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Life sciences · Journal article
Microbial Genomics · August 18, 2026
Early or partial results. Treat as a signal, not a conclusion.
This retrospective genomic analysis of 119 confirmed Vibrio cholerae isolates from 2022–2024 Tanzanian outbreaks identifies two co-circulating pandemic lineages (AFR10 and AFR13) with distinct geographic distribution, shared virulence genes, and resistance to co-trimoxazole and macrolides but retained susceptibility to tetracycline. The findings inform surveillance strategy and support continued use of doxycycline in adults, but are descriptive and do not establish causal links between genotype and clinical outcome or treatment efficacy.
Retrospective genomic epidemiology study. Archived Vibrio cholerae isolates from cholera outbreaks in 16 regions across Tanzania; 144 isolates collected, of which 119 confirmed as V. cholerae.. n = 119. 16 regions across Tanzania, including Lake Tanganyika basin region bordering Democratic Republic of the Congo and Zambia.
Of 144 isolates, 119 confirmed as V. cholerae, of which 109 (91.6%) belonged to sequence type ST69 AFR10 lineage clustered predominantly around Lake Tanganyika basin, bordering Democratic Republic of the Congo and Zambia AFR13 lineage widely distributed across different zones of Tanzania
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Clinicians should note the demonstrated susceptibility to tetracycline supports continued use of doxycycline in adults, but the widespread macrolide resistance (relevant for paediatric treatment alternatives) and detection of antiseptic resistance genes warrant heightened clinical vigilance and ongoing surveillance rather than immediate practice change.
Descriptive genomic epidemiology of archived outbreak isolates identifying circulating lineages and resistance profiles, but without experimental validation, clinical outcome data, or prospective surveillance to confirm transmission dynamics or treatment implications.
As stated by the source record.
Quoted from the source exactly as published.
Clinicians should note the demonstrated susceptibility to tetracycline supports continued use of doxycycline in adults, but the widespread macrolide resistance (relevant for paediatric treatment alternatives) and detection of antiseptic resistance genes warrant heightened clinical vigilance and ongoing surveillance rather than immediate practice change.
Graded across the dimensions that decide whether you should act, each from what the source actually supports. There is no single score, and where a dimension was not assessed it says so.
Cholera remains a persistent public health challenge in Tanzania, with recurrent outbreaks across multiple regions overwhelming the health systems. Despite the ongoing surveillance to control the transmission, limited genomic characterization of circulating Vibrio cholerae strains has constrained traceability of outbreak sources and transmission dynamics including virulence determinants and antimicrobial resistance profiles to guide clinical and public health interventions. We conducted a genome analysis of 144 archived isolates from 2022 to 2024 cholera outbreaks from 16 regions across Tanzania. Sequencing was performed using Oxford Nanopore platforms. Comprehensive bioinformatics analysis was applied including genome assembly, multi-locus sequence typing, resistance gene detection, virulence profiling and phylogenetic reconstruction. Of 144 isolates, sequencing confirmed 119 to be V. cholerae, of which 109 (91.6%) belonged to sequence type ST69. Phylogenetic analysis identified two distinct transmission lineages: AFR10 (formerly T10) and AFR13 (formerly T13), demonstrating marked geographic stratification. AFR10 isolates clustered predominantly around Lake Tanganyika basin, bordering the Democratic Republic of the Congo and Zambia, whereas AFR13 isolates were widely distributed across different zones of Tanzania. All isolates harboured key virulence genes ( ctxA, ctxB, tcpA ) and multiple resistance genes conferring resistance to co-trimoxazole and macrolides. The catB gene was found to be silenced in these isolates. Notably, tetracycline resistance genes ( tetA/B/C ) were absent. The qacEdelta gene was only detected in AFR13 isolates and has been linked to resistance to quaternary ammonium compounds (antiseptics and disinfectants) in Gram-negative bacteria from other studies. These findings demonstrate the co-circulation of two sublineages (AFR10 and AFR13) of the seventh pandemic El Tor lineage with distinct geographic distribution, suggesting both localized persistence and regional circulation. The observed genotypic and phenotypic susceptibility to tetracycline supports the continued use of doxycycline as a first-line therapy in adults. However, the detected macrolide resistance (an alternative treatment for children) and resistance genes associated with reduced susceptibility to antiseptics underscore the need for extensive monitoring. Strengthened national and cross-border genomic surveillance is essential for effective cholera control.
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