{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T19:47:49Z","timestamp":1785527269501,"version":"3.56.0"},"reference-count":46,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T00:00:00Z","timestamp":1780012800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T00:00:00Z","timestamp":1785369600000},"content-version":"vor","delay-in-days":62,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"Armed Forces Health Surveillance Division (AFHSD), Global Emerging Infections Surveillance (GEIS) Branch","award":["P0080_17_KY, P0119_18_KY, P0136_19_KY, P0114_22_KY, and P0112_23_KY)"],"award-info":[{"award-number":["P0080_17_KY, P0119_18_KY, P0136_19_KY, P0114_22_KY, and P0112_23_KY)"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"DOI":"10.1186\/s12864-026-12997-0","type":"journal-article","created":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T11:45:46Z","timestamp":1780055146000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic analysis of Vibrio cholerae in Western Kenya (2015\u20132023) reveals persistence of pandemic ST69 and presence of the European-associated ST8 lineage"],"prefix":"10.1186","volume":"27","author":[{"given":"Erick C","family":"Kipkirui","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanessa","family":"Natasha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Collins","family":"Kigen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James W","family":"Muturi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronald K","family":"Kirera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margaret C","family":"Koech","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary C","family":"Kirui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nancy C","family":"Kipkemoi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janet N","family":"Ndonye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheilla","family":"Jerotich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis Pow","family":"Sang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lillian","family":"Musila","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth A","family":"Odundo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,29]]},"reference":[{"key":"12997_CR1","unstructured":"Ojeda Rodriguez JA, Hashmi MF, Kahwaji CI. Vibrio cholerae infection. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2024 Jan\u2013. Updated 2024 May 1. Available from: https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK526099\/."},{"issue":"Pt 4","key":"12997_CR2","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1099\/jmm.0.023051-0","volume":"60","author":"M Kitaoka","year":"2011","unstructured":"Kitaoka M, Miyata ST, Unterweger D, Pukatzki S. Antibiotic resistance mechanisms of Vibrio cholerae. J Med Microbiol. 2011;60(Pt 4):397\u2013407.","journal-title":"J Med Microbiol"},{"issue":"1","key":"12997_CR3","doi-asserted-by":"publisher","first-page":"6291","DOI":"10.1038\/s41467-024-50484-w","volume":"15","author":"C Chaguza","year":"2024","unstructured":"Chaguza C, Chibwe I, Chaima D, Musicha P, Ndeketa L, Kasambara W, Mhango C, Mseka UL, Bitilinyu-Bangoh J, Mvula B, Kipandula W, Bonongwe P, Munthali RJ, Ngwira S, Mwendera CA, Kalizang\u2019oma A, Jambo KC, Kambalame D, Kamng\u2019ona AW, Steele AD, Chauma-Mwale A, Hungerford D, Kagoli M, Nyaga MM, Dube Q, French N, Msefula CL, Cunliffe NA, Jere KC. Genomic insights into the 2022\u20132023 Vibrio cholerae outbreak in Malawi. Nat Commun. 