Burkholderia cenocepacia ST-250 in Switzerland

Background: The Burkholderia cepacia complex (Bcc) comprises a group of genetically distinct bacteria. Colonization of the respiratory tract in CF-patients is associated with poor clinical outcome. We aimed to investigate Bcc strains from CF-patients and non-CF patients obtained in our center over a period of 20 years on a genomovar, genetic, and epidemiological level. Materials: We analyzed a total of 100 Bcc strains collected from 2001-2021 in our routine diagnostics using whole-genome sequencing (Illumina MiSeq, paired-end 150nt). We determined the multi-locus sequence types (MLST) from PubMLST. We performed single nucleotide polymorphism (SNP)-analysis in CLC Genomics Workbench v22.0.2. We measured antibiotic susceptibility with disk diffusion using clinical breakpoints from the Clinical and Laboratory Standards Institute (M100 32th edition). Results: The genomovars identified were Burkholderia cenocepacia n=44, B. multivorans n=32, B. contaminans n=15; B. cepacia n=3; B. anthina n=2; B. stabilis n=2; B. gladioli n=1; and B. vietnamensis n=1. MLST revealed B. cenocepacia ST-250 in 18 clinical samples obtained from eight CF-patients, with multiple isolates collected over up to nine years from five patients. SNP-analysis of these ST-250 strains showed clustering of isolates from patients (Figure 1). A within-patient genomic variation of up to 114 SNPs and a between patient variation of 68-252 SNPs were observed, respectively, suggesting that this cluster has a recent common ancestor. B. cenocepacia ST-250 isolates exhibited high resistance towards meropenem (14/18, 77.8%), minocycline (13/18, 72.2%), and trimethoprim-sulfamethoxazole (17/18, 94.4%). Only 12/18 (66.7%) were resistant towards ceftazidime. Isolates derived over time from the same patients displayed a progressive increase in resistance towards different antibiotics. Conclusions: We present whole-genome data from B. cenocepacia ST-250. B. cenocepacia ST-250 isolates from five CF-patients showed within-host diversity over several years of colonization and evolution of antimicrobial resistance. Further analyses are underway to infer the timing of a common ancestor and possible transmission of B. cenocepacia ST-250 isolates.