Patent Publication Number: US-10786560-B1

Title: Streptococcus agalactiae antigens associated with strains virulent in fish

Description:
FIELD OF THE INVENTION 
     The present invention relates to  Streptococcus agalactiae  genes which are required for virulence in fish species. Specifically, the invention provides a selection of fish-associated  S. agalactiae  nucleic acid/amino acid sequences which have application in methods of detecting  S. agalactiae  strains which are pathogenic in fish, diagnostic procedures, methods of raising immune responses, vaccines and the like. 
     BACKGROUND OF THE INVENTION 
       Streptococcus agalactiae  is an important pathogen of fish and has been identified in farmed, wild, and ornamental species (Bowater, Forbes-Faulkner, Anderson, Condon, Robinson, Kong, Gilbert, Reynolds, Hyland, McPherson, Brien &amp; Blyde 2012; Delannoy, Crumlish, Fontaine, Pollock, Foster, Dagleish, Turnbull &amp; Zadoks 2013; Evans, Bohnsack, Klesius, Whiting, Garcia, Shoemaker &amp; Takahashi 2008). Farmed fish affected by  S. agalactiae  include economically important species such as tilapia and ya fish (Delannoy et al. 2013; Geng, Wang, Huang, Chen, Li, Ren, Liao, Zhou, Liu, Du &amp; Lai 2012; Mian, Godoy, Leal, Yuhara, Costa &amp; Figueiredo 2009). Based on multilocus sequence typing (MLST), the main strains of  S. agalactiae  associated with fish are members of a limited number of clonal complexes (CC), i.e. CC7 and CC552 (Delannoy et al. 2013; Evans et al. 2008). Detection of CC7, which is beta-haemolytic, is largely limited to Asia, whereas CC552, which is non-haemolytic, has been reported worldwide and in a large number of fish species. Of the main CCs associated with fish, CC552 has been detected exclusively in poikilothermic species. The vast majority of CC552 isolates originate from fish (Delannoy et al., 2013; Evans et aL, 2008), with a few isolates from frogs described as non-haemolytic, serotype 1 b or ST260 belonging probably or certainly to CC552 (Amborski, Snider, Thune &amp; Culley 1983; Elliott, Facklam &amp; Richter 1990; Lopez-Sanchez, Sauvage, Da Cunha, Clermont, Ratsima Hariniaina, Gonzalez-Zorn, Poyart, Rosinski-Chupin &amp; Glaser 2012). By contrast, CC7 has also been isolated from humans, where it has been associated with asymptomatic carriage in the genitourinary tract and with disease (Jones, Bohnsack, Takahashi, Oliver, Chan, Kunst, Glaser, Rusniok, Crook, Harding, Bisharat &amp; Spratt 2003; Ip, Cheuk, Tsui, Kong, Leung &amp; Gilbert 2006). Many other CCs have been linked to carriage or disease in people and in homeothermic animals, most importantly in cattle, including members of CC1, CC19 and CC23 (Manning, Springman, Lehotzky, Lewis, Whittam &amp; Davies 2009; Zadoks, Middleton, McDougall, Katholm &amp; Schukken 2011). However, none of these CCs have been reported in fish. CC23 is of particular interest because its host range is known to include aquatic mammals, such as seals, and poikilotherms, such as crocodiles (Bishop, Shilton, Benedict, Kong, Gilbert, Gal, Godoy, Spratt &amp; Currie 2007; Delannoy, et al. 2013), yet it has never been identified in fish. 
     Indeed, challenge studies in tilapia using two serotypes of ST23 have demonstrated that this ST is non-virulent in fish (Delannoy C M, Zadoks R N, Crumlish M, Rodgers D, Lainson F A, Ferguson H W, Turnbull J, Fontaine M C. Genomic comparison of virulent and non-virulent  Streptococcus agalactiae  in fish. J Fish Dis. 2014 Nov. 15. doi:10.1111/jfd.12319 and Mian G F, Godoy D T, Leal C A, Yuhara T Y, Costa G M, Figueiredo H C. Aspects of the natural history and virulence of  S. agalactiae  infection in Nile tilapia. Vet Microbiol. 2009 Apr. 14; 136(1-2):180-3. doi: 10.1016/j.vetmic.2008.10.016). 
     Comparative genomic analysis of  S. agalactiae  isolates with distinct clinical origins or host associations has provided insight into potential mechanisms of evolution, virulence and host adaptation. For example, hypervirulence of ST17 in human neonates has been linked to a specific adhesin (Tazi, Disson, Bellais, Bouaboud, Dmytruk, Dramsi, Mistou, Khun, Mechler, Tardieux, Trieu-Cuot, Lecuit &amp; Poyart 2010), presence of the lactose operon has been linked to strains that affect milk production in dairy cattle (Richards, Lang, Pavinski Bitar, Lefébure, Schukken, Zadoks &amp; Stanhope 2011) and reductive evolution has been suggested as contributing to niche restriction of ST260 (Rosinski-Chupin, Sauvage, Mairey, Mangenot, Ma, Da Cunha, Rusniok, Bouchier, Barbe &amp; Glaser 2013). Genomic comparison of piscine, human and bovine strains of  S. agalactiae  has thus far failed to identify specific genes required for virulence in fish (Liu, Zhang &amp; Lu 2013). 
     SUMMARY OF THE INVENTION 
     The present invention is based upon the identification of a number of  Streptococcus agalactiae  genes which are conserved among disease-causing strains and hence are likely to contribute to virulence and hence make good targets for the development of vaccines and diagnostic tests. Specifically, the invention relates to genomic content present in fish-associated  S. agalactiae  strains that is absent from strains which are non-virulent to fish. 
     By analyzing the genomic content of  S. agalactiae  strains known to be virulent in fish and comparing the information obtained with genomic information derived from  S. agalactiae  strains known not to be virulent in fish, the inventors have been able to identify a number of fish-specific/associated genes. Moreover, the inventors have been able to show that these fish-specific/associated genes, are distributed over a number of small clusters or loci. 
     Given that the identified genes are present only in  S. agalactiae  strains known to be virulent in fish, it is suggested that these genes and/or their products facilitate virulence in fish and/or contribute to fitness in the aquatic environment. 
     Specifically, the present invention relates to the  S. agalactiae  genes identified in Table 1. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Candidate fish-specific and fish associated genes identified in the genome of  Streptococcus agalactiae  STIR-Cd-17. Genes were considered as fish-specific if the were identified in genomes of CC552 isolates on and as  
               
               
                 fish-associated if the were identified in the genomes of CC552 and CC7 isolates but not in the genomes of isolates from other clonal complexes (CC). 
               
            
           
           
               
               
               
               
            
               
                 NCBI annotation 
                   
                   
                   
               
            
           
           
               
               
               
               
               
               
            
               
                   
                   
                 Putative function and 
                   
                 Generator  
                 BlastP results based on NCBI search 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Locus tag 
                 Bp 
                 COG 
                 PSORBTb 
                 analysis 
                 Species and strains 
                 Product 
                 BSR 
               
               
                   
               
            
           
           
               
            
               
                 LOCUS 1 
               
               
                 (Contig23) 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 M3M _05402 
                 801 
                 hypothetical protein 
                 C 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_0045 
                 1 
               
               
                   
                   
                   
                   
                   
                   Eremococcus coleocola  ACS-139-V-Col8  
                 oxidoreductase, NAD-binding domain protein 
                 0.072 
               
               
                   
                   
                   
                   
                   
                 
                   Tribolium 
                   castaneum 
                 
                 hypothetical protein TcasGA2_TC008151 
                 0.069 
               
               
                 M3M_05407 
                 591 
                 hypothetical protein 
                 C 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_004 
                 1 
               
               
                   
                   
                   
                   
                   
                 S.  oralis  SK304 
                 hypothetical protein HMPREF1125_1048 
                 0.166 
               
               
                   
                   
                   
                   
                   
                   Campylobacter   jejuni  subsp.  jejuni  BH-01-0142 
                 hypothetical protein CJBH_0152c 
                 0.096 
               
            
           
           
               
            
               
                 LOCUS 2  
               
               
                 (Contig753) 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 M3M_01252 
                 222 
                 hypothetical protein  
                 C 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein gbs0229 
                 1 
               
               
                   
                   
                   
                   
                   
                 S.  agalactiae  515/NEM316 
                 Unknown 
                 0.623 
               
               
                   
                   
                   
                   
                   
                 S.  agalactiae  ATCC 13813 
                 hypothetical protein HMPREF9171_2185 
                 0.617 
               
            
           
           
               
            
               
                 LOCUS 3  
               
               
                 (Contig753) 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 M3M_01147  
                 195 
                 aldose 1-epimerase, 
                 U 
                 A909, 
                 S.  agalactiae  SA20-06 
                 aldose 1-epimerase 
                 1 
               
               
                   
                   
                 interruption-C (galM); 
                   
                 H36B 
                 S.  agalactiae  A909 
                 hypothetical protein SAK_0542 
                 0.993 
               
               
                   
                   
                 COG2017 Galactose 
                   
                   
                 S.  agalactiae  H36B 
                 aldose 1-epimerase 
                 0.993 
               
               
                   
                   
                 mutarotase and related 
                   
                   
                 S.  agalactiae  GD201008-001/ZQ0910  
                 hypothetical protein 
                 0.993 
               
               
                   
                   
                 enzymes  
                   
                   
                   Streptococcus   suis  ST3 
                 galactose mutarotase-like protein 
                   
               
               
                 M3M_01152 
                 564 
                 aldose 1-epimerase, 
                 C 
                 A909, 
                 S.  agalactiae  SA20-06 
                 aldose 1-epimerase 
                 1 
               
               
                   
                   
                 interruption-N (galM); 
                   
                 H36B 
                 S.  agalactiae  A909 
                 hypothetical protein SAK_0539 
                 0.966 
               
               
                   
                   
                 COG2017 Galactose 
                   
                   
                 S.  agalactiae  H36B 
                 aldose 1-epimerase, interruption-N 
                 0.966 
               
               
                   
                   
                 mutarotase and related 
                   
                   
                 S.  agalactiae  GD201008-001/ZQ0910 
                 hypothetical protein 
                 0.964 
               
               
                   
                   
                 enzymes  
                   
                   
                   Streptococcus   suis  ST3  
                 galactose mutarotase-like protein 
                 0.606 
               
               
                 M3M_ 01157 
                 996 
                 UDP-glucose 4-epimerase 
                 U 
                 A909, 
                 S.  agalactiae  SA20-06 
                 UDP-glucose 4-epimerase 
                 0.999 
               
               
                   
                   
                 (galE1); COG1087 UDP-  
                   
                 H36B 
                 S.  agalactiae  A909/h36b/GD201008-001/ZQ0910 
                 UDP-glucose 4-epimerase 
                 0.993 
               
               
                   
                   
                 glucose 4-epimerase 
                   
                   
                 S.  gallolyticus  UCN34 
                 UDP-glucose 4-epimerase 
                 0.834 
               
               
                 M3M_01162 
                 1482 
                 galactose-1-phosphate 
                 C 
                 A909, 
                 S.  agalactiae  SA20-06 
                 galactose-1-phosphate uridylyltransferase 
                 0.996 
               
               
                   
                   
                 uridylyltransferase (galT); 
                   
                 H36B 
                 S.  agalactiae  H36B 
                 galactose-1-phosphate uridylyltransferase 
                 0.991 
               
               
                   
                   
                 COG4468 Galactose-1- 
                   
                   
                 S.  agalactiae  G0201008-001 
                 galactose-1-phosphate uridylyltransferase 
                 0.989 
               
               
                   
                   
                 phosphate 
                   
                   
                 S.  agalactiae  A909/ZQ0910 
                 galactose-1-phosphate uridylyltransferase 
                 0.988 
               
               
                   
                   
                 uridyltransferase 
                   
                   
                 S.  sanguinis  SK355 
                 UTP-hexose-1-phosphate uridylyltransferase 
                 0.693 
               
               
                 M3M_01167  
                 1173 
                 galactokinase (galK); 
                 C 
                   
                 S.  agalactiae  H36B 
                 galactokinase 
                 0.914 
               
               
                   
                   
                 COG0153 Galactokinase 
                   
                 H36B 
                 S.  agalactiae  SA20-06 
                 galactokinase 
                 0.909 
               
               
                   
                   
                   
                   
                   
                 S.  gallolyticus  subsp.  gallolyticus  TX20005 
                 galactokinase 
                 0.771 
               
               
                 M3M_01172 
                 2202 
                 alpha-galactosidase 
                 C 
                 A909, 
                 S.  agalactiae  SA20-06 
                 alpha-galactosidase 
                 0.999 
               
               
                   
                   
                 (galA); COG3345 Alpha- 
                   
                 H36B 
                 S.  agalactiae  A909/GD201008-001/ZQ0910/H36B 
                 alpha-galactosidase 
                 0.993 
               
               
                   
                   
                 galactosidase 
                   
                   
                 S.  canis  FSL Z3-227 
                 alpha-galactosidase 
                 0.692 
               
               
                 M3M_01177 
                 828 
                 ABC transporter 
                 CM 
                 A909, 
                 S.  agalactiae  SA20-06 
                 ABC transporter permease 
                 1 
               
               
                   
                   
                 permease; C0G0395 
                   
                 H36B 
                 S.  agalactiae  A909/GD201008-001/ZQ0910/H36B 
                 ABC transporter permease 
                 1 
               
               
                   
                   
                 ABC-type sugar transport 
                   
                   
                 S.  canis  FSL Z3-227 
                 ABC transporter permease 
                 0.873 
               
               
                   
                   
                 system, permease 
                   
                   
                   
                   
                   
               
               
                   
                   
                 component 
                   
                   
                   
                   
                   
               
               
                 M3M_01182 
                 903 
                 sugar ABC transporter 
                 CM 
                 A909, 
                 S.  agalactiae  SA20-06 
                 binding-protein-dependent transport system 
                 0.997 
               
               
                   
                   
                 permease; COG1175 
                   
                 H36B 
                   
                   
                   
               
               
                   
                   
                 ABC-type sugar transport 
                   
                   
                 S.  agalactiae  A909/GD201008-001/ZQ0910/H36B 
                 sugar ABC transporter permease 
                 0.931 
               
               
                   
                   
                 systems, permease 
                   
                   
                 S.  canis  FSL Z3-227 
                 ABC-type sugar transport system, permease component 
                 0.815 
               
               
                   
                   
                 components 
                   
                   
                 S.  iniae  9117 
                 ABC superfamily ATP binding cassette transporter 
                 0.794 
               
               
                 M3M_01187 
                 1035 
                 sugar ABC transporter 
                 U 
                 A909, 
                   Streptococcus   agalactiae  SA20-06 
                 sugar ABC transporter substrate-binding protein 
                 0.993 
               
               
                   
                   
                 sugar-binding protein; 
                   
                 H36B 
                 S.  agalactiae  A909/GD201008-001/ZQ0910/H36B 
                 sugar ABC transporter sugar-binding protein 
                 0.742 
               
               
                   
                   
                 COG1653 ABC-type 
                   
                   
                   Streptococcus   porcinus  str. Jelinkova 176 
                 ABC transporter, solute-binding protein 
                 0.574 
               
               
                   
                   
                 sugar transport system, 
                   
                   
                   
                   
                   
               
               
                   
                   
                 periplasmic component  
                   
                   
                   
                   
                   
               
               
                 M3M_01192 
                 831 
                 AraC family transcriptional 
                 C 
                 A909, 
                 S.  agalactiae  A909/GD201008-001/ZQ0910/H36B/SA20-06 
                 AraC family transcriptional regulator 
                 1 
               
               
                   
                   
                 regulator; C0G2207 
                   
                 H36B 
                   
                   
                   
               
               
                   
                   
                 AraC-type DNA-binding 
                   
                   
                 S.  canis  FSL Z3-227 
                 transcriptional regulator 
                 0.655 
               
               
                   
                   
                 domain-containing 
                   
                   
                 S.  suis  05ZYH33 
                 transcriptional regulator 
                 0.652 
               
               
                   
