Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing.

Marcelino Garrine,Shan Li,Mathieu Almeida,Nicholas R Thomson,Tacilta Nhampossa,Delfino Vubil,Oscar Colin Stine,Joseph N Paulson,Inácio Mandomando,Daryl Domman,Pedro Alonso,Sozinho Acacio,Susanna Jane Dunachie

doi:10.1371/journal.pntd.0005671

Abstract

Although cholera is a major public health concern in Mozambique, its transmission patterns remain unknown. We surveyed the genetic relatedness of 75 Vibrio cholerae isolates from patients at Manhiça District Hospital between 2002–2012 and 3 isolates from river using multilocus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS). MLVA revealed 22 genotypes in two clonal complexes and four unrelated genotypes. WGS revealed i) the presence of recombination, ii) 67 isolates descended monophyletically from a single source connected to Wave 3 of the Seventh Pandemic, and iii) four clinical isolates lacking the cholera toxin gene. This Wave 3 strain persisted for at least eight years in either an environmental reservoir or circulating within the human population. Our data raises important questions related to where these isolates persist and how identical isolates can be collected years apart despite our understanding of high change rate of MLVA loci and the V. cholerae molecular clock.

Highlights

Cholera remains a public health concern in developing countries with an estimated burden of 1.2–4.3 million cases and 28,000–142,000 deaths per year, worldwide [1]
The peak of a cholera epidemic is often preceded by increasing prevalence of the pathogenic strains in the environment [7] where V. cholerae are harbored in aquatic reservoirs during extended periods between outbreaks [8]
Previous studies have reported the role of environmental factors, such as seasonal fluctuations, that influence the dynamics of V. cholerae in environmental reservoirs [33,34]

Summary

Introduction

Cholera remains a public health concern in developing countries with an estimated burden of 1.2–4.3 million cases and 28,000–142,000 deaths per year, worldwide [1]. South Asia and subSaharan Africa account with the majority of cases and deaths. Between 01 January and 03 June 2013, a total of 25,762 cholera cases and 490 deaths were reported from 18 African countries. Mozambique accounted for 7% (1,861/25,762) of cases and 4% (19/490) of deaths, being the third most affected country after the Democratic Republic of the Congo and Angola [2]. The most recent cholera outbreak in Mozambique started in December 2014 in Nampula [3], where there were 8,835 cases with case fatality rate of 0.7% (65 deaths) in 5 northern and central provinces in five months [4,5]. The most recent cholera outbreak in the south was reported in 2011 [6]. The peak of a cholera epidemic is often preceded by increasing prevalence of the pathogenic strains in the environment [7] where V. cholerae are harbored in aquatic reservoirs during extended periods between outbreaks [8]

Methods

Results

Discussion

Conclusion