2024;15(1):6291.","journal-title":"Nat Commun"},{"key":"12997_CR4","doi-asserted-by":"publisher","first-page":"375","DOI":"10.3389\/fmicb.2013.00375","volume":"4","author":"C Lutz","year":"2013","unstructured":"Lutz C, Erken M, Noorian P, Sun S, McDougald D. Environmental reservoirs and mechanisms of persistence of Vibrio cholerae. Front Microbiol. 2013;4:375.","journal-title":"Front Microbiol"},{"issue":"10","key":"12997_CR5","doi-asserted-by":"publisher","first-page":"2449","DOI":"10.3390\/microorganisms11102449","volume":"11","author":"M Mavhungu","year":"2023","unstructured":"Mavhungu M, Digban TO, Nwodo UU. Incidence and virulence factor profiling of Vibrio species: a study on hospital and community wastewater effluents. Microorganisms. 2023;11(10):2449.","journal-title":"Microorganisms"},{"key":"12997_CR6","doi-asserted-by":"publisher","first-page":"1155751","DOI":"10.3389\/fmed.2023.1155751","volume":"10","author":"DA Montero","year":"2023","unstructured":"Montero DA, Vidal RM, Velasco J, George S, Lucero Y, G\u00f3mez LA, Carre\u00f1o LJ, Garc\u00eda-Betancourt R, O\u2019Ryan M. Vibrio cholerae, classification, pathogenesis, immune response, and trends in vaccine development. Front Med (Lausanne). 2023;10:1155751.","journal-title":"Front Med (Lausanne)"},{"issue":"48","key":"12997_CR7","doi-asserted-by":"publisher","first-page":"E7730","DOI":"10.1073\/pnas.1608732113","volume":"113","author":"D Hu","year":"2016","unstructured":"Hu D, Liu B, Feng L, Ding P, Guo X, Wang M, Cao B, Reeves PR, Wang L. Origins of the current seventh cholera pandemic. Proc Natl Acad Sci U S A. 2016;113(48):E7730\u20139.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"12997_CR8","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/s13099-017-0210-0","volume":"9","author":"S Anandan","year":"2017","unstructured":"Anandan S, Devanga Ragupathi NK, Muthuirulandi Sethuvel DP, Thangamani S, Veeraraghavan B. Prevailing clone (ST69) of Vibrio cholerae O139 in India over 10 years. Gut Pathog. 2017;9:60.","journal-title":"Gut Pathog"},{"key":"12997_CR9","doi-asserted-by":"crossref","unstructured":"Dutta D, Chowdhury G, Pazhani GP, Guin S, Dutta S, Ghosh S, Rajendran K, Nandy RK, Mukhopadhyay AK, Bhattacharya MK, Mitra U, Takeda Y, Nair GB, Ramamurthy T. Vibrio cholerae non-O1, non-O139 serogroups and cholera-like diarrhea, Kolkata, India. Emerg Infect Dis. 2013;19(3):464-7.","DOI":"10.3201\/eid1903.121156"},{"key":"12997_CR10","doi-asserted-by":"publisher","first-page":"5453","DOI":"10.2147\/IDR.S420095","volume":"16","author":"J Tang","year":"2023","unstructured":"Tang J, Li S, Zhang M, Li F, Tang Y, Yang F. Whole genome analysis of a Non-O1, Non-O139 Vibrio cholerae detected from human blood in China. Infect Drug Resist. 2023;16:5453\u201361.","journal-title":"Infect Drug Resist"},{"issue":"4","key":"12997_CR11","doi-asserted-by":"publisher","first-page":"698","DOI":"10.17305\/bb.2022.8745","volume":"23","author":"YH Xiang","year":"2023","unstructured":"Xiang YH, Hu QQ, Liu Y, Sheng R, Wang J, Li WJ, Shi J, Li X, Lu SH. Etiology and clinical features of non-O1\/non-O139 Vibrio cholerae infection in an inland city in China. Biomol Biomed. 2023;23(4):698\u2013704.","journal-title":"Biomol Biomed"},{"key":"12997_CR12","doi-asserted-by":"publisher","first-page":"1603736","DOI":"10.3389\/fmicb.2025.1603736","volume":"16","author":"LM Mageto","year":"2025","unstructured":"Mageto LM, Aboge GO, Mekuria ZH, Gathura P, Juma J, Mugo M, Kebenei CK, Imoli D, Ongadi BA, Kering K, Mbae CK, Kariuki S. Genomic characterization of Vibrio cholerae isolated from clinical and environmental sources during the 2022\u20132023 cholera outbreak in Kenya. Front Microbiol. 