                   
                 proteins  
                   
                   
                   
                   
                   
               
               
                 M3M_01197 
                 285 
                 phosphotransferase 
                 CM 
                 A909, 
                 S.  agalactiae  SA20-06 
                 PTS system lactose/cellobiose specific transporter 
                 1 
               
               
                   
                   
                 system, galactitol-specific 
                   
                 H36B 
                 S.  agalactiae  A909/GD201008-001/ZQ0910/H36B 
                 PTS system galactitol-specific transporter subunit IIB 
                 0.989 
               
               
                   
                   
                 IIB component; C0G3414 
                   
                   
                 S.  ictaluri  707-05 
                 PTS system, Lactose/Cellobiose specific IIB subunit 
                 0.832 
               
               
                   
                   
                 Phosphotransferase 
                   
                   
                 S.  pseudoporcinus  SPIN 20026  
                 putative PTS system, galactitol-specific IIB component 
                   
               
               
                   
                   
                 system, galactitol-specific 
                   
                   
                   
                   
                   
               
               
                   
                   
                 IIB component 
                   
                   
                   
                   
                 0.821 
               
               
                 M3M _01202 
                 1332 
                 PTS system, galactitol- 
                 CM 
                 A909, 
                 S.  agalactiae  A909/GD201008-001/ZQ0910/H36B 
                 PTS system galactitol-specific transporter subunit IIC 
                 0.995 
               
               
                   
                   
                 specific IIC component; 
                   
                 H36B 
                 S.  agalactiae  SA20-06 
                 PTS system component 
                 0.923 
               
               
                   
                   
                 COG3775 
                   
                   
                   Granulicatella   adiacens  ATCC 49175  
                 PTS system, galactitol-specific IIC component 
                 0.831 
               
               
                   
                   
                 Phosphotransferase 
                   
                   
                 S.  iniae  9117 
                 PTS family galactitol (gat) porter component IIC 
                 0.811 
               
               
                   
                   
                 system, galactitol-specific 
                   
                   
                   
                   
                   
               
               
                   
                   
                 IIC component 
                   
                   
                   
                   
                   
               
               
                 M3M_01207 
                 465 
                 PTS system, galactitol- 
                 C 
                 A909, 
                 S.  agalactiae  SA20-06 
                 PTS system galactitol-specific transporter subunit IIA 
                 0.99 
               
               
                   
                   
                 specific IIA component; 
                   
                 H36B 
                 S.  agalactiae  A909/GD201008-001/ZQ0910/H36B 
                 PTS system, galactitol-specific IIA component, putative 
                 0.977 
               
               
                   
                   
                 COG1762 
                   
                   
                   
                   
                   
               
               
                   
                   
                 Phosphotransferase 
                   
                   
                   
                   
                   
               
               
                   
                   
                 system mannitol/fructose- 
                   
                   
                   
                   
                   
               
               
                   
                   
                 specific IIA domain 
                   
                   
                   Granulicatella   elegans  ATCC 700633 
                 PTS system IIA component 
                 0.451 
               
               
                 M3M_01212 
                 831 
                 rhamnulose-1-phosphate 
                 C 
                 A909, 
                 S.  agalactiae  A909/GD201008-001/ZQ0910/H36B  
                 rhamnulose-1-phosphate aldolase 
                 0.997 
               
               
                   
                   
                 aldolase; COG0235 
                   
                 H36B 
                 S.  agalactiae  SA20-06 
                 rhamnulose-1-phosphate aldolase 
                 0.995 
               
               
                   
                   
                 Ribulose-5-phosphate 4- 
                   
                   
                 S.  anginosus  subsp.  whileyi  CCUG 39159 
                 putative rhamnulose-1-phosphate aldolase 
                 0.705 
               
               
                   
                   
                 epimerase and related 
                   
                   
                   
                   
                   
               
               
                   
                   
                 epimerases and aldolases 
                   
                   
                   
                   
                   
               
               
                 M3M_01217 
                 1338 
                 PTS system, galactitol- 
                 CM 
                 A909, 
                   
                   
                   
               
               
                   
                   
                 specific IIC component; 
                   
                 H36B 
                 S.  agalactiae  SA20-06 
                 PTS system sugar-specific transporter permease 
                 1 
               
               
                   
                   
                 COG3775 
                   
                   
                 S.  agalactiae  A909/GD201008-001/Z00910 
                 PTS system galactitol-specific transporter subunit IIC 
                 0.995 
               
               
                   
                   
                 Phosphotransferase 
                   
                   
                 S. anginosus subsp. whileyi CCUG 39159 
                 PTS system sugar-specific permease protein 
                 0.905 
               
               
                   
                   
                 system, galactitol-specific 
                   
                   
                   
                   
                   
               
               
                   
                   
                 IIC component 
                   
                   
                   
                   
                   
               
               
                 M3M_01222 
                 279 
                 PTS system galactitol- 
                 U 
                 A909, 
                 S.  agalactiae  SA20-06 
                 PTS system lactose/cellobiose specific transporter 
                 1 
               
               
                   
                   
                 specific enzyme IIB 
                   
                 H36B 
                 S.  agalactiae  A909/GD201008-001/ZQ0910/H36B 
                 PTS system galactitol-specific transporter subunit IIB 
                 0.984 
               
               
                   
                   
                 component; COG3414 
                   
                   
                   
                   
                   
               
               
                   
                   
                 Phosphotransferase 
                   
                   
                 S.  anginosus  subsp.  whileyi  CCUG 39159 
                 PTS system, lactose/cellobiose-specific IIB subunit 
                 0.886 
               
               
                   
                   
                 system, galactitol-specific 
                   
                   
                   Granulicatella   elegans  ATCC 700634 
                 PTS system galactitol-specific transporter subunit IIB 
                 0.864 
               
               
                   
                   
                 IIB component 
                   
                   
                   Streptococcus  ictaluri 707-05 
                 PTS system, Lactose/Cellobiose specific IIB subunit 
                 0.842 
               
               
                 M3M_01227 
                 450 
                 PTS system, galactitol- 
                 C 
                 A909, 
                 S.  agalactiae  A909/GD201008-001/ZQ0910/H36B/SA20-06 
                 PTS system galactitol-specific transporter subunit IIA 
                 1 
               
               
                   
                   
                 specific IIA component; 
                   
                 H36B 
                 S.  porcinus  str. Jelinkova 176 
                 phosphoenolpyruvate-dependent sugar PTS family porter 
                 0.219 
               
               
                   
                   
                 COG1762 
                   
                   
                   
                   
                   
               
               
                   
                   
                 Phosphotransferase 
                   
                   
                 S. anginosus subsp. whileyi CCUG 39159 
                 phosphoenolpyruvate-dependent sugar PTS family porter 
                 0.217 
               
               
                   
                   
                 system mannitol/fructose- 
                   
                   
                   
                   
                   
               
               
                   
                   
                 specific IIA domain 
                   
                   
                   
                   
                   
               
               
                 M3M_01232 
                 2043 
                 PTS system IIA domain- 
                 C 
                 A909, 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_0403 
                 0.999 
               
               
                   
                   
                 containing protein; 
                   
                 H36B 
                 S.  agalactiae  ZQ0910 
                 PTS system IIA domain-containing protein 
                 0.996 
               
               
                   
                   
                 COG3711 Transcriptional 
                   
                   
                 S.  agalactiae  A909/GD201008-001 
                 PTS system IIA domain-containing protein 
                 0.996 
               
               
                   
                   
                 antiterminator 
                   
                   
                 S.  agalactiae  H36B 
                 MW0309, putative 
                 0.986 
               
               
                   
                   
                   
                   
                   
                   Coprobacillus  sp. 29_1 
                 hypothetical protein HMPREF9488_00517 
                 0.247 
               
            
           
           
               
            
               
                 LOCUS 4 
               
               
                 (Contig753) 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 M3M_01047 
                 294 
                 hypothetical protein; 
                 C 
                 — 
                 S.  agalactiae  SA20-06 
                 CRISPR-associated endoribonuclease Cas2 
                 1 
               
               
                   
                   
                 COG1343 
                   
                   
                 S.  constellatus  subsp.  constellatus  SK53 
                 CRISPR-associated endoribonuclease Cas2 
                 0.945 
               
               
                   
                   
                 Uncharacterized protein 
                   
                   
                 S.  mutans  UA159 
                 hypothetical protein SMU_1753c 
                 0.935 
               
               
                   
                   
                 predicted to be involved in 
                   
                   
                   
                   
                   
               
               
                   
                   
                 DNA repair 
                   
                   
                   
                   
                   
               
               
                   
                   
                 csd1 pseudogene 
                   
                   
                   
                   
                   
               
               
                 M3M_01062 
                 672 
                 putative RecB family 
                 C 
                 — 
                 S.  agalactiae  SA20-06 
                 CRISPR-associated protein Cas4 
                 1 
               
               
                   
                   
                 exonuclease; COG1468 
                   
                   
                 S.  mutans  LJ23 
                 CRISPR-associated protein cas4 
                 0.879 
               
               
                   
                   
                 RecB family exonuclease 
                   
                   
                 S.  mutans  UA159 
                 hypothetical protein 
                 0.864 
               
               
                 M3M_01068 
                 850 
                 hypothetical protein; 
                 C 
                 — 
                 S.  agalactiae  SA20-06 
                 Csd2 family CRISPR-associated protein 
                 1 
               
               
                   
                   
                 COG3649 
                   
                   
                 S.  dysgalactiae  subsp.  equisimilis  RE378 
                 putative cytoplasmic protein 
                 0.981 
               
               
                   
                   
                 Uncharacterized protein 
                   
                   
                 S.  dysgalactiae  subsp.  equisimilis  SK1251 
                 hypothetical protein HMPREF9963_1905 
                 0.979 
               
               
                   
                   
                 predicted to be involved in 
                   
                   
                   
                   
                   
               
               
                   
                   
                 DNA repair 
                   
                   
                   
                   
                   
               
               
                 M3M_01097 
                 729 
                 hypothetical protein 
                 C 
                 515 
                 S.  agalactiae  SA20-06 
                 CRISPR-associated protein Cas5 
                 1 
               
               
                   
                   
                   
                   
                   
                 S.  dysgalactiae  subsp.  equisimilis  AC-2713 
                 hypothetical protein SDSE_1670 
                 0.964 
               
               
                   
                   
                   
                   
                   
                 S.  canis  FSL Z3-227 
                 hypothetical protein SCAZ3_08370 
                 0.962 
               
               
                 M3M_01102 
                 2424 
                 ATP-dependent RNA 
                 C 
                 515, 
                 S.  agalactiae  SA20-06 
                 CRISPR-associated helicase Cas3 
                 0.997 
               
               
                   
                   
                 helicase; COG1203 
                   
                 COH1, 
                 S.  dysgalactiae  subsp.  equisimilis  SK1250 
                 CRISPR-associated helicase Cas3 
                 0.956 
               
               
                   
                   
                 Predicted helicases 
                   
                 FSL- 
                 S.  dysgalactiae  subsp.  equisimilis  AC-2713 
                 Pre-mRNA-processing ATP-dependent RNA helicase 
                 0.953 
               
               
                   
                   
                   
                   
                 S3-026 
                   
                 PRP5 
                   
               
               
                 M3M_01107 
                 222 
                 Fic protein family; 
                 U 
                 515 
                 S.  agalactiae  515 
                 Fic protein family family 
                 0.968 
               
               
                   
                   
                 COG2184 Protein 
                   
                   
                 S.  suis  05ZYH33 
                 hypothetical protein SSU05_0462 
                 0.613 
               
               
                   
                   
                 involved in cell division 
                   
                   
                 S.  suis  ST1 
                 hypothetical protein SSUST1_0463 
                 0.613 
               
            
           
           
               
            
               
                 LOCUS 5  
               
               
                 (Contig751) 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 misc_feature 
                 — 
                 CHAP domain protein 
                 — 
                 — 
                 — 
                 — 
                 — 
               
               
                 — 
                 — 
                 — 
                 — 
                 — 
                 — 
                 — 
                 — 
               
               
                 — 
                 — 
                 — 
                 — 
                 — 
                 — 
                 — 
                 — 
               
               
                 misc_feature 
                   
                 resolvase family site- 
                   
                   
                   
                   
                   
               
               
                   
                   
                 specific recombinase 
                   
                   
                   
                   
                   
               
               
                 misc_feature 
                   
                 resolvase family site- 
                   
                   
                   
                   
                   
               
               
                   
                   
                 specific recombinase 
                   
                   
                   
                   
                   
               
               
                 M3M_00445 
                 204 
                 bacteriocin 
                 E 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_0545 
                 1 
               
               
                   
                   
                   
                   
                   
                 S.  equi  subsp.  zooepidemicus  MGCS10565 
                 bacteriocin BlpN-like 
                 0.576 
               
               
                   
                   
                   
                   
                   
                 S.  equi  subsp.  equi   
                   Streptococcus  equi subsp. equi 404 
                 0.57 
               
               
                 M3M_00450 
                 231 
                 hypothetical protein 
                 U 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_0544 
                 1 
               
               
                   
                   
                   
                   
                   
                 S.  pneumoniae  SP6-BS73 
                 bacteriocin BIpM 
                 0.687 
               
               
                   
                   
                   
                   
                   
                 S.  equi  subsp.  equi  4047 
                 bacteriocin 
                 0.649 
               
               
                 misc_feature 
                   
                 abortive infection protein 
                   
                   
                   
                   
                   
               
               
                   
                   
                 AbiGII 
                   
                   
                   
                   
                   
               
               
                 M3M_00465 
                 582 
                 hypothetical protein; 
                 C 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_0542 
                 1 
               
               
                   
                   
                 COG1672 Predicted 
                   
                   
                 S.  macedonicus  ACA-DC 198 
                 Abortive infection protein AbiGI 
                 0.691 
               
               
                   
                   
                 ATPase (AAA+ 
                   
                   
                 S.  dysgalactiae  subsp.  dysgalactiae  ATCC 27957 
                 hypothetical protein SDD27957_04365 
                 0.686 
               
               
                   
                   
                 superfamily) 
                   
                   
                   
                   
                   
               
               
                 M3M_00470 
                 138 
                 Tn5252 Orf28; COG3942 
                 U 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_0541 
                 0.971 
               
               
                   
                   
                 Surface antigen 
                   
                   
                 S.  intermedius  F0395 
                 hypothetical protein HMPREF9682_00655 
                 0.869 
               
               
                   
                   
                   
                   
                   
                 S.  suis  D12 
                 hypothetical protein SSUD12_0897 
                 0.783 
               
               
                 M3M_00475 
                 327 
                 hypothetical protein; 
                 C 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_0540 
                 1 
               
               
                   
                   
                 COG0270 Site-specific 
                   
                   
                 S.  agalactiae  NEM316 
                 hypothetical protein 
                 0.371 
               
               
                   
                   
                 DNA methylase 
                   
                   
                 S.  pneumoniae  NorthCarolina6A-23 
                 modification methylase Hpall 
                 0.357 
               
            
           
           
               
            
               
                 LOCUS 6  
               
               
                 (Contig751)  
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 M3M_00390 
                 270 
                 hypothetical protein 
                 U 
                 — 
                 
                   Ashbya 
                   gossypii 
                 
                 AAR142Cp 
                 0.192 
               
               
                   
                   
                   
                   
                   
                 
                   delta 
                   proteobacterium 
                 
                 Response regulator receiver 
                 0.192 
               
               
                   
                   
                   
                   
                   
                 
                   Photorhabdus 
                   asymbiotica 
                 
                 Gramicidin S synthetase 2 
                 0.187 
               
               
                 M3M_00395 
                 897 
                 hypothetical protein 
                 C  
                 — 
                   Krokinobacter  sp. 
                 hypothetical protein 
                 0.06 
               
               
                   
                   
                   
                   
                   
                 — 
                 — 
                   
               
               
                   
                   
                   
                   
