Epidemiology and genetic diversity of Burkholderia pseudomallei from Riau Province, Indonesia

Melioidosis is a bacterial infection caused by Burkholderia pseudomallei. It is common in tropical and subtropical countries including Southeast Asia and Northern Australia. Many melioidosis cases in Indonesia remain unreported, and the magnitude of undiagnosed and untreated melioidosis across the country remains unclear. Given its proximity to regions with high infection rates, Riau Province on Sumatera Island is anticipated to have endemic melioidosis. This study reports retrospectively collected data on 68 culture-confirmed melioidosis cases from two hospitals in Riau Province between January 1, 2009, and December 31, 2021. We also describe whole genome sequencing and genotypic analysis of six isolates of B. pseudomallei. Ages ranged from 3 to 71 years (median 48 years), with 5/68 (7.4%) being children under 15 years. 55/68 (80.9%) were male and the most common risk factor was diabetes mellitus (42/55 approximately (76.4%)). Pulmonary infection was the commonest presentation (23/57 approximately (40.4%)), with a mortality rate of 43.9% (29/66). Multilocus sequence typing analysis identified three sequence types (STs), namely ST1794 (n = 3), ST46 (n = 2), and ST289 (n = 1). ST1794 is a novel ST while ST46 is widespread in Southeast Asia and ST289 has also been found in Thailand, Malaysia and Singapore. A Phylogeographical analysis of the Riau B. pseudomallei genomic data in comparison to a global dataset of genomes clearly distinguished the genomes of B. pseudomallei in Indonesia from the ancestral Australian clade and definitively classified them within the Asian clade. This study expands the known presence of B. pseudomallei within Indonesia and confirms that Indonesian B. pseudomallei are genetically linked to those in the rest of Southeast Asia. It is anticipated that melioidosis will be found in other locations across Indonesia as laboratory capacities improve and standardized protocols for detecting and confirming suspected cases of melioidosis are more widely implemented.