# Patent

## Title
Nucleic acid fragments and specific detection method by molecular identification of different bacteria species of the genus Acinetobacter

## Abstract

RpoB gene sequences of various species of Acinetobacter bacteria, and a method of detection by molecular identification of various species of Acinetobacter bacteria using rpoB gene sequences.

## Background
The present invention relates to the area of diagnosis. More precisely, the invention concerns a method for the molecular identification of bacteria of the genus Acinetobacter using nucleic acid amplifying and sequencing techniques with oligonucleotide primers.
Bacteria of the genus Acinetobacter are bacteria appearing in the form of Gram-negative cocco-bacilli, having aerobic growth. Currently almost 60 species are known and 2 sub-species.
These bacteria are essentially, but not solely, agents of nosocomial infection. Their spectrum ranges from mere colonization to life-threatening infections, in particular pneumonia, urinary infection, bacteraemia and meningitis (van Dessel et al., 2004). Their excellent survival capacity in the external hospital environment and their ability to develop rapid resistance to most antibiotics are major factors in their emergence as agents of nosocomial infections, in particular in intensive care units (Bergogne-Berezin and Towner, 1996; Towner, 1997).
Although most species are responsible for infections in man, some species have only been isolated in the environment (Nemec et al., 2001, 2003; Carr et al., 2003).
Whereas in the genus Acinetobacter, 32 species have been proposed (van Dessel et al, 2004), 24<<genomic species>> according to nomenclature currently in force and abbreviated below to <<genospecies>> or <<g.sp.>>) are recognized and only 17 species have a validated name (Nemec et al., 2003; Carr et al., 2003). Unfortunately, the members of this genus have very broad intra-specific phenotype variability, and therefore cannot be differentiated at phenotype level. The increase in the number of infections related to these agents has prompted research into analysis methods for the identification and taxonomy of these bacteria. It has therefore been shown that identification methods based on phenotypical characteristics and sequencing of the 16S ribosomal RNA gene by comparison with DNA-DNA hybridisation are not valid. Therefore the search for rapid identification methods of these bacteria is still an issue (Gerner-Smidt et al., 1991; Ibrahim et al., 1997; Rainey et al., 1994). In particular, molecular techniques based on sequencing of the 16S ribosomal RNA gene do not allow a distinction to be made between the closest species, in particular due the lack of polymorphism of this gene within this genus. (Yamamoto and Harayama, 1998; Ochman and Wilson, 1987; Stackebrandt and Goebel, 1994). Additionally, owing to this lack of polymorphism, there is a need to determine the complete sequence of the 16S rRNA gene if it is wished to be able to identify a species. This requires sequencing the entirety of the gene which has around 1600 base pairs. The practical consequence is that sequencing must be based on a minimum of 6 sequencing reactions in addition to the amplification reaction to obtain an assessable result. Phylogenetic attempts have been made using the comparison of gyrB genes (Yamamoto and Harayama, 1996; Yamamoto et al., 1999) and recA genes (Krawczyk et al., 2002) as an alternative to the 16S ribosomal RNA gene (Ibrahim et al., 1997). Unfortunately, the sequences of these genes have not been determined on the 10 most recent species (Nemec et al., 2001, 2003; Carr et al., 2003).
There is therefore still a demand for a molecular identification tool to identify the bacteria species of genus Acinetobacter, which can be routinely used in bacteriology laboratories, in particular having a sufficiently polymorphic gene so that the determination of a short sequence (less than 500 base pairs) with only 1 amplification reaction and two sequence reactions is identifying i.e. can be amplified and sequenced using a single set of primers.
The inventors have discovered and shown according to the present invention that:

    
    
        the rpoB gene and its non-coding boundary sequences, namely
        the non-coding sequences at 5′ between the sequences of the rp/L and rpoB genes (called “rplL-rpoB spacers” or <<rp/L-rpoB intergenic fragments>> below), and
        the non-coding sequences at 3′ between the sequences of the rpoC and rpoB genes (called “rpoB-rpoC spacers” or <<rpoB-rpoC intergenic fragments>> below),
    
    


form a genetic marker allowing the detection and specific identification of the bacterium of each species of genus Acinetobacter, and in particular of the following 24 species: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus. 
The genomic species 1 to 16 (“genomic species>>) correspond to strains referenced in GENBANK, for some of which (no 3, 6, 9, 10, 13 and 16) no name has yet been given.
The inventors have discovered some hypervariable regions between the different species and hence specific to each species, flanked by conserved sequences between the different species, which can be used to implement a molecular identification method of the different species of Acinetobacter bacteria by amplification, using primers chosen from the conserved sequences and hybridisation and/or sequencing of the specific sequences so amplified.
More particularly, the present invention concerns sequences of nucleic acids specific to each species of genus Acinetobacter cited above whose nucleotide sequence is drawn from the rpoB gene of said bacteria.
According to Lazcano et al. [J. Mol. Evol. (1988) 27:365-376], the RNA polymerases are divided into two groups according to their origin, one consisting of RNA- or DNA-dependent viral RNA polymerises, and the other of DNA-dependent RNA polymerases of eukaryote or prokaryote origin (archaebacteria and eubacteria). The eubacterial, DNA-dependent RNA polymerases are characterized by a simple, conserved, multimeric constitution called a “core enzyme”, represented by αββ′, or “holoenzyme” represented by αββ′σ [Yura and Ishihama, Ann. Rev. Genet. (1979) 13:59-97]. Numerous studies have evidenced the functional role, within the multimeric enzymatic complex, of the β subunit of the eubacterial RNA polymerase. On the other hand, the archaebacterial, eukaryote RNA polymerases have a more complex structure which may reach around ten, even thirty subunits [Pühlet et al. Proc. Natl. Acad. Sci. USA (1989) 86:4569-4573].
The genes encoding the different αββ′σ subunits of DNA-dependent RNA polymerase in eubacteria, respectively the rpoA, rpoB, rpoC and rpoD genes, are classified in different groups comprising the genes coding for constituent proteins of the ribosomal subunits or for enzymes involved in the replication and repair of the genome [Yura and Yshihma, Ann. Rev. Genet. (1979) 13:59-97]. Some authors have shown that the sequences of the rpoB and rpoC genes could be used to construct phylogenetic trees [Rowland et al. Biochem. Soc. Trans. (1992) 21:40 S] allowing separation of the different branches and sub-branches of the living kingdoms.
Before setting forth the invention in detail, different terms used in the description and claims are defined as follows:

    
    
        by “nucleic acid extracted from bacteria” is meant either the total nucleic acid, or the genomic DNA, or the messenger RNAs, or the DNA obtained from reverse transcription of the messenger RNAs;
        “nucleotide fragment” or “oligonucleotide” are two synonymous terms designating a chain of nucleotide patterns characterized by an information sequence of the natural (or possibly modified) nucleic acids and able to hybridise, like the natural nucleic acids, with a complementary or substantially complementary nucleotide fragment, under predetermined high-stringency conditions. The chain may contain nucleotide patterns having a different structure to that of the natural nucleic acids. A nucleotide fragment (or oligonucleotide) may for example contain up to 100 nucleotide patterns. It generally contains at least 10, preferably from 18 to 35 nucleotide patterns and can be obtained from a natural nucleic acid molecule and/or by genetic recombination and/or by chemical synthesis,
        a nucleotide pattern is derived from a monomer which may be a natural nucleotide of nucleic acid whose constituent elements are a sugar, a phosphate group and a nitrogen-containing base chosen from among adenine (A), guanine (G), uracil (U), cytosine (C), thymine (T); or else the monomer is nucleotide of which at least one of the three previous constituent elements is modified; for example the modification may concern a base, with modified bases such as inosine which can hybridise with any base A, T, U, C or G, methyl-5-deoxycytidine, deoxyuridine, dimethylamino-5-deoxyuridine or any other modified base capable of hybridisation either at the sugar e.g. the replacement of at least one deoxyribose by a polyamide [Nielsen P E et al., Science (1991) 254:1497-1500], or at the phosphate group e.g. through replacement by esters chosen in particular from among the diphosphates, alkylphosphonates and phosphorothioates,
        by “hybridisation”, is meant the process during which, under suitable conditions, two nucleotide fragments having sufficiently complementary sequences are able to combine under stable specific hydrogen bonds to form a double strand. The hybridisation conditions are determined by “stringency”, i.e. the strictness of operating conditions. Hybridisation is all the more specific the higher the stringency under which it is conducted. Stringency is related in particular to the base composition of a probe/target duplex, and to the extent of mismatch between two nucleic acids. Stringency may also be related to parameters of the hybridisation reaction, such as concentration and the type of ion species present in the hybridisation solution, the type and concentration of denaturing agents and/or hybridisation temperature. The stringency of the conditions under which a hybridisation reaction must be performed depends in particular on the probes used. All these data items are well known and the suitable conditions can possibly be determined in each case by routine experiments. In general, depending on the length of the probes used, the temperature for the hybridisation reaction lies between approximately 20 and 65° C., in particular between 35 and 65° C. in a saline solution at a concentration of approximately 0.8 to 1 M.
        a “probe” is a nucleotide fragment having hybridisation specificity under determined conditions to form a hybridisation complex with a nucleic acid having, in the present case, a nucleotide sequence included either in a messenger RNA, or in a DNA obtained by reverse transcription of said messenger RNA, a transcription product; a probe may be used for diagnostic purposes (capture or detection probes in particular) or for therapeutic purposes,
        a probe may be immobilized or able to immobilized on a solid support by any suitable means, e.g. by covalency, by adsorption, or by direct synthesis on a solid. Examples of supports comprise microtitration plates and DNA chips,
        a “probe” is generally labelled with a marking agent chosen for example from among radioactive isotopes, enzymes, in particular enzymes able to act on a chromogenic, fluorigenic or luminescent substrate (in particular a peroxydase or an alkaline phosphatase), or from among chromophorous chemical compounds, chromogenic, fluorigenic or luminescent chemical compounds, analogs of nucleotide bases. This marking may be direct between the DNA and said marker, or indirect i.e. via ligands such as biotin or other molecule able to bind to markers,
        a “species probe” is a probe allowing specific identification of the species of a bacterium of a given genus, Acinetobacter in this case,
        a “genus probe” is a probe allowing specific identification of the genus of the bacterium, irrespective of the species of the bacterium of said genus, under certain hybridisation conditions,
        a “primer” is a probe comprising for example 10 to 100 nucleotide patterns and having hybridisation specificity under determined conditions for enzymatic amplification reactions,
        by “genus primer”, is meant a set of primers allowing specific amplification of any bacterium of one same given genus, with no distinction as to species, under certain hybridisation and amplification conditions (the “genus primers” are also called “consensus primers” or “universal primers” in the present application),
        by “amplification reaction” is meant an enzymatic polymerisation reaction, e.g. in an amplification technique such as PCR, initiated by primer oligonucleotides and using a DNA polymerase,
        by “sequencing reaction”, is meant a reaction leading to determination of the sequence of a nucleic acid fragment, or of a complete gene by an abortive polymerisation process starting with oligonucleotide primers and using said dideoxynucleotides (Sanger F, Coulson A R (1975), J. Mol. Biol. 94: 441) or by multiple hybridisations with multiple probes fixed onto a solid support such as used in DNA chips for example, or other techniques known to those skilled in art.
    
    


The inventors have determined the complete sequences of the rpoB genes and their non-coding boundary sequences separating them from the rp/L and rpoC genes (“rplL-rpoB spacer” and “rpoB-rpoC spacer”) of 24 species of the genus Acinetobacter. A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus. 
To arrive at determining said complete sequences of rpoB and its flanking sequences in all the species of Acinetobacter bacteria, the inventors after a large number of unsuccessful tests and from the sole rpoB sequence and its non-coding boundary regions in bacteria of genus Acinetobacter—were firstly compelled to determine 51 primers (Table 2) of corresponding sequences of bacteria which they identified as being close and available from GENBANK, namely Acinetobacter sp. ADP1 (GenBank accession number NC—005966), Pseudomonas syringae pv. tomato str.DC3000 (GenBank accession number NC—004578) and P. putida KT2440 (GenBank accession number NC—006347).
Acinetobacter strain sp. ADP1 is a strain which had not been characterized before the invention, and which does not correspond to any of the pathogenic strains described in the present patent application and listed below.
The subject-matter of the present invention is therefore a complete rpoB gene of a bacterium of the genus Acinetobacter chosen from among the following 23 species: A. calcoaceticus (genomic species 1), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, characterized in that its sequence comprises and more particularly consists of a sequence chosen from among the sequences such as described in sequences SEQ. ID. no 9 and 11 to 32 respectively, and the sequences having at least 98% similarity, and their complementary sequences.
A further subject of the present invention concerns nucleic acid fragments comprising and more particularly consisting of a non-coding fragment flanking the rpoB gene of a bacterium of the genus Acinetobacter chosen from among the following 24 species: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, characterized in that its sequence comprises and more particularly consists of a sequence chosen from among the sequences such as described in sequences SEQ. ID. no 121 to 144 respectively, and sequences SEQ. ID. no 165 to 188 respectively, and the sequences having at least 98% similarity and their complementary sequences.
The said sequences having similarity rates of at least 98% with said sequences SEQ. ID. 9 to 32, 121 to 144 and 165 to 188 correspond to the possible variations between the different strains of one same species possibly corresponding to sub-species. Therefore sequences SEQ. ID. no 145 to 164 and 189 to 208 correspond to various strains of A. baumannii having at least 98% homology with sequences SEQ. ID. no 122 and 166 respectively.
By “similarity rate” or “homology percentage”, is meant a percentage of sequence identity i.e. a percentage of nucleotides of the sequences which are identical at the same position with respect to another sequence.
Sequences SEQ. ID. no 121 to 144 correspond to the 5′ flanking sequences representing the complete rpoB spacer bordering the rpoB gene between genes rp/L and rpoB, having a length of between 301 and 310 bp, for each species of the bacterium of the genus Acinetobacter, in the 24 above-mentioned species.
Sequences SEQ. ID. no 165 to 188 correspond to 3′ flanking sequences representing the complete rpoB-rpoc spacer bordering the rpoB gene between the rpoB and rpoC genes, having a length of between 86 and 177 bp, for each species of the bacterium of genus Acinetobacter, in the 24 above-mentioned species.
The spacers rpoB-rpoC and rp/L-rpoB which border the rpoB gene, and the complete sequence of the rpoB gene can be used to identify the bacterium not only as probe and/or by investigating its primary sequence, but also by investigating the secondary and tertiary structures of the messenger RNA derived from transcription of the complete DNA sequence.
In these rpoB genes and their non-coding boundary sequences (rplL-rpoB spacer and rpoB-rpoC spacer) of Acinetobacter, the inventors have evidenced consensus sequences SEQ. ID. no 1, 2, 3, 4, 5, 6, 7 and 8 (Table 3) which are conserved sequences between all bacteria of the genus Acinetobacter, i.e. able to be used as primers to amplify the same portion of the rpoB gene and its non-coding boundary regions (rp/L-rpoB spacer and rpoB-rpoC spacer) of all said Acinetobacter bacteria, namely:

    
    
        SEQ. ID. no 1, and 2 for a first region of the rpoB gene,
        SEQ. ID. no 3, and 4 for a second region of the rpoB gene,
        SEQ. ID. no 5, and 6 for the rp/L-rpoB spacer and
        SEQ. ID. no 7, and 8 for the rpoB-rpoC spacer,
        SEQ. ID. no 1 to 4 and 6-7 lie inside the rpoB gene, with:
        SEQ. ID. no 8 and 6 are close to the 5′ ends of the rpoB and rpoC genes respectively,
        SEQ. ID. no 7 and 5 are close to the 3′ ends of the rp/L and rpoB genes respectively.
    
