Scientific Publications by FDA Staff

Appl Environ Microbiol 2016 Jun 13;82(13):3900-12

Virulence gene profiles and clonal relationships of Escherichia coli O26:H11 isolates from feedlot cattle by whole genome sequencing.

Gonzalez-Escalona N, Toro M, Rump LV, Cao G, Nagaraja TG, Meng J

Escherichia coli O26 is the second most important enterohemorragic E. coli (EHEC) worldwide. Serogroup O26 strains are categorized mainly into two groups: enteropathogenic (EPEC) O26, mostly causing mild diarrhea, and Shiga toxigenic (STEC) O26 that carry shiga toxin (stx) gene, responsible for more severe outcomes. stx-negative O26 can further be split into two groups. One O26 group differs significantly from O26 EHEC, whereby the other O26 EHEC-like shows all characteristics of EHEC O26, except production of STX. In order to determine the different populations of O26 E. coli present in the US cattle, we sequenced 42 O26:H11 strains isolated from feedlot cattle and compared them to 37 O26:H11 genomes available at GenBank. Phylogenetic analysis by whole genome multilocus sequence typing (wgMLST) showed that O26:H11/H- in US cattle were highly diverse. Most strains were sequence type 29 (ST29). By wgMLST two clear lineages could be distinguished among cattle strains: Lineage 1 consisted of O26:H11 EHEC-like (ST29) (4 strains) and O26:H11 EHEC (ST21) (2 strains), and Lineage 2 (36 strains) consisted of O26:H11 EPEC (ST29). Overall our analysis showed US cattle carried pathogenic (ST21, stx1+, ehxA+, toxB+) and also potentially pathogenic (ST29, ehxA+, toxB+) O26:H11 E. coli strains. Furthermore, in silico analysis showed that 70% of the cattle strains carried at least one antimicrobial resistance gene. Our results showed that whole genome sequence analysis is a robust and valid approach to identify, and genetically characterize E. coli O26:H11, which is of importance for food safety and public health. IMPORTANCE: Escherichia coli O26 is the second most important enterohemorragic E. coli (EHEC) worldwide. Serogroup O26 strains are categorized into two groups: enteropathogenic (EPEC) carrying LEE, causing mild diarrhea, and Shiga toxigenic (STEC) carrying stx gene, responsible for more severe outcomes. However, there are currently problems in determining one group from the other. Furthermore several O26 stx negative strains are consistently misidentified as either EHEC-like or EPEC. The use of whole genome sequence (WGS) analysis of O26 strains of cattle from the US allowed for: 1) identification of O26 strains present in US cattle, 2) determined O26 strain diversity, 3) solved the misidentification problem, and 4) screened for the presence of antimicrobial resistance and virulence genes in those strains. This study provided a framework on how to easily and rapidly use WGS information to identify and genetically characterize E. coli O26:H11, which is of importance for food safety and public health.