Phenotypic and Genomic Analyses of Burkholderia stabilis Clinical Contamination, Switzerland

Abstract

A recent hospital outbreak related to premoistened gloves used to wash patients exposed the difficulties of defining Burkholderia species in clinical settings. The outbreak strain displayed key B. stabilis phenotypes, including the inability to grow at 42°C; we used whole-genome sequencing to confirm the pathogen was B. stabilis. The outbreak strain genome comprises 3 chromosomes and a plasmid, sharing an average nucleotide identity of 98.4% with B. stabilis ATCC27515 BAA-67, but with 13% novel coding sequences. The genome lacks identifiable virulence factors and has no apparent increase in encoded antimicrobial drug resistance, few insertion sequences, and few pseudogenes, suggesting this outbreak was an opportunistic infection by an environmental strain not adapted to human pathogenicity. The diversity among outbreak isolates (22 from patients and 16 from washing gloves) is only 6 single-nucleotide polymorphisms, although the genome remains plastic, with large elements stochastically lost from outbreak isolates.

Keywords: Bcc; Burkholderia stabilis; DNA; Switzerland; bacteria; hospital-associated infections; resistance; virulence; whole-genome sequencing.

Figure 1

Comparison of the genome of Burkholderia stabilis strain CH16 from Switzerland (top bar) with that of B. stabilis reference strain BAA-67 (bottom bar). Alternating orange and brown bar sections represent chromosomes 1, 2, 3, and a plasmid. Scale bar indicates identity between the genomes (determined by blastn, http://blast.ncbi.nlm.nih.gov). Colors above the CH16 genome indicate the following: purple, regions of difference between the 2 strains; green, putative integrative and conjugative element; blue, phage; and red, the plasmid.

Figure 2

Phylogeny of outbreak isolates of Burkholderia stabilis strain CH16 from Switzerland based on high-quality single nucleotide polymorphisms (SNPs). This phylogeny of all sequenced outbreak isolates might represent a conservative estimate of SNP numbers. Given the large genome size and possible mismapping to repeats, it is difficult to determine the ultimate number of SNPs between samples. This phylogeny was confirmed using several parameters and manual checking of called SNPs. The root was arbitrarily chosen to give the fewest root to tip SNPs (n = 6). Numbers represent isolates from patients; letters represent isolates from washing gloves, located in the root position. Scale bar indicates 1 SNP.