    


The present invention therefore provides oligonucleotides which have conserved sequences of an Acinetobacter bacterium chosen from among the said 24 species comprising a sequence of at least 12, preferably at least 18 consecutive nucleotide patterns included in one of the sequences chosen from the sequences such as described in following sequences SEQ. ID. no 1 to 8, and their complementary sequences, and preferably consisting of said sequences:









SEQ ID NO: 1:



5′-TAYCGYAAAGAYTTGAAAGAAG-3′,



 



SEQ ID NO: 2:



5′-CMACACCYTTGTTMCCRTGA-3′,



 



SEQ ID NO: 3:



5′-GTGATAARATGGCBGGTCGT-3′,



 



SEQ ID NO: 4:



5′-CGBGCRTGCATYTTGTCRT-3′,



 



SEQ ID NO: 5:



5′-GAAGARCTTAAGAMDAARCTTG-3′



 



SEQ ID NO: 6:



5′-CGTTTCTTTTCGGTATATGAGT-3′,



 



SEQ ID NO: 7:



5′-GTTCTTTAGGTATCAACATTGAA-3′,



 



SEQ ID NO: 8:



5′-GACGCAAGACCAATACGRAT-3′,






in which:

    
    
        D represents A, G or T,
        Y represents C or T,
        B represents C, G or T,
        R represents A or G, and
        M represents A or C.
    
    


At the position corresponding to a nucleotide D, Y, B, M or R in sequences SEQ. ID. no 1 2, 3, 4, 5 and 8, variable nucleotides are found in the complementary target sequences in relation to the species of bacterium under consideration, but all the other nucleotides are conserved in all the species of bacteria of the genus Acinetobacter. 
Sequences SEQ. ID. no 1, 3, 5 and 7 are used as primers on the direct strand, and sequences SEQ. ID. no 2, 4, 6 and 8 are used as primer on the indirect strand. Sequences SEQ. ID. no 2, 4, 6 and 8 therefore correspond to sequences complementary to those of the direct strand.
To be used as consensus primers, these oligonucleotides of sequences SEQ. ID. no 1, 2, 3, 4, 5 and 8 are therefore used in the form of equimolar mixtures of oligonucleotides of different sequences, said oligonucleotides of different sequences for each sequence SEQ. ID. no 1 to 8 meeting the various possible definitions of respective sequences no 1, 2, 3, 4, 5 and 8.
These equimolar mixtures of oligonucleotides are obtained through the use, during oligonucleotide synthesis, of equimolar mixtures of the different nucleotides concerned, respectively:

    
    
        A, G and T for D,
        C and T for Y,
        C, G and T for B,
        A and G for R,
        A and C for M.
    
    


The mixtures of oligonucleotides, meeting the definition nucleotides of sequences SEQ. ID. no 1 2, 3, 4, 5 and 8, are therefore able to hybridise with the different target complementary sequences included in the rpoB genes and at the ends of the rp/L and rpoC genes flanking their boundary non-coding regions (rplL-rpoB spacer and rpoB-rpoC spacer) of all the species of bacteria of the genus Acinetobacter and, more particularly, the 24 above-mentioned species.
The capacity of these primers to amplify rpoB gene fragments and their non-coding boundary regions (rplL-rpoB spacer and rpoB-rpoC spacer), of all species of Acinetobacter, allows the consideration to be made that these primers will be efficient in identifying additional species of Acinetobacter which may be described in the future.
A further subject of the invention is therefore a mixture of oligonucleotides characterized in that it comprises an equimolar mixture of oligonucleotides of different sequences comprising at least 12, preferably at least 18 consecutive nucleotide patterns included in one of sequences SEQ. ID. no 1 to 5 and 8, or the oligonucleotides of complementary sequences.
More particularly, the subject of the present invention is the following mixtures of oligonucleotides:

    
    
        an equimolar mixture of 8 oligonucleotides of different sequences, consisting of sequence SEQ. ID. no 1 or oligonucleotides of complementary sequences.
        an equimolar mixture of 16 oligonucleotides of different sequences, consisting of sequence SEQ. ID. no 2 or oligonucleotides of complementary sequences.
        an equimolar mixture of 6 oligonucleotides of different sequences, consisting of sequence SEQ. ID. no 3 or oligonucleotides of complementary sequences.
        an equimolar mixture of 24 oligonucleotides of different sequences, consisting of sequence SEQ. ID. no 4 or oligonucleotides of complementary sequences.
        an equimolar mixture of 24 oligonucleotides of different sequences, consisting of sequence SEQ. ID. no 5 or oligonucleotides of complementary sequences.
        sequence oligonucleotide consisting of sequence SEQ. ID. no 6 or a complementary sequence.
        sequence oligonucleotide consisting of sequence SEQ. ID. no 7 or a complementary sequence.
        an equimolar mixture of 2 oligonucleotides of different sequences consisting of sequence SEQ. ID. no 8 or oligonucleotides of complementary sequences.
    
    


The oligonucleotides or mixtures of oligonucleotides comprising a sequence included in one of sequences SEQ. ID. no 1 to 8 according to the invention, can be used as genus primers for bacteria of the genus Acinetobacter. 
As mentioned previously, the consensus sequences SEQ. ID. no 1, 2, 3, 4, 5 and 8, so defined, also flank hypervariable sequences whose sequence is specific to each species of the genus Acinetobacter. 
The inventors were therefore able to evidence sequences specific to species for each of the 24 above-cited bacteria species, corresponding to sequences:

    
    
        SEQ. ID. no 33 to 56, flanked by consensus sequences SEQ. ID. no 1 and 2 (hereafter “region 1 of rpoB”);
        SEQ. ID. no 77 to 100, flanked by consensus sequences SEQ. ID. no 3 and 4 (hereunder “region 2 of rpoB”);
        SEQ. ID. no 121 to 144, flanked by consensus sequences SEQ. ID. no 5 and 6 (hereunder “rpo/L-rpoB spacer”); and
        SEQ. ID. no 165 to 188, flanked by consensus sequences SEQ. ID. no 7 and 8 (hereunder “rpoB-rpoC spacer”);
    
    


The oligonucleotides of sequences flanked by SEQ. ID. no 1 2, 3, 4, 5, 6, 7 and 8, can therefore be used as species primer for bacteria of the genus Acinetobacter. 
Said specific hypervariable sequences SEQ. ID. no 33 to 56 flanked by sequences SEQ. ID. no 1 and 2, represent a fragment of the rpoB gene of length 350 bp, with less than 96% similarity between the different species (Table 7) with the exception of the pairs A. baylii/genospecies 11 and A. grimontii/A. junii, which means that they form a short specific target sequence for the specific identification of each species of the bacterium of the genus Acinetobacter, more precisely for the 24 above-mentioned species, with the exception of the pairs A. baylii/genospecies 11 and A. grimontii/A. junii. 
Said specific hypervariable sequences SEQ. ID. no 77 to 100 flanked by sequences SEQ. ID. no 3 and 4, represent a fragment of the rpoB gene of length 450 bp with less than 96% similarity between the different species (Table 8) with the exception of the pairs A. baylii/genospecies 11 and A. grimontii/A. junii, which means that they form a second short specific target sequence to specifically identify each bacterium species of the genus Acinetobacter, more precisely for the 24 above-mentioned species, with the exception of the pairs A. baylii/genospecies 11 and A. grimontii/A. juni. 
Said specific hypervariable sequences SEQ. ID. no 121 to 164 flanked by sequences SEQ. ID. no 5 and 6, represent the rplL-rpoB spacer bordering the rpoB gene by a length of between 301 and 310 bp with less than 97% similarity between the different species (see Table 5 below) with the exception of the pairs A. baylii/genospecies 11, A. grimontii/A. junii, and A. lwoffi/genospecies 9, which means that they form a third short specific target sequence to specifically identify each bacterium species of the genus Acinetobacter, more precisely for the 24 above-mentioned species, with the exception of the pairs A. baylii/genospecies 11, A. grimontii/A. junii, and A. lwoffi/genospecies 9.
Finally, said specific hypervariable sequences SEQ. ID. no 165 to 188 flanked by sequences SEQ. ID. no 7 and 8, represent the rpoB-rpoC spacer bordering the rpoB gene by a length of between 86 and 177 bp with less than 97% similarity between the different species (see Table 6 below) with the exception of the pairs A. grimontii/A. junii and species of the Acb group (A. baumannii, A. calcoaceticus and genospecies 3), so that they form a fourth short specific target sequence for the specific identification of each bacterium species of the genus Acinetobacter, more precisely for the 24 above-mentioned species, with the exception of the pairs A. grimontii/A. junii and species of the Acb group (A. baumannii, A. calcoaceticus and genospecies 3).
A further subject of the present invention is therefore an rpoB gene fragment of a bacterium of genus Acinetobacter chosen from among the 24 species: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, characterized in that its sequence consists of a sequence chosen from among the sequences such as described in sequences SEQ. ID. no 33 to 56 respectively, and sequences SEQ. ID. no 77 to 100 respectively, and the sequences having at least 98% similarity and their complementary sequences.
A further subject of the present invention is an rpoB gene fragment of a bacterium of the genus Acinetobacter chosen from among the 23 species: A. calcoaceticus (genomic species 1), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, characterized in that its sequence comprises a sequence chosen from among the sequences such as described in sequences SEQ. ID. no 33 and 35 to 56 respectively, and sequences SEQ. ID. no 77 and 79 to 100 respectively, and the sequences having at least 98% similarity and their complementary sequences.
The said sequences having similarity rates of at least 98% with said sequences SEQ. ID. no 33 to 56 and 77 to 100 correspond to possible variations between the different strains of one same species, possibly and more particularly corresponding to sub-species. Therefore the sequences SEQ. ID. no 57 to 76 and 101 to 120 correspond to various strains of A. baumannii having at least 98% homology with SEQ. ID. no 34 and 78 respectively.
The subject of the present invention is therefore also the use, as species probe, of a rpoB, rp/L or rpoC gene fragment according to the invention or of an oligonucleotide of sequences specific to a said species of Acinetobacter bacterium according to the invention.
More precisely, the present invention provides a method of detection by molecular identification to identify a bacterium of one of the species of the genus Acinetobacter, characterized in that the following are used:

    
    
        the complete rpoB gene of said bacterium according to the invention, comprising a said sequence SEQ. ID. no 9 to 32, or preferably consisting of a said sequence SEQ. ID. no 9 to 32, or the complementary sequences, or sequences having at least 98% similarity,
        an rpoB gene fragment of a said bacterium according to the invention, comprising a said sequence SEQ. ID. no 33 to 56 or 77 to 100, or consisting of a said sequence SEQ. ID. no 33 to 56 or 77 to 100, or the complementary sequences, or sequences having at least 98% similarity,
        an rpoB gene fragment of a said bacterium according to the invention, comprising a said sequence SEQ. ID. no 77 to 100, or preferably, consisting of a said sequence SEQ. ID. no 77 to 100, or complementary sequences, or sequences having at least 98% similarity,
        a gene fragment comprising a complete rplL-rpoB or rpoB-rpoC intergenic fragment of said bacterium according to the invention, comprising a said sequence SEQ. ID. no 121 to 144 or 165 to 188, or preferably consisting of a said sequence SEQ. ID. no 121 to 144 or 165 to 188, the complementary sequences or sequences having at least 98% similarity,
        an oligonucleotide having a sequence specific to an Acinetobacter bacterium chosen from among the 24 above-cited species, preferably with at least 18, further preferably 18 to 35 consecutive nucleotide patterns included in one of the sequences chosen from among the sequences such as described in sequences:
        SEQ. ID. no 33 to 56 respectively,
        SEQ. ID. no 77 to 100 respectively,
        SEQ. ID. no 121 to 144 respectively,
        SEQ. ID. no 165 to 188 respectively, and
        the sequences having at least 98% similarity and their complementary sequences, or
        an oligonucleotide or equimolar mixture of oligonucleotides according to the invention, comprising a sequence of at least 12, preferably 18 consecutive nucleotides included in one of sequences SEQ. ID. no 1 2, 3, 4, 5, 6, 7 and 8 or their complementary sequences, or preferably consisting of one of said sequences SEQ. ID. no 1 2, 3, 4, 5, 6, 7 and 8.
    
    


In a first embodiment of a bacterium detecting method of the invention, it is sought specifically to detect a given species of an Acinetobacter bacterium chosen from among the following 24 species: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, a method in which:
1—a sample containing or likely to contain nucleic acids of at least one said bacterium is contacted with at least one species probe consisting of an oligonucleotide or gene fragment according to the invention, preferably a gene fragment respectively consisting of one of said sequences chosen from among:

    
    
        SEQ. ID. no 33 to 56 respectively,
        SEQ. ID. no 77 to 100 respectively,
        SEQ. ID. no 121 to 144 respectively,
        SEQ. ID. no 165 to 188 respectively, and
        the sequences having at least 98% similarity and their complementary sequences.
    
    


2—the formation or non-formation of a hybridisation complex is determined between said probe and the nucleic acids of the sample, and it is thereby determined whether said species of Acinetobacter is present in the sample if a hybridisation complex is formed.
In a second embodiment of a method to detect a specific species of a bacterium of the genus Acinetobacter, the steps are performed in which:
1—amplification primers comprising said mixtures of oligonucleotides of the invention are contacted with a sample containing or likely to contain nucleic acids of at least one said bacterium of the genus Acinetobacter, and nucleic acid amplification is performed by enzymatic polymerisation reaction comprising:

    
    
        as 5′ primer, at least one oligonucleotide or mixture oligonucleotides according to the invention comprising a sequence included in one of sequences SEQ. ID. no 1, 3, 5 and 7, preferably consisting of said complete sequence SEQ. ID. no 1, 3, 5 and 7 or the complementary sequences, and
        as 3′ primer, at least one oligonucleotide or mixture of oligonucleotides according to the invention comprising sequences included in one of sequences SEQ. ID. no 2, 4 6, and 8 respectively, preferably consisting of said complete sequence SEQ. ID. no 2, 4, 6, and 8, or respectively a complementary sequence.
    
