title: Whole-genome sequencing of a quarter-century melioidosis outbreak in temperate Australia uncovers a region of low-prevalence endemicity.
abstract: Melioidosis, caused by the highly recombinogenic bacteriumBurkholderia pseudomallei, is a disease with high mortality. Tracing the origin of melioidosis outbreaks and understanding how the bacterium spreads and persists in the environment are essential to protecting public and veterinary health and reducing mortality associated with outbreaks. We used whole-genome sequencing to compare isolates from a historical quarter-century outbreak that occurred between 1966 and 1991 in the Avon Valley, Western Australia, a region far outside the known range ofB. pseudomalleiendemicity. All Avon Valley outbreak isolates shared the same multilocus sequence type (ST-284), which has not been identified outside this region. We found substantial genetic diversity among isolates based on a comparison of genome-wide variants, with no clear correlation between genotypes and temporal, geographical or source data. We observed little evidence of recombination in the outbreak strains, indicating that genetic diversity among these isolates has primarily accrued by mutation. Phylogenomic analysis demonstrated that the isolates confidently grouped within the AustralianB. pseudomalleiclade, thereby ruling out introduction from a melioidosis-endemic region outside Australia. Collectively, our results point toB. pseudomalleiST-284 being present in the Avon Valley for longer than previously recognized, with its persistence and genomic diversity suggesting long-term, low-prevalence endemicity in this temperate region. Our findings provide a concerning demonstration of the potential for environmental persistence ofB. pseudomalleifar outside the conventional endemic regions. An expected increase in extreme weather events may reactivate latentB. pseudomalleipopulations in this region.
authors.affiliation: 1​Melbourne Medical School, University of Melbourne, Melbourne, Victoria, Australia.|2​Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.
authors.forename: Stephanie N J
authors.initials: SNJ
authors.lastname: Chapple
authors.affiliation: 2​Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.
authors.forename: Derek S
authors.initials: DS
authors.lastname: Sarovich
authors.affiliation: 3​School of Medicine, Medical and Biological Sciences, University of St Andrews, St Andrews, UK.|4​Wellcome Trust Sanger Institute, University of Cambridge, Cambridge, UK.
authors.forename: Matthew T G
authors.initials: MTG
authors.lastname: Holden
authors.affiliation: 4​Wellcome Trust Sanger Institute, University of Cambridge, Cambridge, UK.|5​University of Cambridge, Cambridge, UK.
authors.forename: Sharon J
authors.initials: SJ
authors.lastname: Peacock
authors.affiliation: 6​Department of Agriculture and Food Western Australia, Perth, Western Australia, Australia.
authors.forename: Nicky
authors.initials: N
authors.lastname: Buller
authors.affiliation: 7​Sir Charles Gairdner Hospital, Perth, Western Australia, Australia.
authors.forename: Clayton
authors.initials: C
authors.lastname: Golledge
authors.affiliation: 2​Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.
authors.forename: Mark
authors.initials: M
authors.lastname: Mayo
authors.affiliation: 2​Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.|8​Department of Infectious Diseases and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia.
authors.forename: Bart J
authors.initials: BJ
authors.lastname: Currie
authors.affiliation: 2​Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.
authors.forename: Erin P
authors.initials: EP
authors.lastname: Price
mesh_terms: D016957:Burkholderia pseudomallei / Q000235:genetics*; D004196:Disease Outbreaks; D019353:Endemic Diseases; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D008554:Melioidosis / Q000453:epidemiology* / Q000382:microbiology*; D015995:Prevalence; D014904:Western Australia / Q000453:epidemiology
keywords: Australia; Burkholderia pseudomallei; endemicity; evolution; melioidosis; temperate