                   
                 — 
                 — 
                   
               
               
                 M3M_00400 
                 1017 
                 hypothetical protein; 
                 C 
                 — 
                 
                   Gloeobacter violaceus 
                 
                 hypothetical protein 
                 0.057 
               
               
                   
                   
                 COG0457 FOG: TPR 
                   
                   
                   Helicobacter   pylori  F32 
                 hypothetical protein HPF32_0454 
                 0.052 
               
               
                   
                   
                 repeat 
                   
                   
                   
                   
                   
               
               
                   
                   
                   
                   
                 — 
                 — 
                   
                   
               
               
                 M3M_00405 
                 1263 
                 serine 
                 C 
                 — 
                   Fusobacterium  sp. 
                 conserved hypothetical protein 
                 0.321 
               
               
                   
                   
                 hydroxymethyltransferase; 
                   
                   
                   Coprococcus   eutactus  ATCC 27759 
                 hypothetical protein COPEUT_02118 
                 0.293 
               
               
                   
                   
                 COG0112 Glycine/serine 
                   
                   
                   
                   
                   
               
               
                   
                   
                 hydroxymethyltransferase 
                   
                   
                   Erysipelotrichaceae  bacterium 3_1_53 
                 hypothetical protein HMPREF0983_03234 
                 0.246 
               
               
                 M3M_00410 
                 318 
                 integrase; COG4974 Site- 
                 U 
                 — 
                   Streptococcus   porcinus  str. Jelinkova 176 
                 phage integrase, N-terminal SAM domain protein 
                 0.73 
               
               
                   
                   
                 specific recombinase 
                   
                   
                   Streptococcus   anginosus  subsp.  whileyi  CCUG 39159 
                 site-specific recombinase, phage integrase family 
                 0.707 
               
               
                   
                   
                 XerD 
                   
                   
                   Streptococcus   mitis  by. 2 str. SK95 
                 phage integrase, N-terminal SAM domain protein 
                 0.66 
               
            
           
           
               
            
               
                 LOCUS 7 
               
               
                 (Contig371) 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 M3M_04250 
                 357 
                 integrase; COG0582 
                 U 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_0928 
                 0.992 
               
               
                   
                   
                 Integrase 
                   
                   
                 S.  pneumoniae  70585 
                 Integrase 
                 0.633 
               
               
                   
                   
                   
                   
                   
                 S.  pneumoniae  2061617 
                 phage integrase family protein 
                 0.633 
               
               
                 M3M_04255 
                 189 
                 hypothetical protein 
                 U 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_0927 
                 1 
               
               
                   
                   
                   
                   
                   
                 S.  pneumoniae  GA47461 
                 hypothetical protein SPAR97_1602 
                 0.675 
               
               
                   
                   
                   
                   
                   
                 S.  pneumoniae  GA17484  
                 hypothetical protein SPAR47_088 
                 0.675 
               
               
                 M3M_04260 
                 126 
                 Cro/Cl family 
                 U 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_0926 
                 1 
               
               
                   
                   
                 transcriptional regulator 
                   
                   
                 S.  pneumoniae  CCRI 1974 
                 hypothetical protein SpneC1_02124 
                 0.681 
               
               
                   
                   
                   
                   
                   
                 S.  pneumoniae  CCRI 1974M2 
                 hypothetical protein SpneC19_10413 
                 0.681 
               
               
                 M3M_04265 
                 339 
                 hypothetical protein  
                 U 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_0925 
                 0.693 
               
               
                   
                   
                   
                   
                   
                 Oenococcus  oeni  AWRIB429 
                 hypothetical protein AWRIB429_1949 
                 0.155 
               
               
                   
                   
                   
                   
                   
                 Oenococcus  oeni  AWRIB548 
                 phage terminase large subunit 
                 0.155 
               
               
                 M3M_04270 
                 792 
                 hypothetical protein 
                 U  
                 — 
                   Bacillus   amyloliquefaciens  DC-12 
                 hypothetical protein BamyaD_16251 
                 0.137 
               
               
                   
                   
                   
                   
                   
                   Bacillus  sp. 5B6 
                 hypothetical protein MY7_0533 
                 0.135 
               
               
                   
                   
                   
                   
                   
                   Bacillus   amyloliquefaciens  AS43.3 
                 hypothetical protein B938_03325 
                 0.129 
               
               
                 M3M_04275 
                 639 
                 hypothetical protein; 
                 CM 
                 — 
                   Clostridiales  bacterium OBRC5-5 
                 hypothetical protein HMPREF1135_01905 
                 0.402 
               
               
                   
                   
                 COG0477 Permeases of 
                   
                   
                   Lachnospiraceae  oral taxon 107 str. F0167  
                 hypothetical protein HMPREF0491_01439 
                 0.368 
               
               
                   
                   
                 the major facilitator 
                   
                   
                   Staphylococcus   hominis  SK119 
                 multidrug resistance protein 1 
                 0.114 
               
               
                   
                   
                 superfamily 
                   
                   
                   
                   
                   
               
               
                 M3M_04280 
                 369 
                 beta-hydroxyacyl-(acyl- 
                 U 
                 — 
                   Geobacillus   thermoleovorans  CCB_US3_UF5 
                 putative thioester dehydrase 
                 0.311 
               
               
                   
                   
                 carrier-protein) 
                   
                   
                   Coraliomargarita   akajimensis  DSM 45221 
                 beta-hydroxyacyl-dehydratase FabA/FabZ 
                 0.292 
               
               
                   
                   
                 dehydratase FabA/FabZ; 
                   
                   
                   Pirellula   staleyi  DSM 6068 
                 beta-hydroxyacyl- dehydratase FabA/FabZ 
                 0.289 
               
               
                   
                   
                 COG0764 3- 
                   
                   
                   
                   
                   
               
               
                   
                   
                 hydroxymyristoyl/3- 
                   
                   
                   
                   
                   
               
               
                   
                   
                 hydroxydecanoyl- 
                   
                   
                   
                   
                   
               
               
                   
                   
                 dehydratases 
                   
                   
                   
                   
                   
               
               
                 M3M_04285 
                 540 
                 PadR family 
                 C 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_0923 
                 1 
               
               
                   
                   
                 transcriptional regulator 
                   
                   
                   Lachnospiraceae  oral taxon 107 str. F0167 
                 hypothetical protein HMPREF0491_01453 
                 0.255 
               
               
                   
                   
                 COG1695 Predicted 
                   
                   
                   Clostridiales  bacterium OBRC5-5  
                 hypothetical protein HMPREF1135_01904 
                 0.254 
               
               
                   
                   
                 transcriptional regulators 
                   
                   
                   
                   
                   
               
            
           
           
               
            
               
                 LOCUS 8 
               
               
                 (Contig381) 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 M3M_01921 
                 618 
                 DJ-1/Pfpl family protein; 
                 U 
                 — 
                 S.  agalactiae  SA20-06 
                 hypothetical protein SaSA20_1488 
                 1 
               
               
                   
                   
                 COG0693 Putative 
                   
                   
                 S.  criceti  HS-6 
                 hypothetical protein STRCR_0670 
                 0.761 
               
               
                   
                   
                 intracellular 
                   
                   
                   
                   
                   
               
               
                   
                   
                 protease/amidase 
                   
                   
                 S.  sanguinis  SK1087  
                 ThiJ/Pfpl family intracellular protease 
                 0.613 
               
               
                 M3M_01926 
                 531 
                 hypothetical protein; 
                 C 
                 — 
                 S.  agalactiae  SA20-06 
                   Streptococcus   agalactiae  SA20-06 
                 1 
               
               
                   
                   
                 COG3797 
                   
                   
                 S.  suis  ST1 
                 hypothetical protein SSUST1_1897  
                 0.725 
               
               
                   
                   
                 Uncharacterized protein 
                   
                   
                 S.  suis  R61 
                 hypothetical protein SSUR61_0033 
                 0.706 
               
               
                   
                   
                 conserved in bacteria 
                   
                   
                   
                   
                   
               
               
                   
               
            
           
         
       
