Genomic and molecular insights into AMR, virulence, and toxin of Shiga toxin–producing Escherichia coli isolated from local curd foodborne outbreak in Manipur

This study reports the isolation, characterization, and genome analysis of Escherichia coli isolated from curd, revealing potential pathogenic and multidrug-resistant characteristics.15 individuals who consumed the suspected contaminated local curd developed symptoms included acute diarrhoea, dehydration, abdominal pain, and fever. Microbiological analysis confirmed the presence of E. coli in the curd, with characteristic greenish-metallic-sheen colonies on Eosin Methylene Blue and formed pink colour lactose fermentation in MaConkey agar. It exhibited positive biochemical reactions, including IMViC, catalase, citrate utilization, and sugar fermentation tests. Gram staining further confirmed the isolate is Gram-negative bacteria. PCR-based detection revealed the presence of diarrhoeagenic E. coli , specifically Shiga toxin-producing E. coli , with successful amplification of the stx2 gene. Antimicrobial susceptibility testing demonstrated resistance to ampicillin, cephalosporins, ciprofloxacin, and tetracycline, with sensitivity to chloramphenicol, gentamicin, and carbapenems. Genome sequencing identified the isolate as E. coli strain WOB, with a genome size of ~ 5.3 Mb and a GC content of 50.5%. Genomic typing classified the E. coli WOB under serotype O17/O77:H18 and phylogroup D, with sequence type ST370991. Phylogenetic analysis using EnteroBase cgMLST V2, HierCC V1 clustering, and the NINJA algorithm revealed a highly diverse population structure among selected 901 E. coli genomes from India, comprising 784 unique cgMLST profiles distributed across multiple well-defined phylogenetic clusters. The genome harboured antimicrobial resistance genes, including blaTEM-1B , tet(B) , and sul2 , as well as a plasmid (IncFIB). Notably, both stx1 and stx2 genes and 36 virulence factors were identified. Comparative genomics further revealed similarities to pathogenic EHEC strains, including E. coli O157:H7. The findings highlight the public health risk posed by informal food processing, underscoring the need for improved hygiene, surveillance, and genomic monitoring.