Genetic Characterization of Vibrio cholerae O1 isolates from outbreaks between 2011 and 2015 in Tanzania

Yazid Kachwamba,M Matonya,J Mghamba,R Kishimba,A A Mohammed,H Lukupulo,M Almeida,S Nyanga,O C Stine,S Li,F Mosha,L Urio,D Domman,M Majigo,J Lusekelo,S.Y Massele

doi:10.1186/s12879-017-2252-9

Abstract

BackgroundCholera outbreaks have occurred in Tanzania since 1974. To date, the genetic epidemiology of these outbreaks has not been assessed.Methods96 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).ResultsOf 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 3rd wave of the 7th pandemic and were found in four clades related to isolates from Kenya and Asia.ConclusionsWe conclude that genetically related V. cholerae cluster in outbreaks, and distinct strains circulate simultaneously.

Highlights

Cholera outbreaks have occurred in Tanzania since 1974
Outbreaks have been reported in various regions, including Dar es Salaam, Dodoma, Kigoma, Lindi, Mbeya, Morogoro, Mtwara, Pwani and Tanga; case fatality rates (CFR) have ranged from 1.3% to 11.7% [3]
Further exploration to determine the genetic relatedness of these genotypes revealed three multi-locus variable-number tandem-repeat analysis (MLVA)-Clonal complex (CC), each comprising genotypes that differed from the other genotypes by a single allelic change

Summary

Introduction

Cholera outbreaks have occurred in Tanzania since 1974. To date, the genetic epidemiology of these outbreaks has not been assessed. Vibrio cholerae is the causative agent of cholera, a secretory diarrheal disease resulting in high mortality among humans, if untreated [1]; cholera continues to be a significant public health problem in countries with poor socio-economic conditions. The burden of this disease is estimated to be 3–5 million cases, with 100,000–120,000 deaths annually [2], and the number of cholera cases reported to the World Health Organization continues to rise. Outbreaks have been reported in various regions, including Dar es Salaam, Dodoma, Kigoma, Lindi, Mbeya, Morogoro, Mtwara, Pwani and Tanga; case fatality rates (CFR) have ranged from 1.3% to 11.7% [3]. Between 2011 and 2016 seven outbreaks have been reported from six regions, including Dar es Salaam, Kigoma, Morogoro, Singida, Tanga, and Mara

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Results

Conclusion