2025;16:1603736.","journal-title":"Front Microbiol"},{"issue":"3","key":"12997_CR13","doi-asserted-by":"publisher","first-page":"e0021121","DOI":"10.1128\/cmr.00211-21","volume":"35","author":"F Chowdhury","year":"2022","unstructured":"Chowdhury F, Ross AG, Islam MT, McMillan NAJ, Qadri F. Diagnosis, management, and future control of cholera. Clin Microbiol Rev. 2022;35(3):e0021121.","journal-title":"Clin Microbiol Rev"},{"issue":"11","key":"12997_CR14","doi-asserted-by":"publisher","first-page":"2151","DOI":"10.3201\/eid1711.110720","volume":"17","author":"M Sj\u00f6lund-Karlsson","year":"2011","unstructured":"Sj\u00f6lund-Karlsson M, Reimer A, Folster JP, Walker M, Dahourou GA, Batra DG, Martin I, Joyce K, Parsons MB, Boncy J, Whichard JM, Gilmour MW. Drug-resistance mechanisms in Vibrio cholerae O1 outbreak strain, Haiti, 2010. Emerg Infect Dis. 2011;17(11):2151\u20134.","journal-title":"Emerg Infect Dis"},{"issue":"1","key":"12997_CR15","doi-asserted-by":"publisher","first-page":"879","DOI":"10.1186\/s12879-025-11259-w","volume":"25","author":"D Chisompola","year":"2025","unstructured":"Chisompola D, Nzobokela J, Moono R, Chinyante E, Chipipa A, Chapuswike N, Chakopo M, Mukuma N, Chakulya M. Emerging antibiotic resistance in Vibrio cholerae: a study of cholera prevalence and resistance patterns in Zambia\u2019s Copperbelt Province. BMC Infect Dis. 2025;25(1):879.","journal-title":"BMC Infect Dis"},{"key":"12997_CR16","unstructured":"World Health Organization. Multi-country outbreak of cholera: epidemiological update no. 33. 2026. Available from: https:\/\/www.who.int\/publications\/m\/item\/multi-country-outbreak-of-cholera--epidemiological-update--33--27-january-2026 Accessed February 1, 2026."},{"issue":"3","key":"12997_CR17","doi-asserted-by":"publisher","first-page":"e0414022","DOI":"10.1128\/spectrum.04140-22","volume":"11","author":"MM Shah","year":"2023","unstructured":"Shah MM, Bundi M, Kathiiko C, Guyo S, Galata A, Miringu G, Ichinose Y, Yoshida LM. Antibiotic-resistant Vibrio cholerae O1 and Its SXT elements associated with two cholera epidemics in Kenya in 2007 to 2010 and 2015 to 2016. Microbiol Spectr. 2023;11(3):e0414022.","journal-title":"Microbiol Spectr"},{"issue":"3","key":"12997_CR18","doi-asserted-by":"publisher","first-page":"e0011166","DOI":"10.1371\/journal.pntd.0011166","volume":"17","author":"C Kiama","year":"2023","unstructured":"Kiama C, Okunga E, Muange A, Marwanga D, Langat D, Kuria F, Amoth P, Were I, Gachohi J, Ganda N, Martinez Valiente M, Njenga MK, Osoro E, Brunkard J. Mapping of cholera hotspots in Kenya using epidemiologic and water, sanitation, and hygiene (WASH) indicators as part of Kenya\u2019s new 2022\u20132030 cholera elimination plan. PLoS Negl Trop Dis. 2023;17(3):e0011166.","journal-title":"PLoS Negl Trop Dis"},{"key":"12997_CR19","doi-asserted-by":"crossref","unstructured":"Imoli D, Maingi JM, Mbae C, Kavai SM, Wairimu C, Mundalo S, Odityo G, Wairimu M, Mekuria Z, Gebreyes W, Kariuki S. Genomic characterization of multidrug-resistant extended-spectrum \u03b2-lactamase-producing Vibrio cholerae O1 strains from 2022 cholera outbreak in Kenya. J Antimicrob Chemother. 