     
     As noted in Table 1 above, the candidate genes which are the subject of this invention have been identified as belonging to a number of distinct clusters—referred to herein as “loci”. The Table shows that the inventors have identified 8 loci. 
     While the invention relates to each of the genes identified in Table 1, it further relates to proteins and peptides (the gene “products”) encoded by the same. 
     For convenience and simplicity, the genes identified in Table 1 and their peptide/protein products, shall be referred to hereinafter as “fish-associated sequences”. 
     It should be understood that the term “fish-associated sequences” encompasses not only all of the genes and gene products identified in Table 1 but also the homologous/identical sequences, fragments, fusions, derivatives, variants antigens and the like described in more detail below. 
     In addition to the specific fish-associated sequences identified in Table 1, this invention may relate to similar or homologous sequences from other streptococci or  S. agalactiae  strains. Similar or homologous sequences within the scope of this invention may share some identity and/or homology to or with the nucleic acid and/or amino acid sequences of the genes and/or their protein products identified in Table 1. For example, homologous or identical sequences (both nucleic acid and/or amino acid) which are to be considered as encompassed within the scope of this invention may include those that exhibit at least about 60% to about 99% sequence identity to the nucleic acid or amino acid sequences of the genes and proteins identified in Table 1. For example homologous or identical sequences (both nucleic acid and amino acid) may exhibit at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97% or 98% identity or homology to the nucleic acid or amino acid sequences of the genes and proteins identified in Table 1. 
     The various genes and their protein products identified in Table 1 may be referred to as reference (fish-associated) sequences. Thus, homologous or identical sequences within the scope of this invention embraces those exhibiting homology or identity (as defined above) to the reference sequences disclosed herein. 
     The degree of (or percentage) “homology” between two or more (amino acid or nucleic acid) sequences may be determined by aligning the sequences and determining the number of aligned residues which are identical or which are not identical but which differ by redundant nucleotide substitutions (the redundant nucleotide substitution having no effect upon the amino acid encoded by a particular codon, or conservative amino acid substitutions). 
     A degree (or percentage) “identity” between two or more (amino acid or nucleic acid) sequences may also be determined by aligning the sequences and ascertaining the number of exact residue matches between the aligned sequences and dividing this number by the number of total residues compared—multiplying the resultant figure by 100 would yield the percentage identity between the sequences. 
     In addition, the invention may concern fragments of any of the fish-associated sequences disclosed herein. A fragment of a nucleic acid or amino acid sequence (including those described herein) may comprise, consist or consist essentially of from about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 (amino acid or nucleic acid) residues to n−1 residues, where “n” is the total number of (amino acid or nucleic acid) residues in the relevant complete or native sequence. For the avoidance of doubt, the complete or native sequence may be any of the reference (fish-associated) sequences to which this invention relates. 
     The fragments of this invention may be functional fragments—that is to say the fragment retains one or more functional properties of the native or complete gene or protein sequence from which it is derived. Additionally or alternatively, the fragments of this invention may be antigenically and/or immunologically similar or identical to the native or complete gene/protein sequence (for example any of the sequences identified in Table 1) from which they are derived. 
     Fragments of any of the fish-associated sequences of this invention may comprise a number of contiguous or consecutive residues of a complete sequence. Fragments may alternatively or additionally comprise or consist (essentially) of, one or more domains and/or sequences of discontinuous residues from any of the complete fish-associated sequences of this invention. 
     The invention also relates to oligonucleotide and/or peptide probes and/or primers with specificity for any part of the fish-associated sequences described herein. For example the oligonucleotide and/or protein probes or primers of this invention may comprise sequences which are complementary to all or part of the sequence of a fish-associated sequence of this invention. Oligonucleotide primers may be used in PCR based methods or isothermal amplification procedures to amplify nucleic acid sequences of interest and therefore primers of this invention (which are complementary to sequences of the fish-associated sequences of this invention) may be exploited in order to facilitate the amplification of all or part of the fish-associated sequences or in methods of detecting the same. Such methods may find application in the detection or identification of Streptococci which are pathogenic to fish. 
     The probes/primers of this invention may be labeled with optically detectable tags and/or mass tags or the like. Optically detectable tags may include fluorescent tags such as fluorophores and the like. For example, the probes/primers of this invention may be labeled with cyanine, fluorescein, rhodamine, Alexa Fluors, Dylight fluors, ATTO Dyes, BODIPY Dyes, SETA Dyes and SeTau Dyes. The probes and/or primers may be modified so as to comprise sequences designed to create restriction sites in amplified sequences. 
     The invention may further relate to variants, derivatives or mutants of any of the fish-associated sequences described herein. One of skill will appreciate that a variant, derivative or mutant sequence may comprise or be encoded by, a nucleic acid or amino acid sequence which itself comprises one or more nucleotide and/or amino acid substitutions, inversions, additions and/or deletions relative to a reference sequence. As stated, in the context of this invention, a reference sequence may be any of the fish-associated sequences disclosed in Table 1. The term “substitution” may encompass one or more conservative substitution(s). The term “conservative substitution” is intended to embrace the act of replacing one or more amino acids of a protein or peptide with an alternate amino acid with similar properties and which does not substantially alter the physico-chemical properties and/or structure or function of the native (or wild-type) protein. 
     Sequences which are to be regarded as derived from (or derivatives of) any of the fish-associated sequences described herein may comprise one or more modifications to the structure or sequence. For example, derivative fish-associated sequences may comprise one or more synthetic or artificial amino acid/nucleic acid sequences. As described elsewhere, derivative or modified fish-associated sequences of this invention may be recombinantly produced. 
     As is well known in the art, the degeneracy of the genetic code permits substitution of one or more bases in a codon without changing the primary amino acid sequence. Consequently, although this specification presents a number of specific fish-associated sequences, the degeneracy of the code may be exploited to yield variant fish-associated nucleic acid sequences. These variant nucleic acid sequences may encode proteins/peptides (or fragments thereof) detailed in Table 1, but may differ from wild-type or native sequences by one or more nucleic acid residues. As stated, these variant nucleic acid sequences may encode primary amino acid sequences which are substantially identical to the wild-type primary sequences of those (fish-associated) proteins described in Table 1. 
     The invention may further relate to sequences, for example nucleic acid sequences, which have been codon optimised, perhaps for expression in certain cellular (for example bacterial) systems. As such, the term “fish-associated sequences” encompasses codon-optimised nucleic acid sequences encoding any of the proteins/peptides described in Table 1. 
     The invention may exploit nucleic acid (for example oligonucleotide) and/or amino acid (protein/peptide) fusions comprising any of the fish-associated sequences described herein. A fusion may comprise a fish-associated sequence fused, conjugated, bound or otherwise associated to or with some heterologous (for example a non-fish-associated sequence) sequence or moiety. Where the fusion is a fusion protein, the fusion may comprise a fish-associated sequence and a heterologous sequence (for example a non-fish-associated sequence) fused (directly or indirectly via a linker moiety) thereto. 
     Fusions may be generated using, for example, the recombinant (cloning and PCR based) technologies described herein. 
     The fish-associated sequences (for example any of the proteins identified in Table 1 and/or disclosed herein) may be purified directly from the relevant  S. agalactiae  strains, cultures and/or cell wall preparations thereof. For example, cell lysis and/or centrifugation techniques may be used to harvest internal (cytoplasmic) proteins as well as cell surface proteins. Nucleic acids may be extracted from cells by a number of known techniques including those which exploit the use of PCR and cloning procedures, silica-based nucleic acid extraction techniques (mini-spin columns and the like) and agarose gel extraction protocols. 
     The invention provides recombinant or synthetic forms of any of the fish-associated sequences described herein. Recombinant sequences (both nucleic acid and/or protein) may be produced by any number of well-known methods including those using PCR, cloning and protein/nucleic acid purification techniques. 
     Recombinant fish-associated sequences may be modified (relative to the corresponding wild-type sequence) to include synthetic (nucleic acid or amino acid) residues and/or sequences encoding tagging or labelling moieties. Additionally or alternatively, the recombinant fish-associated sequences may lack certain wild-type sequences or domains such as, for example, secretion signal peptide domains and the like. 
     One of skill in this field will appreciate that PCR techniques may be exploited to selectively amplify the appropriate gene sequences from a variety of sources including, for example, stored  S. agalactiae  isolates, clinical isolates, diseased (tissue) material and the like. Cloned fish-associated sequences of this invention may be introduced into a vector (such as a plasmid or expression cassette). In one embodiment, the vector may further comprise a nucleotide sequence of a tag or label to assist in protein purification procedures. The vector may encode a heterologous (relative to the fish-associated sequence) sequence which is to be fused to a fish-associated sequence of this invention. 
     A cell may be transformed or transfected with a vector of this invention—such cells may be referred to as “host cells”. As such, the invention provides transformed/transfected host cells. A transformed/transfected cell may be maintained under conditions suitable to induce expression of any fish-associated sequence encoded by the vector. Prokaryotic or eukaryotic cells, such as, for example bacterial, plant, insect, mammalian and/or fungal cells, may be transformed or transfected with one or more of the vectors described herein. One of skill in this field will be familiar with the techniques used to introduce heterologous or foreign nucleic acid sequences, such as expression vectors, into cells, and these may include, for example, heat-shock treatment, use of one or more chemicals (such as calcium phosphate) to induce transformation/transfection, the use of viral carriers, microinjection and/or techniques such as electroporation. Further information regarding transformation/transfection techniques may be found in Current Protocols in Molecular Biology, Ausuble, F. M., ea., John Wiley &amp; Sons, N.Y. (1989) which is incorporated herein by reference. In one embodiment, the host cell is a bacterial cell such as, for example, an  Escherichia coli  cell. 
     Techniques used to purify recombinant proteins generated in this way are known and, where the recombinant protein is tagged or labelled, these may include the use of, for example, affinity chromatography techniques. 
     In view of the above, this invention may provide or relate to expression vectors comprising one or more of the fish-associated ( S. agalactiae ) gene sequences and host cells transformed therewith. As a reminder, it should be understood that the term “fish-associated sequences” as used herein, encompasses all of the fragments, variants, homologous/identical and derivative sequences described herein. 
     The fish-associated sequences of this invention may find application in a variety of compositions, methods and procedures. 
     For example, the fish-associated sequences disclosed herein may be regarded as markers which indicate the ability of certain  Streptococcus  species or strains, for example strains of  S. agalactiae , to cause disease in fish. As such, one or more of the fish-associated sequences of this invention may form the basis of tests to detect or identify  S. agalactiae  strains which have the potential to cause disease or be pathogenic in fish. 
     Thus, in a first aspect, the invention provides a method of screening for or detecting or identifying streptococci which are pathogenic in fish, said method providing a strain or species of  Streptococcus  to be tested and detecting the expression and/or presence of one or more of the genes and/or proteins identified in Table 1, wherein detection of the expression and/or presence of one or more of the genes and/or proteins identified in Table 1 indicates that the  Streptococcus  is a  Streptococcus  which is pathogenic in fish. 
     For example, the invention may exploit one or more of the genes contained within one or more of loci 1-8 identified in Table 1 above. The invention may further exploit one or more genes encoding components of pathways which have now been associated with virulence in fish. For example, the invention may exploit one or more of the genes of locus 3 and/or one or more genes encoding components of the Leloir pathway. The invention may exploit one or more genes encoding one or more of the following proteins/enzymes/pathway components: 
     (i) Alpha-galactosidase; 
     (ii) rhamnulose-1-phosphate aldolase; 
     (iii) aldose 1-epimerase; 
     (iv) galactose mutarotase; 
     (v) galactokinase; 
     (vi) D-galactose-1-phosphate uridyltransferase; 
     (vii) UDP-galactose 4-epimerase; 
     (viii) ABC transporter permease; 
     (ix) sugar ABC transporter permease; 
     (x) sugar ABC transporter sugar-binding protein; 
     (xi) AraC family transcriptional regulator; 
     (xii) phosphotransferase system, galactitol-specific IIB component; 
     (xiii) PTS system, galactitol-specific IIC component; 
     (xiv) PTS system, galactitol-specific IIA component; 
     (xv) PTS system, galactitol-specific IIC component; 
     (xvi) PTS system galactitol-specific enzyme IIB component; 
     (xvii) PTS system, galactitol-specific IIA component; and 
     (xviii) PTS system IIA domain-containing protein. 
     It should be understood that the term “pathogenic” embraces any  Streptococcus  species or strain which has the ability to infect and/or cause disease in fish. Thus, the methods disclosed herein may be used to detect or identify those streptococci which are most likely to cause disease in fish. 
     The methods may be further applied to screening samples for the presence or absence of streptococci that are pathogenic to fish. For example, samples may be probed for the presence of one or more of the genes or proteins identified in Table 1. 
     Samples which may be subject to the methods of this invention may include any sample of matter which could contain streptococci potentially pathogenic to fish. In particular, samples derived from matter to which fish are likely to be exposed may be tested using the methods of this invention. For example, the term “sample” may include biological samples such as, for example, tissue biopsies and/or samples of cells, secretion, scrapings fluids, blood and the like. For example, biopsies from fish may be screened and/or probed for the presence or absence of pathogenic streptococci. The term “samples” may also encompass samples of water, food and substrates such as soil, sand, water body (for example lake, loch, pond, stream, river, sea or ocean) bed substrates. A sample may be a sample of a material, product or substrate used in a tank or other vessel suitable for holding fish. 
     In view of the above, the present invention may find particular application in the field of fish farming and aquaculture where the fish-associated sequences of this invention may form the basis of protocols useful to screen for streptococci which may cause disease. 
     The methods of the first and second aspects of this invention may be immunological and/or molecular/amplification based methods. One of skill will appreciate that immunological methods may exploit binding agents, for example antibodies and the like, with affinity and/or specificity for (i.e. an ability to bind to) any of the fish-associated sequences (in particular the proteinaceous products) described herein. Suitable immunological techniques include, for example ELISA and other types of immunoassay. Amplification methods may comprise, for example, isothermal amplification procedures and/or LAMP (loop mediated amplification: an alternative to PCR) as a method to detect oligonucleotides. 
     PCR (or molecular) methods may exploit oligonucleotides capable of binding to or interacting with one or more of the fish-associated sequences disclosed herein. For example, the invention may provide methods which exploit oligonucleotide or peptide sequences complementary to a sequence of one or more of the fish-associated sequences of this invention. The complementary sequences of the oligonucleotides or peptides of this invention may span, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or about 50 residues of any of the fish-associated sequences of this invention. 
     In view of the above and in a third aspect, this invention provides antibodies, including polyclonal and/or monoclonal antibodies (or antigen binding fragments thereof) that bind (or have affinity or specificity for) any of the fish-associated sequences provided by this invention. Production and isolation of polyclonal/monoclonal antibodies specific for protein/peptide sequences is routine in the art, and further information can be found in, for example “Basic methods in Antibody production and characterisation” Howard &amp; Bethell, 2000, Taylor &amp; Francis Ltd. Such antibodies may be used in diagnostic procedures to, for example, detect or diagnose  S. agalactiae  infection/infestations in an animal (for example, fish) species, as well as for passive immunisation. 
     One of skill will appreciate that, where a method of this invention exploits an immunological technique, one or more of the fish-associated sequences (for example one or more of the proteins identified in Table 1) may be immobilised to a substrate and the immobilised moiety used to probe a sample for the presence of antibodies reactive thereto. After a suitable period of incubation between the immobilised moiety and the sample, the presence or absence of antibodies may be detected by means of a secondary binding agent (for example an antibody) optionally conjugated to a detectable component, with specificity for the relevant antibody. The presence of antibody in a sample may indicate the presence of a streptococcal strain which is pathogenic to fish. 
     Alternatively, binding agents (for example aptamers (oligonucleotide/peptide type aptamers)) or antibodies with specificity to one or more of the  S. agalactiae  antigens described herein may be immobilised onto a substrate. The substrate may then be used to probe a sample for the presence of one or more  S. agalactiae  antigens. After a suitable period of incubation between the sample and the immobilised antibody, the substrate may be contacted with a secondary binding agent or antibody with specificity for the relevant antigen. The secondary binding agent or antibody may be conjugated to a detectable moiety. Alternatively, the immobilised binding agent:antigen:binding agent complexes may be further probed with a tertiary binding agent or antibody capable of binding to the secondary binding agent. The tertiary binding agent may be conjugated to a detectable moiety. 
     Other immunological techniques, such as immunohistochemical staining, may exploit binding agents (for example antibodies/conjugated antibodies) with specificity for one or more of the  S. agalactiae  antigens described herein to detect the presence or absence of  S. agalactiae  or  S. agalactiae  antigens in a sample. 
     It should be noted that while traditional ELISA and/or molecular (for example PCR) based methods may be used to execute the various methods of this invention, other techniques exploiting nanotechnology, microfluidics, electrochemistry (changes in electrical conductivity that result from the binding of a target (eg streptococcal) sequence to an aptamer bound to a carbon nanotube) may also be useful. Molecular methods useful to detect the presence of  S. agalactiae  or antigens therefrom in a sample may exploit primer sequences which amplify sequences encoding one or more of the fish-associated sequences/antigens of this invention. These primers may be used to probe samples for the presence of  S. agalactiae  nucleic acid. Further information regarding these (PCR-based) techniques may be found in, for example, PCR Primer: A Laboratory Manual, Second Edition Edited by Carl W. Dieffenbach &amp; Gabriela S. Dveksler: Cold Spring Harbour Laboratory Press and Molecular Cloning: A Laboratory Manual by Joseph Sambrook &amp; David Russell: Cold Spring Harbour Laboratory Press. Further information on isothermal amplification methods may be found, for example, in Yan L, Zhou J, Zheng Y, Gamson A S, Roembke B T, Nakayama S, Sintim H O. Isothermal amplified detection of DNA and RNA. Mol Biosyst. 2014 May; 10(5):970-1003. doi: 10.1039/c3mb70304e. 
     The present invention also extends to kits comprising reagents and compositions suitable for diagnosing and/or detecting  S. agalactiae  infections. For example, depending on whether or not the kits are intended to be used to identify levels of  S. agalactiae  antigen or antibodies thereto in samples, the kits may comprise substrates having  S. agalactiae  antigens (for example any of those identified in Table 1 or any of the fish-associated sequences/antigens described herein) or agents capable of binding any of the fish-associated sequences to which this invention relates, bound thereto. In addition, the kits may comprise agents capable of binding fish-associated sequences (antibodies, aptamers and the like)—particularly where the kit is to be used to identify levels of  S. agalactiae  antigen in samples. In other embodiments, the kit may comprise agents capable of binding the  S. agalactiae  antigens, for example specifically raised polyclonal antibodies or monoclonal antibodies. Kits for use in detecting the presence or expression of genes encoding the fish-associated sequences may comprise one or more of the oligonucleotides/primers described herein. The kits may also comprise other reagents to facilitate, for example, sequencing and/or PCR or isothermal analysis. All kits described herein may further comprise instructions for use. 
     The invention further provides immunogenic compositions comprising one or more of the fish-associated sequences described herein. In particular, the invention provides immunogenic compositions comprising one or more of the fish-associated protein sequences identified in Table 1. These protein sequences (or for example, any variants, derivatives, homologous and/or immunogenic fragments thereof) may be antigenic (antigens) and capable of eliciting or raising immune responses in animals. 
     The immunogenic compositions of this invention may find application as vaccines and thus the invention further provides vaccines and vaccine compositions. 
     For convenience, those sequences disclosed in this specification which encode antigens useful in the compositions or vaccines of this invention shall be referred to as “fish-associated antigens”. Thus the vaccines and vaccine/immunogenic compositions of this invention may comprise one or more of the fish-associated antigens of this invention (for example those described in Table 1). The fish-associated antigens may (in use) elicit a “protective” immune response. One of skill will appreciate that the precise nature of the response (humoral and/or cellular, for example) may depend on the formulation of the antigen, its route of administration, the presence or absence of adjuvant, and the type of adjuvant employed. 
     In a fourth aspect, the invention provides an immunogenic composition comprising one or more of the fish-associated antigens described herein. 
     In a fifth aspect, the invention provides a vaccine or vaccine composition comprising one or more of the fish-associated antigens described herein. 
     The compositions or vaccine of the fourth and fifth aspects of this invention may comprise excipients such as pharmaceutically acceptable and/or sterile excipients, carriers and/or diluents. Additionally, or alternatively, the compositions or vaccines of this invention may further comprise or be admixed with, another component or components, such as another polypeptide and/or an adjuvant. Additionally, or alternatively, vaccines or vaccine compositions provided by this invention may, for example, contain viral, fungal, bacterial or other parasite whole cells/particles and/or antigens used to control other diseases/infections or infestations. For example, the vaccine or vaccine composition may be included within a multivalent vaccine, which includes antigens against other piscine pathogens/diseases. 
     In addition to compositions and/or vaccines which comprise fish-associated antigens, the invention further provides immunogenic compositions and vaccines which comprise attenuated or killed strains of  S. agalactiae  which express or harbour one or more of the fish-associated sequences described herein. The attenuated or killed  S. agalactiae  strains may not express one or more of the fish associated sequences of this invention. For example, the genome of a  S. agalactiae  strain to be used as a vaccine may be modified so as to (i) lack one or more of the genes encoding one or more of the fish-associated sequences described herein and/or (ii) comprise one or more genes modified to prevent functional expression of one or more of the fish-associated sequences of this invention. 
     The vaccines of this invention may also take the form of DNA type vaccines (used in association with an appropriate delivery system, such as liposomes, microspheres, attenuated bacterial vectors and the like). A DNA vaccine for use in an invention of this type may comprise sequences encoding one or more of the fish-associated sequences of this invention. 
     In view of the above, a further aspect of this invention provides a composition, immunogenic composition or vaccine composition comprising one or more of the fish-associated antigens described herein, for use in raising an immune response in an animal. In one embodiment, the immune response is a protective response. A protective immune response may be a response which neutralizes, inhibits or prevents a  Streptococcus agalactiae  infection and/or a disease or condition caused thereby or associated therewith. 
     In a further embodiment, the animal may be any animal susceptible to infection by or with an  S. agalactiae  strain (for example a strain which is pathogenic in fish). For example, the animal may be a fish. 
     In a yet further aspect, the invention provides the use of one or more of the fish-associated antigens described herein for the manufacture of a medicament or vaccine for use in the treatment and/or prevention of a  Streptococcus agalactiae  infection and/or a disease or condition caused thereby or associated therewith. 
     Moreover, the invention may provide one or more compounds which modulate any aspect of the function, activity and/or expression of one or more of the fish-associated sequences of this invention. Such compounds may be collectively referred to as “modulator compounds”. For example, the modulator compounds may take the form of small organic molecules, antibodies (monoclonal or polyclonal and/or antigen (fish-associated sequence) binding fragments thereof) with affinity for any of the fish-associated sequences described herein (such antibodies are described above), proteins, peptides, carbohydrates, nucleic acids (RNA and/or DNA), aptamers. 
     One of skill in this field will appreciate that compounds which exhibit an ability to modulate (for example increase or decrease) aspects of the function, expression and/or activity of any of the fish-associated sequences of this invention may easily be prepared and tested. For example, a compound (a test agent) may be tested for an ability to modulate a fish-associated sequence of this invention by contacting the agent with an  S. agalactiae  strain expressing one or more of the fish-associated sequences of this invention and determining (perhaps after a period of incubation) any modulation of the level of expression, function and/or activity of the fish associated sequence. 
     Modulation of a level of expression, function and/or activity of a fish-associated sequence may be determined by comparison with the level of expression function and/or activity of the same or a corresponding fish-associated sequence(s) in a control system—for example an  S. agalactiae  strain which has not been contacted with the test agent. The detection of any difference in the expression, function and/or activity of one or more of the fish-associated sequences indicates that the test agent may be a compound which is capable of modulating the expression, function and/or activity of one or more of the fish-associated sequences. 
     Compounds which modulate the expression, function or activity of one or more of the fish-associated sequences (for example compounds which block or neutralize the function, expression or activity of a fish-associated sequence) may find application (as medicament) in the treatment or prevention of diseases, conditions or infections caused or contributed to by  S. agalactiae  in fish. Such compounds may also be useful in methods of treating or preventing diseases, conditions or infections caused or contributed to by  S. agalactiae  in fish, the methods comprising administering therapeutically effective amounts of the compounds described herein. 
     The invention further provides a method of raising an anti- Streptococcus agalactiae  immune response in an animal, said method comprising the step of administering to an animal, an immunogenic amount of one or more  Streptococcus  antigen(s) or fragment(s) thereof, sufficient to induce an anti- Streptococcus agalactiae  immune response. 
     The vaccines, vaccine/immunogenic compositions and antigens of this invention may find application in the treatment, prevention and/or control of  S. agalactiae  infections and/or associated diseases in fish hosts. The vaccine may be a polypeptide or polynucleotide vaccine—the polypeptides and/or polynucleotides providing, or encoding, one or more of the  S. agalactiae  fish-associated sequences/antigens described herein. 
     The vaccines, vaccine/immunogenic compositions and antigens of this invention may be used not only to raise immune responses in animals (in particular fish) but also in the treatment or prevention of diseases caused or contributed to by streptococcal species, including for example,  S. agalactiae . The various therapeutic agents discussed herein (vaccines, immunogenic compositions, antigens and the like) may be used to treat or prevent diseases such as, for example, septicaemia and meningo-encephalitis as might occur in freshwater and saltwater fish species. Thus, the immunogenic compositions, vaccines and antigens of this invention have significant utility in any fish species susceptible or predisposed to a disease, condition or infection caused or contributed to by a streptococcal species or, more specifically, by  S. agalactiae . For example, the vaccines, immunogenic compositions and antigens of this invention may be used to raise immune responses and/or prevent or treat diseases and/or infections (such as  S. agalactiae -associated diseases, conditions or infections) in tilapia. 
     The compositions of this invention, including, for example the immunogenic and vaccine compositions, may be formulated for enteral (including oral), topical (including dermal and sublingual), parenteral (including subcutaneous, intradermal, intramuscular, intraperitoneal and intravenous), transdermal and/or mucosal administration. The compositions of this invention, including, for example the immunogenic and vaccine compositions, may be formulated for “immersion” or “bath” administration—specifically, the compounds may be added to water into which an animal (for example a fish) to be treated is placed. As the fish passes water through its body and over its gills, it is brought into contact with any compositions that have been added to the water. 
    
