Stress Resistance and Virulence Gene Profiles Associated with Phylogeny and Phenotypes of Escherichia coli from Cattle

• Published in: Journal of food protection 2023-09, Vol.86 (9), p.100122-100122, Article 100122
• Main Authors: Fang, Yuan, Tran, Frances, Stanford, Kim, Yang, Xianqin
• Format: Article
• Language: English
• Subjects: Acid resistance; Biofilm; Phylogeny; Shiga toxin; tLST; Top seven E. coli; Virulence profile
• ISSN: 0362-028X; 1944-9097
• DOI: 10.1016/j.jfp.2023.100122

•Top 7 E. coli genomes (n = 155) were analyzed for phylogeny, virulence factors (VF) and stress genes.•Carriage of stx and the extreme heat resistance marker tLST was mutually exclusive.•A novel O84:H2 strain carrying stx1a was identified.•All heat-resistance genes and most metal resistance genes were in phylogroup A.•No specific genes associated with acid resistance or biofilm formation phenotypes were identified.•VFs were more abundant in the acid resistant group. Seven serogroups of E. coli (Top seven E. coli) are frequently implicated in foodborne outbreaks in North America, largely due to their carriage of Shiga toxin genes (stx). This study aimed to profile resistance genes and virulence factors (VF), and their potential association with phylogeny and phenotypes of Top seven E. coli originating from cattle in Canada. 155 Top seven E. coli isolates previously characterized for heat and acid resistance and biofilm-forming ability were whole-genome sequenced and analyzed for phylogeny, VF, and stress resistance genes. The 155 E. coli strains belonged to six phylogroups: A (n = 32), B1 (n = 93), C (n = 3), D (n = 11), E (n = 15), and G (n = 1). Different phylogroups were clearly separated on the core genome tree, with strains of the same serotype closely clustered. The carriage of stx and the transmissible locus of stress tolerance (tLST), the extreme heat resistance marker, was mutually exclusive, in 33 and 15 genomes, respectively. A novel O84:H2 strain carrying stx1a was also identified. In total, 70, 41, and 32 VF, stress resistance genes and antibiotic resistance genes were identified. The stress resistance genes included those for metal (n = 29), biocides/acid (n = 4), and heat (n = 8) resistance. All heat resistance genes and most metal-resistance genes that were differentially distributed among the phylogroups were exclusively in phylogroup A. VF were least and most present in phylogroups A and D, respectively. No specific genes associated with acid resistance or biofilm formation phenotypes were identified. VF were more abundant (P