Virulence gene profiles and phylogeny of Shiga toxin-positive Escherichia coli strains isolated from FDA regulated foods during 2010-2017

• DOI: 10.1371/journal.pone.0214620
• Publication Date: 2019-04-01T17:30:02Z
• Authors: Narjol González-E...; Julie Ann Kase
• Keywords: 0301 basic medicine; Food Safety; Science; Food Contamination; Shiga Toxin; 03 medical and health sciences; Humans; Escherichia coli Infections; Phylogeny; 2. Zero hunger; Shiga-Toxigenic Escherichia coli; Virulence; United States Food and Drug Administration; Q; R; Legislation, Food; United States; Bacterial Typing Techniques; 3. Good health; Food; Hemolytic-Uremic Syndrome; Food Microbiology; Government Regulation; Medicine; Transcriptome; Hazard Analysis and Critical Control Points; Research Article; Multilocus Sequence Typing

AbstractIllnesses caused by Shiga toxin-producingEscherichiacoli (STECs) can be life threatening, such as hemolytic uremic syndrome (HUS). The STECs most frequently identified by USDA’s Microbiological Data Program (MDP) carried toxin gene subtypesstx1aand/orstx2a. Here we describe the genome sequences of 331 STECs isolated from foods regulated by the FDA 2010-2017, determining their genomic identity, serotype, sequence type, virulence potential, and prevalence of antimicrobial resistance. Isolates were selected from the MDP archive, routine food testing by field labs (ORA), food testing by a contract company, and our laboratory (ORS). Only 276 (83%) were confirmed as STECs byin silicoanalysis. Foods from which STECs were recovered included cilantro (6%), spinach (25%), lettuce (11%), and flour (9%). Phylogenetic analysis using core genome MLST revealed these STEC genomes were highly variable, with some clustering associated with ST types and serotypes. We detected 95 different sequence types (ST); several ST were previously associated with HUS: ST21 and ST29 (O26:H11), ST11 (O157:H7), ST33 (O91:H14), ST17 (O103:H2), and ST16 (O111:H-).in silicovirulome analyses showed ~ 51% of these strains were potentially pathogenic [besidesstxgene they also carriedeae(25%) or 26%subA(26%)]. Virulence gene prevalence was also determined:stx1 only (19%) -variants a and c;stx2 only (66%) – variants a, b, c, d, e, and g; andstx1/sxt2 (15%). Our data form a new WGS database that can be used to support food safety investigations and monitor the recurrence/emergence ofE. coliin foods.ImportanceShiga toxin-producingEscherichiacoli (STECs) are associated with foodborne outbreaks worldwide; however, surveillance has not previously included genomic analyses for phylogenetics, prevalence, or potential virulence. We constructed the first genomic database of isolates from FDA-regulated foods to help monitor the emergence of new pathogenic STECs. Although only ~30 STECs were isolated per year, 50% of these carried markers associated with pathogenesis either a combination ofeaeplusstx, orsubAplusstx. Moreover, those strains also carried virulence genes associated with severe illnesses. Here we showed that WGS enabled comparisons across isolates to establish phylogeny, help in identification of antibiotic resistance by monitoring the presence of antimicrobial resistance genes, and determined the presence of known virulence genes that have been linked with illnesses. Future food safety investigations will benefit from improved source tracking and risk assessments made possible by these analyses and new WGS database.