Draft Genome Sequences of Six Different Staphylococcus epidermidis Clones, Isolated Individually from Preterm Neonates Presenting with Sepsis at Edinburgh's Royal Infirmary

Walsh, Paul; Bekaert, Michaël; Carroll, John M.; Manning, Timmy; Kelly, Brian; O'Driscoll, Aisling; Lu, Xiangwu; Smith, Claire; Dickinson, Paul; Templeton, Kate; Ghazal, Peter; Sleator, Roy D.

doi:10.1128/genomea.00471-15

Cited by 3 publications

(4 citation statements)

References 14 publications

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“…Our results suggest that qacA4 is distributed in pediatric oncology populations at centers across the United States and Canada. In addition, we identified 39 isolates carrying qacA4 collected at institutions in 5 countries (29,33,35,37,38). This suggests that qacA4 follows the wide distribution of both the S. epidermidis ST2 clone and qacA (36,48) and is likely disseminated throughout health care settings globally.…”

Section: Discussionmentioning

confidence: 83%

“…We identified isolates proven or presumed to carry qacA4 from 22 patients enrolled in a multicenter, randomized controlled CHG bathing trial at 14 participating study centers across the United States and Canada. Furthermore, we identified qacA4 in clinical S. epidermidis isolates collected in prior studies at centers without patients participating in our CHG bathing trial (29,33,35,37,38). Previous studies have characterized three alleles of qacA: qacA1, qacA2, and qacA3 (18,21).…”

Section: Discussionmentioning

confidence: 96%

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A Novel, Widespread qacA Allele Results in Reduced Chlorhexidine Susceptibility in Staphylococcus epidermidis

Addetia¹,

Greninger

Adler³

et al. 2019

Antimicrob Agents Chemother

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Chlorhexidine gluconate (CHG) is a topical antiseptic widely used in health care settings. In Staphylococcus spp., the pump QacA effluxes CHG, while the closely related QacB cannot due to a single amino acid substitution. We characterized 1,050 cutaneous Staphylococcus isolates obtained from 173 pediatric oncology patients enrolled in a multicenter CHG bathing trial. CHG susceptibility testing revealed that 63 (6%) of these isolates had elevated CHG MICs (≥4 μg/ml). Screening of all 1,050 isolates for the qacA/B gene (the same qac gene with A or B allele) by restriction fragment length polymorphism (RFLP) yielded 56 isolates with a novel qacA/B RFLP pattern, qacA/B273. The CHG MIC was significantly higher for qacA/B273-positive isolates (MIC50, 4 μg/ml; MIC range, 0.5 to 4 μg/ml) than for other qac groups: qacA-positive isolates (n = 559; MIC50, 1 μg/ml; MIC range, 0.5 to 4 μg/ml), qacB-positive isolates (n = 17; MIC50, 1 μg/ml; MIC range, 0.25 to 2 μg/ml), and qacA/B-negative isolates (n = 418, MIC50, 1 μg/ml; MIC range, 0.125 to 2 μg/ml) (P = 0.001). A high proportion of the qacA/B273-positive isolates also displayed methicillin resistance (96.4%) compared to the other qac groups (24.9 to 61.7%) (P = 0.001). Whole-genome sequencing revealed that qacA/B273-positive isolates encoded a variant of QacA with 2 amino acid substitutions. This new allele, named qacA4, was carried on the novel plasmid pAQZ1. The qacA4-carrying isolates belonged to the highly resistant Staphylococcus epidermidis sequence type 2 clone. By searching available sequence data sets, we identified 39 additional qacA4-carrying S. epidermidis strains from 5 countries. Curing an isolate of qacA4 resulted in a 4-fold decrease in the CHG MIC, confirming the role of qacA4 in the elevated CHG MIC. Our results highlight the importance of further studying qacA4 and its functional role in clinical staphylococci.

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Section: Discussionmentioning

confidence: 83%

Section: Discussionmentioning

confidence: 96%

A Novel, Widespread qacA Allele Results in Reduced Chlorhexidine Susceptibility in Staphylococcus epidermidis

Addetia¹,

Greninger

Adler³

et al. 2019

Antimicrob Agents Chemother

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“…Furthermore, some genomes represented other bacterial species incorrectly classified as S. epidermidis . Using the outlined selection/exclusion criteria, a curated list of 15 genomes from three different projects [two published ( Roach et al , 2015 ; Walsh et al , 2015 ), one unpublished PRJNA246628] was obtained (Table S1). To determine how the newly closed BPH0662 isolate related to international ST2 strains, analysis of these 15 representative, publically available, draft ST2 genomes together with the four existing complete S. epidermidis genomes was performed using BPH0662 as a reference ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis

et al. 2016

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Staphylococcus epidermidis is a significant opportunistic pathogen of humans. The ST2 lineage is frequently multidrug-resistant and accounts for most of the clinical disease worldwide. However, there are no publically available, closed ST2 genomes and pathogenesis studies have not focused on these strains. We report the complete genome and methylome of BPH0662, a multidrug-resistant, hospital-adapted, ST2 S. epidermidis, and describe the correlation between resistome and phenotype, as well as demonstrate its relationship to publically available, international ST2 isolates. Furthermore, we delineate the methylome determined by the two type I restriction modification systems present in BPH0662 through heterologous expression in Escherichia coli, allowing the assignment of each system to its corresponding target recognition motif. As the first, to our knowledge, complete ST2 S. epidermidis genome, BPH0662 provides a valuable reference for future genomic studies of this clinically relevant lineage. Defining the methylome and the construction of these E. coli hosts provides the foundation for the development of molecular tools to bypass restriction modification systems in this lineage that has hitherto proven intractable.

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“…110,111 The project has sequenced and analyzed the genomes of 12 bacterial pathogens, identifying biomarkers for the rapid diagnosis of neonatal infections. [112][113][114][115][116][117][118]…”

Section: In Silico Diagnosticsmentioning

confidence: 99%

Under the microscope: From pathogens to probiotics and back

Sleator¹

2015

Bioengineered

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Draft Genome Sequences of Six Different Staphylococcus epidermidis Clones, Isolated Individually from Preterm Neonates Presenting with Sepsis at Edinburgh's Royal Infirmary

Abstract: Herein, we report the draft genome sequences of six individual Staphylococcus epidermidis clones, cultivated from blood taken from different preterm neonatal sepsis patients at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.

Cited by 3 publications

References 14 publications

A Novel, Widespread qacA Allele Results in Reduced Chlorhexidine Susceptibility in Staphylococcus epidermidis

A Novel, Widespread qacA Allele Results in Reduced Chlorhexidine Susceptibility in Staphylococcus epidermidis

Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis

Under the microscope: From pathogens to probiotics and back

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