title: Genetic Characterization of Vibrio cholerae O1 isolates from outbreaks between 2011 and 2015 in Tanzania.
abstract: Cholera outbreaks have occurred in Tanzania since 1974. To date, the genetic epidemiology of these outbreaks has not been assessed.
  
  
  
  96 Vibrio cholerae O1 isolates from five regions were characterized, and their genetic relatedness assessed using multi-locus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS).
  
  
  
  Of the 48 MLVA genotypes observed, 3 were genetically unrelated to any others, while the remaining 45 genotypes separated into three MLVA clonal complexes (CCs) - each comprised of genotypes differing by a single allelic change. In Kigoma, two separate outbreaks, 4 months apart (January and May, 2015), were each caused by genetically distinct strains by MLVA and WGS. Remarkably, one MLVA CC contained isolates from both the May outbreak and ones from the 2011/2012 outbreak in Dar-es-Salaam. However, WGS revealed the isolates from the two outbreaks to be distinct clades. The outbreak that started in August 2015 in Dar-es-Salaam and spread to Morogoro, Singida and Mara was comprised of a single MLVA CC and WGS clade. Isolates from within an outbreak were closely related differing at fewer than 5 nucleotides. All isolates were part of the 3rdwave of the 7thpandemic and were found in four clades related to isolates from Kenya and Asia.
  
  
  
  We conclude that genetically related V. cholerae cluster in outbreaks, and distinct strains circulate simultaneously.
authors.affiliation: Muhimbili University of Health and Allied Sciences, Dar es Salaam, United Republic of Tanzania.|Tanzania Field Epidemiology and Laboratory Training Program, Dar es Salaam, United Republic of Tanzania.
authors.forename: Yazid
authors.initials: Y
authors.lastname: Kachwamba
authors.affiliation: Tanzania Field Epidemiology and Laboratory Training Program, Dar es Salaam, United Republic of Tanzania.
authors.forename: A A
authors.initials: AA
authors.lastname: Mohammed
authors.affiliation: Muhimbili University of Health and Allied Sciences, Dar es Salaam, United Republic of Tanzania.|Tanzania Field Epidemiology and Laboratory Training Program, Dar es Salaam, United Republic of Tanzania.
authors.forename: H
authors.initials: H
authors.lastname: Lukupulo
authors.affiliation: Tanzania Field Epidemiology and Laboratory Training Program, Dar es Salaam, United Republic of Tanzania.
authors.forename: L
authors.initials: L
authors.lastname: Urio
authors.affiliation: Muhimbili University of Health and Allied Sciences, Dar es Salaam, United Republic of Tanzania.
authors.forename: M
authors.initials: M
authors.lastname: Majigo
authors.affiliation: National Health Laboratory, Quality Assurance and Training Centre, Dar es Salaam, United Republic of Tanzania.
authors.forename: F
authors.initials: F
authors.lastname: Mosha
authors.affiliation: National Health Laboratory, Quality Assurance and Training Centre, Dar es Salaam, United Republic of Tanzania.
authors.forename: M
authors.initials: M
authors.lastname: Matonya
authors.affiliation: Tanzania Field Epidemiology and Laboratory Training Program, Dar es Salaam, United Republic of Tanzania.|Tanzania Ministry of Health, Community Development, Gender, Elderly and Children, Dar es Salaam, United Republic of Tanzania.
authors.forename: R
authors.initials: R
authors.lastname: Kishimba
authors.affiliation: Tanzania Field Epidemiology and Laboratory Training Program, Dar es Salaam, United Republic of Tanzania.|Tanzania Ministry of Health, Community Development, Gender, Elderly and Children, Dar es Salaam, United Republic of Tanzania.
authors.forename: J
authors.initials: J
authors.lastname: Mghamba
authors.affiliation: National Health Laboratory, Quality Assurance and Training Centre, Dar es Salaam, United Republic of Tanzania.
authors.forename: J
authors.initials: J
authors.lastname: Lusekelo
authors.affiliation: National Health Laboratory, Quality Assurance and Training Centre, Dar es Salaam, United Republic of Tanzania.
authors.forename: S
authors.initials: S
authors.lastname: Nyanga
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.
authors.forename: M
authors.initials: M
authors.lastname: Almeida
authors.affiliation: Department of Epidemiology and Public Health, University of Maryland, Baltimore, Maryland, USA.
authors.forename: S
authors.initials: S
authors.lastname: Li
authors.affiliation: Wellcome Trust Sanger Instititue, Hinxton, England.
authors.forename: D
authors.initials: D
authors.lastname: Domman
authors.affiliation: Muhimbili University of Health and Allied Sciences, Dar es Salaam, United Republic of Tanzania.
authors.forename: S Y
authors.initials: SY
authors.lastname: Massele
authors.affiliation: Department of Epidemiology and Public Health, University of Maryland, Baltimore, Maryland, USA. ostin001@umaryland.edu.
authors.forename: O C
authors.identifier: 0000-0003-3974-3752
authors.initials: OC
authors.lastname: Stine
mesh_terms: D002771:Cholera / Q000453:epidemiology* / Q000821:virology; D004279:DNA, Viral / Q000032:analysis; D004196:Disease Outbreaks; D005838:Genotype; D060005:Genotyping Techniques; D006801:Humans; D018598:Minisatellite Repeats; D017720:Molecular Epidemiology; D010802:Phylogeny; D013636:Tanzania / Q000453:epidemiology; D041241:Vibrio cholerae O1 / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D004279:DNA, Viral