Whole-genome sequencing analysis of Burkholderia pseudomallei comparing drug-resistant and pan-susceptible isolates reveals novel biomarkers for drug resistance

Melioidosis, caused by the gram-negative bacterium Burkholderia pseudomallei (Bp), poses a significant health threat due to its potential for drug resistance, which can severely limit available treatment options. To investigate this, we conducted a comparative genomic analysis of 38 drug-resistant (DR) and 300 drug-susceptible (DS) Bp isolates to identify genetic markers associated with antimicrobial resistance. Our study identified seven significant single-nucleotide polymorphisms (SNPs) linked to drug resistance: two with ceftazidime (CAZ), and five with meropenem (MEM). Pathway analysis revealed that AMC resistance was associated with alterations in fatty-acid metabolism, whereas CAZ resistance was associated with changes in membrane protein pathways. These findings highlighted how Bp develops resistance to key antibiotics through various mechanisms. In addition, we discovered 21 novel genetic variants in known drug-resistance genes, including 15 SNPs and six short insertions or deletions (indels). These previously unreported variants could contribute to resistance, highlighting the genetic diversity and adaptability to antimicrobial pressures of Bp. These findings deepen our understanding of Bp drug resistance and offer valuable insights into genetic markers with the potential to enhance diagnostic precision. By enriching the resistance database, this work provides prospective tools for early resistance prediction, facilitating prompt and effective treatment strategies. Furthermore, it emphasizes the critical role of genetic investigations in addressing the challenge of antibiotic resistance in melioidosis.