Rapid confirmation of autochthonous origin in suspected cases of melioidosis from French overseas departments in the Caribbean and the Indian Ocean by PCR-high resolution melting (HRM) analysis

Burkholderia pseudomallei, a soil-borne bacterium that causes melioidosis, endemic in South and Southeast Asia and northern Australia, is now emerging in new regions. Since the 1990s, cases have been reported in French overseas departments, including Martinique and Guadeloupe in the Caribbean, and Reunion Island and Mayotte in the Indian Ocean, suggesting a local presence of the bacterium. Our phylogenetic analysis of 111 B. pseudomallei genomes isolated worldwide, including three strains from Martinique, revealed distinct geography-specific clades for Africa, the Americas, Asia and Australasia. Single nucleotide polymorphisms (SNP) that define clade branches in the phylogeny were identified; we selected those specific to three regions relevant to the French overseas departments: the Indian Ocean, the Americas and a unique subset specific to Martinique. Three SNP markers (one per region) were used to develop a PCR-high resolution melting tool to discriminate between local and imported strains in each region. Blind tests on B. pseudomallei strains from French patients, from overseas departments and mainland France, were used for validation. Our method accurately predicted the geographic origin of the patient as recorded from the patient travel history and/or from the multilocus sequence typing data. This rapid typing method, which allows timely identification of local cases and targeted public health interventions, is particularly valuable in the French overseas departments where melioidosis is emerging and regulatory constraints limit the handling of B. pseudomallei. Although initially tailored to specific regions, this tool can be adapted for use in other areas to support local epidemiological surveillance of melioidosis.