The 2010 Cholera Outbreak in Haiti: How Science Solved a Controversy

Orata, Fabini D.; Keim, Paul; Boucher, Yan

doi:10.1371/journal.ppat.1003967

Cited by 107 publications

(75 citation statements)

References 20 publications

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“…This study was also important because WGS was performed in conjugation with bioinformatic analysis and the results were used to infer a molecular clock, which determined that the most recent common ancestor of the Haitian and Nepalese strains was estimated to be between 23 July and 17 October 2010. This aligned the cholera outbreak in Nepal and the arrival of Nepalese soldiers in Haiti with the start of the Haitian outbreak (145). WGS provided particularly strong evidence that Nepalese UN peacekeeping troops brought cholera to Haiti (154)(155)(156).…”

Section: Vibrio Choleraementioning

confidence: 76%

“…In the first few weeks of the outbreak, the U.S. CDC analyzed the strain by PFGE and evidence suggested that the etiological strain originated in South Asia and was probably brought to the region by United Nations (UN) workers; however, several argued that this was not conclusive, as PFGE does not yield a detailed enough fingerprint for such a conclusion (144). Independent researchers proposed that, instead of human introduction, the cause was climate change that led to increases in temperature and salinity in the river estuaries around the Bay of Saint Marc in Haiti, leading to the competing climate hypothesis (145,146). The main challenge in Vibrio outbreak source tracing is that the most common PFGE patterns tend to drift over the course of an outbreak, indicating that multiple concurrent outbreaks may be occurring, a possibility that, in this case, also challenged the singlesource introduction hypothesis (147).…”

Section: Vibrio Choleraementioning

confidence: 99%

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Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

et al. 2016

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SUMMARYThe epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generatein silicoresults for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques.

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Section: Vibrio Choleraementioning

confidence: 76%

Section: Vibrio Choleraementioning

confidence: 99%

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

et al. 2016

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“…Recent examples include the 2011 German E. coli O104:H4 outbreak, in which the open-access data and crowd-sourced analysis resulted in valuable epidemiological results in less than 1 week (238). Other recent examples of globally collaborative outbreak investigations attributable to data sharing include the H1N1 influenza A (swine flu) virus outbreak of 2009 (239), the Haitian V. cholerae outbreak in 2010 (240,241), and the West African Ebola outbreak in 2014 (242).…”

Section: Global Accessibility Of Genomics Datamentioning

confidence: 99%

A Primer on Infectious Disease Bacterial Genomics

et al. 2016

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SUMMARYThe number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies. The use of HTS for bacterial infectious disease research is attractive because one whole-genome sequencing (WGS) run can replace multiple assays for bacterial typing, molecular epidemiology investigations, and more in-depth pathogenomic studies. The computational resources and bioinformatics expertise required to accommodate and analyze the large amounts of data pose new challenges for researchers embarking on genomics projects for the first time. Here, we present a comprehensive overview of a bacterial genomics projects from beginning to end, with a particular focus on the planning and computational requirements for HTS data, and provide a general understanding of the analytical concepts to develop a workflow that will meet the objectives and goals of HTS projects.

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“…The two main virulence factors expressed by V. cholerae O1 and O139 are the thermo-labile cholera toxin (CT) responsible for aqueous diarrhea [7,8] and the pilus co-regulator of toxin, which modulates the formation of adhesion factors and is a regulator of intestinal colonization [9][10][11]. The simultaneous expression of both has serious damaging infectious effects [12].…”

Section: Introductionmentioning

confidence: 99%