    


2—and the formation or non-formation of an amplification product is determined, and the presence of absence of said bacterium in the sample is thereby respectively determined if an amplification product is or is not formed.
More particularly, it is sought to determine a given species of an Acinetobacter bacterium chosen from among the following 24 species: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, and, at step 2 above, the presence or absence of the given species of a said bacterium is determined by conducting the steps in which:
a) a sequencing reaction is conducted of a gene fragment is amplified with said primers, and
b) the sequence of said amplified fragment obtained is compared with the sequence of a gene fragment of said bacterium respectively comprising:

    
    
        said sequences SEQ. ID. no 33 to 56, when said 5′ and 3′ primers are oligonucleotides of sequences included in sequences SEQ. ID. no 1 and 2 respectively,
        said sequences SEQ. ID. no 77 to 100, when said 5′ and 3′ primers are oligonucleotides of sequences included in sequences SEQ. ID. no 3 and 4 respectively, and
        said sequences SEQ. ID. no 121 to 144, when said 5′ and 3′ primers are oligonucleotides of sequences included in sequences SEQ. ID. no 5 and 6 respectively, and
        said sequences SEQ. ID. no 165 to 188, when said 5′ and 3′ primers are oligonucleotides of sequences included in sequences SEQ. ID. no 7 and 8 respectively.
    
    


In another variant of said second embodiment of a method to detect a specific species of a bacterium of the genus Acinetobacter, it is sought to detect a specific species of an Acinetobacter bacterium chosen from among the 24 following species: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, A. parvus, and at step 2 above the presence or absence of the given species of said bacterium is determined by conducting the steps in which:
a—a sample containing or likely to contain amplified nucleic acids of at least one said bacterium is contacted with at least one species probe consisting of an rpoB gene fragment or a specific oligonucleotide of the invention, preferably a fragment consisting respectively of one of said sequences chosen from among:

    
    
        SEQ. ID. no 33 to 56 respectively, when said 5′ and 3′ primers are oligonucleotides of sequences included in sequences SEQ. ID. no 1 and 2 respectively,
        SEQ. ID. no 77 to 100 respectively, when said 5′ and 3′ primers are oligonucleotides of sequences included in sequences SEQ. ID. no 3 and 4 respectively, and
        SEQ. ID. no 121 to 144 respectively, when said 5′ and 3′ primers are oligonucleotides of sequences included in sequences SEQ. ID. no 5 and 6 respectively, and
        SEQ. ID. no 165 to 188 respectively, when said 5′ and 3′ primers are oligonucleotides of sequences included in sequences SEQ. ID. no 7 and 8 respectively, and
    
    


b—the formation or non-formation of a hybridisation complex is determined between said probe and the amplified nucleic acids of the sample, and the presence or absence in the sample of said species of Acinetobacter is thereby determined according to whether or not a hybridisation complex is formed.
In one preferred embodiment of a method according to the invention, the steps are performed comprising:
1—a first amplification of the nucleic acid of said sample with a pair of 5′ and 3′ primers chosen from among said mixtures of oligonucleotides of the invention, comprising sequences respectively included in sequences SEQ. ID. no 1 and SEQ. ID. no 2, preferably consisting of said sequences SEQ. ID. no 1 and 2, or the complementary sequences, and
2—a first determination of the onset or absence of an amplification product containing the nucleic acids of at least one said bacterium, by hybridisation or optionally sequencing, and comparison of the amplicons obtained at step 1 with the fragments respectively consisting of one of said sequences chosen from among SEQ. ID. no 33 to 56 and 34 to 76 respectively, and

    
    
        if, at this step 2, the presence of species A. grimontii or A. junii is determined, the following is also performed:
    
    


3a—a second amplification reaction with avec 5′ and 3′ primers chosen from among said oligonucleotide mixtures according to the invention, comprising sequences respectively included in sequences SEQ. ID. no 3 and SEQ. ID. no 4, preferably consisting of said sequences SEQ. ID. no 3 and 4, or the complementary sequences, and
4a—determining the formation or non-formation of an amplification product containing nucleic acids of at least one said bacterium, by hybridisation or optionally sequencing, and comparing the amplicons obtained at step 3a with the fragments respectively consisting of one of said sequences chosen from among SEQ. ID. no 77 to 100 respectively, or

    
    
        if, at first step 2, the presence of species A. baylii or genomic species 11 is determined, the following is also performed:
    
    


3b—a second amplification reaction with 5′ and 3′ primers chosen from among said mixtures of oligonucleotides according to the invention containing sequences respectively included in sequences SEQ. ID. no 7 and SEQ. ID. no 8, preferably consisting of said sequences SEQ. ID. no 7 and 8, or the complementary sequences, and
4b—determining the formation or non-formation of an amplification product containing nucleic acids of at least one said bacterium, by hybridisation or optionally sequencing, and comparison of the amplicons obtained at step 3b with the fragments respectively consisting of one of said sequences chosen from among SEQ. ID. no 165 to 188 respectively.
Sequences SEQ. ID. no 1 to 208 can be prepared by genetic engineering and/or by automatic synthesis or chemical synthesis using techniques well known to those skilled in the art.
The probes of the invention can be used for diagnostic purposes, as mentioned above, by determining the formation or non-formation of a hybridisation complex between the probe and a target nucleic acid in a sample, using any known hybridisation technique and in particular so-called “DOT-BLOT” techniques [Maniatis et al. (1982) Molecular Cloning, Cold Spring Harbor], DNA transfer techniques called “SOUTHERN BLOT” [Southern E. M., J. Mol. Biol. (1975) 98:503], RNA transfer techniques called “NORTHERN BLOT”, or so-called “sandwich” techniques, in particular with a capture probe and/or detection probe, said probes being able to hybridise with two different regions of the target nucleic acid, and at least one of said probes (generally the detection probe) being able to hybridise with a target region specific to the species, on the understanding that the capture probe and the detection probe must have nucleotide sequences that are at least partly different.
The nucleic acid to be detected (target) may be DNA or RNA (the first obtained after PCR amplification). When detecting a target of double strand nucleic acid type, this acid must be denatured before initiating the detection method. The target nucleic acid may be obtained by extraction using known methods for nucleic acids of a sample to be tested. The denaturing of a double strand nucleic acid can be performed using known chemical, physical or enzymatic denaturing methods, in particular by heating to a suitable temperature of more than 80° C.
To implement the above-cited hybridisation techniques, in particular the “sandwich” techniques, a probe of the invention, called a capture probe, is immobilized on a solid support, and another probe of the invention, called a detection probe, is labelled with a marking agent. The examples of support and marking agent are as previously defined.
Advantageously, one species probe is immobilized on a solid support, and another species probe is labelled with a marking agent.
Another application of a said mixture of oligonucleotides of the invention is its use as nucleotide primer comprising a monocatenary oligonucleotide chosen from among oligonucleotides having a sequence of at least 12 nucleotide patterns included in one of sequences SEQ. ID. no 1 to 8, which can be used for the synthesis of a nucleic acid in the presence of a polymerase using a method known as such, in particular in amplification methods using said synthesis in the presence of a polymerase (PCR, RT-PCR, etc.). In particular, a primer of the invention can be used for the specific reverse transcription of a messenger RNA sequence of a bacterium species of the genus Acinetobacter, to obtain a corresponding complementary DNA sequence. Said reverse transcription may form the first stage of the RT-PCR technique, the following stage being PCR amplification of the complementary DNA obtained.
In one particular case, said primer comprising an oligonucleotide of the invention also comprises the sense or anti-sense sequence of a promoter recognized by an RNA polymerase (promoters T7, T3, SP6 for example [Studier F W, B A Moffatt (1986) J. Mol. Biol. 189:113]: said primers can be used in nucleic acid amplification methods involving a transcription step such as, for example, NASBA or 3SR techniques [Van Gemen B. et al. Abstract MA 1091, 7th International Conference on AIDS (1991) Florence, Italy].
A further subject of the invention is a nucleotide primer comprising a mixture of monocatenary oligonucleotides chosen from among the oligonucleotides having sequences comprising one of sequences SEQ. ID. no 1 to 8 or preferably consisting of one of sequences SEQ. ID. no 1 to 8, which can be used for total or partial sequencing of the rpoB gene or of the rplL-rpoB spacer or rpoB-rpoC spacer of any species of the genus Acinetobacter. 
The sequencing of the complete or partial rpoB gene or of the rplL-rpoB spacer or rpoB-rpoC spacer in any bacterium of the genus Acinetobacter allows the identification of any Acinetobacter bacterium by bio-computerized analysis of this sequence and allows the recognition of new species of unknown Acinetobacter bacteria.
Preferably, for use as primer or to sequence the rpoB genes or the rplL-rpoB spacer or rpoB-rpoC spacer, said mixtures of oligonucleotides of sequence SEQ. ID. no 1 and 2 are used.
A further subject of the present invention is a diagnosis kit which can be used in a method of the invention, containing at least one said rpoB gene fragment or rplL-rpoB spacer or rpoB-rpoC spacer according to the invention, comprising or consisting of one of sequences SEQ. ID. no 9 to 188 or an oligonucleotide or said equimolar mixture of oligonucleotides according to the invention, comprising sequences included in sequences SEQ. ID. no 1 to 8 and the oligonucleotides and rpoB gene fragments or rplL-rpoB spacer or rpoB-rpoC spacer of complementary sequences such as defined above, and, preferably, reagents which can be used for hybridisation reactions or amplification reactions or for sequencing accordingly.
As mentioned in the definitions, an oligonucleotide or nucleic acid fragment according to the invention, may be in the form of a deoxyribonucleic acid (DNA) or a ribonucleic acid (RNA) for which T is replaced by U in this case.
Finally, a last subject of the invention is a gene therapy probe to treat infections caused by a strain belonging to a species of the genus Acinetobacter, said probe comprising an oligonucleotide such as defined previously. This gene therapy probe, able to hybridise on the messenger RNA and/or on the genomic DNA of said bacteria, is able to block phenomena of translation and/or transcription and/or replication.
The principle of gene therapy methods is known and is based in particular on the use of a probe corresponding to an anti-sense strand: the formation of a hybrid between the probe and the sense strand is capable of disturbing at least one of the decoding steps of genetic data. Gene therapy probes can therefore be used as antibacterial medicinal products, to combat infections caused by bacteria species of the genus Acinetobacter. 
Other characteristics and advantages of the present invention will become apparent and the invention will be better understood with the help of the description given below of the experiments conducted to implement the invention, together with their results, which are given solely by way of illustration.
Table 1, below, reproduces the list of species of Acinetobacter for which rpoB sequences and the rplL-rpoB spacer and rpoB-rpoC spacer were determined, the mentioned strains were obtained from the collection Collection de l'Institut Pasteur (CIP), sequences SEQ. ID. no 1 to 208 are described in the sequence listing appended to the description.
Table 2 lists the different primers used for amplification and sequencing of the rpoB genes.
When Table 2 gives sequences comprising nucleotides W, H, Y, V, R, B, M, K, S or D, these have the meanings known to persons skilled in the art, and in equally conventional fashion these primers are used in the form of an equimolar mixture of oligonucleotides of different sequences in the place of said nucleotides as explained above.
Table 3 gives comparisons of similarities of the sequences of the 16S rRNA and rpoB genes between the two sub-species C. affermentans and between the 11 pairs of species considered as close for which similarities between sequences of 16S rRNA genes are 98.5% or over, with a statistical comparison of the mean similarities obtained.



FIG. 1 is a graphical representation of the variability rate (range site variability: RSV (Y axis)) of the sequences of the rpoB genes and flanking sequences of the different species of genus Acinetobacter investigated per window of 50 nucleotides (X axis). The hypervariable regions, bounded by the conservative regions and used for species identification using consensus primers, are boxed.
FIG. 2 is a dendogram showing the phylogenetic relationships between the different species of Acinetobacter using the “neighbour-joining” method. The tree was constructed by aligning sequences of the rpoB gene. “Bootstrap” sampling values (percentage probability of node accuracy) calculated on the basis of a sample of 1000 trees, are given at each node, only values of 75% or higher being indicated.
FIG. 3 is a dendogram showing the phylogenetic relationships between different species of Acinetobacter using the “neighbour-joining” method. The tree was constructed by aligning hypervariable sequences (region 1 and region 2) of the rpoB gene. The “bootstrap” values (percentage probability of node accuracy) calculated on the basis of a sample of 1000 trees, are indicated at each node.
FIG. 4 is a dendogram showing the phylogenetic relationships between the different species of Acinetobacter using the “neighbour-joining” method. The 4 trees were constructed by aligning sequences of the rpoB, 16SRNA, rpoB, gyrB, recA genes. The “bootstrap” sampling values (percentage probability of node accuracy) calculated on the basis of a sample of 1000 trees, are given at each node, solely values of 75% or higher being indicated.



