Cholera nanopore data
Background: Cholera remains a persistent public health challenge in Tanzania, with recurrent outbreaks across multiple regions overwhelming the health systems. Despite ongoing surveillance to control the transmission, limited genomic characterization of circulating Vibrio cholerae (V. cholerae) strains has constrained traceability of outbreak  Page 2 of 4 Standard_article_template  sources and transmission dynamics including virulence determinants and antibiogram to guide clinical and public health interventions. Methods: 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, multilocus sequence typing (MLST), resistance gene detection, virulence profiling, and phylogenetic reconstruction. Results: Of 144 isolates, 119 were confirmed as V. cholerae isolates by sequencing, of which 109 (91.6%) belonged to sequence type (ST) 69. Phylogenetic analysis identified two distinct transmission lineages: AFR10 (formerly T10; 20.2%) and AFR13 (formerly T13; 79.8%), demonstrating marked geographic stratification. AFR10 isolates clustered predominantly in southern highland and Lake Tanganyika basin, bordering the Democratic Republic of the Congo and Zambia, whereas AFR13 isolates were widely distributed across northern, eastern, central parts of Tanzania, and across the coastal zone. All isolates harboured key virulence genes (ctxA, ctxB, tcpA) and multiple resistance genes including catB9, sul1, dfrA1, mph(A), and mph(E) conferring resistance for chloramphenicol, co-trimoxazole and macrolides. The catB7 was found to be a silenced gene in the cholera isolates. Notably, tetracycline resistance genes (tetA/B/C) were absent. AFR13 isolates carried ctxB7 allele associated with highly virulent, multidrug-resistant outbreak strains and qacEdelta gene, which confers resistance to quaternary ammonium compounds (antiseptics and disinfectants). Conclusion: Cholera outbreaks in Tanzania 2022-2024 were driven by two sublineages (AFR10 and AFR13) of the 7th pandemic El Tor (7PET) lineage with distinct geographic distribution, suggesting both endemic persistence and cross-border transmission. The absence of resistance to tetracycline supports continued use of doxycycline as a first-line therapy in adults. However, the detected macrolide resistance, an alternative treatment to children, as well as resistance genes to antiseptics, underscores the need for extensive monitoring. Strengthened national and cross-border genomic surveillance is essential for effective cholera prevention, control and response.
Background: Cholera remains a persistent public health challenge in Tanzania, with recurrent outbreaks across multiple regions overwhelming the health systems. Despite ongoing surveillance to control the transmission, limited genomic characterization of circulating Vibrio cholerae (V. cholerae) strains has constrained traceability of outbreak  Page 2 of 4 Standard_article_template  sources and transmission dynamics including virulence determinants and antibiogram to guide clinical and public health interventions. Methods: 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, multilocus sequence typing (MLST), resistance gene detection, virulence profiling, and phylogenetic reconstruction. Results: Of 144 isolates, 119 were confirmed as V. cholerae isolates by sequencing, of which 109 (91.6%) belonged to sequence type (ST) 69. Phylogenetic analysis identified two distinct transmission lineages: AFR10 (formerly T10; 20.2%) and AFR13 (formerly T13; 79.8%), demonstrating marked geographic stratification. AFR10 isolates clustered predominantly in southern highland and Lake Tanganyika basin, bordering the Democratic Republic of the Congo and Zambia, whereas AFR13 isolates were widely distributed across northern, eastern, central parts of Tanzania, and across the coastal zone. All isolates harboured key virulence genes (ctxA, ctxB, tcpA) and multiple resistance genes including catB9, sul1, dfrA1, mph(A), and mph(E) conferring resistance for chloramphenicol, co-trimoxazole and macrolides. The catB7 was found to be a silenced gene in the cholera isolates. Notably, tetracycline resistance genes (tetA/B/C) were absent. AFR13 isolates carried ctxB7 allele associated with highly virulent, multidrug-resistant outbreak strains and qacEdelta gene, which confers resistance to quaternary ammonium compounds (antiseptics and disinfectants). Conclusion: Cholera outbreaks in Tanzania 2022-2024 were driven by two sublineages (AFR10 and AFR13) of the 7th pandemic El Tor (7PET) lineage with distinct geographic distribution, suggesting both endemic persistence and cross-border transmission. The absence of resistance to tetracycline supports continued use of doxycycline as a first-line therapy in adults. However, the detected macrolide resistance, an alternative treatment to children, as well as resistance genes to antiseptics, underscores the need for extensive monitoring. Strengthened national and cross-border genomic surveillance is essential for effective cholera prevention, control and response.