Phenotypic and Genomic Analyses ofBurkholderia stabilisClinical 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. B urkholderia is a diverse genus of gram-negative bacteria, with isolates identified from a variety of environments, and ever more species being identified and classified. Whereas some Burkholderia species are associated with bioremediation potential and antimicrobial and antifungal production, others are animal and human pathogens that generally fall within the B. cepacia complex (Bcc) (1). Burkholderia bacteria have large, flexible, multi-replicon genomes, a large metabolic repertoire, various virulence factors, and inherent resistance to many antimicrobial drugs (2,3). An outbreak of B. stabilis was identified among hospitalized patients across several cantons in Switzerland during 2015-2016 (4). The bacterium caused bloodstream infections, noninvasive infections, and wound contaminations. The source of the infection was traced to contaminated commercially available, premoistened washing gloves used for bedridden patients. After hospitals discontinued use of these gloves, the outbreak resolved. Many instances of Bcc strain contamination of medical devices and solutions have been described (4), including an outbreak in Korea associated with a 0.5% chlorhexidine solution (5). B. stabilis also has been identified in nosocomial infections (6-8). We conducted in-depth characterization of the B. stabilis strain from the Switzerland outbreak by using clinical methods and whole-genome sequencing (WGS). We generated a complete draft genome by combining short-and long-read genomic data and compared it to other outbreak isolates to provide a complete genomic assessment of this strain. We provide a thorough comparative genomic analysis of this outbreak strain. Methods Bacterial Isolate Collection Isolates were collected from 22 patients (labeled 1-22) and 16 contaminated washing gloves (labeled A-P) across Switzerland during the outbreak (4). For comparison, we

Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity

“…in the loss of plasmids, increased antimicrobial resistance and a subset of genes that undergo positive selection [38,40,[42][43][44].…”