1—MATERIAL AND METHODS
1.1—Bacterial Strains
The bacterial strains used are listed in Table 1. All the strains were cultured on Columbia agar, 5% sheep blood, and were incubated 48 h at 37° C. under aerobic conditions.
1.2—Amplification and Sequencing of the rpoB Gene and of Spacers rplL-rpoB and rpoB-rpoC
The sequence of the rpoB gene and of its boundary intergenic spacers in the closest species were aligned to produce a consensus sequence. The sequences chosen were those of Acinetobacter sp. ADP1 (GenBank accession number NC—005966), Pseudomonas syringae pv. tomato str.DC3000 (GenBank accession number NC—004578) and P. putida KT2440 (GenBank accession number NC—006347). The consensus sequence allowed determination of the primers subsequently used for PCR techniques, “genome walking” and sequencing. Some primers were determined after analysis of the results obtained. The primers are given in Table 2 below.
The bacterial DNA was extracted from strain suspensions using the QIAamp blood kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations. All the PCR reaction mixtures contained 2.5×10−2 U Taq polymerase per μl, 1× Taq buffer, 1.8 mM MgCl2 (Gibco BRL, Life Technologies, Cergy Pontoise, France), 200 μM dATP, dCTP, dTTP and dGTP (Boehringer Manheim GmbH, Hilden, Germany), and 0.2 μM of each primer (Eurogentec, Seraing, Belgium). The PCR reaction mixtures were subjected to 35 denaturing cycles at 94° C. for 30 s, hybridisation of the primers for 30 s, and elongation at 72° C. for 2 min. Each amplification programme started with a denaturing step at 95° C. for 2 min. and ended with an elongation step at 72° C. for 10 min. Determination of the sequence of the gene ends was performed using the Universal GenomeWalker Kit (Clontech Laboratories, Palo Alto, Calif.). In short, genomic DNA was digested by Eco RV, Dra I, Pvu II, Stu I and Sca I. The DNA fragments were bound with the GenomeWalker adaptor, PCR was conducted by incorporating the “adaptor primer” provided by the manufacturer and the specific primers. For amplification, 1.5 U of ELONGASE enzyme (Boehringer Manheim) were used with 10 pmol of each primer, 20 mM of each dNTP, 10 mM Tris-HCl, 50 mM KCl, 1.6 mM MgCl2 and 5 μl digested DNA for a final volume of 50 μl. The amplicons were purified with the “QIAquick spin PCR purification kit” (Qiagen). The sequence reactions were performed using reagents of the ABI Prism 3100 ADN sequencer (dRhod.Terminator RR Mix, Perkin Elmer Applied Biosystems).
These conditions for DNA extraction, PCR amplification and sequencing were described in Khamis et al 2003.
1.3—Determination of the Partial Discriminating Sequences in the rpoB Gene
To detect the sequence portions with high variability flanked by conserved regions, we used the SVARAP programme (Sequence VARiability Analysis Program). Once this analysis was made, the most polymorphic regions of the rpoB gene were determined and universal primers, chosen in the conserved boundary regions, were designated after different unsuccessful attempts. The PCR conditions incorporating the universal primers were the same as previously mentioned. These primers were used for amplification and sequencing of the 4 hypervariable regions for all the strains tested.
These primers are given in Table 3 below and FIG. 1.
1.4—Analysis of rpoB Sequences and their Boundary Intergenic Spacers
The fragments of rpoB gene sequences and of boundary intergenic spacers obtained in this study were analysed using “Sequence Analysis Software” (Applied Biosystems), and the partial sequences were combined into a single consensus sequence using “Sequence Assembler Software” (Applied Biosystems). All the deposit references of the strains with Collection de l'Institut Pasteur (<<CIP>>) (France, Paris) are listed in Table 1. The multiple alignments and similarity percentages between the genes of the different species were performed using CLUSTAL W on the EMBL-EBI server (Thompson et al. 1994). Phylogenetic trees were made from the sequences using the “neighbour—joining” method (Felsenstein et al. 1989). “Bootstrap” values were calculated to assess the solidity of the nodes, using SEQBOOT in PHYLIP software.
2—RESULTS
a. Complete Sequences of the rpoB Genes of the Different Acinetobacter Species
The designated primers allowed amplification of the test regions in all working strains; the size of the complete gene is 4089 bp for all species. The similarity percentages between strains vary from 83 to 94%, with the exception of 2 pairs of species (Table 4). Two pairs of species A. junii/A. grimontii and A. baylyi/genomic species 11 have similarities of 99%. The other species have less than 95% similarity with each other.
b. Identification of the Different Species of Acinetobacter Based on the Partial Sequences of the rpoB Gene
The SVARAP programme enabled identification of 2 variable regions bounded by conserved regions, allowing the generation of universal primers:

    
    
        region 1: between positions 2900 and 3250, and
        region 2: between positions 3250 and 3700 bp (FIG. 1).
    
    


These regions were amplified using primers from all species of Acinetobacter and all strains of A. baumannii. The size of region 1 is 350 bp and region 2 has 450 bp. The similarity percentage between the different species of region 1 varies from 78.6 to 95.4% for all species except 2 pairs. As for the complete sequence, A. baylyi/genomic species 11 and A. junii/A. grimontii have the highest similarity values, respectively 98 and 99.1%, whereas the other species have less than 96%. The similarity percentage for region 2 is between 75.8 and 95.3% for all species, again with the exception of species A. junii/A. grimontii and A. baylyi/genospecies 11 which have the highest similarities i.e. 98.8 et 99.6% respectively, whereas the other species have less than 96% similarity between each other.
The intra-specific similarity of the different strains of A. baumannii for region 1 varies from 98.3 to 100% with the exception of strain CIP 103655. This latter strain only has between 94.9 and 95.7% similarity with the other strains. In the same manner, region 2 varies from 98.7 to 100% for all strains of A. Baumanii with the exception of strain CIP 103655. This strain has similarities of between 93.6 and 94.4% with the other strains of the species. The closest species to A. baumannii are genomic species 3 for region 1 and A. calcoaceticus for region 2, with similarities of 95.1% and 93.6% respectively. These are much lower values than for intraspecific variability with the exception of strain CIP 103655 for which the most distant strain of A. baumannii has 94.9% and 93.6% similarity in regions 1 and 2 respectively.
Overall, sequence variability ranges from 0.4 to 24.2% for the partial sequences, compared with 0.8 to 16.9% for complete rpoB sequences. The 2 partial sequences therefore allow non-ambiguous identification of the 24 species.
c. Analysis of the Regions Flanking the rpoB Gene (Intergenic Spacer rplL-rpoB and Intergenic Spacer rpoB-rpoC)
The size of the 2 intergenic spacers varies according to species. The size of the spacer between rplL and rpoB varies from 301 to 310 bp (Table 1). Between species, the similarity rate of this rp/L-rpoB spacer varies from 80.8 to 96.9%, except that the intergenic spacer is identical between A. junnii and A. grimontii, and the pairs of species such as A. baylyi-genomic species 11 and A. lwoffii-genomic species 9 have similarity rates of between 98.4 and 99.7%.
The size of the intergenic spacer between rpoB and rpoC varies from 86 to 177 bp (Table 1) with similarity rates between species of between 70.2 and 96.5%, except for A. junnii/A. grimontii which have a high similarity of 99.5%, and within the Acb complex (A. calcoaceticus, A. baumannii and genomic species 3) whose similarity rates lie between 98.5 and 99.0% for the intergenic spacer rpoB-rpoC. On the other hand, compared with the spacer rplL-rpoB, A. baylyi-genomic species 11 and A. lwoffii-genomic species 9 only have 83.8 and 87.9% similarity respectively for the rpoB-rpoC intergenic spacer.
Within the A. baumannii species, the size of the rplL-rpoB intergenic spacer is 305 bp for all strains, with the exception of strain CIP 103655 for which the size is 304 bp. The rpoB-rpoC intergenic spacer has a size of 86 bp for all strains. Again in this species, the similarity rate in the rpolL-rpoB spacer varies from 99 to 100% for all strains with the exception of strain CIP 103655. This latter strain has between 96.1 and 96.4% similarity with the other strains. The other intergenic spacer rpoB-rpoC has 100% similarity for all strains with the exception of strain CIP 103655 for which it has 97.7 to 98.8% similarity with the other strains. The closest species to A. baumannii is genomic species 3 for the rplL-rpoB spacer and A. calcoaceticus for the rpoB-rpoC spacer, with respective similarities of 95.9% and 98.5%. These are much higher values than intra-specific similarity, with the exception of strain CIP 103655 for which species of A. baumannii have similarities of 96.1% and 97.7% respectively for intergenic spacers rplL-rpoB and rpoB-rpoC.
As arises from the positions of the primers of sequences SEQ. ID. no 5, 6, 7 and 8, the fragments corresponding to the amplicons obtained using these primers have sequences which overspan those of the actual intergenic spacers at the 5′ and 3′ ends, but sequences SEQ. ID. no 121 to 144 and 165 to 188 given in the sequence listing appended to this description correspond to the complete intergenic spacers and do not overspan genes rp/L, rpoB and rpoC respectively.
d. Phylogenetic Analysis of Acinetobacter Species
The phylogenetic tree constructed with the complete sequences of the rpoB gene and constructed using the neighbour-joining technique, is supported by very high bootstrap values (FIG. 2). The number of bootstrap values ≧75% is 17/22 when using the complete rpoB gene, whereas it is only 7/22 when using the 16S rRNA gene (p<0.01). All the species are well separated into different groups. The tree based on the partial rpoB gene (concatenated region 1 and region 2) shows a homogeneous group of A. baumannii strains. Strain CIP 103655 appears in the same group but is clearly separate from the other isolates of A. baumannii. This grouping is supported by a bootstrap value of 85%.
2.4—Discussion
With the exception of the 16S rRNA gene, there currently does not exist any sequencing of house-keeping genes on all species of Acinetobacter. The sequences of genes gyrB and recA are not available for the 10 species most recently described. Yamamoto et al (1996, 1999) and Krawczyk et al (2002) have sequenced the gyrB and recA genes of 14 species and compared this technique with DNA-DNA hybridisation (Bouvet and Jeanjean, 1989; Bouvet and Grimont, 1986; Tjernberg and Ursing, 1989). By constructing a tree based on the rpoB gene which incorporates 14 species, no congruency is observed between the different species. However, the tree based on the rpoB gene has significantly more bootstrap values of ≧75% (11/12) than the tree based on the 16S rRNA gene (4/12), gyrB (5/12) and recA (6/12) (p<0.01, p=0.01 and p=0.02 respectively) (FIG. 4). This demonstrates the robustness of the tree based on the rpoB gene. A. lwoffi and Acinetobacter genomic species 9 are 100% identical on the gyrB gene, but are separated on the sequence of gyrD and recA (Yamamoto et al., 1999; Krawczyk et al (2002). The species that are ill-delimited by the rpoB gene are the pairs A. grimontii/A. junii and A. baylii/genospecies 9. Unfortunately, it is impossible to compare them at gyrB and recA, the sequences of A. grimontii and A. baylii not being available.
For the routine molecular identification of Acinetobacter bacteria, each of the partial sequences of the rpoB gene and of its 2 boundary intergenic spacers can be used on account of its discriminatory power and length. The disadvantage of using only one of these sequences is the lack of good discrimination between the pairs A. grimontii/A. junii and A. baylii/genomic species 9 (Tables 4 to 11). However, this disadvantage can be reduced by combining the sequence of at least 2 of these hypervariable sequences. Owing to its size we believe it is preferable to start with the sequence of region 1 since it can be used for perfect identification of 20 species out of 24. If the sequences obtained are those of A. grimontii/A. junii, it is better to subsequently to carry out the sequence of region 2 which better differentiates between these 2 species. If the sequence obtained is closer to A. baylii/genospecies 9, it is preferable to determine the sequence of the rpoB-rpoC spacer which discriminates better between these 2 species.
The intra-specific variability of the short fragments observed in the A. baumannii species shows that, with the exception of strain CIP 103655, all the isolates have distinctly lower similarities than those observed between A. baumannii and the species closest to it. However the low similarities observed between the A. baumannii strain CIP 103655 and the other isolates of the species show that the identification of some isolates of this species may remain ambiguous. The A. baumannii species is the most frequent species affecting man. The results show that the CIP 103655 strain is different to the 24 categorized species and is probably not a strain of the A. baumannii species.
To conclude, the results obtained through the use of partial sequences of the rpoB gene and the intergenic spacers rplL-rpoB and rpoB-rpoC show that these tools are efficient for the routine molecular identification of Acinetobacter strains. However, owing to the strong similarity between some species, additional work to examine intra-specific similarities in several species will be necessary. Also, the status of some strains such as strain A. baumannii CIP 103655 and of some species such as A. grimontii and A. baylii, must be investigated by DNA-DNA hybridisation and sequences of other house-keeping genes (recA and gyrB).







TABLE 1







Acinetobacter strains investigated.












SEQ. ID.
SEQ. ID
SEQ. ID.
complete intergenic spacers













rpoB-
rpoB-
rpoB-
rp/L-rpoB
rpoB-rpoC















Species
Strain
complete
region 1
region 2
SEQ. ID. no
Size
SEQ. ID.
Size


















genomic species 1,
CIP 81.8T
9
33
77
121
305
165
86


A. calcoaceticus










genomic species 2,
CIP 70.34T
10
34
78
122
305
166
86


baumannii











1072.1 (ref)

57
101
144
305
189
86



CIP 53.77

58
102
145
305
190
86



CIP 53.79

59
103
146
305
191
86



CIP 54.97

60
104
147
305
192
86



CIP 54.147

61
105
148
305
193
86



CIP 64.1

62
106
149
305
194
86



CIP 68.38

63
107
150
305
195
86



CIP 70.8

64
108
151
305
196
86



CIP 70.9

65
109
152
305
197
86



CIP 70.10

66
110
153
305
198
86



CIP 70.21

67
111
154
305
199
86



CIP 70.22

68
112
155
305
200
86



CIP 70.24

69
113
156
305
201
86



CIP 70.28

70
114
157
305
202
86



CIP 70.32

71
115
158
305
203
86



CIP 70.33

72
116
159
305
204
86



CIP 70.35

73
117
160
305
205
86



CIP 103572

74
118
161
305
206
86



CIP 103655

75
119
162
304
207
86



CIP 105742

76
120
163
304
208
86


genomic species 3
CIP 70.15
11
35
79
123
305
167
86


genomic species 4,
CIP 64.3T
12
36
80
124
308
168
172


A. haemolyticus










genomic species 5,
CIP 64.5T
13
37
81
125
308
169
149


A. junii










genomic species 6
CIP A165
14
38
82
126
308
170
170


genomic species 7,
CIP 64.6T
15
39
83
127
301
171
141


A. johnsonii










genomic species 8,
CIP 64.10T
16
40
84
128
308
172
177


A. lwoffii










genomic species 9
CIP 64.7
17
41
85
129
306
173
150


genomic species 10
CIP 70.12
18
42
86
130
307
174
144


genomic species 11
CIP 63.46
19
43
87
131
304
175
154


genomic species 12,
CIP 103788T
20
44
88
132
304
176
89


A. radioresistens










genomic species 13
CIP 70.18
21
45
89
133
309
177
154


genomic species 16
CIP 64.2
22
46
90
134
309
178
153


A. schindleri
CIP 107287T
23
47
91
135
310
179
159


A. ursingii
CIP 107286T
24
48
92
136
308
180
136


A. baylyi
CIP 107474T
25
49
93
137
304
181
88


A. bouvetii
CIP 107468T
26
50
94
138
305
182
156


A. gerneri
CIP 107464T
27
51
95
139
309
183
170


A. grimontii
CIP 107470T
28
52
96
140
308
184
150


A. tandoii
CIP 107469T
29
53
97
141
306
185
156


A. tjernbergiae
CIP 107465T
30
54
98
142
307
186
143


A. towneri
CIP 107472T
31
55
99
143
307
187
157


A. parvus
CIP 108168T
32
56
100
144
308
188
143
















TABLE 2







Primers used to amplify, the rpoB gene and its


flanking regions

















SEQ






Tm
ID


No.
Primer
Sequence (5′-3′)
Position
(° C.)
NO:















 1.
AcintFa
GGTAAAGTDACRCCTAAAGGT

60° C.
209


 


 2.
AcintRa
GTATGAACGTGGGDCAGATT

58° C.
210


 


 3.
Ac28Fa
GTDGGTACVGGYATGGAA

52° C.
211


 


 4.
Ac1754Ra
GAACGYGCRTGCATYTTGTCA

60° C.
212


 


 5.
Ac822F
CGYAAAGAYTTGAAAGAAGA

54° C.
213


 


 6.
Ac840R
CTTCTTTCAARTCTTTRCGRT

60° C.
214


 


 7.
Ac660F
GAYGTDAAAGAYTCATCTTTA

54° C.
215


 


 8.
Ac1720R
GAACGYGCRTGCATYTTGT

60° C.
216


 


 9.
Ac660R
CGTAAAGATGARTCTTTHAC

54° C.
217


 


10.
Ac1700F
GACAARATGCAYGCRCGTT

60° C.
218


 


11.
Ac696F*
TAYCGYAAAGAYTTGAAAGAAG

60° C.
1


 


12.
Ac1093R*
CMACACCYTTGTTMCCRTGA

60° C.
2


 


13.
Ac1055F*
GTGATAARATGGCBGGTCGT

60° C.
3


 


14.
Ac1598R*
CGBGCRTGCATYTTGTCRT

58° C.
4


 


15.
Acint1Fb
AAGAAGCWGGYGCTAMAG
−
55° C.
219


 


16.
Acint2Fb
CTKGGYCTKAAAGAAGCYAA
−
58° C.
220


 


17.
Acint3Fb
CTGCTGCYGYTGTTGAAGA
−
58° C.
221


 


18.
Acint1Rb
GGTAGTTRATGGTTTCMGG
+
56° C.
222


 


19.
Acint2Rb
GTTRATGGTTTCMGGCTTYTT
+
59° C.
223


 


20.
Acint3Rb
GGTTTCMGGCTTYTTAACTT
+
56° C.
224


 












21.
Ac1Fa
ATGGCWTACTCAYATACYGA
1
57° C.
225


 


22.
Ac4Fa
GCWTACTCATAYACYGARAA
4
56° C.
226


 


23.
Ac8Fa
ACTCATAYACYGARAARAAAC
8
56° C.
227


 


24.
Ac361F
GARCAAGAAGTMTACATGGG
361
58° C.
228


 


25.
Ac1215F
GTTCAACCGYCGTWTSGGT
1215
59° C.
229


 


26.
Ac1503F
GATCAACGCCAAGCCDGT
1503
57° C.
230


 


27.
Ac2071F
GGYTCRAACATGCAGCGT
2071
56° C.
231


 


28.
Ac2267F
GYGTVGAYATCTACAACCT
2267
55° C.
232


 


29.
Ac3684F
TGAYGGHCGTACDGGYG
3684
56° C.
233


 


30.
Ac3753F
CCAYTTRGTDGAYGACAAAAT
3753
56° C.
234


 


31.
Ac3850F
TTCGGTGGTCAGCGYTTC
3850
57° C.
235


 


32.
Ac28R
GTTTYTTYTCRGTRTATGAGT
28
56° C.
236


 


33.
Ac55R
GCAAYTTRCYAAARTYCTT
55
59° C.
237


 


34.
Ac211R
CAGCATTGCCRGARTARCT
211
57° C.
238


 


35.
Ac380R
CCCATGTAKACTTCTTGYTC
380
58° C.
239


 


36.
Ac1221R
GTTGAACTTCATVCGDCCWA
1221
55° C.
240


 


37.
Ac1523R
GCHACHGGCTTGGCGTT
1523
56° C.
241


 


38.
Ac2093R
GCCTGACGCTGCATGTT
2093
55° C.
242


 


39.
Ac2314Ra
TGTTCTGGTTBGAACGVGT
2314
56° C.
243


 


40.
Ac2928Ra
GHGCHGCTTCTTCRAAGA
2928
55° C.
244


 


41.
Ac2936Ra
CGYTCACGHGCHGCTTCT
2936
55° C.
245


 


42.
Ac1170F
GCTTCCATYTGGCGHACRT
1170
58° C.
246


 


43.
Ac1705F
GTACGTCACGBACYTCRAA
1705
58° C.
247


 


44.
Ac1804F
TCCATRAACTGDGAYAAYTG
1804
56° C.
248


 


45.
Ac2231F
GTATCACGYGCDACACAHGA
2231
60° C.
249


 


46.
Ac2348F
GTCATGAAYGCDACRCGCA
2348
58° C.
250


 


47.
Ac1379R
CGGTTACCYAARTGRTCRAT
1379
58° C.
251


 


48.
Ac1391R
GAACGNACRCGVCGGTTA
1391
58° C.
252


 


49.
Ac2325R
GTTRATACADGTRTTYTGGTT
2325
56° C.
253


 


50.
Ac2439R
GAACGCRACRCGCATGTT
2439
56° C.
254


 


51.
Ac2442R
CATGAACGCRACRCGCAT
2442
56° C.
255
















TABLE 3







Primers used to amplify and sequence region 1 and region 2


of the rpoB gene and its boundary spacers in the Acineto-


bacter species subject of the present study.













SEQ.







ID.


Tm



Primers
no
Sequence (5′-3′)
Position*
(° C.)
Target





Ac696F
1
TAYCGYAAAGAYTTGAAAGAAG
+2916
60° C.
rpoB region 1


 


Ac1093R
2
CMACACCYTTGTTMCCRTGA
+3267
60° C.
rpoB region 1


 


Ac1055F
3
GTGATAARATGGCBGGTCGT
+3263
60° C.
rpoB region 2


 


Ac1598R
4
CGBGCRTGCATYTTGTCRT
+3773
58° C.
rpoB region 2


 


AcintLBF
5
GAAGARCTTAAGAMDAARCTTG
−361
60° C.
Spacer rp/L-rpoB


 


AcintLBR
6
CGTTTCTTTTCGGTATATGAGT
+29
60° C.
Spacer rp/L-rpoB


 


AcintBCF
7
GTTCTTTAGGTATCAACATTGAA
+4048
60° C.
Spacer rpoB-rpoC


 


AcintBCR
8
GACGCAAGACCAATACGRAT
+4207
59° C.
Spacer rpoB-rpoC





*i.e. the position of the first nucleotide of the primer sequence relative to the rpoB gene.













TABLE 4





Comparison of similarity rates (%) of the rpoB gene (4089 bp) between the different Acinetobacter species






























1
2
3
4
5
6
7
8
9
10
11
12





 [1]
A. calcoaceticus














 [2]
A. genospecies 3
93.9













 [3]
A. baumannii
92.0
93.8












 [4]
A. genospecies 16
88.6
88.7
89.4











 [5]
A. parvus
87.9
88.3
89.0
93.9










 [6]
A. genospecies 13
89.4
89.5
90.0
94.4
93.7









 [7]
A. tjernbergiae
89.4
89.0
89.4
91.9
91.6
93.3








 [8]
A. grimonti
87.7
87.9
88.6
91.8
91.7
92.1
90.1







 [9]
A. junii
87.5
87.8
88.6
91.6
91.8
92.0
90.0
99.2






[10]
A. haemolyticus
88.0
88.3
89.1
92.5
91.8
92.1
90.4
91.7
91.9





[11]
A. genospecies 6
87.8
87.8
87.5
90.1
89.5
90.4
89.8
90.1
90.1
90.6




[12]
A. bouvetii
84.8
85.2
85.6
85.8
85.4
86.1
85.4
84.3
84.4
85.3
84.8



[13]
A. johnsonii
86.6
86.8
87.2
87.8
87.7
88.4
87.6
86.8
86.7
87.3
86.6
88.6


[14]
A. genospecies 9
85.5
86.3
86.2
86.5
86.1
86.2
85.2
85.1
85.0
85.9
85.1
87.6


[15]
A. lwoffi
85.7
86.4
85.9
86.8
85.9
86.9
85.7
85.2
85.0
86.1
85.4
86.9


[16]
A. schindleri
86.0
86.7
86.9
87.2
86.8
87.4
86.4
85.9
85.7
86.3
85.7
88.4


[17]
A. towneri
85.1
85.2
85.7
86.2
86.0
86.5
85.5
86.4
86.5
86.5
86.0
86.0


[18]
A. tandoii
86.4
87.0
86.7
87.5
87.4
88.0
87.2
87.3
87.4
87.9
87.1
86.4


[19]
A. baylyi
86.5
86.6
87.2
87.4
86.7
87.6
86.6
86.6
86.7
87.2
86.3
86.2


[20]
A. genospecies 11
86.6
86.9
87.3
87.6
87.0
87.9
86.9
86.8
86.9
87.4
86.5
86.3


[21]
A. genospecies 10
86.6
86.9
87.3
87.4
87.7
88.2
87.6
87.2
87.2
87.5
86.9
86.4


[22]
A. gerneri
86.5
86.7
87.6
86.9
86.9
87.7
87.4
87.3
87.3
87.5
86.9
86.8


[23]
A. ursingii
85.7
86.0
85.6
85.4
85.7
85.9
86.3
85.3
85.3
86.2
86.5
84.3


[24]
A. radioresistense
84.2
84.5
84.9
84.6
84.4
84.4
84.1
84.4
84.2
84.4
84.2
83.1


























13
14
15
16
17
18
19
20
21
22
23






 [1]
A. calcoaceticus














 [2]
A. genospecies 3














 [3]
A. baumannii














 [4]
A. genospecies 16














 [5]
A. parvus














 [6]
A. genospecies 13














 [7]
A. tjernbergiae














 [8]
A. grimonti














 [9]
A. junii














[10]
A. haemolyticus














[11]
A. genospecies 6














[12]
A. bouvetii














[13]
A. johnsonii














[14]
A. genospecies 9
88.4













[15]
A. lwoffi
88.4
93.3












[16]
A. schindleri
88.7
90.7
90.5











[17]
A. towneri
88.0
87.3
86.7
87.0










[18]
A. tandoii
87.9
86.4
86.8
87.4
87.1









[19]
A. baylyi
87.0
86.9
86.9
86.7
86.0
86.7








[20]
A. genospecies 11
87.3
87.1
87.2
86.9
86.1
86.8
99.2







[21]
A. genospecies 10
87.4
86.6
86.7
87.4
85.5
87.4
92.3
92.5






[22]
A. gerneri
87.7
86.3
86.4
86.7
87.0
87.6
88.7
88.9
89.0





[23]
A. ursingii
85.5
85.1
84.9
85.2
85.3
86.5
85.3
85.5
85.3
86.1




[24]
A. radioresistense
83.2
84.6
84.3
84.9
84.6
83.9
84.1
84.0
83.7
84.3
85.2
















TABLE 5





Comparison of similarity rates (%) of sequences (301-310 bp) of the rp/L-rpoB spacer in the different


Acinetobacter species.






























1
2
3
4
5
6
7
8
9
10
11
12





 [1]
A. calcoaceticus














 [2]
genospecies 3
92.8













 [3]
A. baumannii
90.6
95.9












 [4]
genospecies 13
84.0
86.8
86.5











 [5]
genospecies 16
86.5
87.4
86.8
93.4










 [6]
A. parvus
83.0
86.2
86.5
96.9
93.4









 [7]
A. tjernbergiae
85.5
87.1
86.5
95.0
93.7
94.0








 [8]
A. junii
87.7
88.4
88.4
91.5
93.4
91.2
93.1







 [9]
A. grimontii
87.7
88.4
88.4
91.5
93.4
91.2
93.1
100.0






[10]
A. haemolyticus
85.8
87.1
86.5
93.4
93.7
92.1
93.1
93.4
93.4





[11]
genospecies 6
87.1
87.4
86.2
91.2
93.1
90.6
92.1
93.1
93.1
91.2




[12]
genospecies 9
87.7
86.8
86.8
84.0
85.8
83.0
85.2
86.5
86.5
85.5
85.8



[13]
A. lwoffii
86.8
86.5
86.5
83.0
84.6
82.7
85.2
85.5
85.5
84.6
85.5
98.4


[14]
A. schindleri
87.4
87.7
88.1
83.6
85.5
83.6
85.8
87.4
87.4
85.5
85.8
96.2


[15]
A. bouvetii
87.7
86.5
86.5
84.6
85.2
84.3
86.2
86.5
86.5
86.2
85.5
91.8


[16]
A. johnsonii
84.3
84.6
84.9
81.1
82.4
80.8
82.7
82.1
82.1
82.4
82.1
88.1


[17]
A. towneri
84.9
85.8
87.1
87.1
85.5
86.5
87.4
84.6
84.6
85.8
84.9
89.0


[18]
A. tandoii
86.2
85.8
85.8
84.0
84.3
83.6
85.2
84.9
84.9
84.3
84.3
89.0


[19]
A. baylyi
82.7
82.4
83.0
81.4
83.6
82.4
82.7
83.6
83.6
81.8
82.7
86.2


[20]
genospecies 11
83.0
82.7
83.3
81.8
84.0
82.7
83.0
84.0
84.0
82.1
82.7
86.5


[21]
genospecies 10
84.9
84.6
84.9
84.3
85.5
84.9
85.5
86.2
86.2
83.6
84.9
88.1


[22]
A. gerneri
86.8
85.5
85.8
83.0
84.6
83.6
84.9
85.2
85.2
83.6
84.0
88.4


[23]
A. radioresistense
86.2
87.1
88.4
86.8
87.4
86.2
86.8
87.7
87.7
86.8
85.2
86.8


[24]
A. ursingii
85.8
84.9
85.5
85.2
86.5
84.9
86.8
85.5
85.5
84.9
85.2
85.5


























13
14
15
16
17
18
19
20
21
22
23






 [1]
A. calcoaceticus














 [2]
genospecies 3














 [3]
A. baumannii














 [4]
genospecies 13














 [5]
genospecies 16














 [6]
A. parvus














 [7]
A. tjernbergiae














 [8]
A. junii














 [9]
A. grimontii














[10]
A. haemolyticus














[11]
genospecies 6














[12]
genospecies 9














[13]
A. lwoffii














[14]
A. schindleri
95.9













[15]
A. bouvetii
91.2
91.5












[16]
A. johnsonii
87.7
87.4
86.5











[17]
A. towneri
88.4
89.3
91.2
87.4










[18]
A. tandoii
88.4
89.3
93.1
84.9
90.3









[19]
A. baylyi
85.2
85.8
85.5
89.3
87.1
84.9








[20]
genospecies 11
85.5
86.2
85.8
89.6
87.4
85.2
99.7







[21]
genospecies 10
87.1
87.7
90.3
86.8
89.3
89.6
92.5
92.8






[22]
A. gerneri
88.4
87.7
88.7
85.5
88.4
88.1
91.5
91.8
92.8





[23]
A. radioresistense
86.2
85.8
86.2
84.9
86.5
84.9
83.0
83.3
86.5
86.5




[24]
A. ursingii
85.5
84.9
87.7
85.5
85.8
86.2
85.2
85.5
86.8
87.7
90.3
















TABLE 6





Similarity rates (%) of sequences (301-310 bp) of the rpoB-rpoC spacer (86-177 bp) in the different


Acinetobacter species.






