2025;80(9):2399\u20132407.","DOI":"10.1093\/jac\/dkaf224"},{"issue":"Suppl 1","key":"12997_CR20","first-page":"12","volume":"28","author":"EO Oyugi","year":"2017","unstructured":"Oyugi EO, Boru W, Obonyo M, Githuku J, Onyango D, Wandeba A, Omesa E, Mwangi T, Kigen H, Muiruri J, Gura Z. An outbreak of cholera in western Kenya, 2015: a case control study. Pan Afr Med J. 2017;28(Suppl 1):12.","journal-title":"Pan Afr Med J"},{"issue":"7","key":"12997_CR21","doi-asserted-by":"publisher","first-page":"758","DOI":"10.1093\/trstmh\/traf032","volume":"119","author":"LM Mageto","year":"2025","unstructured":"Mageto LM, Mutono N, Aboge G, Gathura P, Okunga E, Muange A, Mbae CK, Thumbi SM, Kariuki S. Spatio-temporal pattern and risk factors associated with cholera outbreaks in selected high-risk areas of Kenya. Trans R Soc Trop Med Hyg. 2025;119(7):758\u201366.","journal-title":"Trans R Soc Trop Med Hyg"},{"issue":"5","key":"12997_CR22","doi-asserted-by":"publisher","first-page":"e0010928","DOI":"10.1371\/journal.pntd.0010928","volume":"17","author":"W Boru","year":"2023","unstructured":"Boru W, Xiao S, Amoth P, Kareko D, Langat D, Were I, Ali M, Sack DA, Lee EC, Debes AK. Prioritizing interventions for cholera control in Kenya, 2015\u20132020. PLoS Negl Trop Dis. 2023;17(5):e0010928.","journal-title":"PLoS Negl Trop Dis"},{"issue":"6","key":"12997_CR23","doi-asserted-by":"publisher","first-page":"e0013078","DOI":"10.1371\/journal.pntd.0013078","volume":"19","author":"C Kiama","year":"2025","unstructured":"Kiama C, Okunga E, Makwe C, Muange A, Livinus M, Langat D, Brunkard J, Loarec A. Mapping of cholera Priority Areas for Multisectoral Interventions (PAMIs) using the 2023 GTFCC guidance: the Kenya experience. PLoS Negl Trop Dis. 2025;19(6):e0013078.","journal-title":"PLoS Negl Trop Dis"},{"key":"12997_CR24","unstructured":"Clinical and Laboratory Standards Institute (CLSI). Performance standards for antimicrobial susceptibility testing. 3rd ed. CLSI supplement M45. Wayne (PA): CLSI; 2018."},{"key":"12997_CR25","unstructured":"Andrews S. FastQC: a quality control tool for high throughput sequence data. Cambridge (UK): Babraham Bioinformatics; 2010. Available from: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/"},{"issue":"5","key":"12997_CR26","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","volume":"37","author":"M Kolmogorov","year":"2019","unstructured":"Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019;37(5):540\u2013 6","journal-title":"Nat Biotechnol"},{"key":"12997_CR27","doi-asserted-by":"crossref","unstructured":"Wick RR, Holt KE. Polypolish: short-read polishing of long-read bacterial genome assemblies. PLoS Comput Biol. 2022;18(1):e1009802.","DOI":"10.1371\/journal.pcbi.1009802"},{"issue":"8","key":"12997_CR28","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","volume":"29","author":"A Gurevich","year":"2013","unstructured":"Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072\u20135.","journal-title":"Bioinformatics"},{"issue":"1","key":"12997_CR29","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","volume":"17","author":"BD Ondov","year":"2016","unstructured":"Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016;17(1):132.","journal-title":"Genome Biol"},{"issue":"1","key":"12997_CR30","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","volume":"9","author":"C Jain","year":"2018","unstructured":"Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9(1):5114.","journal-title":"Nat Commun"},{"issue":"4","key":"12997_CR31","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1128\/JCM.06094-11","volume":"50","author":"MV Larsen","year":"2012","unstructured":"Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pont\u00e9n T, Ussery DW, Aarestrup FM, Lund O. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012;50(4):1355\u201361.","journal-title":"J Clin Microbiol"},{"issue":"1","key":"12997_CR32","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1038\/s41467-022-35713-4","volume":"14","author":"NL Sherry","year":"2023","unstructured":"Sherry NL, Horan KA, Ballard SA, Gon\u04abalves da Silva A, Gorrie CL, Schultz MB, Stevens K, Valcanis M, Sait ML, Stinear TP, Howden BP, Seemann T. An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance. Nat Commun. 