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 bacterium Burkholderia 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 of B. pseudomallei endemicity. 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 Australian B. pseudomallei clade, thereby ruling out introduction from a melioidosis-endemic region outside Australia. Collectively, our results point to B. pseudomallei ST-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 of B. pseudomallei far outside the conventional endemic regions. An expected increase in extreme weather events may reactivate latent B. pseudomallei populations in this region.

Burkholderia pseudomallei distribution in Australasia is linked to paleogeographic and anthropogenic history

“…For example, a clonal B . pseudomallei population thought to have been introduced circa 1966 into southwestern Australia has persisted without additional introductions [ 34 , 35 ]. Other terrestrially linked populations may have remained in isolation for much longer periods.…”

Staphylococcus aureus from patients with chronic rhinosinusitis show minimal genetic association between polyp and non-polyp phenotypes

“…In silico multilocus sequence typing (MLST) was performed on all genome-sequenced isolates to confirm sequence type (ST) assignments using SRST2v0.1.8 [ 15 ], and all strains were confirmed to be S. aureus according to a positive nucA [ 16 ] result upon BLAST analysis. Draft assemblies of the S. aureus genomes were constructed using an optimized assembly pipeline of Velvet [ 17 ], PAGIT [ 18 ], SSPACE [ 19 ] and Gapfiller [ 20 ], which have been wrapped in MGAP [ 21 , 22 ]. Draft assemblies were annotated using Prokka v1.11 [ 23 ].…”

Melioidosis: An Australian Perspective

“…Melioidosis is endemic across northern, tropical Australia north of latitude 20° S [ 4 , 5 , 6 , 7 ], with focal areas of endemicity described in much more southern, temperate regions (latitude 31° S) [ 8 , 9 , 10 ]. Outbreaks, related to contaminated water, have been described in pigs in south-east Queensland (latitude 25.5° S) [ 11 ] and human and bovine cases have also been identified in the same region [ 12 , 13 , 14 ].…”

“…Due to concerns regarding adherence to prolonged oral antibiotics, in the NT a longer intensive phase has been developed [ 10 ] ( Table 2 ). Using this strategy, the rates of relapse in the NT are very low, even when there is poor adherence to oral eradication therapy [ 6 , 53 ].…”