1
2
3
4
5
6
7
8
9
10
11
12





 [1]
genospecies 6














 [2]
A. haemolyticus
92.4













 [3]
A. junii
90.4
89.4












 [4]
A. grimontii
90.9
89.9
99.5











 [5]
A. calcoaceticus
90.4
89.9
91.4
91.4










 [6]
genospecies 3
90.9
89.9
91.9
91.9
99.0









 [7]
A. baumannii
90.4
89.9
91.4
91.4
98.5
98.5








 [8]
genospecies 13
76.3
75.3
78.8
79.3
92.9
93.4
92.9







 [9]
genospecies 16
75.3
75.3
77.8
78.3
91.9
92.4
91.9
96.5






[10]
A. parvus
79.3
79.3
79.8
80.3
91.4
91.4
91.4
86.4
85.9





[11]
A. tjernbergiae
80.3
80.8
81.3
81.8
93.4
93.4
93.4
86.4
86.9
91.4




[12]
A. tandoii
74.2
77.8
75.8
76.3
90.4
91.4
90.4
79.8
80.3
77.3
79.8



[13]
A. towneri
74.2
77.3
78.8
79.3
88.4
89.4
88.9
76.8
76.8
76.3
78.8
85.4


[14]
A. baylyi
82.8
81.8
80.3
80.8
88.4
87.9
87.9
84.8
86.4
87.4
87.4
85.9


[15]
genospecies 11
78.3
79.8
77.3
77.8
88.9
89.9
89.4
77.3
77.8
79.3
81.3
84.3


[16]
genospecies 10
75.3
77.3
77.3
76.8
88.4
88.4
88.9
79.3
79.8
81.8
84.8
72.7


[17]
A. gerneri
78.3
78.8
80.3
80.8
89.4
90.4
89.4
74.7
75.3
74.2
75.3
76.8


[18]
A. bouvetii
70.7
73.7
74.7
75.3
89.9
90.9
89.9
89.4
91.4
84.3
85.4
81.8


[19]
A. schindleri
70.2
73.7
72.7
73.2
90.9
91.9
90.9
88.9
90.4
84.3
85.9
80.8


[20]
A. johnsonii
75.3
77.8
74.2
73.7
89.4
89.4
89.4
73.2
73.7
75.8
76.8
76.3


[21]
genospecies 9
76.8
79.8
80.8
81.3
90.4
91.4
90.4
80.3
82.3
79.3
81.3
81.8


[22]
A. lwoffii
74.7
77.3
78.8
79.3
90.4
91.4
90.4
82.3
83.8
81.3
82.8
83.8


[23]
A. radioresistense
86.4
86.4
85.4
85.4
94.9
94.9
94.9
88.4
87.9
91.9
93.4
87.9


[24]
A. ursingii
77.3
75.3
79.8
79.3
90.9
91.4
91.9
81.3
82.8
85.4
88.4
77.8


























13
14
15
16
17
18
19
20
21
22
23






 [1]
genospecies 6














 [2]
A. haemolyticus














 [3]
A. junii














 [4]
A. grimontii














 [5]
A. calcoaceticus














 [6]
genospecies 3














 [7]
A. baumannii














 [8]
genospecies 13














 [9]
genospecies 16














[10]
A. parvus














[11]
A. tjernbergiae














[12]
A. tandoii














[13]
A. towneri














[14]
A. baylyi
82.8













[15]
genospecies 11
84.3
83.8












[16]
genospecies 10
75.3
82.8
80.8











[17]
A. gerneri
71.7
82.3
70.7
74.7










[18]
A. bouvetii
79.8
83.3
75.3
76.3
74.2









[19]
A. schindleri
78.3
84.3
75.3
77.8
71.7
92.9








[20]
A. johnsonii
74.2
81.8
72.2
75.8
77.3
76.3
77.8







[21]
genospecies 9
82.8
82.3
78.8
77.3
76.3
84.8
84.8
80.8






[22]
A. lwoffii
82.3
85.9
78.3
76.8
74.2
83.8
81.8
73.2
87.9





[23]
A. radioresistense
86.4
90.9
85.9
89.9
84.3
86.9
85.4
86.4
86.9
87.4




[24]
A. ursingii
77.8
85.4
79.3
81.3
72.2
77.8
77.8
76.8
77.8
78.3
88.4
















TABLE 7





Comparison of similarity rates (%) of sequences (350 bp) of the partial sequences of rpoB region 2 in


the different Acinetobacter species.






























1
2
3
4
5
6
7
8
9
10
11
12





 [1]
A. baumannii














 [2]
genospecies 3
95.1













 [3]
A. calcoaceticus
88.3
90.6












 [4]
A. grimonti
87.1
86.6
88.0











 [5]
A. junii
86.9
86.3
87.1
99.1










 [6]
genospecies 16
86.0
84.3
84.6
90.3
89.4









 [7]
A. parvus
87.1
85.7
84.0
91.4
90.6
95.4








 [8]
genospecies 13
87.4
86.9
85.7
90.6
89.7
93.4
93.1







 [9]
A. johnsonii
85.1
84.3
84.6
90.0
89.4
89.4
91.1
91.7






[10]
A. tjernbergiae
87.1
86.3
85.4
90.6
89.7
92.3
92.9
93.1
93.1





[11]
genospecies 6
83.7
82.9
82.9
87.4
87.1
89.4
88.3
87.1
87.7
87.7




[12]
A. haemolyticus
87.7
85.4
85.1
87.7
87.4
92.0
89.7
91.1
89.1
90.0
90.3



[13]
A. schindleri
84.6
84.0
82.9
89.1
88.6
87.7
88.0
88.3
86.0
87.1
85.4
86.3


[14]
A. baylyi
85.1
84.0
82.6
85.1
84.9
86.0
85.4
84.6
86.0
85.1
85.7
85.7


[15]
genospecies 11
85.1
84.3
82.9
85.1
84.9
85.7
85.1
84.9
85.7
85.4
85.7
85.7


[16]
A. bouvetii
84.6
84.6
81.1
85.4
85.7
84.9
85.4
85.4
86.0
84.9
83.7
84.9


[17]
genospecies 10
82.9
82.6
80.6
84.6
83.7
84.9
84.9
85.1
84.3
84.9
82.6
84.9


[18]
A. gerneri
84.9
85.7
82.3
89.1
88.9
85.4
86.9
85.7
87.4
86.9
85.4
85.1


[19]
genospecies 9
85.4
84.3
82.3
83.7
84.0
86.0
85.1
85.7
86.0
84.9
84.6
86.0


[20]
A. lwoffii
83.7
85.1
83.1
83.4
83.7
85.7
84.6
87.1
85.1
84.6
84.0
85.7


[21]
A. towneri
81.7
80.9
81.4
85.1
85.4
84.9
84.0
83.7
87.1
83.4
83.4
84.0


[22]
A. ursingii
82.6
82.0
82.0
84.9
84.6
82.9
84.0
83.7
83.7
85.1
84.6
82.9


[23]
A. tandoii
83.4
82.6
82.0
88.6
88.3
89.4
90.0
86.9
88.0
88.3
86.9
88.0


[24]
A. radioresistense
79.7
78.9
78.6
82.0
81.1
82.0
82.0
80.0
79.4
81.7
80.6
79.4


























13
14
15
16
17
18
19
20
21
22
23






 [1]
A. baumannii














 [2]
genospecies 3














 [3]
A. calcoaceticus














 [4]
A. grimonti














 [5]
A. junii














 [6]
genospecies 16














 [7]
A. parvus














 [8]
genospecies 13














 [9]
A. johnsonii














[10]
A. tjernbergiae














[11]
genospecies 6














[12]
A. haemolyticus














[13]
A. schindleri














[14]
A. baylyi
84.9













[15]
genospecies 11
85.7
98.0












[16]
A. bouvetii
86.3
90.0
89.4











[17]
genospecies 10
85.1
88.6
88.0
85.1










[18]
A. gerneri
85.7
87.1
87.1
89.1
86.0









[19]
genospecies 9
86.9
86.0
86.9
86.3
85.1
86.6








[20]
A. lwoffii
86.0
85.4
86.6
85.4
84.3
86.3
93.7







[21]
A. towneri
82.0
83.7
83.1
83.4
80.9
86.3
86.3
84.0






[22]
A. ursingii
83.4
82.0
82.6
84.0
81.7
85.4
80.6
81.7
82.0





[23]
A. tandoii
85.7
83.4
83.7
85.4
82.3
87.4
85.1
85.7
84.9
83.7




[24]
A. radioresistense
82.0
78.6
79.4
80.3
79.7
83.1
80.0
80.0
78.6
80.0
83.4
















TABLE 8





Comparison of similarity rates (%) of sequences (450 bp) of the partial sequences of rpoB region 2 in the


different Acinetobacter species.






























1
2
3
4
5
6
7
8
9
10
11
12





 [1]
A. calcoaceticus














 [2]
genospecies 3
94.2













 [3]
A. baumannii
93.6
91.8












 [4]
genospecies 13
89.3
90.0
88.4











 [5]
A. tjernbergiae
90.0
90.7
89.1
93.8










 [6]
genospecies 16
88.2
88.7
89.1
93.3
93.1









 [7]
A. parvus
88.4
88.7
89.6
93.6
93.1
94.9








 [8]
A. baylyi
84.7
84.9
84.4
86.9
85.6
86.2
86.2







 [9]
genospecies 11
84.2
84.9
84.4
86.4
85.6
86.2
86.2
99.6






[10]
genospecies 10
84.0
84.2
84.9
84.4
83.8
87.3
86.9
94.9
95.3





[11]
A. bouvetii
86.2
85.8
85.1
83.8
86.0
85.6
84.9
87.3
87.3
88.0




[12]
A. schindleri
82.9
85.1
84.2
83.6
83.3
85.3
84.7
87.1
87.1
87.3
90.9



[13]
A. johnsonii
84.7
85.3
85.8
85.8
86.0
86.7
86.2
87.1
87.1
86.4
89.8
88.7


[14]
genospecies 9
83.6
85.1
83.8
83.6
83.8
85.1
86.0
86.0
86.0
85.8
86.4
88.0


[15]
A. lwoffii
83.6
85.6
83.3
84.4
84.0
85.8
84.2
86.4
86.4
85.8
86.4
88.0


[16]
A. gerneri
81.8
80.0
82.0
81.6
80.9
82.4
81.6
87.3
87.3
86.7
84.0
83.3


[17]
A. tandoii
82.2
82.7
83.1
83.3
83.3
83.1
83.1
82.9
82.9
82.2
83.1
81.8


[18]
A. towneri
83.6
83.6
83.6
83.1
82.4
82.9
83.3
83.3
83.3
83.8
84.0
84.9


[19]
A. haemolyticus
83.3
83.1
84.4
81.3
82.4
82.7
82.0
84.7
84.7
83.8
81.8
81.8


[20]
genospecies 6
82.0
82.0
82.0
82.0
82.0
83.8
82.2
81.8
81.8
81.8
81.3
80.7


[21]
A. ursingii
81.8
81.3
80.7
81.6
82.2
79.6
79.8
80.0
79.6
78.2
79.1
81.1


[22]
A. grimonti
80.9
81.6
81.6
82.2
82.2
83.6
83.1
80.2
80.2
81.6
78.2
80.7


[23]
A. junii
80.4
80.9
81.6
81.6
81.1
82.4
82.9
80.4
80.4
81.3
78.4
79.6


[24]
A. radioresistense
75.8
76.0
77.1
77.1
76.9
78.0
77.8
78.7
78.2
78.7
77.1
78.2


























13
14
15
16
17
18
19
20
21
22
23






 [1]
A. calcoaceticus














 [2]
genospecies 3














 [3]
A. baumannii














 [4]
genospecies 13














 [5]
A. tjernbergiae














 [6]
genospecies 16














 [7]
A. parvus














 [8]
A. baylyi














 [9]
genospecies 11














[10]
genospecies 10














[11]
A. bouvetii














[12]
A. schindleri














[13]
A. johnsonii














[14]
genospecies 9
86.0













[15]
A. lwoffii
86.7
95.1












[16]
A. gerneri
83.6
82.2
82.4











[17]
A. tandoii
82.4
80.9
80.7
83.1










[18]
A. towneri
83.8
85.1
85.1
85.3
88.7









[19]
A. haemolyticus
82.4
83.8
82.2
85.1
84.7
86.7








[20]
genospecies 6
81.8
81.3
81.8
84.7
83.8
84.7
87.3







[21]
A. ursingii
79.8
78.9
79.3
81.1
83.1
84.0
81.6
85.8






[22]
A. grimonti
80.9
82.7
83.3
80.9
83.1
84.7
84.9
85.8
81.6





[23]
A. junii
80.7
80.9
81.8
81.3
83.6
84.2
85.6
86.0
80.9
98.0




[24]
A. radioresistense
76.0
80.7
79.6
80.4
79.1
80.2
80.4
81.8
81.6
83.6
82.4
















TABLE 9





Comparison of similarity rates (%) of sequences (350 bp) of the partial sequences


of rpoB region 1 in the different A. baumannii strains.

























