Genomic insights into an extensively drug-resistant and hypervirulent Burkholderia dolosa N149 isolate of a novel sequence type (ST2237) from a Vietnamese patient hospitalised for stroke

Quang Huy Nguyen; Cam Linh Nguyen; Thai Son Nguyen; Bich Ngoc Do; Thi Thanh Tam Tran; Thi Thu Hang Le; Thanh Thuyet Bui; Huu Song Le; Dong Van Quyen; Juliette Hayer; Anne-Laure Bañuls; Tien Sy Bui

doi:10.1016/j.jgar.2024.02.009

Genomic insights into an extensively drug-resistant and hypervirulent Burkholderia dolosa N149 isolate of a novel sequence type (ST2237) from a Vietnamese patient hospitalised for stroke

J Glob Antimicrob Resist. 2024 Feb 24:37:44-47. doi: 10.1016/j.jgar.2024.02.009. Online ahead of print.

Affiliations

¹ LMI DRISA, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam. Electronic address: nguyen-quang.huy@usth.edu.vn.
² LMI DRISA, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam.
³ Department of Microbiology, 108 Military Central Hospital, Hanoi, Vietnam; Vietnamese-German Center for Medical Research, Hanoi, Vietnam.
⁴ Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam.
⁵ LMI DRISA, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam; UMR MIVEGEC (University of Montpellier- IRD-CNRS), Montpellier, France.

PMID: 38408562
DOI: 10.1016/j.jgar.2024.02.009

Abstract

Objectives: Burkholderia dolosa is a clinically important opportunistic pathogen in inpatients. Here we characterised an extensively drug-resistant and hypervirulent B. dolosa isolate from a patient hospitalised for stroke.

Methods: Resistance to 41 antibiotics was tested with the agar disc diffusion, minimum inhibitory concentration, or broth microdilution method. The complete genome was assembled using short-reads and long-reads and the hybrid de novo assembly method. Allelic profiles obtained by multilocus sequence typing were analysed using the PubMLST database. Antibiotic-resistance and virulence genes were predicted in silico using public databases and the 'baargin' workflow. B. dolosa N149 phylogenetic relationships with all available B. dolosa strains and Burkholderia cepacia complex strains were analysed using the pangenome obtained with Roary.

Results: B. dolosa N149 displayed extensive resistance to 31 antibiotics and intermediate resistance to 4 antibiotics. The complete genome included three circular chromosomes (6 338 630 bp in total) and one plasmid (167 591 bp). Genotypic analysis revealed various gene clusters (acr, amr, amp, emr, ade, bla and tet) associated with resistance to 35 antibiotic classes. The major intrinsic resistance mechanisms were multidrug efflux pump alterations, inactivation and reduced permeability of targeted antibiotics. Moreover, 91 virulence genes (encoding proteins involved in adherence, formation of capsule, biofilm and colony, motility, phagocytosis inhibition, secretion systems, protease secretion, transmission and quorum sensing) were identified. B. dolosa N149 was assigned to a novel sequence type (ST2237) and formed a mono-phylogenetic clade separated from other B. dolosa strains.

Conclusions: This study provided insights into the antimicrobial resistance and virulence mechanisms of B. dolosa.

Keywords: Burkholderia cepacia complex; Burkholderia dolosa; Complete genome; Extensively-drug resistance; Hypervirulence; Novel MLST.