Prevalence and Genomic Characterization of Escherichia coli O157:H7 in Cow-Calf Herds throughout California

Abstract

Escherichia coli serotype O157:H7 is a zoonotic food-and waterborne bacterial pathogen that causes a high hospitalization rate and can cause lifethreatening complications. Increasingly, E. coli O157:H7 infections appear to originate from fresh produce. Ruminants, such as cattle, are a prominent reservoir of E. coli O157:H7 in the United States. California is one of the most agriculturally productive regions in the world for fresh produce, beef, and milk. The close proximity of fresh produce and cattle presents food safety challenges on a uniquely large scale. We performed a survey of E. coli O157:H7 on 20 farms in California to observe the regional diversity and prevalence of E. coli O157:H7. Isolates were obtained from enrichment cultures of cow feces. Some farms were sampled on two dates. Genomes from isolates were sequenced to determine their relatedness and pathogenic potential. E. coli O157:H7 was isolated from approximately half of the farms. The point prevalence of E. coli O157:H7 on farms was highly variable, ranging from zero to nearly 90%. Within farms, generally one or a few lineages were found, even when the rate of isolation was high. On farms with high isolation rates, a single clonal lineage accounted for most of the isolates. Farms that were visited months after the first visit might have had the same lineages of E. coli O157:H7. Strains of E. coli O157:H7 may be persistent for months on farms.IMPORTANCE This survey of 20 cow-calf operations from different regions of California provides an in depth look at resident Escherichia coli O157:H7 populations at the molecular level. E. coli O157:H7 is found to have a highly variable prevalence, and with whole-genome sequencing, high prevalences in herds were found to be due to a single lineage shed from multiple cows. Few repeat lineages were found between farms in this area; therefore, we predict that E. coli O157:H7 has significant diversity in this area beyond what is detected in this survey. All isolates from this study were found to have pathogenic potential based on the presence of key virulence gene sequences. This represents a novel insight into pathogen diversity within a single subtype and will inform future attempts to survey regional pathogen populations.

Clostridioides difficile on Ohio swine farms (2015): A comparison of swine and human environments and assessment of on‐farm risk factors

“…Surprisingly, large-herd farms had significantly lower odds of C. difficile recovery as compared to farms with fewer swine. This association is contradictory to associations commonly found between farm herd-size and the prevalence of other highly studied enteric pathogens (e.g., Salmonella, Campylobacter, Escherichia coli O157:H7) (Adesiyun et al, 2014;Guerin et al, 2007;Worley et al, 2017). It may be that the swine farms in this study with larger herds had more stringent hygiene and biosecurity protocols in place or greater worker adherence to such protocols than those with smaller herds.…”

Whole genome shotgun sequencing revealed highly polymorphic genome regions and genes in Escherichia coli O157:H7 isolates collected from a single feedlot

“…Particularly, the clade 8 is more likely to be associated with the severe disease cases. These results were quite different from those reported recently by our group based on a survey that involved 20 cattle farms from various regions in California, which revealed that the clade 8 was the most dominant group [ 51 ], probably reflecting certain geographic effects on the E . coli O157:H7 lineage distribution, as our current strains were from a feedlot located in the South Western region of the US.…”

Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli (STEC) on New Zealand Dairy Farms: Application of a Culture-Independent Assay and Whole-Genome Sequencing

“…This finding has been reflected in other studies, where STEC strains isolated from calves from the same pen showed low variability, indicating frequent within-pen transmission ( 28 ). Unique STEC O157 lineages also proliferated among cattle on US dairy farms with a high STEC O157 prevalence ( 29 ). SNP analysis indicated that STEC O157 populations on a farm were dominated by a single clonal type, but differences occurred between farms, and some clonal types were still present during resampling 11 months later ( 29 ).…”

“…Unique STEC O157 lineages also proliferated among cattle on US dairy farms with a high STEC O157 prevalence ( 29 ). SNP analysis indicated that STEC O157 populations on a farm were dominated by a single clonal type, but differences occurred between farms, and some clonal types were still present during resampling 11 months later ( 29 ). Pulsed-field gel electrophoresis (PFGE) analysis of O26:H11 isolates ( n = 11) on three Australian farms also found unique strains at each farm ( 30 ).…”