ABSTRACTMostEscherichia colistrains are nonpathogenic. However, for clinical diagnosis and food safety analysis, current identification methods for pathogenicE. colieither are time-consuming and/or provide limited information. Here, we utilized a custom DNA microarray with informative genetic features extracted from 368 sequence sets for rapid and high-throughput pathogen identification. The FDAEscherichia coliIdentification (FDA-ECID) platform contains three sets of molecularly informative features that together stratify strain identification and relatedness. First, 53 known flagellin alleles, 103 alleles ofwzxandwzy, and 5 alleles ofwzmprovide molecular serotyping utility. Second, 41,932 probe sets representing the pan-genome ofE. coliprovide strain-level gene content information. Third, approximately 125,000 single nucleotide polymorphisms (SNPs) of available whole-genome sequences (WGS) were distilled to 9,984 SNPs capable of recapitulating theE. coliphylogeny. We analyzed 103 diverseE. colistrains with available WGS data, including those associated with past foodborne illnesses, to determine robustness and accuracy. The array was able to accurately identify the molecular O and H serotypes, potentially correcting serological failures and providing better resolution for H-nontypeable/nonmotile phenotypes. In addition, molecular risk assessment was possible with key virulence marker identifications. Epidemiologically, each strain had a unique comparative genomic fingerprint that was extended to an additional 507 food and clinical isolates. Finally, a 99.7% phylogenetic concordance was established between microarray analysis and WGS using SNP-level data for advanced genome typing. Our study demonstrates FDA-ECID as a powerful tool for epidemiology and molecular risk assessment with the capacity to profile the global landscape and diversity ofE. coli.IMPORTANCEThis study describes a robust, state-of-the-art platform developed from available whole-genome sequences ofE. coliandShigellaspp. by distilling useful signatures for epidemiology and molecular risk assessment into one assay. The FDA-ECID microarray contains features that enable comprehensive molecular serotyping and virulence profiling along with genome-scale genotyping and SNP analysis. Hence, it is a molecular toolbox that stratifies strain identification and pathogenic potential in the contexts of epidemiology and phylogeny. We applied this tool to strains from food, environmental, and clinical sources, resulting in significantly greater phylogenetic and strain-specific resolution than previously reported for available typing methods.
PacBio Genome Sequences of Escherichia coli Serotype O157:H7, Diffusely Adherent E. coli, and Salmonella enterica Strains, All Carrying Plasmids with an mcr-1 Resistance Gene