Population Genetics of Vibrio cholerae from Nepal in 2010: Evidence on the Origin of the Haitian Outbreak

National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
mBio (Impact Factor: 6.79). 06/2011; 2(4):e00157-11. DOI: 10.1128/mBio.00157-11
Source: PubMed


Cholera continues to be an important cause of human infections, and outbreaks are often observed after natural disasters, such as the one following the 2010 earthquake in Haiti. Once the cholera outbreak was confirmed, rumors spread that the disease was brought to Haiti by a battalion of Nepalese soldiers serving as United Nations peacekeepers. This possible connection has never been confirmed. We used whole-genome sequence typing (WGST), pulsed-field gel electrophoresis (PFGE), and antimicrobial susceptibility testing to characterize 24 recent Vibrio cholerae isolates from Nepal and evaluate the suggested epidemiological link with the Haitian outbreak. The isolates were obtained from 30 July to 1 November 2010 from five different districts in Nepal. We compared the 24 genomes to 10 previously sequenced V. cholerae isolates, including 3 from the Haitian outbreak (began July 2010). Antimicrobial susceptibility and PFGE patterns were consistent with an epidemiological link between the isolates from Nepal and Haiti. WGST showed that all 24 V. cholerae isolates from Nepal belonged to a single monophyletic group that also contained isolates from Bangladesh and Haiti. The Nepalese isolates were divided into four closely related clusters. One cluster contained three Nepalese isolates and three Haitian isolates that were almost identical, with only 1- or 2-bp differences. Results in this study are consistent with Nepal as the origin of the Haitian outbreak. This highlights how rapidly infectious diseases might be transmitted globally through international travel and how public health officials need advanced molecular tools along with standard epidemiological analyses to quickly determine the sources of outbreaks.

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    • "Microbial whole-genome sequencing using bench-top sequencing technologies holds great promises to enhance diagnostic and public health microbiology [1]–[3]. Its great value in describing and improving our understanding of bacterial evolution, outbreaks and transmission events has been shown in a number of recent studies, including Staphylococcus aureus [4]–[6], Vibrio cholera [7], Escherichia coli [8], Mycobacterium tuberculosis [9] and surveillance of antimicrobial resistance [10]. All of these studies have however, been done retrospectively, (except [8], which was done prospectively) and conducted using the same technology and performed in a single laboratory. "
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    ABSTRACT: Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. We developed two different procedures for identifying variable sites and inferring phylogenies in WGS data across multiple platforms. The methods were evaluated on three bacterial data sets and sequenced on three different platforms (Illumina, 454, Ion Torrent). We show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. It is concluded that the cause of the success of these new procedures is due to a validation of all informative sites that are included in the analysis. The procedures are available as web tools.
    Full-text · Article · Aug 2014 · PLoS ONE
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    • "DNA prepared from 57 clinical and 40 environmental isolates (Table S1 and Table S2) were sequenced and the data generated was compared to previously published V. cholerae sequences taken from Mutreja et al. [14] and Hendriksen et al. [31]. The initial consensus phylogenetic tree generated from this data (Figure 1a) showed that 27 of the environmental isolates clustered well outside of the seventh pandemic lineage and differed by more than 50,000 SNPs from the reference. "
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    Full-text · Article · Sep 2013 · PLoS ONE
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    • "The whole genome sequence analysis here provided not only an ability to accurately identify phylogenetically informative SNPs but also the ability to conduct whole genome SNP typing (WGST) to compare to the SNP assays, spa typing, MLVA and MLST. WGST has been previously used for advanced molecular typing of MRSA [20,21], as well as for other bacteria [22,23] and fungal pathogens [24-26]. WGST has proven to be far superior to other typing methodologies for determining genetic assignment (genotype) and phylogenetic relatedness (phylotype), given its ability to interrogate genome-wide character states. "
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