    
     
       DETAILED DESCRIPTION 
       The present invention will now be described in detail with reference to the following Figures which show: 
         FIG. 1 : Kaplan-Meier curves comparing survival of tilapia following intraperitoneal injection of  Streptococcus agalactiae  strain STIR-CD-17 (sequence type (ST) 260) at doses corresponding to 10 2 , 10 5  and 10 7  cfu per fish. No mortality was observed for the negative control fish (sham dose). Curves are significantly different (Mantel-Cox log rank test, P&lt;0.05). 
         FIG. 2 : Minimal mobile elements containing fish specific genes are clustered in Locus 1 (A), with clonal complex (CC) specific genomic content inserted between flanking genes purK and purB, and in Locus 8 (B), which shows lineage-specific content for CC552 but not for other CCs of  Streptococcus agalactiae . In this analysis, CC552 includes isolates STIR-CD-17 and SA20-06; CC7 includes isolates GD201008-001, ZQ0910 and A909; and CC23 includes isolates NEM316, 515 and MRI Z1-201. Hypo=hypothetical protein. 
         FIG. 3 : Bayesian phylogenetic tree based on 22,484 concatenated SNPs from the core genome of 16 isolates of  Streptococcus agalactiae  showing sequence type (ST), serotype and host of origin (fish, seal, bovine, human or unknown origin). Clonal complex (CC) of isolates included in the analysis are also indicated, using nomenclature that predates the amalgamation of CC1, CC7, CC17 and CC19. Posterior probabilities are shown at each node and the scale bar represents the substitutions per site. 
         FIG. 4 : (A) Genetic structure of locus 5, which carries 5 genes (full arrows), and 3 pseudogenes (dashed arrows). Locus 5 disrupts a conserved gene encoding a putative outer-membrane protein in  S. agalactiae  A909 (ST7). Direct repeats (DR) flank the extremities of locus 5 and a similar sequence is found in the corresponding integration position in  S. agalactiae  A909. (B) Alignment of the DR sequences as found in STIR-CD-17 (sequence 2 and 3) with the corresponding sequence as found in A909 (sequence 1). Black blocks indicate sequence identity and grey blocks indicate single nucleotide polymorphisms. Hypo, Hypothetical protein; Abi, abortive infection protein. 
         FIG. 5 : Western blot of  Streptococcus agalactiae  recombinant proteins (SDS-PAGE 4-12% Bis-Tris polyacrylamide gel). (A) M3M-01212—rhamnulose-1-phosphate aldolase; (B) V193-02470—aldose epimerase; (C) M3M-01172—alpha-galactosidase. Lanes: (1) negative control fish serum (1/20; (2) immunised fish serum (1/20); (3) Coomassie blue stained gel. Band of interest is indicated with an arrow. 
     
    
    
