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 life-threatening 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.

Keywords: California; Escherichia coli; O157:H7; STEC; cattle; food-borne pathogens; genomics.

FIG 1

Map of California showing the counties from which cow-calf herds were sampled. Counties which had a herd return at least one E. coli O157:H7 isolate are indicated in gray. Counties with no positive samples are filled with diagonal lines. Map created using ArcMap 10.5 (ESRI, Redlands, CA).

FIG 2

SNP-based collapsed phylogenetic tree of the strains used in this study. The scale bar represents the number of nucleotide substitutions per site. Groups of strains have a triangle connector whose length represents the range of nucleotide substitution rates within the group. Brackets group strains based on stx gene alleles. The introduction of a short insertion into the tir gene is indicated with text on the corresponding branch. The tree without collapsed branches is presented as Fig. S1 in the supplemental material.

FIG 3

Minimum-spanning tree (MST) of the strains used in this study plus selected strains from the NCBI genome database. The MST was created using the number of allelic differences between genome sequences, using E. coli O157:H7 Sakai as the reference and not counting gene absences. The identities of the strains are indicated by color, with the exception of yellow-filled circles, which have the letter of the corresponding herd adjacent. Connections are shown by black lines, with the allelic distance to the nearest interior node indicated within the circle, except for those along the main path relative to strain O8BKT061141, which are indicated along the line. Line thickness is increased for connections with many differences: >250, double; >500, triple; >1,000, quadruple. A detailed tree with all isolate names is presented in Fig. S3 in the supplemental material. *, the raw produce outbreak strains are from a previous report (39).

FIG 4

Presence or absence of virulence genes in the genome sequences. Presence of a gene was called at 60% of the total sequence being represented in homologous sequences with 90% sequence identity. Blue squares represent presence in at least half of the isolates, while gray squares represent absence in more than half. Numbers show how many sequences had a positive call when not all sequences were positive. Additional detail and genes are presented in Data Set S2 in the supplemental material.