2023;14(1):60.","journal-title":"Nat Commun"},{"key":"12997_CR33","unstructured":"Seemann T. ABRicate: mass screening of contigs for antibiotic resistance genes [Internet]. Melbourne (AU): GitHub; 2016. Available from: https:\/\/github.com\/tseemann\/abricate"},{"issue":"3","key":"12997_CR34","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gku1196","volume":"43","author":"NJ Croucher","year":"2015","unstructured":"Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, Parkhill J, Harris SR. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 2015;43(3):e15.","journal-title":"Nucleic Acids Res"},{"key":"12997_CR35","unstructured":"Alexey M. Kozlov, Alexandros Stamatakis. Using RAxML-NG in practice. In: Celine Scornavacca, Frederic Delsuc, Nicolas Galtier, editors. Phylogenetics in the Genomic Era. No commercial publisher; 2020. Chapter 1.3, p. 1.3:1\u20131.3:25."},{"issue":"W1","key":"12997_CR36","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","volume":"52","author":"I Letunic","year":"2024","unstructured":"Letunic I, Bork P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 2024;52(W1):W78\u201382.","journal-title":"Nucleic Acids Res"},{"issue":"14","key":"12997_CR37","doi-asserted-by":"publisher","first-page":"6614","DOI":"10.1093\/nar\/gkw569","volume":"44","author":"T Tatusova","year":"2016","unstructured":"Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44(14):6614\u201324.","journal-title":"Nucleic Acids Res"},{"key":"12997_CR38","doi-asserted-by":"crossref","unstructured":"Abdou Fayad, Rima Rafei, Eric Njamkepo, et al. An unusual two-strain cholera outbreak in Lebanon, 2022\u20132023: a genomic epidemiology study. Nature Communications. 2024;15:4148.","DOI":"10.1038\/s41467-024-51428-0"},{"issue":"12","key":"12997_CR39","doi-asserted-by":"publisher","first-page":"e0007934","DOI":"10.1371\/journal.pntd.0007934","volume":"13","author":"YMG Hounmanou","year":"2019","unstructured":"Hounmanou YMG, Leekitcharoenphon P, Kudirkiene E, Mdegela RH, Hendriksen RS, Olsen JE, Dalsgaard A. Genomic insights into Vibrio cholerae O1 responsible for cholera epidemics in Tanzania between 1993 and 2017. PLoS Negl Trop Dis. 2019;13(12):e0007934.","journal-title":"PLoS Negl Trop Dis"},{"key":"12997_CR40","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.2147\/IDR.S245806","volume":"13","author":"X Zhang","year":"2020","unstructured":"Zhang X, Lu Y, Qian H, Liu G, Mei Y, Jin F, Xia W, Ni F. Non-O1, Non-O139 Vibrio cholerae (NOVC) Bacteremia: case report and literature review, 2015\u20132019. Infect Drug Resist. 2020;13:1009\u201316.","journal-title":"Infect Drug Resist"},{"issue":"4","key":"12997_CR41","doi-asserted-by":"publisher","first-page":"818","DOI":"10.3390\/microorganisms12040818","volume":"12","author":"Q Zhang","year":"2024","unstructured":"Zhang Q, Alter T, Fleischmann S. Non-O1\/Non-O139 Vibrio cholerae-an underestimated foodborne pathogen? An overview of its virulence genes and regulatory systems involved in pathogenesis. Microorganisms. 2024;12(4):818.","journal-title":"Microorganisms"},{"key":"12997_CR42","doi-asserted-by":"publisher","first-page":"1025633","DOI":"10.3389\/fpubh.2022.1025633","volume":"10","author":"A Shariati","year":"2022","unstructured":"Shariati A, Arshadi M, Khosrojerdi MA, Abedinzadeh M, Ganjalishahi M, Maleki A, Heidary M, Khoshnood S. The resistance mechanisms of bacteria against ciprofloxacin and new approaches for enhancing the efficacy of this antibiotic. Front Public Health. 