     MATERIALS AND METHODS 
     Challenge Study 
       Streptococcus agalactiae  Strains. 
     For the challenge study, isolates representing CC552 and ST23 were selected. CC552 was represented by isolate STIR-CD-17, which was isolated in 2008 during a clinical outbreak of streptococcosis affecting farmed tilapia ( Oreochromis  sp.) in Honduras. This isolate is non-haemolytic, belongs to ST260 and serotype Ib and it was negative by PCR for all surface protein genes and mobile genetic elements (MGE) that were evaluated as part of standardized 3-set genotyping (Delannoy et al. 2013). ST23 was represented by isolate MRI Z1-201, which was recovered by lung swab from a grey seal ( Halichoerus grypus ) found dead in 2003 in Scottish coastal waters. Post-mortem examination of the seal identified a systemic infectious process as the cause of death, but it was not clear whether this was caused by the  S. agalactiae  strain. MRI Z1-201 is beta-haemolytic, belongs to serotype Ia and contains genes encoding an alpha-like protein (alp1) and 3 insertion sequences (IS1381, ISSag1 and ISSag2) (Delannoy et al., 2013). This combination of ST, molecular serotype, surface protein-encoding genes and insertion sequences has been reported from poikilothermic animals, including being a cause of necrotizing fasciitis in crocodiles ( Crocodylus porosus ) (Bishop et al. 2007). 
     Fish. 
     Nile tilapia ( Oreochromis niloticus ) were reared in the Tropical Aquarium at the Institute of Aquaculture (University of Stirling, UK) and maintained in a re-circulating water system in aquaria at 28±2° C. under constant aeration and filtration. The fish were fed twice daily with commercial pellets (Skretting, UK) and kept on a 12 h light/12 h dark cycle. Prior to bacterial challenge, three fish were sacrificed and sampled for bacterial recovery as described (Crumlish, Thanh, Koesling, Tung &amp; Gravningen 2010); briefly, a sterile plastic bacteriological loop (Fisher Scientific, Loughborough, UK) was inserted into the kidney and used to inoculate a tryptone soya agar plate (TSA; Oxoid Ltd., Basingstoke, UK). Plates were incubated at 28° C. for 72 h and examined for the presence of bacterial colonies. Absence of microbial colonisation was confirmed, and clinically healthy animals originating from the same groups and weighing 40±5 g were transferred to the Aquatic Research Challenge Facility (Institute of Aquaculture, University of Stirling, UK) for subsequent use in passage and challenge studies. All animal experiments were conducted at the Institute of Aquaculture in accordance with the Animals (Scientific Procedures) Act 1986. 
     Passage and Challenge. 
     Fish were lightly anaesthetized by immersion in a benzocaine bath (Sigma-Aldrich, Irvine, UK). For intraperitoneal (i.p.) challenge, a 0.1 mL inoculum was administered via a needle, mounted on a 1 mL syringe, inserted cephalad into the midline of the abdomen just posterior to the pectoral fins. Fish were fasted for 24 h prior to injection and for 12 h following injection, at which time daily feeding was resumed. Fish from different experimental groups (10 animals per group), as defined by strain, dose and follow-up period, were kept in separate 10 L aquaria with separate flow-through water systems, a temperature of 28±2° C. and a 12 h light/12 h dark cycle. Fish were monitored at least 3 times daily for signs of disease and death. All moribund and dead fish were removed, and moribund fish were euthanized with an overdose of benzocaine. 
     Prior to the challenge experiment, ST260 and ST23 were passaged through fish to enhance their virulence post-storage (Eldar, Bejerano, Livoff, Horovitcz &amp; Bercovier 1995). For each strain, a single colony from a pure culture was used to inoculate 4 mL of tryptone soya broth (TSB; Oxoid Ltd.) and cultures were incubated aerobically for 8 h (ST23, fast growing) or 24 h (ST260, slow growing) at 28° C. with gentle shaking (140 rpm). These cultures were then used to seed 36 mL aliquots of TSB, and cultures were incubated for 16 h at 28° C. and 140 rpm. Cultures were then centrifuged at 3,293 rcf for 15 min and the supernatants were discarded. Centrifugation was repeated several times for ST260 because it produced a fragile cell pellet. Cell pellets were resuspended in sterile 0.85% saline and the OD 600 nm  was adjusted to 1, corresponding to approximately 10 9  viable colony forming units (cfu) per mL for ST260 and 10 8  viable cfu per mL for ST23, as determined by plating serial ten-fold dilutions according to the method of Miles, Misra &amp; Irwin (1938). Inocula containing a high concentration of bacteria (approximately 10 7  cfu per fish) were injected into a single fish. For ST260, this procedure was only performed on a single occasion, because the fish died as a direct consequence of infection within 3 days post-inoculation (p.i.). Fish challenged with ST23 were euthanized at 3 days p.i.,  S. agalactiae  was cultured from the brain and kidney and the procedure was repeated twice, whereby isolates from the sacrificed fish were used to prepare the inoculum for the next passage. One colony isolated from the brain after the 1 st  passage (ST260) or the 3 rd  passage (ST23) was sub-cultured onto 5% (v/v) sheep blood agar plates (SBA; E&amp;O Laboratories, Bonnybridge, UK) and used for challenge experiments. 
     Based on results from the pre-experimental passages, challenge with ST260 was conducted at three doses (10 2 , 10 5  and 10 7  cfu per mL; 3 groups of 10 animals each) whereas challenge with ST23 was only conducted at the highest dose (10 7  cfu per mL; 2 groups of 10 animals each). A sixth group (10 animals) was mock-challenged with 0.85% sterile saline. The maximum follow-up period was 16 days. For fish challenged with ST260, moribund individuals were euthanized as well as the fish remaining at day 16 p.i. For fish challenged with ST23, one group was euthanized at day 7 p.i. while the second group and the negative control group were euthanized at day 16 p.i. Euthanized fish were aseptically sampled for bacterial recovery from the kidney (Crumlish et al. 2010). Kaplan-Meier curves were used to compare survival rates of tilapia challenged with different doses of ST260 and significance of differences was determined using a log rank test (Graph Pad Software version 5, San Diego, Calif., USA). 
     Genome Comparison 
     Genomic DNA Preparation. 
     The ST260 isolate, STIR-CD-17, was streaked onto SBA and grown aerobically at 28° C. for 72 h to assess purity and absence of haemolysis. A single colony was used to inoculate 5 mL of Brain Heart Infusion broth (BHI; Oxoid Ltd.). After overnight static incubation at 28° C. in an aerobic environment, genomic DNA was extracted from cells harvested from 1 mL of culture using an Epicentre MasterPure Gram-positive DNA purification kit (Epicentre, Madison, Wis., USA), with slight modifications; briefly, the bacterial culture was repeatedly centrifuged (due to loose pellet), supernatant was removed and cells were re-suspended in 150 μL of TE Buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA), 6 μL of mutanolysin (5 U per μL; Sigma-Aldrich, Irvine, UK) and 1 μL of ready-to-use lysozyme (as provided by the kit manufacturer), and incubated at 37° C. for 1 h. The remainder of the protocol was performed according to manufacturer&#39;s instructions, except for the extension of the Proteinase K/Gram-Positive Lysis Solution incubation time (30 min instead of 15 min) and the RNase incubation time (1 h instead of 30 min). DNA concentration was quantified using a NanoDrop 1000 (Thermo Scientific, Loughborough, UK) and genomic DNA (0.5 μg) was visualized over UV light to assess absence of shearing following electrophoresis through a Gel Red (Cambridge Bioscience, Cambridge, UK)—containing 0.8% (w/v) agarose gel (at 100 V cm −1  for 1 h). 
     Genome Sequencing, Assembly and Annotation. Genome sequencing and de novo assembly of reads was performed at the GenePool sequencing core facility (University of Edinburgh, UK) using an Illumina Solexa Genome Analyzer and VELVET 0.6. Of 208 contiguous sequences (contigs), 96 were more than 200 nucleotides long and were annotated using the Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) of the National Centre for Biotechnology Information (NCBI). The draft genome sequence of  S. agalactiae  STIR-CD-17 has been deposited in GenBank under accession number ALXB00000000 (Delannoy, Zadoks, Lainson, Ferguson, Crumlish, Turnbull &amp; Fontaine 2012). Functional categories of proteins were identified by PGAAP based on the analysis of Clusters of Orthologous Genes (COGs) using the COGnitor program (Tatusov, Fedorova, Jackson, Jacobs, Kiryutin, Koonin, Krylov, Mazumder, Mekhedov, Nikolskaya, Rao, Smirnov, Sverdlov, Vasudevan, Wolf, Yin &amp; Natale 2003). When a functional category could not be identified using COG analysis, nucleotide sequences were screened for conserved Pfam domains (http://pfam.sanger.ac.uk/search) to determine the putative function of hypothetical proteins. Finally, in silico prediction of subcellular localization of proteins encoded by the genome was performed using the PSORTb program version 3.0.2 (Yu, Wagner, Laird, Melli, Rey, Lo, Dao, Sahinalp, Ester &amp; Foster 2010), using the module for Gram-positive bacteria. Prediction categories included cytoplasmic, cytoplasmic membrane, cell wall, extracellular and unknown localization. 
     Comparative Genomic Analysis. 
     For comparative analysis, representative  S. agalactiae  genomes were selected, including those from subpopulations found in fish and humans (CC7), in terrestrial and aquatic mammals but not in fish (CC23), in humans only (CC17), in cattle only (CC67), and in humans and cattle (CC1, CC19) (Delannoy et al. 2013; Zadoks et al. 2011). 
     Genomes were compared by means of reciprocal BLAST comparison of the translated products of predicted open reading frames (ORF) of STIR-CD-17 against each of 10 reference genomes (Table 2). The BLASTP score was used to express the level of homology and to identify reciprocal best hits. Predicted protein sequences from STIR-CD-17 that did not find a reciprocal best hit with a BLAST score &gt;80 in any of the other genomes were identified, and their corresponding genes were considered putatively fish-specific. Predicted protein sequences from STIR-CD-17 with a reciprocal best hit and BLAST score &gt;80 in genomes belonging to CC7 only were also identified, and their corresponding genes were considered putatively fish-associated because isolates belonging to CC7 occur in fish as well as in people. Subsequently, amino acid sequences encoded by the predicted putatively fish-specific or fish-associated genes were searched against the NCBI protein database (http://www.ncbi.n-lm.nih.gov/BLAST; last accessed 13 Jan. 2013) to determine whether homologues existed beyond the 10 selected  S. agalactiae  genomes. Homology between predicted proteins was analysed whilst correcting for query length using normalised BLAST score ratio (BSR) analysis (Rasko, Myers &amp; Ravel 2005). For each protein, the BLASTP bit-score for the alignment against itself (REF_SCORE) and for the most similar proteins within the database (QUE_SCORE) was obtained and normalized by dividing the QUE_SCORE by the REF_SCORE. Amino acid sequences with a normalized bit-score ≥0.8 were considered homologous. Normalized bit-scores &lt;0.8 were taken as an indication of divergence (0.4&lt;BSR&lt;0.8) or uniqueness (BSR≤0.4) (Rasko et al. 2005). Finally, to overcome potential annotation discrepancies, selected genomes were compared pairwise using the Artemis Comparison Tool (ACT; Carver, Berriman, Tivey, Patel, Bohme, Barrell, Parkhill &amp; Rajandream 2008) and the DOUBLE ACT v2 web interface (http://www.hpa-bioinfotools.org.uk/pise/double_act.html) with BLASTN and default settings. The ACT comparison also provided insight into the genetic organisation and conservation of sequences flanking regions of interest. 
     Finally, the genome of STIR-CD-17 (ST260) was compared with the unannotated genome of MRI Z1-201 (ST23; NCBI accession number ANQL00000000). Both genomes were analysed by BLAST search and ACT comparisons for the presence of known  S. agalactiae  virulence genes, including adhesins, invasins and evasins (Table 3). Pairwise ACT comparisons between STIR-CD-17 and MRI Z1-201 were also performed to evaluate presence of the putatively fish-specific genes and fish-associated genes within MRI Z1-201 and results were confirmed by PCR (discussed below). Lastly, the relatedness between the challenge study isolates and other fish-derived  S. agalactiae  isolates was explored based on the phylogeny of their core genome. In addition to the challenge study isolates and the annotated genomes listed in Table 2, this analysis included genomes of the fish-derived isolates SA20-06 (ST553; Pereira, Rodrigues, Hassan, Aburjaile, Soares, Ramos, Carneiro, Guimarães, Silva, Diniz, Barbosa, Gomes de Sã, Ali, Bakhtiar, Dorella, Zerlotini, Araújo, Leite, Oliveira, Miyoshi, Silva, Azevedo &amp; Figueiredo 2013), ZQ0910 (ST7; Wang, Jian, Lu, Cai, Huang, Tang &amp; Wu 2012), GD201008-001 (ST7; Liu, Zhang &amp; Lu 2012) and STIR-CD-25 (ST283; NCBI accession number ANEK01000001; Delannoy et al. 2013). The Panseq v.2.0. Web server (Laing, Buchanan, Taboada, Zhang, Kropinski, Villegas, Thomas &amp; Gannon 2010) was used for automated extraction, concatenation and alignment of nucleotide sequences from the core genome, using default settings except that the core genome threshold was set to 16 so that any region not found in all 16 genomes was removed. The resulting nexus file consisting of 22,484 concatenated single-nucleotide polymorphisms (SNPs) from the core genome was used for phylogenetic analysis and model optimisation in TOPALi v2.5 (Milne, Wright, Rowe, Marshall, Husmeier &amp; McGuire 2004). The selected model (Symmetrical Model [SYM]) was used to estimate a Bayesian phylogenetic tree in MrBayes (Ronquist &amp; Huelsenbeck 2003) launched from TOPALi. The MrBayes settings were 2 runs of 625,000 generations and a burn-in period of 125,000 generations, with trees sampled every 10 generations. The consensus tree was imported into DENDROSCOPE v3.2.1 (Huson, Richter, Rausch, Dezulian, Franz &amp; Rupp 2007) for visualization and editing. 
     Population Screening 
     Isolate Collection. 
     To complement the in silico identification of putatively fish-specific or fish-associated genes, which was largely based on comparison with  S. agalactiae  of human origin, the presence of genes of interest was assessed among a panel of unsequenced  S. agalactiae  isolates from fish, aquatic mammals and cattle. Fish and sea mammal isolates used have previously been described in detail (Delannoy et al. 2013). Briefly, fish isolates originated from an outbreak of streptococcosis in wild mullet ( Liza klunzinger ) in Kuwait (1 outbreak, 5 isolates), from outbreaks of streptococcosis in farmed tilapia ( Oreochromis  spp.) from Colombia (1 outbreak, 1 isolate), Costa Rica (1 outbreak, 4 isolates), Honduras (1 outbreak, 3 isolates), Vietnam (1 isolate), Thailand (7 isolates from 7 unrelated outbreaks) and Belgium (1 isolate) and from 3 fish (rosy barb, golden ram, and unidentified species) from unrelated aquaria in Australia. Thus, 16 epidemiologically unrelated events were represented. The sequenced strain, STIR-CD-17, originated from the outbreak in Honduras. Sea mammal isolates originated from a bottlenose dolphin ( Tursiops truncatus ) and 5 grey seals ( Halichoerus grypus ) that had stranded in the UK in unrelated incidents. Bovine isolates were obtained from aseptically collected quarter milk samples from 6 farms in Denmark and, based on pulsed-field gel electrophoresis and multi-locus sequence typing (unpublished data), represented 19 macro-restriction profiles and 6 STs from 3 CCs (CC1, 19 and 23). 
     PCR Screening. 
     Final volumes of 250 μL of bacterial lysates were prepared by digestion with lysozyme and proteinase K (Delannoy et al. 2013). Species identity of all isolates was confirmed using primers that target a species-specific fragment of the 16S-23S intergenic spacer region (Delannoy et al. 2013). Intragenic primers were designed from the genome of STIR-CD-17 to allow amplification of 2 putatively fish-specific genes and 3 fish-associated genes using the Primer Select module in Lasergene (DNASTAR Inc., Madison, Wis., USA) (Table 4). PCR reactions for species confirmation and detection of putatively fish-specific and fish-associated genes were performed in 25 μL volumes containing 12.5 μL of GoTaq Green Master Mix (Promega, Madison, Wis., USA), 0.25 μM of each primer and 2 μL of DNA template. Thermal cycling consisted of a denaturation step at 94° C. for 5 min followed by 35 cycles of 94° C. for 1 min, target-specific annealing temperature for 45 s, and 72° C. for 30 s with a final step at 72° C. for 7 min. Annealing temperatures were based on the melting temperatures of the respective primer sets, as provided by the manufacturer (Eurofins MWG Operon, Munich, Germany). The PCR products for all reactions were visualized over UV light following electrophoresis through 1.5% (w/v) agarose gels containing Gel Red. Strain STIR-CD-17, from which the genome and primer sequences were derived, was included in each assay as positive control and a water blank was included as negative control. 
     Results 
     Challenge Study 
     Fish challenged with ST260 showed dose-dependent mortality ( FIG. 1 ). Most deaths occurred between days 1 and 7 p.i., and at termination of the experiment only 1 fish remained alive. Fish that died within 48 hr p.i. did not show any clinical signs of disease prior to death. The first clinical signs appeared 2 to 5 days p.i. depending on the dose administered, and consisted of lethargy and anorexia which were always followed by signs of ataxia 24 to 48 h prior to death. Most fish remaining alive after day 7 (only fish from the groups receiving 10 2  and 10 6  cfu per fish) exhibited uni- or bilateral exophthalmia together with corneal opacity and peri-ocular haemorrhage. Occasionally, fish exhibited abdominal extension due to accumulation of ascitic fluid ranging from translucent to purulent.  Streptococcus agalactiae  was recovered from the kidneys of all tested tilapia (n=10). 
     Among fish challenged with ST23, no mortality or clinical signs were observed after 7 days p.i. One group of 10 fish was sacrificed and bacteria were recovered from the kidneys of 3 of these fish, demonstrating infection in the absence of clinical disease. After day 7, there was one dead fish but death was attributed to fighting and cannibalism. Sampling for bacterial recovery was not possible for this fish due to absence of its carcass. The second group of 10 fish was euthanized at the end of the experiment (16 days p.i.). No bacteria were recovered from the kidneys of this group. No morbidity or mortality was recorded in mock-challenged control fish nor were any bacteria recovered from these fish. 
     Genome Comparison 
     The draft genome of STIR-CD-17 contained 1,805,303 nucleotides, 21 rRNA genes and 80 tRNA genes. The average G+C content was 35%. In addition, 102 pseudogenes were identified which contained multiple stop codons due to frameshift and nonsense mutations. 
     Several putatively fish-specific genes and fish-associated genes were identified (Table 1). Genes were considered to be putatively fish-specific if they were identified only in the genome of ST260 during whole genome comparison and only in isolates from CC552 in subsequent BSR analysis, which included additional sequence information from NCBI. Genes were considered to be fish-associated if they were only identified in the genome of ST260 and ST6 or ST7 (both CC7) during whole genome comparison and only in isolates from CC552 or CC7 in subsequent BSR analysis but not in members of other CCs. Putatively fish-specific and fish-associated genes were distributed over 8 small clusters or loci, which are discussed in the following sections. The largest locus, locus 3, was considered fish-associated whereas the remaining 7 loci were fish-specific. Locus 4 included a few genes that were shared with other strains of  S. agalactiae , implying that some elements of this locus were not fish-specific; however, rather than being split into multiple fish-specific and non-specific elements, this locus will be described as if it were fish-associated. The first and last loci, namely locus 1 and locus 8, were located between sets of genes considered well-conserved across  S. agalactiae  genomes. Locus 1 contained two fish-specific ORF, the translated products of which were predicted to be localised within the cytoplasm (due to the absence of any secretion-associated motifs), but did not contain any known domain from which a putative function could be derived. The 2 ORF were located between genes (purK and purB encoding an ATPase subunit and an adenylosuccinate lyase, respectively) that are well-conserved across  S. agalactiae  genomes, including those from fish. ACT comparison of genomes from different CCs showed that the region delimited by purK and purB is occupied by distinct genes in different lineages, whereas the region is identical between isolates that belong to the same CC. For example, the same hypothetical proteins were found in the genome of 2 piscine isolates belonging to CC552 (STIR-CD-17 and SA20-06), whereas a putative membrane protein was shared by CC7 strains of human and piscine origin (A909 and GD201008-001 and ZQ0910) ( FIG. 2A ). Locus 8 also contained 2 fish-specific ORF, the first of which was predicted to encode a putative cytoplasmic protein containing a conserved domain of unknown function (PF08002). The translated product of the second ORF was identified as a DJ-1/Pfpl family protein (COG0693/PF01965), which includes proteins with intracellular protease function or transcriptional regulators (Halio, Blumentals, Short, Merrill &amp; Kelly 1996; Ohnishi, Yamazaki, Kato, Tomono &amp; Horinouchi 2005). As in locus 1, the ORF were inserted between 2 well-conserved genes, in this case ksgA (encoding a 16S ribosomal RNA methyltransferase KsgA/Diml family protein) and rnmV (encoding a primase-like protein). Locus 8 showed less diversity than locus 1, whereby the observed sequence in isolates from CC552 was conserved and distinct from the sequence in isolates from other CCs, but isolates from CC7 and CC23 contained homologous regions between ksgA and mmV ( FIG. 2B ). 
     Locus 2, 3 and 4 were all found close to each other, with locus 3 located approximately 1.7 kb downstream of locus 2, and locus 4 approximately 5.1 kb downstream of locus 3. Locus 2 was located within putative pathogenicity island (PAI) IV from human  S. agalactiae  (Glaser, Rusniok, Buchrieser, Chevalier, Frangeul, Msadek, Zouine, Couve, Lalioui, Poyart, Trieu-Cuot &amp; Kunst 2002; Herbert, Beveridge, McCormick, Aten, Jones, Snyder &amp; Saunders 2005), and contained a single ORF, the translated product of which was predicted to encode a cytoplasmic protein of unknown function. This ORF was only found within the genomes of CC552 isolates. Based on ACT comparison, this fish-specific gene occupied the region that contains the virulence genes rib or bca in genomes of human  S. agalactiae , genes that are absent from CC552 isolates (Delannoy et al. 2013; this study). Locus 3 was located just external to PAI IV (inserted between gbs0486 and gbs0487 in NEM316, PAI IV being delimited by gbs0458-0486; Glaser et al. 2002; Herbert et al. 2005) and comprised 18 ORF. The translated products shared homology with proteins found in all  S. agalactiae  from fish, i.e. isolates belonging to CC552 and CC7, and in human isolates belonging to CC7, but not with human isolates from other CCs. This locus therefore comprises genes designated as fish-associated in  S. agalactiae , even though homologues of some genes were found in other streptococcal species (Table 1). With the exception of 1 ORF encoding a putative transcriptional regulator, the ORF in locus 3 encoded products predicted to be involved in carbohydrate transport and metabolism, including those involved in the transport and degradation of galactose (GalK, GalE, GalM) and the hydrolysis of galactose-containing oligosaccharides (GalA). Concerning locus 4, its composition and organisation was found to correspond to a CRISPR-cas module (clustered regularly interspaced short palindromic repeats-CRISPR associated proteins) with sequence identity to subtype IC (Makarova, Haft, Barrangou, Brouns, Charpentier, Horvath, Moineau, Mojica, Wolf &amp; Yakunin 2011). Three ORF from this locus were found in  S. agalactiae  from CC552 only. Frame-shifts within 2 of the ORF in this locus resulted in the early termination of the coding sequences, meaning the resulting pseudogenes are unlikely be functional. Some components of the locus are also found in human or bovine strains of  S. agalactiae  belonging to ST17, ST23 and ST67, whilst homologues of some elements are found in other streptococcal species such as  S. mutans, S. canis  and  S. dysgalactiae  subsp.  equisimilis  (Table 1). 
     Locus 5 and 6 were identified within PAI VI (Glaser et al. 2002; Herbert et al. 2005). Locus 5 was flanked by 159 bp direct repeats and integrated at the position of a similar 159 bp sequence into a conserved gene encoding a putative outer membrane protein in human  S. agalactiae  strains. Locus 5 was fish-specific and contained 5 ORF and 4 probable pseudogenes ( FIG. 4 ). The translated product of the first ORF, although of unknown function, contained a conserved DNA methylase domain (PF00145). The second ORF encoded a putative surface-anchored protein containing a CHAP domain (pfam05257). The following 2 ORFs encoded hypothetical proteins only found in isolates from CC552, while the final ORF encoded a putative bacteriocin. The pseudogenes encoded a putative phage abortive infection protein, AbiGII and two resolvases; however, frame-shift mutations in each resulted in premature termination of the coding sequence. Comparison of these 4 pseudogenes with the equivalent region in the SA20-06 genome revealed identical frame-shifts in each coding sequence. Locus 6 was located approximately 4.3 kb downstream from locus 5. Locus 6 was unique to STIR-CD-17, containing 5 ORF, 3 encoding hypothetical proteins with no domains of known function, 1 encoding a putative serine hydroxymethyltransferase (SHMT) and 1 encoding a putative integrase. The locus was integrated into and disrupted a gene with hypothetical function that is conserved among other strains of  S. agalactiae.    
     Locus 7 was composed of 8 ORF, of which 3 were unique to STIR-CD-17 and 5 where shared with SA20-06 (CC552), making the latter fish-specific by our terminology. The 3 unique ORF encoded a putative permease, a putative betahydroxyl dehydratase involved in fatty acid biosynthesis (M3M_04280; PF07977) and a hypothetical protein. The translated products of the ORF that were shared within CC552 included two putative transcriptional regulators, two hypothetical proteins and a putative integrase, suggesting that these ORF form part of a MGE. Indeed, Locus 7 was inserted into a 6-phospho-beta-glucosidase-encoding gene, found intact in other  S. agalactiae  such as A909 (ST7). 
     Comparison of Challenge Strains 
     Numerous genes that are recognised as encoding virulence determinants in human  S. agalactiae  were present in the ST23 strain but not in the ST260 strain used for the challenge experiments (Table 3), including genes encoding adhesins (fbsA and Imb) and an immune evasin (scpB). Other genes were conserved in both strains, including those encoding putative adhesins (fbsA, pavA, srrl, and bibA), invasins (cfb and hylB) and immune evasins (cps and neu operon, ponA, and sodA). The allelic variants of bibA differed between ST260 (gbs2018-6) and ST23 (gbs2018-1; Brochet, Couve, Zouine, Vallaeys, Rusniok, Lamy, Buchrieser, Trieu-Cuot, Kunst, Poyart &amp; Glaser 2006), as did pilus-encoding genes (PI2b in ST260 and PI-2a in ST23). In ST260, the backbone protein of PI2b was truncated, and a sortase appeared as a pseudogene due to the introduction of stop codons. Unlike ST23, ST260 was found to have an incomplete cyl operon, where only cylA and incomplete cylE and cylB were present. Based on ACT analysis, the non-virulent ST23 isolate did not contain fish-specific or fish-associated genes that were identified through comparison of annotated genes. 
     Phylogenetic analysis of the core genome showed that CC552 is distantly related to ST23, CC7 and other strains found in cattle and humans ( FIG. 3 ). Within ST23, challenge strain MRI Z1-201 was genetically highly similar to human reference strain 515. Both strains belong to serotype Ia and were genetically divergent from NEM316, which belongs to ST23 and serotype III; in fact, the genetic distance between the serotype Ia and III isolates within ST23 was larger than the distance between distinct members of other clonal complexes, e.g. ST260 and ST553 in CC552, ST19 and ST110 in CC19, and ST6, ST7 and ST283 in CC7. 
     Population Screening 
     In silico analysis of genomic data from a limited number of  S. agalactiae  strains allowed the identification of putatively fish-specific and fish-associated genes. To determine whether the findings at genome level were representative of gene distribution at population level, a collection of isolates was screened by PCR for presence of the fish-specific genes M3M_04280 (locus 7) and M3M_01062 (locus 4) and the fish-associated genes M3M_01167, M3M_01172 and M3M_01182 (locus 3). The distribution of those targets across host species based on in silico analysis and PCR screening is shown in Table 5. Five profiles of gene presence/absence were identified, ranging from lack of detection of any of the 5 target genes (Profile 1) to detection of the full complement of target genes (Profile 5). Profile 1 was the most common, and was associated with isolates from multiple homeothermic species (humans, cattle and seals), multiple CCs (CC1, CC17, CC19, CC23 and CC67) and multiple continents. Profile 5 was associated exclusively with ST260, with all representatives of this ST having originated from disease outbreaks in farmed tilapia in South America. ST261, which can also be considered a member of CC552 (Delannoy et al., 2013), lacked the M3M_01062 amplicon, whilst testing positive for the remaining targets. This profile, Profile 4, was not uniquely associated with ST261 but was shared with ST7 isolates from a natural outbreak of disease in mullet in Kuwait. Other ST7 isolates from fish and from humans were positive for 3 or 4 target genes, resulting in 2 additional profiles (Profiles 2 and 3). Profile 2 was associated with human and piscine isolates from Thailand, China and the USA. Profile 3 was identified in piscine isolates from 2 continents (Asia and South America) and 2 CCs (CC7, including ST283, and CC552). There was a strong correlation between PCR profile, host species and ST, with two notable exceptions: one bovine isolate of ST1 was PCR-positive for the 3 fish-associated genes, and one dolphin isolate of ST399 was PCR-positive for the 3 fish-associated genes as well as one of the two putatively fish-specific genes. 
     Western Blots ( FIG. 5 ) 
     The blots show that fish immunized with  S. agalactiae  proteins (M3M-01212 (-rhamnulose-1-phosphate aldolase), V193-02470 (aldose epimerase) and M3M-01172 alpha-galactosidase) raise an immune response against the immunogen. The same immune response was not seen in the control, non-immunised, fish. It should be noted that the multiple ‘other’ bands in each lane derive from the fact that the recombinant proteins were not 100% purified, and so the fish were also effectively “immunized” with other (unrelated) material from the expression host. 
     DISCUSSION 
     Despite the wide range of  S. agalactiae  STs and CCs associated with carriage and disease in humans, the only CCs to be associated with disease in fish are members of CC7 and CC552. Even ST23, which has a host range including humans, cattle, dogs, aquatic mammals (seals) and poikilotherms (crocodiles) (Bishop et al. 2007; Brochet, Couve, Zouine, Vallaeys, Rusniok, Lamy, Buchrieser, Trieu-Cuot, Kunst, Poyart &amp; Glaser 2006; Delannoy et al. 2013, Sorensen, Poulsen, Ghezzo, Margarit &amp; Kilian 2010), has not been identified in fish. Within ST23, two subpopulations are recognized, one predominantly associated with humans and belonging to serotype Ia and the other predominantly associated with cattle and belonging to serotype III (Sørensen et al 2010). Phylogenetic analysis of the core genome shows that the two subpopulations are genetically distinct, despite sharing ST23 ( FIG. 3 ). Neither ST23 serotype Ia (this study) nor ST23 serotype III (Mian et al. 2009) cause disease in tilapia after intraperitoneal challenge. We demonstrated the presence of our ST23 strain in the brain and kidney of tilapia at 3 to 7 days post-challenge, but the infection remained asymptomatic and was cleared by day 16 p.i. Numerous genes recognised as encoding virulence determinants in human  S. agalactiae  are present in the genome of ST23 but not ST260 (Table 3), including genes encoding adhesins (fbsA, Imb) and an immune evasin (scpB). Absence of scpB has also been reported for bovine-associated  S. agalactiae  (Sorensen et al. 2010). Other genes were found to be only partially present or altered in STIR-CD-17, such as the genes from the Cyl operon and genes encoding the pilus 2b, explaining the non-haemolytic phenotype and suggesting the absence of pilus on the surface of STIR-CD-17. 
     The combination of challenge experiments and genomic analysis presented above shows that numerous known virulence genes do not contribute to disease in fish, implying that other virulence factors may play a role. Whilst previous authors have already observed that members of CC552 have a smaller genome than strains that affect other host species (approximately 1.8 Mb compared to 2.0 to 2.4 Mb for human and bovine derived  S. agalactiae ; Liu et al. 2013; Rosinski-Chupin et al. 2013), few efforts have been made to identify genome content that may explain virulence in fish. Using whole genome comparison, ACT analysis and BLAST score ratios we identified putatively fish-specific or fish-associated gene content. Fish-specific and fish-associated genes tended to be clustered in regions that carried signatures of MGEs, as previously described for bovine  S. agalactiae  (Richards et al. 2011). Supplementing the in silico analysis with PCR-based detection of 5 selected targets in a collection of field isolates from fish, sea mammals and cattle confirmed the exclusive or predominant association of these genes with CCs that are found in fish. All targets were detected in more than one ST, more than one host species and more than one country, but, with one exception, not in isolates from seals or cattle, nor in isolates belonging to CCs other than CC7 and CC552. One bovine isolate did not match the generic pattern whereby it belonged to CC1 and contained 3 genes that were clustered in locus 3. The fact that associations between genes and host species are rarely absolute has been demonstrated before in comparative analysis of human and bovine  S. agalactiae  populations (Richards et al. 2011). Based on the definition of CC sensu stricto (Feil, Li, Aanensen, Hanage &amp; Spratt 2004), former CC1, CC7, CC17 and CC19 are currently all members of a single CC. To facilitate comparison with literature predating the amalgamation of those CCs, we have adhered to the old nomenclature and clusters. Based on analysis of the core phylogeny, ST283 was grouped under CC7 for the sake of the current discussion ( FIG. 3 ). 
     Several fish-associated loci were flanked by conserved regions that can act as substrates for homologous recombination between strains, allowing for formation of minimal mobile elements (MMEs; Saunders &amp; Snyder, 2002). For example, Locus 1 was located in the region between purK and purB ( FIG. 2A ). This region is a well-recognized MME containing variable inserts within the genome sequence of several pathogenic streptococci, including  Streptococcus pneumoniae  and  Streptococcus pyogenes  (Herbert et al., 2005). Locus 8 also fulfilled the criteria for an MME ( FIG. 2B ). In most  S. agalactiae  genomes of human isolates, this region is occupied by a histidine triad nucleotide-binding protein, which is replaced in  S. agalactiae  of CC552 by a hypothetical protein and DJ-1/Pfp family protein. This family includes proteins with intracellular protease function or transcriptional regulators (Halio et al., 1996; Ohnishi et al., 2005), but its role in fish-associated  S. agalactiae  is unknown. Locus 5 was not flanked by conserved regions but by direct repeats of 159 bp (Figure S1). The corresponding region for this locus is occupied by the same single 159 bp sequence in other  S. agalactiae  strains, suggesting that in STIR-CD-17 it may have been a MGE that lost its mobility through inactivation of resolvases, which were present as pseudogenes within the locus. 
     Presence of other MGEs was associated with putative integrases, e.g. for Locus 7 and 6. Locus 7 contained genes encoding products involved in fatty acid biosynthesis (PF07977) and a major facilitator family transporter (PF07690); the latter protein was predicted to be localised in the cytoplasmic membrane where it could contribute to transport of small solutes in response to chemiosmotic ion gradients (Pao, Paulsen &amp; Saier 1998). Locus 6, which was found only in the genome of STIR-CD-17, contains a serine hydroxymethyltransferase (SHMT)-encoding gene. SHMT catalyzes the reversible cleavage of serine to form glycine and monocarbonic groups, essential in several biosynthetic pathways. SHMT of halotolerant bacteria is up-regulated under conditions of high salinity, resulting in an increased salinity tolerance due to an accumulation of glycine betaine within the cell (Waditee-Sirisattha, Sittipol, Tanaka &amp; Takabe 2012). Non-haemolytic  S. agalactiae  can infect a wide range of marine fishes (Bowater et al. 2012) and SHMT could potentially play a role in persistence within the marine environment. 
     Other fish-associated loci were located in putative PAI described in human  S. agalactiae  strains, with Loci 5 and 6 located in PAI VI and Locus 2 in PAI IV (Glaser et al. 2002; Herbert et al. 2005). Locus 2 occupied a region that corresponds to a cluster of genes that include either the virulence gene rib (e.g. in 2603V/R) or bca (e.g. in A909). These genes are mutually exclusive and form part of a 3-set genotyping system for  S. agalactiae  (Kong, Gowan, Martin, James &amp; Gilbert 2002). In PCR-based screening of CC552 isolates for rib and bac, all isolates tested negative (Delannoy et al. 2013), which would be explained by the replacement of these genes by Locus 2. This locus is predicted to encode a cytoplasmic protein, but the function is unknown. Locus 3, which is located just outside PAI IV, contains a number of genes whose corresponding proteins are not found in  S. agalactiae  genomes other than CC7 and CC552; some of these, however, are well-conserved in other streptococci, including the fish-pathogenic species  Streptococcus ictaluri  and  Streptococcus iniae , and species that affect other hosts, such as  Streptococcus suis  (pigs) and  Streptococcus canis  (dogs). The proteins encoded by this locus are involved in carbohydrate transport and metabolism and include the beta-galactosidase, GalA, an enzyme that catalyzes the hydrolysis of galactose-containing oligosaccharides. It also contains genes for all enzymes of the Leloir pathway (GalK, GalE, GalM and GalT), which is involved in the transport and degradation of galactose. These genes have been well-characterised in lactic acid bacteria (Grossiord, Vaughan, Luesink &amp; de Vos 1998). Galactose is present in dairy products, but also in fish tissues like the brain, where it is a component of glycolipids and glycoproteins (Tocher 2003). The presence of these genes in meningoencephalitis-causing bacteria such as piscine  S. agalactiae  may therefore provide some metabolic advantages. In  S. thermophilus , the primary role for Leloir pathway enzymes is to produce precursor sugars for assembly of exopolysaccharides (EPS; Levander &amp; Rådström 2001). EPS are secreted externally and differ from the capsular polysaccharides (CPS) that are tightly-associated with the cell surface (Levander &amp; Rådström 2001). The production of EPS in bacteria leads to a loose ‘fluffy’ pellet phenotype following centrifugation (Forde &amp; Fitzgerald 2002). To our knowledge, EPS formation has not been describe in  S. agalactiae , but isolates from CC552 do form fluffy pellets. Genes responsible for EPS production in  S. thermophilus  share a high level of homology with capsular polysaccharide (CPS) genes from  S. agalactiae  (Stingele, Neeser &amp; Mollet 1996), suggesting a common origin of these genes. The  S. agalactiae  capsule is composed of numerous polysaccharides that include glucose, galactose and rhamnose (Cieslewicz, Chaffin, Glusman, Kasper, Madan, Rodrigues, Fahey, Wessels &amp; Rubens 2005) and it is conceivable that enzymes encoded by Locus 3 play a role in the production of precursors involved in the capsule rather than EPS formation. 
     Although the functional relevance of putatively fish-specific genome content of CC552 strains remains to be determined, the reduced genome content of members of CC552 may well explain why their host range is restricted to poikilothermic animals. It seems unlikely that these strains, which are thermosensitive (limited to no growth up to 37° C.) and have undergone extensive niche restriction and genome reduction (Lopez-Sanchez et al. 2012) would revert to virulence for humans, a concern raised in the context of the use of doctor fish for pedicure (Verner-Jeffreys, Baker-Austin, Pond, Rimmer, Kerr, Stone, Griffin, White, Stinton, Denham, Leigh, Jones, Longshaw &amp; Feist 2012). Conversely, acquisition of fish-associated virulence factors by strains with a primary homeothermic host range may pose a risk for emergence of additional strains with high virulence in fish. Epidemiological studies, MLST data and phylogenetic analysis have shown that ST7 and ST283 form part of a large group of amalgamated CCs that are primarily associated with carriage and infection in humans, implying that spill-over has occurred in the human-to-fish direction rather than vice versa (Delannoy et al. 2013; Liu et al. 2013). Fish-associated genes, particularly those detected in all piscine and CC7 isolates examined in the current study, could potentially be used as diagnostic markers to indicate the ability of  S. agalactiae  strains to cause disease in fish. 
     In conclusion, the genome of fish-derived strain STIR-CD-17 (ST260) showed evidence of niche restriction, which is in agreement with epidemiological observations. Comparison of the ST260 genome with genomes of  S. agalactiae  strains derived from humans and cattle led to identification of 8 loci that were found only in the fish-derived strains, including a locus encoding the Leloir pathway. Additional in silico analysis and PCR-based screening of a collection of isolates from humans, cattle, fish and sea mammals showed that elements of those loci are shared by all  S. agalactiae  CCs known to infect fish (CC7, CC552), regardless of host or country of origin, whereas they are absent from CCs that have not been detected in fish. The 8 loci are also absent from strain MRI Z1-201 (ST23), which failed to cause morbidity or mortality after intraperitoneal injection in tilapia. 
     Tables 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                   Streptococcus agalactiae  genome sequences included in genomic 
               
