Analysis of fine-scale phylogeny of Burkholderia pseudomallei in relation to regional geography and drug susceptibility in Thailand

Abstract

Abstract Melioidosis caused by Burkholderia pseudomallei (Bp) is a public health threat. Genomic-epidemiology research on this deadly disease is scarce. We investigated whole-genome sequences of Bp isolates in relation to environmental source and drug susceptibility. In total, 563 Bp isolates were collected from 11 Northeast Thai provinces during the period 2004–2021. Patients (n = 530 isolates), infected animals (n = 8), and environmental sources (n = 25) provided samples. Phylogenetic analysis revealed genetic diversity among the Bp isolates, including numerous well-supported clusters of varying sizes. Through in-depth analysis of 38 monophyletic clades (MCs), we found eleven associated with province of origin (p-value < 0.001). Closely related clusters (CRCs) within MCs resembled MLST-identified “sequence types” (STs). We found 102 known and 52 novel STs. ST-70 was the most prevalent in this area (n = 78; 13.85%). Sample type (human/environmental) and sampling time intervals were not correlated with genetic distance among clonal Bp isolates. Some members of 12 CRCs had acquired resistance to co-trimoxazole and one against amoxicillin-clavulanic acid. Within Northeast Thailand, there is an association between Bp genotype and geographical origin.

Keywords

• Next-generation sequencing
• Whole-genome sequencing
• Burkholderia pseudomallei
• Genetic diversity
• Drug resistance
• Phylogenetic analysis