2022;10:1025633.","journal-title":"Front Public Health"},{"key":"12997_CR43","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.plasmid.2018.08.001","volume":"99","author":"SJ Ambrose","year":"2018","unstructured":"Ambrose SJ, Harmer CJ, Hall RM. Evolution and typing of IncC plasmids contributing to antibiotic resistance in Gram-negative bacteria. Plasmid. 2018;99:40\u201355.","journal-title":"Plasmid"},{"issue":"10","key":"12997_CR44","doi-asserted-by":"publisher","first-page":"1787","DOI":"10.1038\/s41564-023-01472-1","volume":"8","author":"F Lassalle","year":"2023","unstructured":"Lassalle F, Al-Shalali S, Al-Hakimi M, Njamkepo E, Bashir IM, Dorman MJ, Rauzier J, Blackwell GA, Taylor-Brown A, Beale MA, Cazares A, Al-Somainy AA, Al-Mahbashi A, Almoayed K, Aldawla M, Al-Harazi A, Quilici ML, Weill FX, Dhabaan G, Thomson NR. Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen. Nat Microbiol. 2023;8(10):1787\u201398.","journal-title":"Nat Microbiol"},{"issue":"4","key":"12997_CR45","doi-asserted-by":"publisher","first-page":"742","DOI":"10.1093\/jac\/dkl538","volume":"59","author":"T Frank","year":"2007","unstructured":"Frank T, Gautier V, Talarmin A, Bercion R, Arlet G. Characterization of sulphonamide resistance genes and class 1 integron gene cassettes in Enterobacteriaceae, Central African Republic (CAR). J Antimicrob Chemother. 2007;59(4):742\u20135.","journal-title":"J Antimicrob Chemother"},{"issue":"10","key":"12997_CR46","doi-asserted-by":"publisher","first-page":"2072","DOI":"10.3201\/eid2910.230554","volume":"29","author":"CN Mavian","year":"2023","unstructured":"Mavian CN, Tagliamonte MS, Alam MT, Sakib SN, Cash MN, Moir M, Jimenez JP, Riva A, Nelson EJ, Cato ET, Ajayakumar J, Louis R, Curtis A, De Rochars VMB, Rouzier V, Pape JW, de Oliveira T, Morris JG Jr, Salemi M, Ali A. Ancestral origin and dissemination dynamics of reemerging toxigenic Vibrio cholerae, Haiti. Emerg Infect Dis. 2023;29(10):2072\u201382.","journal-title":"Emerg Infect Dis"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12864-026-12997-0","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-026-12997-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-026-12997-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T18:10:45Z","timestamp":1785521445000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12864-026-12997-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,29]]},"references-count":46,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["12997"],"URL":"https:\/\/doi.org\/10.1186\/s12864-026-12997-0","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,29]]},"assertion":[{"value":"17 February 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 May 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 May 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The investigators have adhered to the policies for protection of human subjects as described in US Army Regulation 70\u201325 (approval no. WRAIR#1549\/1549A). Ethics approval was obtained from the Kenya Medical Research Institutional Review Board (approval no. SERU#1549). Written informed consent was obtained from all participants prior to enrollment and before any study procedures were performed. For all participants younger than 16 years of age, written informed consent to participate was obtained from a parent or legal guardian prior to inclusion in the study. All study procedures were conducted in accordance with the ethical principles of World Medical Association Declaration of Helsinki.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not Applicable.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"643"}}