               
                 comparison. 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Host 
                 Strain 
                 Source 
                 CC 
                 ST  
                 Serotype  
                 Accession Number 
                 References 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Human 
                 CJB111 
                 Blood 
                 1 
                 1 
                 V 
                 NZ_AAJQ00000000 
                 Tettelin et al. 2005 
               
               
                   
                 H36B 
                 Umbilicus 
                 7 
                 6 
                 Ib 
                 NZ_AAJS00000000  
                 Tettelin et al. 2005 
               
               
                   
                 A909 
                 Umbilicus 
                 7 
                 7 
                 la 
                 NC_007432 
                 Tettelin et al. 2005 
               
               
                   
                 COH1 
                 Blood 
                 17 
                 17 
                 III 
                 NZ_AAJR00000000  
                 Tettelin et al. 2005 
               
               
                   
                 18RS21 
                 Umbilicus 
                 19 
                 19 
                 II 
                 NZ_AAJO00000000 
                 Tettelin et al. 2005 
               
               
                   
                 2603V/R 
                 Unknown 
                 19 
                 110 
                 V 
                 NC_004116 
                 Tettelin et al. 2002 
               
               
                   
                 515 
                 Cerebrospinal fluid 
                 23 
                 23 
                 Ia 
                 NZ_AAJP00000000  
                 Tettelin et al. 2005 
               
               
                 Bovine 
                 ATCC 13813 
                 Milk 
                 67 
                 *61 
                 II 
                 AEQQ00000000 
                 N/A 
               
