Phylogeography and Molecular Epidemiology of Yersinia pestis in Madagascar

Abstract

BackgroundPlague was introduced to Madagascar in 1898 and continues to be a significant human health problem. It exists mainly in the central highlands, but in the 1990s was reintroduced to the port city of Mahajanga, where it caused extensive human outbreaks. Despite its prevalence, the phylogeography and molecular epidemiology of Y. pestis in Madagascar has been difficult to study due to the great genetic similarity among isolates. We examine island-wide geographic-genetic patterns based upon whole-genome discovery of SNPs, SNP genotyping and hypervariable variable-number tandem repeat (VNTR) loci to gain insight into the maintenance and spread of Y. pestis in Madagascar.Methodology/Principal FindingsWe analyzed a set of 262 Malagasy isolates using a set of 56 SNPs and a 43-locus multi-locus VNTR analysis (MLVA) system. We then analyzed the geographic distribution of the subclades and identified patterns related to the maintenance and spread of plague in Madagascar. We find relatively high levels of VNTR diversity in addition to several SNP differences. We identify two major groups, Groups I and II, which are subsequently divided into 11 and 4 subclades, respectively. Y. pestis appears to be maintained in several geographically separate subpopulations. There is also evidence for multiple long distance transfers of Y. pestis, likely human mediated. Such transfers have resulted in the reintroduction and establishment of plague in the port city of Mahajanga, where there is evidence for multiple transfers both from and to the central highlands.Conclusions/SignificanceThe maintenance and spread of Y. pestis in Madagascar is a dynamic and highly active process that relies on the natural cycle between the primary host, the black rat, and its flea vectors as well as human activity.

Genetic diversity of Yersinia pestis in Brazil

“…However, analysis of the 12 VNTR loci in the three parental strains and their derived cultures did not reveal changes in the studied regions, confirming their stability as previously observed (Adair et al, 2000;Keim et al, 2000). Furthermore, according to Vogler et al (2011), the rate of VNTR evolution in the laboratory, even with passaging, should be much slower than in nature. While these isolates may not be exactly the same as when they were first isolated, they should be quite similar to the original isolates.…”

“…The global expansion of Y. pestis strains from central Asian plague foci was demonstrated by Li et al (2009) with an MLVA of 25 VNTRs. MLVA was also successfully employed to study the maintenance and spread of Y. pestis in Madagascar (Vogler et al, 2011).…”

“…Alternatively, the strains could be inaccurate representatives of the original isolates, and these differences could be due to handling procedures during the prolonged storage of the strains in the laboratory since their isolation (Revazishvili et al, 2008;Vogler et al, 2011). Leal et al (2000) and Leal-Balbino et al (2004, 2006 observed spontaneous changes in the genome (both plasmid and chromosomal) of Brazilian Y. pestis following prolonged storage and laboratory handling.…”

“…In almost every case, no differences between isolates were found, even across multiple host species, different geographic origins, or years (Sobreira M and Leal NC, unpublished results). Molecular subtyping of Y. pestis for epidemiological tracking has been difficult due to the great genetic similarity among isolates (Vogler et al, 2011). However, analysis of multiple-locus variable number of tandem repeats (VNTR), also known as MLVA, has become a valuable tool to discriminate Y. pestis strains.…”

“…However, analysis of multiple-locus variable number of tandem repeats (VNTR), also known as MLVA, has become a valuable tool to discriminate Y. pestis strains. Using MLVA, it is possible to trace the dispersion routes of bacterial populations at the local, regional and global levels (Adair et al, 2000;Klevytska et al, 2001;Achtman et al, 2004;Girard et al, 2004;Pourcel et al, 2004;Lowell et al, 2005;Vogler et al, 2011).…”