Diverse Genotypes of Yersinia pestis Caused Plague in Madagascar in 2007

Abstract

Background Yersinia pestis is the causative agent of human plague and is endemic in various African, Asian and American countries. In Madagascar, the disease represents a significant public health problem with hundreds of human cases a year. Unfortunately, poor infrastructure makes outbreak investigations challenging.Methodology/Principal FindingsDNA was extracted directly from 93 clinical samples from patients with a clinical diagnosis of plague in Madagascar in 2007. The extracted DNAs were then genotyped using three molecular genotyping methods, including, single nucleotide polymorphism (SNP) typing, multi-locus variable-number tandem repeat analysis (MLVA), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) analysis. These methods provided increasing resolution, respectively. The results of these analyses revealed that, in 2007, ten molecular groups, two newly described here and eight previously identified, were responsible for causing human plague in geographically distinct areas of Madagascar.Conclusions/SignificancePlague in Madagascar is caused by numerous distinct types of Y. pestis. Genotyping method choice should be based upon the discriminatory power needed, expense, and available data for any desired comparisons. We conclude that genotyping should be a standard tool used in epidemiological investigations of plague outbreaks.

Local-Scale Genotype Diversity of Yersinia Pestis: A Case Study from Ambohitromby, Ankazobe District (2003-2016), Madagascar

“…Our ndings are consistent with this idea as almost half of the R. rattus we examined were seropositive, suggesting many rats in Ambohitromby can survive Y. pestis infection and serve as local reservoirs for plague. Y. pestis subgroup s13 may have been recently transported to Ambohitromby as no other isolates from Ambohitromby or from any other locations within Ankazobe District examined in this or previous studies [4,18] were assigned to subgroup s13. Movement of Y. pestis, likely via inadvertent human-mediated movement of infected rats and/or ea vectors, has been documented in Madagascar [4], and isolation of this subgroup from a rat captured in Ambohitromby suggest it is now ecologically-established in this area.…”

“…Third, the human infection was likely obtained locally in Ambohitromby [18] from a subgroup (s05) that had been persisting in this region for more than a decade, as the human isolate is closely-related to seven other human and rat isolates from this commune obtained from 2003-2014 that are also assigned to this same subgroup; previous studies also have documented this subgroup in an adjacent commune within Ankazobe District [4,18]. Local, long-term persistence of Y. pestis in Madagascar likely occurs in R. rattus populations [4,[18][19][20].…”

Whole genome multilocus sequence typing as an epidemiologic tool for Yersinia pestis

“…Based on the perfect matches observed for other linked isolates and the differences among group 2 strains resulting from SNPs, opposed to more rapidly changing VNTRs, we hypothesize that multiple strains were circulating in the area at the time of the patient’s exposure. Indeed, Santa Fe County, New Mexico, has been shown to produce multiple Y. pestis genotypes in a single year (Gibbons et al, 2012), a phenomenon that has also been noted in both China and Madagascar (Riehm et al, 2015; Zhang et al, 2009). wgMLST of additional Y. pestis isolates derived from fleas collected in the patient’s yard will be important for determining if an exact match to the patient isolate can be identified.…”

“…Currently, a hierarchal approach is used for molecular typing of Y. pestis strains. These assays are PCR based and rely on canonical SNPs (discovered from sequencing a limited number of full genomes) to first determine phylogenetic placement followed by a higher discriminatory secondary typing method, such as 43 locus VNTR analysis, for strain differentiation (Riehm et al, 2015; Riehm et al, 2012; Vogler et al, 2013). …”

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“…Being a traditional object for the spoligotyping, a special type of genotyping based on the spacer nucleotide analysis, CRISPR systems of Y. pestis strains often served as a model for CRISPR-based evolutionary studies. All three separate genomic CRISPR loci were described in detail (Pourcel et al, 2005), including numerous strains without complete genomes (Vergnaud et al, 2007;Cui et al, 2008;Riehm et al, 2012;Barros et al, 2014;Riehm et al, 2015). Relationships between strains were studied using the distance based on shared and differential spacers content only (Barros et al, 2014) or taking into account the principles of evolutionary cassette dynamics.…”