Complete Genome Sequences for Three Chromosomes of the Burkholderia stabilis Type Strain (ATCC BAA-67)

Bugrysheva, Julia V.; Cherney, Blake; Sue, David; Conley, Andrew B.; Rowe, Lori A.; Knipe, Kristen; Frace, Michael; Loparev, Vladimir N.; Avila, Julie R.; Anderson, Kevin; Hodge, David R.; Pillai, Segaran P.; Weigel, Linda M.

doi:10.1128/genomea.01294-16

Cited by 5 publications

(3 citation statements)

References 5 publications

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“…Molecular epidemiological investigations were carried out using core genome multilocus sequence typing (cgMLST) analysis with Ridom SeqSphere+ v3.2.1 (Ridom, Münster, Germany) [ 41 ]. Reads were quality trimmed to ≥ Q30 and mapped against the reference genome of B. stabilis type strain ATCC27515 BAA-67 (GenBank accession numbers CP016442–4) [ 42 ]. A minimum coverage of 10x was needed for mapping.…”

Section: Methodsmentioning

confidence: 99%

Burkholderia stabilis outbreak associated with contaminated commercially-available washing gloves, Switzerland, May 2015 to August 2016

Sommerstein

Führer²,

Priore

et al. 2017

Eurosurveillance

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We describe an outbreak of Burkholderia stabilis associated with contaminated washing gloves, a commercially available Class I medical device. Triggered by an increase in Burkholderia cepacia complex (BCC) bacteremias and the detection of BCC in unopened packages of washing gloves, an ad hoc national outbreak committee comprising representatives of a public health organisation, a regulatory agency, and an expert association convened and commissioned an outbreak investigation. The investigation included retrospective case finding across Switzerland and whole genome sequencing (WGS) of isolates from cases and gloves. The investigation revealed that BCC were detected in clinical samples of 46 cases aged 17 to 91 years (33% females) from nine institutions between May 2015 and August 2016. Twenty-two isolates from case patients and 16 from washing gloves underwent WGS. All available outbreak isolates clustered within a span of < 19 differing alleles, while 13 unrelated clinical isolates differed by > 1,500 alleles. This BCC outbreak was rapidly identified, communicated, investigated and halted by an ad hoc collaboration of multiple stakeholders. WGS served as useful tool for confirming the source of the outbreak. This outbreak also highlights current regulatory limitations regarding Class I medical devices and the usefulness of a nationally coordinated outbreak response.

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Section: Methodsmentioning

confidence: 99%

Burkholderia stabilis outbreak associated with contaminated commercially-available washing gloves, Switzerland, May 2015 to August 2016

Sommerstein

Führer²,

Priore

et al. 2017

Eurosurveillance

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“…This draft comprises 1 contig for each of the 3 chromosomes. Comparison with the genome of B. stabilis BAA-67 ( 16 ) showed that the genomes are syntenic with the exception of a rearrangement on chromosome 1 between the rRNA operons, which might be a real inversion or an assembly artifact in 1 of the genomes (Figure 1). We detected a separate contig representing a predicted plasmid sequence, whereas none was found within strain BAA-67 (J. Bugrysheva, US Centers for Disease Control and Prevention, pers.…”

Section: Resultsmentioning

confidence: 99%

“…We manually compared assemblies in Artemis and ACT ( 14 , 15 ) to circularize and split chromosomes 1 and 2 according to the genome of B. stabilis BAA-67 (GenBank accession nos. CP016442–4) ( 16 ). We found chromosome 3 is a single contig that was not obviously circularizable.…”

Section: Methodsmentioning

confidence: 99%

Phenotypic and Genomic Analyses ofBurkholderia stabilisClinical Contamination, Switzerland

Seth-Smith¹,

Casanova²,

Sommerstein³

et al. 2019

Emerg. Infect. Dis.

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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.

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A combined de novo assembly approach increases the quality of prokaryotic draft genomes

Çabuk

Ünlü

2022

Folia Microbiol

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Complete Genome Sequences for Three Chromosomes of the Burkholderia stabilis Type Strain (ATCC BAA-67)

Cited by 5 publications

References 5 publications

Burkholderia stabilis outbreak associated with contaminated commercially-available washing gloves, Switzerland, May 2015 to August 2016

Burkholderia stabilis outbreak associated with contaminated commercially-available washing gloves, Switzerland, May 2015 to August 2016

Phenotypic and Genomic Analyses ofBurkholderia stabilisClinical Contamination, Switzerland

A combined de novo assembly approach increases the quality of prokaryotic draft genomes

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