4 research outputs found
Additional file 1: of Vancomycin-resistant Enterococcus faecium sequence type 796 - rapid international dissemination of a new epidemic clone
Table S1. A summary of the isolates with their epidemiological and meta-data. (XLSX 22 kb
Whole Genome Comparisons Suggest Random Distribution of <i>Mycobacterium ulcerans</i> Genotypes in a Buruli Ulcer Endemic Region of Ghana
<div><p>Efforts to control the spread of Buruli ulcer – an emerging ulcerative skin infection caused by <i>Mycobacterium ulcerans</i> - have been hampered by our poor understanding of reservoirs and transmission. To help address this issue, we compared whole genomes from 18 clinical <i>M</i>. <i>ulcerans</i> isolates from a 30km<sup>2</sup> region within the Asante Akim North District, Ashanti region, Ghana, with 15 other <i>M</i>. <i>ulcerans</i> isolates from elsewhere in Ghana and the surrounding countries of Ivory Coast, Togo, Benin and Nigeria. Contrary to our expectations of finding minor DNA sequence variations among isolates representing a single <i>M</i>. <i>ulcerans</i> circulating genotype, we found instead two distinct genotypes. One genotype was closely related to isolates from neighbouring regions of Amansie West and Densu, consistent with the predicted local endemic clone, but the second genotype (separated by 138 single nucleotide polymorphisms [SNPs] from other Ghanaian strains) most closely matched <i>M</i>. <i>ulcerans</i> from Nigeria, suggesting another introduction of <i>M</i>. <i>ulcerans</i> to Ghana, perhaps from that country. Both the exotic genotype and the local Ghanaian genotype displayed highly restricted intra-strain genetic variation, with less than 50 SNP differences across a 5.2Mbp core genome within each genotype. Interestingly, there was no discernible spatial clustering of genotypes at the local village scale. Interviews revealed no obvious epidemiological links among BU patients who had been infected with identical <i>M</i>. <i>ulcerans</i> genotypes but lived in geographically separate villages. We conclude that <i>M</i>. <i>ulcerans</i> is spread widely across the region, with multiple genotypes present in any one area. These data give us new perspectives on the behaviour of possible reservoirs and subsequent transmission mechanisms of <i>M</i>. <i>ulcerans</i>. These observations also show for the first time that <i>M</i>. <i>ulcerans</i> can be mobilized, introduced to a new area and then spread within a population. Potential reservoirs of <i>M</i>. <i>ulcerans</i> thus might include humans, or perhaps <i>M</i>. <i>ulcerans</i>-infected animals such as livestock that move regularly between countries.</p></div
Micromolecular epidemiology of BU in the Asante Akim North District revealed by <i>M</i>. <i>ulcerans</i> whole genome sequence comparisons.
<p>(A) Median-joining network graph showing the genetic relationship between 18 <i>M</i>. <i>ulcerans</i> clinical isolates comprising the Agogo-1 and Agogo-2 genotypes (shaded), inferred from whole genome sequence alignments. Node sizes in the graph are proportional to the frequency of genotype occurrence and have been colour-coded accordingly. Edges are labelled in red with the number of mutational steps between each node. (B) Map of Asante Akim North District study area, showing the location of endemic villages and the origin of each of the 18 BU cases, with a coloured circle corresponding with the genotype displayed in the network graph in (A). The number “2” within some coloured circles indicates an Agogo-2 genotype.</p
Genetic relationship among the 33 <i>M</i>. <i>ulcerans</i> isolates used in this study.
<p>A maximum-likelihood consensus phylogeny was inferred based on whole genome alignments of each of the isolates against the <i>M</i>. <i>ulcerans</i> Agy99 reference genome. The alignment file from pairwise comparisons of the resulting 320 variable nucleotide positions was used as input for RaxML. Nodes with less than 70% bootstrap support (1000 replicates) were collapsed.</p