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. 2020 Nov 10;5(6):e00726-20.
doi: 10.1128/mSystems.00726-20.

A Persisting Nontropical Focus of Burkholderia pseudomallei with Limited Genome Evolution over Five Decades

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A Persisting Nontropical Focus of Burkholderia pseudomallei with Limited Genome Evolution over Five Decades

Jessica R Webb et al. mSystems. .

Abstract

Burkholderia pseudomallei is the causative agent of the high-mortality disease melioidosis. Although melioidosis is classified as a tropical disease, rare autochthonous cases have been reported from temperate climatic regions, with uncertainty as to whether B. pseudomallei is persistent in the local environment and whether specific genetic mechanisms facilitate the survival of B. pseudomallei outside the tropics. Sporadic cases of melioidosis occurred in a valley region (latitude 31. 6°S) in southwest Western Australia, Australia, between 1966 and 1992. We report a new melioidosis cluster in the same region following high rainfall in January 2017. More than 20 animals died, and B. pseudomallei was isolated from four alpacas, a parrot, and three environmental samples taken from the farm where the alpacas resided. Epidemiological data and genomics revealed that two locations on the farm were the probable sources of the alpaca infections. We determined that B. pseudomallei isolates from the 2017 cluster belonged to sequence type 284 (ST-284), as did all isolates recovered from 1966 to 1992. Genomic analysis confirmed that the ST-284 isolates were clonal and contained conserved genomic islands and limited evidence of recombination. We identified protein-coding regions unique to these isolates that might influence the persistence of B. pseudomallei in this temperate region VSports手机版. We demonstrate the environmental persistence of B. pseudomallei in a temperate region for over 50 years, with limited genetic changes suggesting a latent state and with activation, potential aerosolization, and local dispersal following unusually high rainfall. IMPORTANCE Burkholderia pseudomallei is predominantly a tropical pathogen uncommonly found in the environment of temperate climatic regions. It is unclear if introduction into temperate regions is sporadic and temporary or if B. pseudomallei can persist in such environments. B. pseudomallei was identified in the environment of southwest Western Australia with melioidosis cases between 1966 and 1991. We report a new cluster with 23 animal fatalities in the same region from 2017, with B. pseudomallei again being recovered from the environment. Comparison of the isolates from the first and second clusters using genomics revealed a single sequence type, high clonality, and limited recombination, even though the time of recovery of the isolates spanned 51 years. This is a major contrast to the extensive genomic diversity seen in the tropics. Our data support the suggestion that B. pseudomallei has the ability to persist in nontropical environments, potentially in a latent state, and has the ability to activate following favorable conditions (rainfall) and then infect animals and humans. .

Keywords: Burkholderia pseudomallei; clonality; melioidosis; phylogenetics; temperate climate V体育安卓版. .

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FIG 1
FIG 1
Western Australian rainfall totals (in millimeters) in January 2017, the month prior to the melioidosis outbreak in Moondyne of the Avon Valley region, Western Australia. Moondyne Farm is located within the black square, and the color gradient indicates the amount of rainfall (in millimeters). The image is from the Australian Bureau of Meteorology (www.bom.gov.au).
FIG 2
FIG 2
Map of Moondyne Farm (the area within the white border) showing the 10 locations that were environmentally sampled. Locations 7, 9, and 10 were positive for B. pseudomallei (indicated by the yellow triangles), and B. pseudomallei was not identified elsewhere. The image was created using Inkscape 0.92.3.
FIG 3
FIG 3
Geography of the region of southwest Western Australia, where the endemicity of melioidosis is low. (A) Geographical origin of B. pseudomallei isolates within southwest Western Australia. Isolates from the first melioidosis cluster are from Chittering and Toodyay, which are in the Avon Valley region of southwest Western Australia, and Gidgegannup, which, despite bordering Avon Valley, is not considered a part of Avon Valley. The isolates from the second melioidosis cluster are from Moondyne, which is located within the Avon Valley or Gidgegannup. The exact locations of the farms are not presented here to maintain privacy. The regions have been segregated and assigned as outlined by the Australian Bureau of Statistics (https://www.abs.gov.au/; statistical area level 3), and the map was created using the ArcGIS program (https://www.arcgis.com/index.html). (B) A map of the mean rainfall in Australia (January 1981 to December 2010) that demonstrates the location of temperate southwest Western Australia in comparison to that of tropical Darwin, where melioidosis is highly endemic. The image and data were supplied by the Australian Bureau of Meteorology (www.bom.gov.au) and adapted with its permission.
FIG 4
FIG 4
Midpoint-rooted maximum parsimony phylogeny of B. pseudomallei ST-284 isolates (n = 22) from southwest Western Australia, based on 532 core-genome SNPs. Bootstrapping revealed that the phylogenetic tree had moderately supported to well-supported nodes, with the branch support values ranging from 80 to 100. Branch colors indicate cluster 1 or cluster 2 (with the first cluster occurring between 1966 and 1992 and the second cluster occurring in 2017); the inner strip delineates the location of isolation; the outer strip delineates the isolate source, which is followed by the year in which the sample was collected and the BAPS cluster for each isolate, as defined by the RhierBAPS program; and the gray highlighted regions delineate transmission events. The geographical location for isolate MSHR0164 is unknown, and so the location of MSHR0164 was not included. Black circles on the branches denote bootstrap values of >80. The consistency index for the tree was 0.9963, and the homoplasy index was 0.0037.
FIG 5
FIG 5
Maximum parsimony phylogenetic analysis of ST-284 isolates on a global scale (n = 318). The phylogeny is based on 216,486 core-genome SNPs. The analysis is rooted with MSHR0668, the most ancestral B. pseudomallei strain, as identified in a large phylogenetic study (59). (A) Maximum parsimony phylogeny of global B. pseudomallei genomes, including the 22 southwest Western Australia strains (blue branches). The ring delineates the global geographical region of origin. (B) Positions of the 22 southwest Western Australia strains from the first and the second clusters (strains highlighted by the gray rectangle) among Australasian strains. The node belonging to the non-Australasian strains (indicated by the gray circle, containing 124 strains) has been collapsed. The consistency index for the tree was 0.1620, and the homoplasy index was 0.8380.
FIG 6
FIG 6
Maximum parsimony phylogenetic analysis of ST-284 isolates with an Australian set of isolates. The phylogeny is based on 206,357 core-genome SNPs. (A) Maximum parsimony phylogeny. The strip delineates the Australian region of origin. (B) Presence/absence of the 14 protein-coding regions that were unique to the ST-284 isolates, as annotated in isolate MSHR0169. Each cell provides the BSR values: 0 represents no alignment (white), and 1 represents identical alignment (red). The consistency index for the tree was 0.1775, and the homoplasy index was 0.8225.

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