This report describes a 2017 outbreak of twelve E. coli O157:H7 infections that were likely linked to contact with animal manure.

Shiga-toxin-producing E. coli (STEC) is a leading causing of bacterial foodborne and zoonotic illnesses in the USA. Whole-genome sequencing (WGS) is a powerful tool used in public health and microbiology for the detection, surveillance, and outbreak investigation of STEC. In this study, we applied three WGS-based subtyping methods, high quality single-nucleotide polymorphism (hqSNP) analysis, whole genome multi-locus sequence typing using chromosome-associated loci [wgMLST (chrom)], and core genome multi-locus sequence typing (cgMLST), to isolate sequences from 11 STEC outbreaks. For each outbreak, we evaluated the concordance between subtyping methods using pairwise genomic differences (number of SNPs or alleles), linear regression models, and tanglegrams. Pairwise genomic differences were highly concordant between methods for all but one outbreak, which was associated with international travel. The slopes of the regressions for hqSNP vs. allele differences were 0.432 (cgMLST) and 0.966 wgMLST (chrom); the slope was 1.914 for cgMLST vs. wgMLST (chrom) differences. Tanglegrams comprised of outbreak and sporadic sequences showed moderate clustering concordance between methods, where Baker’s Gamma Indices (BGIs) ranged between 0.35 and 0.99 and Cophenetic Correlation Coefficients (CCCs) were ≥0.88 across all outbreaks. The K-means analysis using the Silhouette method showed the clear separation of outbreak groups with average silhouette widths ≥0.87 across all methods. This study validates the use of cgMLST for the national surveillance of STEC illness clusters using the PulseNet 2.0 system and demonstrates that hqSNP or wgMLST can be used for further resolution.

In July 2017, a Shiga toxin-producing Escherichia coli (STEC) outbreak was reported among 18 individuals with exposure to untreated recreational water at a California lake. Ten cases were hospitalized and five (ages 1–5 years) developed hemolytic-uremic syndrome. An environmental investigation was conducted to confirm STEC transmission via the lake and determine the outbreak strain contamination source. Large-volume water and sediment samples were collected in August 2017 and July 2018 and tested for STEC and molecular microbial source tracking markers. The STEC O157:H7 outbreak strain was recovered from the suspected exposure location and from goose scat, and goose genetic material was detected in every 2017 environmental sample, confirming lake water as the transmission vehicle and implicating the lake’s resident Canada goose population in disseminating the pathogen. An unrelated STEC O157:H7 strain and ruminant fecal contamination were detected the following year, suggesting repeated STEC introductions to the lake environment. Subsequent large-scale outbreaks of the same highly virulent STEC O157:H7 strain were associated with romaine lettuce and ground beef, resulting in its designation as the reoccurring, emerging, or persisting (REP) strain REPEXH01. The severe illnesses associated with outbreaks of virulent pathogen strains like REPEXH01 are more likely to be detected. Conducting environmental investigations in response to these reoccurring outbreaks allows for the collection of incremental evidence about the patterns of transmission and sources of consequential pathogens and strains. Such information can provide critical insights for mitigation strategies to interrupt ongoing transmission and prevent future outbreaks.