Scientific Publications
A multi-isolate genomic approach identifies diverse Escherichia coli contamination and antimicrobial resistance carriage on retail foods.
Microbial Genomics
Background. Bacterial pathogens contaminating retail foods can cause foodborne illness. Escherichia coli is commonly enumerated on food to assess unsafe levels of faecal contamination, but E. coli as a species is genetically variable and different types of E. coli may present more of a health risk than others. This enumeration approach provides limited insight into the types of E. coli contaminating food, whereas whole-genome sequencing (WGS) can provide insight into the genetic diversity as well as genes of concern. Current WGS studies have focused on the selection of pathogenic or antimicrobial-resistant E. coli, which has provided limited insight into the diversity and potential risk to consumers. Methods. To assess the diversity and potential risk of E. coli on food, food samples were collected from retail stores across Norfolk, UK. In this study, 126 chicken, 52 leafy green, 115 pork, 75 prawn and 33 salmon E. coli-positive samples were investigated. Up to four E. coli were isolated per sample and underwent WGS. E. coli genomes underwent in silico multi-locus sequence typing, where sequence types (STs) were investigated at the single nucleotide polymorphism (SNP) level. Furthermore, virulence genes and antimicrobial resistance (AMR) determinants were investigated .Results. From the total of 401 food samples, 1,067 E. coli genomes were isolated, sequenced and classified into 238 known STs and 54 unknown STs. Of the 145?samples in which four isolates were sequenced, 17 revealed four different STs, suggesting a high within-sample diversity. Within-sample within-ST comparisons revealed up to 845 pairwise non-recombinant SNPs. E. coli genomes contained between 0 and 14 AMR determinants. Up to four different AMR determinant combinations within a sample were identified, with 34.7% (n=139/401?samples) of all E. coli-positive samples containing three or more AMR determinants. In this dataset, 26 putative extraintestinal pathogenic E. coli (ExPEC) were identified. Discussion. A multi-isolate WGS approach identified a high diversity of STs, different AMR profiles and putative ExPEC within individual food samples which would have been missed by traditional enumeration approaches. Collecting multiple isolates and WGS is therefore necessary for ensuring thorough microbial hazard characterization for the consumer.
Microbial Genomics
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