Genome Sequences and Phylogenetic Analysis of K 88-and F 18-Positive 1 Porcine Enterotoxigenic Escherichia coli 2 3

15 Porcine enterotoxigenic Escherichia coli (ETEC) continue to result in major morbidity 16 and mortality to the swine industry via post-weaning diarrhea. The key virulence 17 factors of these strains, their serotypes, and their fimbrial components have been 18 well studied. However, most studies to date have focused on plasmid-encoded traits 19 related to colonization and toxin production, and the chromosomal backgrounds of 20 these strains have been largely understudied. Here, we generated the genomic 21 sequences of K88-positive and F18-positive porcine ETEC and examined the 22 phylogenetic distribution of clinical porcine ETEC and their plasmid-associated 23 genetic content. The genomes of porcine ETEC strains UMNK88 and UMNF18 were 24 both found to contain remarkable plasmid complements containing known virulence 25 factors, potential novel virulence factors, and antimicrobial resistance-associated 26 elements. The chromosomes of these strains also possessed several unique 27 genomic islands containing hypothetical genes with similarity to classical virulence 28 factors, although phage-associated genomic islands dominated the accessory 29 genomes of these strains. Phylogenetic analysis of 78 clinical isolates associated 30 with neonatal and porcine diarrhea revealed that a limited subset of porcine ETEC 31 lineages exist that generally contain common toxin and fimbrial profiles, with many of 32 the isolates belonging to the ST10, ST23, and ST169 MLST types. These lineages 33 were generally distinct from existing human ETEC database isolates. Overall, most 34 porcine ETEC appear to have emerged from a limited subset of E. coli lineages that 35 either have an increased propensity to carry plasmid-encoded virulence factors, or 36 have the appropriate ETEC core genome required for virulence. 37 on D ecem er 2, 2017 by gest http/jb.asm . rg/ D ow nladed fom INTRODUCTION 38 Diarrhea is a major cause of morbidity and mortality to young pigs, resulting in 39 significant production losses to the swine industry (10). Enterotoxigenic Escherichia 40 coli (ETEC) are the most common cause of diarrhea in young pigs, resulting in a 41 disease known as enteric colibacillosis (10). Neonatal and post-weaning pigs are 42 most susceptible to ETEC. While neonatal ETEC diarrhea is generally well 43 controlled by using fimbrial-based vaccines, post-weaning enteric colibacillosis has 44 been more difficult to control. Porcine ETEC are characterized by the production of 45 specific adhesins and enterotoxins. The adhesins most common in porcine ETEC 46 are fimbrial adhesins K88 (also called F4), K99 (F5), 987P (F6), F41, and F18, as 47 well as afimbrial adhesins such as AIDA-I. Porcine ETEC also produce one or more 48 enterotoxins, including heat labile enterotoxin (LT), heat stable enterotoxins a and b 49 (STa and STb), and EAST1 toxin (34). These and other described porcine ETEC 50 virulence factors have mostly been localized to plasmids. Additionally, F18-positive 51 porcine E. coli implicated in edema disease and diarrhea sometimes possess the 52 shiga toxin-encoding gene (stx2e) within their chromosomes (16). 53