               
                   
                 FSL S3-026 
                 Milk 
                 67 
                 67 
                 III 
                 AEXT00000001 
                 Richards etal. 2011 
               
               
                 Unknown 
                 NEM316 
                 Unknown 
                 23 
                 23 
                 III 
                 NC_004368 
                 Glaser etal. 2002; 
               
               
                   
                   
                   
                   
                   
                   
                   
                 Sørensen etal. 2010 
               
               
                   
               
               
                 *The bovine strain ATCC 13813 has been typed by MLST PCR as ST61 (Evans et al. 2008), but it was also reported by Liu et al. (2013) as S1337. ST337 and ST61 differ at locus glcK (allele number 2 and 1 respectively), which is the only locus that we could not investigate from the genome due to its incompleteness (in between 2 contigs). The typing result from Evans et al. (2008) is retained here. N/A, not applicable. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Distribution of adhesins, invasins and immune evasins in  Streptococcus   
               
               
                   agalactiae  highly-pathogenic (STIR-CD-17, ST260, serotype 1b) or non-pathogenic 
               
               
                 (MRI Z1-201, ST23, serotype 1a; NEM316, ST23, serotype III; Mian et al., 2009) to 
               
               
                 fish. Locus tags are provided when available (annotated genomes). 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 Virulence factors 
                 Related gene(s) 
                 STIR-CD-17 
                 MRI Z1-201 
                 NEM316 
               
               
                   
               
            
           
           
               
               
            
               
                   
                 Adhesins 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 Fibrinogen-binding 
                 fbsA 
                 M3M_07935 
                 + 
                 GBS1087 
               
               
                   
                 proteins 
                 fbsB 
                   
                 + 
                 GBS0850 
               
               
                   
                 Fibronectin-binding 
                 pavA 
                 M3M_03075 
                 + 
                 GBS1263 
               
               
                   
                 protein 
                   
                   
                   
                   
               
               
                   
                 Serin-rich protein 
                 srr1 
                 M3M_05192  
                 + 
                 GBS1529 
               
               
                   
                   
                 srr2 
                   
                 − 
                   
               
               
                   
                 Immunogenic 
                 bibA 
                 M3M_09338  
                  +* 
                 GBS2018 
               
               
                   
                 bacterial adhesin 
                   
                   
                   
                   
               
               
                   
                 Pilus island PI-1 
                 PI-1 backbone 
                   
                 − 
                   
               
               
                   
                   
                 protein 
                   
                   
                   
               
               
                   
                   
                 PI-1 ancillary 
                   
                 − 
                   
               
               
                   
                   
                 protein 2 
                   
                   
                   
               
               
                   
                   
                 Sortase family 
                   
                 − 
                   
               
               
                   
                   
                 protein 
                   
                   
                   
               
               
                   
                   
                 Sortase family 
                   
                 − 
                   
               
               
                   
                   
                 protein 
                   
                   
                   
               
               
                   
                   
                 PI-1 ancillary 
                   
                 − 
                   
               
               
                   
                   
                 protein 1 
                   
                   
                   
               
               
                   
                 Pilus Island PI-2a 
                 PI-2a ancillary 
                   
                 + 
                 GBS1474 
               
               
                   
                   
                 protein 2 
                   
                   
                   
               
               
                   
                   
                 Sortase family 
                   
                 + 
                 GBS1475 
               
               
                   
                   
                 protein 
                   
                   
                   
               
               
                   
                   
                 Sortase family 
                   
                 + 
                 GBS1476 
               
               
                   
                   
                 protein 
                   
                   
                   
               
               
                   
                   
                 PI-2a backbone 
                   
                 + 
                 GBS1477 
               
               
                   
                   
                 protein 
                   
                   
                   
               
               
                   
                   
                 PI-2a ancillary 
                   
                 + 
                 GBS1478 
               
               
                   
                   
                 protein 1 
                   
                   
                   
               
               
                   
                 Pilus Island PI-2b 
                 PI-2b ancillary 
                 M3M_06299  
                 − 
                   
               
               
                   
                   
                 protein 1 
                   
                   
                   
               
               
                   
                   
                 PI-2b backbone 
                 M3M _06294* 
                 − 
                   
               
               
                   
                   
                 protein 
                   
                   
                   
               
               
                   
                   
                 Sortase family 
                 Pseudo* 
                 − 
                   
               
               
                   
                   
                 protein 
                   
                   
                   
               
               
                   
                   
                 PI-2b ancillary 
                 M3M_06274  
                 − 
                   
               
               
                   
                   
                 protein 2 
                   
                   
                   
               
               
                   
                   
                 Sortase family 
                 M3M_06269  
                 − 
                   
               
               
                   
                   
                 protein 
                   
                   
                   
               
               
                   
                 Laminin-binding 
                 Imb 
                   
                 + 
                 GBS1307 
               
               
                   
                 protein 
                   
                   
                   
                   
               
            
           
           
               
               
            
               
                   
                 Invasins 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 β-hemolysin/cytolysin 
                 cyIX 
                   
                 + 
                 GBS0644 
               
               
                   
                   
                 cyID 
                   
                 + 
                 GBS0645 
               
               
                   
                   
                 cyIG 
                   
                 + 
                 GBS0646 
               
               
                   
                   
                 acpC 
                   
                 + 
                 GBS0647 
               
               
                   
                   
                 cyIZ 
                   
                 + 
                 GBS0648 
               
               
                   
                   
                 cyIA 
                 M3M_00355 +   
                 + 
                 GBS0649 
               
               
                   
                   
                 cyIB 
                 M3M_00350 
                 + 
                 GBS0650 
               
               
                   
                   
                 cyIE 
                 M3M_00345 +   
                 + 
                 GBS0651 
               
               
                   
                   
                 cyIF 
                   
                 + 
                 GBS0652 
               
               
                   
                   
                 cyII 
                   
                 + 
                 GBS0653 
               
               
                   
                   
                 cyIJ 
                   
                 + 
                 GBS0654 
               
               
                   
                   
                 cyIK 
                   
                 + 
                 GBS0655 
               
               
                   
                 CAMP factor 
                 cfb 
                 M3M_09048 
                 + 
                 GBS2000 
               
               
                   
                 Hyaluronatelyase 
                 hyIB 
                 M3M_03035  
                 + 
                 GBS1270 
               
               
                   
                 Surface protein rib 
                 rib 
                   
                 − 
                 GBS0470 
               
               
                   
                 C-α protein 
                 bca 
                   
                 − 
                   
               
            
           
           
               
               
            
               
                   
                 Immune evasins 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 Capsule 
                 cps and neu genes 
                 M3M_08948- 
                 + 
                 GBS1233-1247 
               
               
                   
                   
                 cluster 
                 09023 
                   
                   
               
               
                   
                 Penicillin-binding 
                 pbp1A/ponA 
                 M3M_06939  
                 + 
                 GBS0288 
               
               
                   
                 protein 1A 
                   
                   
                   
                   
               
               
                   
                 Serine protease cspA 
                 cspA 
                 Pseudo* 
                 + 
                 GBS2008 
               
               
                   
                 C5a peptidase 
                 scpB 
                 — 
                 + 
                 GBS1308 
               
               
                   
                 C-β protein 
                 bac 
                 — 
                 − 
               
               
                   
               
               
                 *Partial gene sequence, or pseudogenes due to the introduction of stop codons. 
               
               
                   + Genes partially present due to sequence deletion. 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Primer pairs for putatively fish-specific† or fish-associated‡ genes of 
               
               
                 Streptococcus agalactiae. 
               
            
           
           
               
               
               
               
               
            
               
                 Host  
                   
                   
                   
                 Tm 
               
               
                 association 
                 Target 
                 Locus tag 
                 Primers 
                 (° C.) 
               
               
                   
               
               
                 Fish- 
                 Beta-hydroxyacyl  
                 M3M_04280 
                 71-AAATAATCCGATTGTTCCTG-91 
                 51.2 
               
               
                 specific 
                 dehydratase FabA/FabZ 
                   
                 346-ATATACTATAAA1TTCCCTTCTAA-321 
                 50.8 
               
               
                   
                 Putative RecB familly  
                 M3M_01062 
                 5-CTATGCCGAAGATGATTATTTG-28 
                 54.7 
               
               
                   
                 exonuclease (cas4) 
                   
                 491-CTTCTTGGCGTAGTTCCTCAGTA-467 
                 60.6 
               
               
                 Fish- 
                 Galactokinase 
                 M3M_01167 
                 466-AAATCGGCAAGCAGACAGAAAATGAAT-494 
                 60.4 
               
               
                 associated 
                   
                   
                 1041-GCAATAGCACAACCGCCAAAACC-1017 
                 62.4 
               
               
                   
                 Alpha galactosidase 
                 M3M_01172 
                 663-AAGGGTGCTAGTAGTGCCGAACATAAT-691 
                 63.4 
               
               
                   
                   
                   
                 1113-AACCAGCCATCATCCATAACAAAAAGT-1085 
                 60.4 
               
               
                   
                 Sugar ABC transporter  
                 M3M_01182 
                 489-ATTGGTATTTGGAGCACTGTAGG-513 
                 58.9 
               
               
                   
                 permease 
                   
                 740-TCTTATTATAGGCCGGACTTGTA-716 
                 57.1 
               
               
                   
               
               
                 †limited to CC552 strains 
               
               
                 ‡limited to CC552 and CC7 
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Distribution of putatively fish-specific (found in CC552 only) and fish-associated (found in CC7 and CC552) genes across 
               
               
                 a range of host species, clonal complexes (CC) and sequence types (ST) of  Streptococcus agalactiae  based on PCR or 
               
               
                 in silico analysis. For each profile and epidemiologically independent source, the number of isolates is shown. 
               
            
           
           
               
               
               
               
               
               
               
               
               
            
               
                   
                 Marker 
                   
                   
                   
                   
                   
                   
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
               
               
            
               
                 Profile 
                 4280 
                 1062 
                 1167 
                 1172 
                 1182 
                 Host 
                 Country 
                 (sub)CC 
                 ST 
                 Method 
                 Comment 
                 Isolates 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
               
               
            
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Cattle 
                 Denmark 
                 1 
                 1 
                 PCR 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Cattle 
                 Denmark 
                 1 
                 1 
                 PCR 
                   
                 2 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Human 
                 Unknow 
                 1 
                 1 
                 In silico 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Cattle 
                 Denmark 
                 1 
                 478 
                 PCR 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Human 
                 Unknow 
                 17 
                 17 
                 In silico 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Cattle 
                 Denmark 
                 19 
                 19 
                 PCR 
                   
                 11 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Human 
                 USA 
                 19 
                 19 
                 In silico 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Cattle 
                 Denmark 
                 19 
                 44 
                 PCR 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Human 
                 Unknow 
                 19 
                 110 
                 In silico 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Cattle 
                 Denmark 
                 23 
                 23 
                 PCR 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Human 
                 Unknow 
                 23 
                 23 
                 In silico 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Seal 
                 UK 
                 23 
                 23 
                 PCR 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Seal 
                 UK 
                 23 
                 23 
                 PCR 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Seal 
                 UK 
                 23 
                 23 
                 PCR 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Seal 
                 UK 
                 23 
                 23 
                 PCR 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Seal 
                 UK 
                 23 
                 23 
                 PCR 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Unknown 
                 Unknown 
                 23 
                 23 
                 In silico 
                 NEM316 
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Cattle 
                 Denmark 
                 23 
                 199 
                 PCR 
                   
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Cattle 
                 USA 
                 67 
                 67 
                 In silico 
                 FSL S3-026 
                 1 
               
               
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 Cattle 
                 USA 
                 67 
                 337 
                 In silico 
                 ATCC13831 
                 1 
               
               
                 2 
                 0 
                 0 
                 1 
                 1 
                 1 
                 Cattle 
                 Denmark 
                 1 
                 1 
                 PCR 
                   
                 1 
               
               
                 2 
                 0 
                 0 
                 1 
                 1 
                 1 
                 Human 
                 USA 
                 7 
                 6 
                 PCR 
                 H36B 
                 1 
               
               
                 2 
                 0 
                 0 
                 1 
                 1 
                 1 
                 Fish 
                 Thailand 
                 7 
                 7 
                 PCR 
                   
                 1 
               
               
                 2 
                 0 
                 0 
                 1 
                 1 
                 1 
                 Fish 
                 Chain 
                 7 
                 7 
                 PCR 
                 ZQ0910 
                 1 
               
               
                 2 
                 0 
                 0 
                 1 
                 1 
                 1 
                 Fish 
                 China 
                 7 
                 7 
                 PCR 
                 FG201008-001 
                 1 
               
               
                 2 
                 0 
                 0 
                 1 
                 1 
                 1 
                 Human 
                 Unknown 
                 7 
                 7 
                 PCR 
                 A909 
                 1 
               
               
                 2 
                 0 
                 0 
                 1 
                 1 
                 1 
                 Fish 
                 Thailand 
                 7 
                 500 
                 PCR 
                   
                 1 
               
               
                 2 
                 0 
                 0 
                 1 
                 1 
                 1 
                 Fish 
                 Thailand 
                 7 
                 500 
                 PCR 
                   
                 1 
               
               
                 3 
                 0 
                 1 
                 1 
                 1 
                 1 
                 Fish 
                 Thailand 
                 7 
                 1 
                 PCR 
                   
                 1 
               
               
                 3 
                 0 
                 1 
                 1 
                 1 
                 1 
                 Fish 
                 Thailand 
                 7 
                 1 
                 PCR 
                   
                 1 
               
               
                 3 
                 0 
                 1 
                 1 
                 1 
                 1 
                 Fish 
                 Thailand 
                 7 
                 1 
                 PCR 
                   
                 1 
               
               
                 3 
                 0 
                 1 
                 1 
                 1 
                 1 
                 Fish 
                 Thailand 
                 7 
                 283 
                 PCR 
                   
                 1 
               
               
                 3 
                 0 
                 1 
                 1 
                 1 
                 1 
                 Dolphin 
                 UK 
                 7 
                 399 
                 PCR 
                   
                 1 
               
               
                 3 
                 0 
                 1 
                 1 
                 1 
                 1 
                 Fish 
                 Vietnam 
                 7 
                 491 
                 PCR 
                   
                 1 
               
               
                 3 
                 0 
                 1 
                 1 
                 1 
                 1 
                 Fish 
                 Brasil 
                 552 
                 553 
                 In silico 
                 SA20-06 
                 1 
               
               
                 4 
                 1 
                 0 
                 1 
                 1 
                 1 
                 Fish 
                 Kuwait 
                 7 
                 7 
                 PCR 
                   
                 5 
               
               
                 4 
                 1 
                 0 
                 1 
                 1 
                 1 
                 Fish 
                 Australia 
                 552 
                 261 
                 PCR 
                   
                 1 
               
               
                 4 
                 1 
                 0 
                 1 
                 1 
                 1 
                 Fish 
                 Australia 
                 552 
                 261 
                 PCR 
                   
                 1 
               
               
                 4 
                 1 
                 0 
                 1 
                 1 
                 1 
                 Fish 
                 Australia 
                 552 
                 261 
                 OCR 
                   
                 1 
               
               
                 4 
                 1 
                 0 
                 1 
                 1 
                 1 
                 Fish 
                 Belgium 
                 552 
                 261 
                 PCR 
                   
                 1 
               
               
                 5 
                 1 
                 1 
                 1 
                 1 
                 1 
                 Fish 
                 Honduras 
                 552 
                 260 
                 PCR 
                 Incl. STIR-CD-17 
                 4 
               
               
                 5 
                 1 
                 1 
                 1 
                 1 
                 1 
                 Fish 
                 Columbia 
                 552 
                 260 
                 PCR 
                   
                 1 
               
               
                 5 
                 1 
                 1 
                 1 
                 1 
                 1 
                 Fish 
                 Cost Rica 
                 552 
                 260 
                 PCR 
                   
                 4 
               
               
                   
               
            
           
         
       
     
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