Whole genome characterisation of Enterotoxigenic Escherichia coli circulating in Zambia

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Abstract
Background: Enterotoxigenic Escherichia coli (ETEC) is a significant cause of diarrheal disease, particularly in low—and middle-income countries, including Zambia. ETEC pathogenesis is driven by colonisation factors (CF) and enterotoxins, and increasing antimicrobial resistance compounds the global health burden. Despite its impact, limited genomic data exists for ETEC strains in Sub-Saharan Africa. Methods: This study conducted whole-genome sequencing of 62 ETEC isolates collected from children under five years old presenting with moderate-to-severe diarrhoea in Lusaka, Zambia. Genomic DNA was extracted, sequenced using the Illumina MiSeq platform, and analysed for phylogenetic relationships, toxin profiles, CF combinations, AMR genes, and plasmid incompatibility groups. Sequences were processed using bioinformatics tools, including SPAdes for genome assembly and Abricate for virulence and AMR profiling. Results: The isolates displayed diverse phylogenetic groupings, predominantly within phylogroups A (22 isolates) and B1 (29 isolates). Forty-five serotypes and 39 sequence types were identified, with ST155, ST4, and ST847 being most prevalent. 35% of isolates lacked a known CF, but CS6-only stains were the most common (8%). The most frequent toxin profile was LTh (31%); AMR analysis revealed 350 resistance genes, with Sul2 (14%) and blaTEM-1 (10%) being predominant. ∼89% of isolates exhibited genomic multidrug resistance. Plasmid analysis identified IncFII as the most prevalent incompatibility group (19%). Conclusion: This study highlights the genomic diversity of ETEC in Zambia, revealing concerns about multidrug resistance and identifying virulence profiles. These findings reiterate the urgent need for enhanced surveillance and targeted interventions, including vaccine development, to combat ETEC-related diarrhoea effectively. Authors Summary: Diarrhoea caused by a bacteria called Escherichia coli is a significant health problem for young children in Zambia and many similar countries. Despite its profound impact, not much is known about the types of ETEC found in Zambia. In this study, we collected this type of bacteria from children under five years old who had diarrhoea and studied them in detail using advanced genetic tools. We discovered that the bacteria are very diverse, with different groups, toxin types, and ways of attaching to the host. Worryingly, most bacteria were resistant to several antibiotics, potentially making treatment challenging. This research helps us understand how ETEC spreads and causes illness in Zambia, showing the urgent need for tracking, improved treatments, and vaccines to protect children from this serious disease.

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