Strains
1
2
3
4
5
6
7
8
9
10





















 [1]
64.1












 [2]
70.9
100.0











 [3]
70.33
100.0
100.0










 [4]
105742
100.0
100.0
100.0









 [5]
53.79
100.0
100.0
100.0
100.0








 [6]
70.8
99.4
99.4
99.4
99.4
99.4







 [7]
54.97
99.4
99.4
99.4
99.4
99.4
100.0






 [8]
70.32
98.3
98.3
98.3
98.3
98.3
98.9
98.9





 [9]
70.34
98.3
98.3
98.3
98.3
98.3
98.9
98.9
100.0




[10]
68.38
98.3
98.3
98.3
98.3
98.3
98.9
98.9
99.4
99.4



[11]
70.24
98.6
98.6
98.6
98.6
98.6
99.1
99.1
99.7
99.7
99.7


[12]
53.77
99.1
99.1
99.1
99.1
99.1
99.7
99.7
99.1
99.1
99.1


[13]
54.147
99.1
99.1
99.1
99.1
99.1
99.7
99.7
99.1
99.1
99.1


[14]
70.10
99.1
99.1
99.1
99.1
99.1
99.7
99.7
98.6
98.6
98.6


[15]
1072.1
98.9
98.9
98.9
98.9
98.9
99.4
99.4
98.3
98.3
98.3


[16]
70.21
99.1
99.1
99.1
99.1
99.1
99.7
99.7
98.6
98.6
98.6


[17]
70.28
98.9
98.9
98.9
98.9
98.9
99.4
99.4
98.3
98.3
98.3


[18]
70.35
98.9
98.9
98.9
98.9
98.9
99.4
99.4
98.3
98.3
98.3


[19]
70.22
99.1
99.1
99.1
99.1
99.1
99.7
99.7
98.6
98.6
98.6


[20]
103572
98.9
98.9
98.9
98.9
98.9
99.4
99.4
98.3
98.3
98.3


[21]
103655
95.4
95.4
95.4
95.4
95.4
95.4
95.4
94.9
94.9
94.9




















Strains
11
12
13
14
15
16
17
18
19
20





















 [1]
64.1












 [2]
70.9












 [3]
70.33












 [4]
105742












 [5]
53.79












 [6]
70.8












 [7]
54.97












 [8]
70.32












 [9]
70.34












[10]
68.38












[11]
70.24












[12]
53.77
99.4











[13]
54.147
99.4
100.0










[14]
70.10
98.9
99.4
99.4









[15]
1072.1
98.6
99.1
99.1
99.7








[16]
70.21
98.9
99.4
99.4
100.0
99.7







[17]
70.28
98.6
99.1
99.1
99.7
99.4
99.7






[18]
70.35
98.6
99.1
99.1
99.7
99.4
99.7
100.0





[19]
70.22
98.9
99.4
99.4
99.4
99.1
99.4
99.7
99.7




[20]
103572
98.6
99.1
99.1
99.1
98.9
99.1
99.4
99.4
99.7



[21]
103655
95.1
95.1
95.1
95.1
94.9
95.1
95.4
95.4
95.7
95.4
















TABLE 10





Comparison of similarity rates (%) of sequences (450 bp) of the partial sequences


of rpoB region 2 in different A. baumannii strains

























Strains
1
2
3
4
5
6
7
8
9
10





















 [1]
70.10












 [2]
70.21
100.0











 [3]
1072.1
99.8
99.8










 [4]
103572
99.8
99.8
100.0









 [5]
53.77
99.1
99.1
99.3
99.3








 [6]
70.22
99.1
99.1
99.3
99.3
99.6







 [7]
70.32
99.3
99.3
99.6
99.6
99.3
99.3






 [8]
70.34
99.3
99.3
99.6
99.6
99.3
99.3
100.0





 [9]
68.38
99.3
99.3
99.6
99.6
99.3
99.3
100.0
100.0




[10]
54.147
99.3
99.3
99.6
99.6
99.3
99.3
100.0
100.0
100.0



[11]
53.79
99.1
99.1
99.3
99.3
99.1
99.6
99.8
99.8
99.8
99.8


[12]
70.9
98.9
98.9
99.1
99.1
98.9
99.3
99.6
99.6
99.6
99.6


[13]
64.1
99.1
99.1
99.3
99.3
99.1
99.6
99.8
99.8
99.8
99.8


[14]
70.33
99.1
99.1
99.3
99.3
99.1
99.6
99.8
99.8
99.8
99.8


[15]
105742
99.1
99.1
99.3
99.3
99.1
99.6
99.8
99.8
99.8
99.8


[16]
54.97
99.1
99.1
99.3
99.3
99.1
99.1
99.8
99.8
99.8
99.8


[17]
70.8
99.1
99.1
99.3
99.3
98.7
98.7
99.3
99.3
99.3
99.3


[18]
70.24
99.6
99.6
99.8
99.8
99.1
99.1
99.8
99.8
99.8
99.8


[19]
70.35
99.6
99.6
99.8
99.8
99.6
99.6
99.8
99.8
99.8
99.8


[20]
70.28
99.6
99.6
99.8
99.8
99.1
99.1
99.3
99.3
99.3
99.3


[21]
103655
94.0
94.0
94.2
94.2
94.2
94.2
93.8
93.8
93.8
93.8




















Strains
11
12
13
14
15
16
17
18
19
20





















 [1]
70.10












 [2]
70.21












 [3]
1072.1












 [4]
103572












 [5]
53.77












 [6]
70.22












 [7]
70.32












 [8]
70.34












 [9]
68.38












[10]
54.147












[11]
53.79












[12]
70.9
99.8











[13]
64.1
100.0
99.8










[14]
70.33
100.0
99.8
100.0









[15]
105742
100.0
99.8
100.0
100.0








[16]
54.97
99.6
99.3
99.6
99.6
99.6







[17]
70.8
99.1
98.9
99.1
99.1
99.1
99.6






[18]
70.24
99.6
99.3
99.6
99.6
99.6
99.6
99.6





[19]
70.35
99.6
99.3
99.6
99.6
99.6
99.6
99.1
99.6




[20]
70.28
99.1
98.9
99.1
99.1
99.1
99.1
99.1
99.6
99.6



[21]
103655
93.8
93.6
93.8
93.8
93.8
93.6
93.6
94.0
94.0
94.4
















TABLE 11





Comparison of similarity rates (%) of the sequences of intergenic spacer rp/L-rpoB


in different A. baumannii strains

























Strains
1
2
3
4
5
6
7
8
9
10





















 [1]
70.8












 [2]
70.33
99.7











 [3]
68.38
100.0
99.7










 [4]
105742
100.0
99.7
100.0









 [5]
64.1
100.0
99.7
100.0
100.0








 [6]
103572
100.0
99.7
100.0
100.0
100.0







 [7]
54.147
100.0
99.7
100.0
100.0
100.0
100.0






 [8]
70.35
100.0
99.7
100.0
100.0
100.0
100.0
100.0





 [9]
70.32
100.0
99.7
100.0
100.0
100.0
100.0
100.0
100.0




[10]
70.28
100.0
99.7
100.0
100.0
100.0
100.0
100.0
100.0
100.0



[11]
70.24
100.0
99.7
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[12]
70.22
100.0
99.7
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[13]
70.21
100.0
99.7
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[14]
70.10
100.0
99.7
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[15]
54.97
100.0
99.7
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[16]
53.79
100.0
99.7
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[17]
53.77
100.0
99.7
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[18]
70.9
100.0
99.7
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[19]
70.34
100.0
99.7
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[20]
1072.1
99.3
99.0
99.3
99.3
99.3
99.3
99.3
99.3
99.3
99.3


[21]
103655
96.7
96.4
96.7
96.7
96.7
96.7
96.7
96.7
96.7
96.7




















Strains
11
12
13
14
15
16
17
18
19
20





















 [1]
70.8












 [2]
70.33












 [3]
68.38












 [4]
105742












 [5]
64.1












 [6]
103572












 [7]
54.147












 [8]
70.35












 [9]
70.32












[10]
70.28












[11]
70.24












[12]
70.22
100.0











[13]
70.21
100.0
100.0










[14]
70.10
100.0
100.0
100.0









[15]
54.97
100.0
100.0
100.0
100.0








[16]
53.79
100.0
100.0
100.0
100.0
100.0







[17]
53.77
100.0
100.0
100.0
100.0
100.0
100.0






[18]
70.9
100.0
100.0
100.0
100.0
100.0
100.0
100.0





[19]
70.34
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0




[20]
1072.1
99.3
99.3
99.3
99.3
99.3
99.3
99.3
99.3
99.3



[21]
103655
96.7
96.7
96.7
96.7
96.7
96.7
96.7
96.7
96.7
96.4
















TABLE 12





Comparison of similarity rates (%) of sequences (301-310 bp) of the


intergenic spacer rpoB-rpoC in different A. baumannii strains.

























Strains
1
2
3
4
5
6
7
8
9
10





















 [1]
54.97












 [2]
103655
98.8











 [3]
70.10
100.0
98.8










 [4]
70.24
100.0
98.8
100.0









 [5]
70.33
100.0
98.8
100.0
100.0








 [6]
70.34
100.0
98.8
100.0
100.0
100.0







 [7]
70.35
100.0
98.8
100.0
100.0
100.0
100.0






 [8]
1072.1
100.0
98.8
100.0
100.0
100.0
100.0
100.0





 [9]
103572
100.0
98.8
100
100.0
100.0
100.0
100.0
100.0




[10]
105742
100.0
98.8
100.0
100.0
100.0
100.0
100.0
100.0
100.0



[11]
70.32
100.0
98.8
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[12]
70.28
100.0
98.8
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[13]
70.22
100.0
98.8
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[14]
70.21
100.0
98.8
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[15]
70.9
100.0
98.8
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[16]
70.8
100.0
98.8
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[17]
68.38
100.0
98.8
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[18]
64.1
100.0
98.8
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[19]
54.147
100.0
98.8
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[20]
53.79
100.0
98.8
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0


[21]
53.77
98.8
97.7
98.8
98.8
98.8
98.8
98.8
98.8
98.8
98.8




















Strains
11
12
13
14
15
16
17
18
19
20





















 [1]
54.97












 [2]
103655












 [3]
70.10












 [4]
70.24












 [5]
70.33












 [6]
70.34












 [7]
70.35












 [8]
1072.1












 [9]
103572












[10]
105742












[11]
70.32












[12]
70.28
100.0











[13]
70.22
100.0
100.0










[14]
70.21
100.0
100.0
100.0









[15]
70.9
100.0
100.0
100.0
100.0








[16]
70.8
100.0
100.0
100.0
100.0
100.0







[17]
68.38
100.0
100.0
100.0
100.0
100.0
100.0






[18]
64.1
100.0
100.0
100.0
100.0
100.0
100.0
100.0





[19]
54.147
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0




[20]
53.79
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0
100.0



[21]
53.77
98.8
98.8
98.8
98.8
98.8
98.8
98.8
98.8
98.8
98.8









BIBLIOGRAPHICAL REFERENCES


    1. Bouvet P J, Jeanjean S. Delineation of new proteolytic espèce génomique in the genus Acinetobacter. Res Microbiol. 1989 May-June; 140(4-5):291-9.
    2. Bouvet, P. J. M., and Grimont, P. A. D. Taxonomy of the genus Acinetobacter with the recognition of Acinetobacter baumannii sp. nov., Acinetobacter haemolyticus sp. nov., Acinetobacter johnsonii sp. nov., and Acinetobacter junii sp. nov. and amended descriptions of Acinetobacter calcoaceticus and Acinetobacter lwoffii. Int. J. Syst. Bacteriol., 1986, 36, 228-240.
    3. Carr E L, Kampfer P, Patel B K, Gurtler V, Seviour R J. Seven novel species of Acinetobacter isolated from activated sludge. Int J Syst Evol Microbiol. 2003 July; 53(Pt 4):953-63.
    4. Felseinstein 1989 1989. PHYLIPphylogeny inference package (version 3.2). Cladistics 5:164-166.
    5. Gerner-Smidt P, Tjernberg I, Ursing J. Reliability of phenotypic tests for identification of Acinetobacter species. J Clin Microbiol. 1991 February; 29(2):277-82.
    6. Gerner-Smidt P. Ribotyping of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex. J Clin Microbiol. 1992 October; 30(10):2680-5.
    7. Ibrahim A, Gerner-Smidt P, Liesack W. Phylogenetic relationship of the twenty-one DNA groups of the genus Acinetobacter as revealed by 16S ribosomal DNA sequence analysis. Int J Syst Bacteriol. 1997 July; 47(3):837-41.
    8. Khamis A, Colson P, Raoult D, Scola B L. Usefulness of rpoB gene sequencing for identification of Afipia and Bosea species, including a strategy for choosing discriminative partial sequences. Appl Environ Microbiol. 2003 November; 69(11):6740-9.
    9. Krawczyk B, Lewandowski K, Kur J. Comparative studies of the Acinetobacter genus and the species identification method based on the recA sequences. Mol Cell Probes. 2002 February; 16(1):1-11.
    10. Nemec A, De Baere T, Tjernberg I, Vaneechoutte M, van der Reijden T J, Dijkshoorn L. Acinetobacter ursingii sp. nov. and Acinetobacter schindleri sp. nov., isolated from human clinical specimens. Int J Syst Evol Microbiol. 2001 September; 51(Pt 5):1891-9
    11. Nemec A, Dijkshoorn L, Cleenwerck I, De Baere T, Janssens D, Van Der Reijden T J, Jezek P, Vaneechoutte M. Acinetobacter parvus sp. nov., a small-colony-forming species isolated from human clinical specimens. Int J Syst Evol Microbiol. 2003 September; 53(Pt 5):1563-7.
    12. Ochman and Wilson A C. R Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J Mol Evol. 1987; 26:74-86.
    13. Stackebrandt, E., and B. M. Goebel. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-849.
    14. Rainey, F. A., E. Lang, and E. Stackebrandt. 1994. The phylogenetic structure of the genus Acinetobacter. FEMS Microbiol. Lett. 124:349-353.
    15. Tjernberg I, Ursing J. Clinical strains of Acinetobacter classified by DNA-DNA hybridization. APMIS. 1989 July; 97(7):595-605.
    16. Towner K J. Clinical importance and antibiotic resistance of Acinetobacter spp. Proceedings of a symposium held on 4-5 Nov. 1996 at Eilat, Israel. J Med Microbiol. 1997 September; 46(9):721-46.
    17. Van Dessel H, Dijkshoorn L, Van Der Reijden T, Bakker N, Paauw A, Van Den Broek P, Verhoef J, Brisse S. Identification of a new geographically widespread multiresistant Acinetobacter baumannii clone from European hospitals. Res Microbiol. 2004 March; 155(2):105-12.
    18. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680
    19. Yamamoto, S., and S. Harayama. 1996. Phylogenetic analysis of Acinetobacter strains based on the nucleotide sequences of gyrB genes and on the amino acid sequences of their products. Int. J. Syst. Bacteriol. 46:506-511.
    20. Yamamoto, S., and S. Harayama. 1998. Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int. J. Syst. Bacteriol. 48:813-819.
    21. Yamamoto, S., P. J. Bouvet, and S. Harayama. 1999. Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization. Int. J. Syst. Bacteriol. 49:87-95.

## Claims

1. A mixture of oligonucleotides comprising:
(a) an equimolar mixture of each different oligonucleotide defined by a first single sequence consisting of at least 18 consecutive nucleotides of a nucleotide sequence set forth in SEQ ID NOS: 1-5 and 8,
where:
D represents A, G, or T,
Y represents C or T,
B represents C, G, or T,
R represents A or G, and
M represents A or C; or

(b) an equimolar mixture of the full-length complementary sequences of the different oligonucleotides set forth in (a).

2. The mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO: 1.

3. A combination of primers comprising:
a 5′ primer comprising the mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 1; and
a 3′ primer comprising a mixture of oligonucleotides selected from the group consisting of:
(i) an equimolar mixture of each different oligonucleotide defined by a second single sequence consisting of at least 12 consecutive nucleotides of SEQ ID NO:2, where M represents A or C, R represents A or G, and Y represents C or T; and
(ii) an equimolar mixture of the full-length complementary sequences of the different oligonucleotides set forth in (i).

4. A method for determining whether a bacterium belonging to the Acinetobacter genus is present in a sample, the method comprising:
(1) contacting the sample with the combination of primers according to claim 3;
(2) amplifying the nucleic acids present in the sample by an enzymatic polymerization reaction; and
(3) determining the presence of amplification product, wherein the presence of amplification product indicates the presence of a bacterium belonging to the Acinetobacter genus in the sample.

5. The method according to claim 4, further comprising:
(4) determining the presence or absence in the sample of at least one Acinetobacter species selected from the group consisting of A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, by carrying out the following steps comprising:
(4a) sequencing the amplification product, and
(4b) comparing the sequence of the amplification product obtained in (4a) with at least one sequence selected from the group consisting of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus.

6. The method according to claim 4, further comprising:
(4) determining the presence or absence in the sample of at least one Acinetobacter species selected from the group consisting of A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, by contacting the amplification product with at least one species probe consisting of an rpoB gene fragment,
wherein formation of a hybridization complex between the species probe and the amplification product is indicative of the presence in the sample of the Acinetobacter species corresponding to the species probe, and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample.

7. A method for detecting whether a species of Acinetobacter selected from the group consisting of: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, is present in a sample, comprising:
(1) contacting the sample with the combination of primers according to claim 3 to obtain a first amplification product; and
(2) identifying the Acinetobacter species from which the first amplification product was obtained by:
sequencing the first amplification product and comparing the sequence of the first amplification product to SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus; or
contacting the first amplification product with a species probe consisting of one of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, wherein formation of a hybridization complex between the species probe and the first amplification product is indicative of the presence in the sample of the species of Acinetobacter corresponding to the species probe and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample; and
if the presence of A. grimontii or A. junii, respectively comprising the rpoB sequences set forth in SEQ ID NO: 28 and SEQ ID NO: 13, is determined, the following steps (3) and (4) are carried out:
(3) obtaining a second amplification product by contacting the sample with:
a 5′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 3, or the complementary sequences thereof, where R represents A or G, and B represents C, G, or T; and
a 3′ primer comprising a mixture of each different oligonucleotide defined by a fourth single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 4, or the complementary sequences thereof, where R represents A or G, B represents C, G, or T, and Y represents C or T; and

(4) determining whether the second amplification product obtained in (3) corresponds to any of the sequences set forth in SEQ ID NOS: 77-100; or
if the presence of A. baylii or genomic species 11, respectively comprising the rpoB the sequences set forth in SEQ ID NO: 25 and SEQ ID NO: 19 is determined, the following steps (5) and (6) are carried out:
(5) obtaining a second amplification product by contacting the sample with:
a 5′ primer comprising at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and a 3′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G; and

(6) determining whether the second amplification product obtained in (5) corresponds to any of the sequences set forth in SEQ ID NOS: 165-188.

8. The combination of primers according to claim 3, wherein the second single sequence consists of at least 18 consecutive nucleotides of the sequence set forth in SEQ ID NO: 2.

9. A method for detecting whether a species of Acinetobacter selected from the group consisting of: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, is present in a sample, comprising:
(1) contacting the sample with the combination of primers according to claim 3 to obtain a first amplification product; and
(2) identifying the species from which the first amplification product was obtained by:
sequencing the first amplification product and comparing the sequence of the first amplification product to SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus; or
contacting the first amplification product with a species probe consisting of one of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, wherein formation of a hybridization complex between the species probe and the first amplification product is indicative of the presence in the sample of the species of Acinetobacter corresponding to the species probe and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample; and
carrying out at least a second amplification wherein the following steps (3) and (4) are carried out:
(3) obtaining a second amplification product by contacting the sample with 5′ and 3′ primers selected from the group consisting of:
(i) a 5′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 3, or the complementary sequences thereof, where R represents A or G, and B represents C, G, or T; and
a 3′ primer comprising a mixture of each different oligonucleotide defined by a fourth single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 4, or the complementary sequences thereof, where R represents A or G, B represents C, G, or T, and Y represents C or T;
(ii) a 5′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 5, or the complementary sequences thereof, where D represents A, G, or T, M represents A or C, and R represents A or G; and
a 3′ primer comprising at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 6, or the complementary sequence thereof; and
(iii) a 5′ primer comprising at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and
a 3′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G; and

(4) determining whether the second amplification product obtained in (3) corresponds to any of the sequences set forth in:
SEQ ID NOS: 77-100, if the 5′ and 3′ primers corresponding to SEQ ID NOS: 3 and 4 are selected in (3);
SEQ ID NOS: 121-144, if the 5′ and 3′ primers corresponding to SEQ ID NOS: 5 and 6 are selected in (3); or
SEQ ID NOS: 165-188, if the 5′ and 3′ primers corresponding to SEQ ID NOS: 7 and 8 are selected in (3).

10. A method for detecting whether a species of Acinetobacter selected from the group consisting of: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, is present in a sample, comprising:
(1) contacting the sample with the combination of primers according to claim 3 to obtain a first amplification product; and
(2) identifying the species from which the first amplification product was obtained by:
sequencing the first amplification product and comparing the sequence of the first amplification product to SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus; or
contacting the first amplification product with a species probe consisting of one of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, wherein formation of a hybridization complex between the species probe and the first amplification product is indicative of the presence in the sample of the species of Acinetobacter corresponding to the species probe and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample; and
if the presence of A. baylii or genomic species 11, respectively comprising the rpoB sequences set forth in SEQ ID NO: 25 and SEQ ID NO: 19 is determined, the following steps (3) and (4) are carried out:
(3) obtaining a second amplification product by contacting the sample with:
a 5′ primer comprising at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and
a 3′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of at least 12 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G; and

(4) determining whether the second amplification product obtained in (3) corresponds to any of the sequences set forth in SEQ ID NOS: 165-188.

11. A method for detecting whether a species of Acinetobacter selected from the group consisting of: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, is present in a sample, comprising:
(1) obtaining a first amplification product by contacting the sample with the combination of primers according to claim 8, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO: 1 and the second single sequence consists of the full-length sequence set forth in SEQ ID NO: 2; and
(2) identifying the species from which the first amplification product was obtained by:
sequencing the first amplification product and comparing the sequence of the first amplification product to SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus; or
contacting the first amplification product with a species probe consisting of one of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, wherein formation of a hybridization complex between the species probe and the first amplification product is indicative of the presence in the sample of the species of Acinetobacter corresponding to the species probe and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample; and
if the presence of A. grimontii or A. junii, respectively comprising the rpoB the sequences set forth in SEQ ID NO: 28 and SEQ ID NO: 13 is determined, the following steps (3) and (4) are carried out:
(3) obtaining a second amplification product by contacting the sample with:
a 5′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of the full-length sequence set forth in SEQ ID NO: 3, or the complementary sequences thereof, where R represents A or G, and B represents C, G, or T; and
a 3′ primer comprising a mixture of each different oligonucleotide defined by a fourth single sequence consisting of the full-length sequence set forth in SEQ ID NO: 4, or the complementary sequences thereof, where R represents A or G, B represents C, G, or T, and Y represents C or T; and

(4) determining whether the second amplification product obtained in (3) corresponds to any of the sequences set forth in SEQ ID NOS: 77-100; or
if the presence of A. baylii or genomic species 11, respectively comprising the rpoB sequences set forth in SEQ ID NO: 25 or SEQ ID NO: 19 is determined, the following steps (5) and (6) are carried out:
(5) obtaining a second amplification product by contacting the sample with:
a 5′ primer consisting of the full-length sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and
a 3′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of the full-length sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G; and

(6) determining whether the second amplification product obtained in (5) corresponds to any of the sequences set forth in SEQ ID NOS: 165-188.

12. A method for detecting whether a species of Acinetobacter selected from the group consisting of: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, is present in a sample, comprising:
(1) obtaining a first amplification product by contacting the sample with the combination of primers according to claim 8, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO: 1 and the second single sequence consists of the full-length sequence set forth in SEQ ID NO:2; and
(2) identifying the species from which the first amplification product was obtained by:
sequencing the first amplification product and comparing the sequence of the first amplification product to SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus; or
contacting the first amplification product with a species probe consisting of one of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, wherein formation of a hybridization complex between the species probe and the first amplification product is indicative of the presence in the sample of the species of Acinetobacter corresponding to the species probe and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample; and
carrying out at least a second amplification wherein the following steps (3) and (4) are carried out:
(3) obtaining a second amplification product by contacting the sample with 5′ and 3′ primers selected from the group consisting of:
(i) a 5′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of the full-length sequence set forth in SEQ ID NO: 3, or the complementary sequences thereof, where R represents A or G, and B represents C, G, or T; and
a 3′ primer comprising a mixture of each different oligonucleotide defined by a fourth single sequence consisting of the full-length sequence set forth in SEQ ID NO: 4, or the complementary sequences thereof, where R represents A or G, B represents C, G, or T, and Y represents C or T;
(ii) a 5′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of the full-length sequence set forth in SEQ ID NO: 5, or the complementary sequences thereof, where D represents A, G, or T, M represents A or C, and R represents A or G; and
a 3′ primer consisting of the full-length sequence set forth in SEQ ID NO: 6, or the complementary sequence thereof; and
(iii) a 5′ primer consisting of the full-length sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and
a 3′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of the full-length sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G; and

(4) determining whether the second amplification product obtained in (3) corresponds to any of the sequences set forth in:
SEQ ID NOS: 77-100, if the 5′ and 3′ primers corresponding to SEQ ID NOS: 3 and 4 are selected in (3);
SEQ ID NOS: 121-144, if the 5′ and 3′ primers corresponding to SEQ ID NOS: 5 and 6 are selected in (3); or
SEQ ID NOS: 165-188, if the 5′ and 3′ primers corresponding to SEQ ID NOS: 7 and 8 are selected in (3).

13. A method for detecting whether a species of Acinetobacter selected from the group consisting of: A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A. schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, respectively comprising the rpoB sequences set forth in SEQ ID NOS: 9-32, is present in a sample, comprising:
(1) obtaining a first amplification product by contacting the sample with the combination of primers according to claim 8, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO: 1 and the second single sequence consists of the full-length sequence set forth in SEQ ID NO:2; and
(2) identifying the species from which the first amplification product was obtained by:
sequencing the first amplification product and comparing the sequence of the first amplification product to SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus; or
contacting the first amplification product with a species probe consisting of one of SEQ ID NOS: 33-56, which describe portions of the rpoB gene specific to, respectively, A. calcoaceticus (genomic species 1), A. baumannii (genomic species 2), genomic species 3, A. haemolyticus (genomic species 4), A. junii (genomic species 5), genomic species 6, A. johnsonii (genomic species 7), A. lwoffii (genomic species 8), genomic species 9, genomic species 10, genomic species 11, A. radioresistens (genomic species 12), genomic species 13, genomic species 16, A schindleri, A. ursingii, A. baylyi, A. bouvetii, A. gerneri, A. grimontii, A. tandoii, A. tjernbergiae, A. towneri, and A. parvus, wherein formation of a hybridization complex between the species probe and the first amplification product is indicative of the presence in the sample of the species of Acinetobacter corresponding to the species probe and the absence of a hybridization complex indicates that the species of Acinetobacter corresponding to the species probe is not present in the sample; and
if the presence of A. baylii or genomic species 11, respectively comprising the rpoB sequences set forth in SEQ ID NO: 28 or SEQ ID NO: 19 is determined, the following steps (3) and (4) are carried out:
(3) obtaining a second amplification product by contacting the sample with:
a 5′ primer consisting of the full-length sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and
a 3′ primer comprising a mixture of each different oligonucleotide defined by a third single sequence consisting of the full-length sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G; and

(4) determining whether the second amplification product obtained in (3) corresponds to any of the sequences set forth in SEQ ID NOS: 165-188.

14. A combination of primers, comprising:
a first pair of primers comprising the combination of primers set forth in claim 8; and
a second pair of primers selected from the group consisting of:
(i) a 5′ primer comprising an equimolar mixture of each different oligonucleotide defined by a third single sequence consisting of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 3, or the complementary sequences thereof, where R represents A or G, and B represents C, G, or T; and
a 3′ primer comprising an equimolar mixture of each different oligonucleotide defined by a fourth single sequence consisting of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 4, or the complementary sequences thereof, where R represents A or G, B represents C, G, or T, and Y represents C or T,
(ii) a 5′ primer comprising an equimolar mixture of each different oligonucleotide defined by a third single sequence consisting of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO:5, or the complementary sequences thereof, where D represents A, G, or T, M represents A or C, and R represents A or G; and
a 3′ primer comprising at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 6, or the complementary sequence thereof; and
(iii) a 5′ primer comprising at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 7, or the complementary sequence thereof; and
a 3′ primer comprising an equimolar mixture of each different oligonucleotide defined by a third single sequence consisting of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 8, or the complementary sequences thereof, where R represents A or G.

15. The mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO: 2.

16. The mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO: 3.

17. The mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO: 4.

18. The mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO: 5.

19. The mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of the full-length sequence set forth in SEQ ID NO: 8.

20. A combination of primers comprising:
a 5′ primer comprising the mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 3; and
a 3′ primer comprising a mixture of oligonucleotides selected from the group consisting of:
(i) an equimolar mixture of each different oligonucleotide defined by a second single sequence consisting of at least 12 consecutive nucleotides of SEQ ID NO:4, where:
B represents C, G, or T,
R represents A or G, and
Y represents C or T; and

(ii) an equimolar mixture of the full-length complementary sequences of the different oligonucleotides set forth in (i).

21. A combination of primers comprising:
a 5′ primer comprising the mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 5; and
a 3′ primer consisting of:
at least 12 consecutive nucleotides of SEQ ID NO: 6; or
the full-length complementary sequence of at least 12 consecutive nucleotides of SEQ ID NO: 6.

22. A combination of primers comprising:
a 3′ primer comprising the mixture of oligonucleotides according to claim 1, wherein the first single sequence consists of at least 18 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NO: 8; and
a 5′ primer consisting of:
at least 12 consecutive nucleotides of SEQ ID NO: 7; or
the full-length complementary sequence of at least 12 consecutive nucleotides of SEQ ID NO:7.