Recombinations in staphylococcal cassette chromosome mec elements compromise the molecular detection of methicillin resistance in Staphylococcus aureus

dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
dc.contributor.authorHill-Cawthorne, Grant A.
dc.contributor.authorHudson, Lyndsey O.
dc.contributor.authorAbd El Ghany, Moataz
dc.contributor.authorPiepenburg, Olaf
dc.contributor.authorNair, Mridul
dc.contributor.authorDodgson, Andrew
dc.contributor.authorForrest, Matthew S.
dc.contributor.authorClark, Taane G.
dc.contributor.authorPain, Arnab
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentPathogen Genomics Laboratory
dc.contributor.institutionMarie Bashir Institute for Infectious Diseases and Biosecurity, Sydney School of Public Health, University of Sydney, Sydney, NSW, Australia
dc.contributor.institutionDepartment of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
dc.contributor.institutionTwistDx Ltd., Babraham, United Kingdom
dc.contributor.institutionMicrobiology Dept, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
dc.contributor.institutionDepartment of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
dc.date.accessioned2014-08-27T09:48:02Z
dc.date.available2014-08-27T09:48:02Z
dc.date.issued2014-06-27
dc.description.abstractClinical laboratories are increasingly using molecular tests for methicillin-resistant Staphylococcus aureus (MRSA) screening. However, primers have to be targeted to a variable chromosomal region, the staphylococcal cassette chromosome mec (SCCmec). We initially screened 726 MRSA isolates from a single UK hospital trust by recombinase polymerase amplification (RPA), a novel, isothermal alternative to PCR. Undetected isolates were further characterised using multilocus sequence, spa typing and whole genome sequencing. 96% of our tested phenotypically MRSA isolates contained one of the six orfX-SCCmec junctions our RPA test and commercially available molecular tests target. However 30 isolates could not be detected. Sequencing of 24 of these isolates demonstrated recombinations within the SCCmec element with novel insertions that interfered with the RPA, preventing identification as MRSA. This result suggests that clinical laboratories cannot rely solely upon molecular assays to reliably detect all methicillin-resistance. The presence of significant recombinations in the SCCmec element, where the majority of assays target their primers, suggests that there will continue to be isolates that escape identification. We caution that dependence on amplification-based molecular assays will continue to result in failure to diagnose a small proportion (?4%) of MRSA isolates, unless the true level of SCCmec natural diversity is determined by whole genome sequencing of a large collection of MRSA isolates. © 2014 Hill-Cawthorne et al.
dc.eprint.versionPublisher's Version/PDF
dc.identifier.citationHill-Cawthorne GA, Hudson LO, El Ghany MFA, Piepenburg O, Nair M, et al. (2014) Recombinations in Staphylococcal Cassette Chromosome mec Elements Compromise the Molecular Detection of Methicillin Resistance in Staphylococcus aureus. PLoS ONE 9: e101419. doi:10.1371/journal.pone.0101419.
dc.identifier.doi10.1371/journal.pone.0101419
dc.identifier.issn19326203
dc.identifier.journalPLoS ONE
dc.identifier.pmcidPMC4074205
dc.identifier.pmid24972080
dc.identifier.urihttp://hdl.handle.net/10754/325341
dc.language.isoen
dc.publisherPublic Library of Science (PLoS)
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.subjectbacterial strain
dc.subjectbacterium detection
dc.subjectbacterium identification
dc.subjectbacterium isolate
dc.subjectcontrolled study
dc.subjectgene cassette
dc.subjectgene insertion
dc.subjectgene sequence
dc.subjectgenetic analysis
dc.subjectgenetic variability
dc.subjectmethicillin resistant Staphylococcus aureus
dc.subjectmultilocus sequence typing
dc.subjectnucleic acid analysis
dc.subjectnucleotide sequence
dc.subjectphenotype
dc.subjectrecombinase polymerase amplification
dc.titleRecombinations in staphylococcal cassette chromosome mec elements compromise the molecular detection of methicillin resistance in Staphylococcus aureus
dc.typeArticle
display.details.left<span><h5>Type</h5>Article<br><br><h5>Authors</h5><a href="https://repository.kaust.edu.sa/search?query=orcid.id:0000-0002-3828-5473&spc.sf=dc.date.issued&spc.sd=DESC">Hill-Cawthorne, Grant A.</a> <a href="https://orcid.org/0000-0002-3828-5473" target="_blank"><img src="https://repository.kaust.edu.sa/server/api/core/bitstreams/82a625b4-ed4b-40c8-865a-d6a5225a26a4/content" width="16" height="16"/></a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Hudson, Lyndsey O.,equals">Hudson, Lyndsey O.</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Abd El Ghany, Moataz,equals">Abd El Ghany, Moataz</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Piepenburg, Olaf,equals">Piepenburg, Olaf</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Nair, Mridul,equals">Nair, Mridul</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Dodgson, Andrew,equals">Dodgson, Andrew</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.author=Forrest, Matthew S.,equals">Forrest, Matthew S.</a><br><a href="https://repository.kaust.edu.sa/search?query=orcid.id:0000-0001-8985-9265&spc.sf=dc.date.issued&spc.sd=DESC">Clark, Taane G.</a> <a href="https://orcid.org/0000-0001-8985-9265" target="_blank"><img src="https://repository.kaust.edu.sa/server/api/core/bitstreams/82a625b4-ed4b-40c8-865a-d6a5225a26a4/content" width="16" height="16"/></a><br><a href="https://repository.kaust.edu.sa/search?query=orcid.id:0000-0002-1755-2819&spc.sf=dc.date.issued&spc.sd=DESC">Pain, Arnab</a> <a href="https://orcid.org/0000-0002-1755-2819" target="_blank"><img src="https://repository.kaust.edu.sa/server/api/core/bitstreams/82a625b4-ed4b-40c8-865a-d6a5225a26a4/content" width="16" height="16"/></a><br><br><h5>KAUST Department</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Biological and Environmental Sciences and Engineering (BESE) Division,equals">Biological and Environmental Sciences and Engineering (BESE) Division</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Bioscience Program,equals">Bioscience Program</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Computational Bioscience Research Center (CBRC),equals">Computational Bioscience Research Center (CBRC)</a><br><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.department=Pathogen Genomics Laboratory,equals">Pathogen Genomics Laboratory</a><br><br><h5>Date</h5>2014-06-27</span>
display.details.right<span><h5>Abstract</h5>Clinical laboratories are increasingly using molecular tests for methicillin-resistant Staphylococcus aureus (MRSA) screening. However, primers have to be targeted to a variable chromosomal region, the staphylococcal cassette chromosome mec (SCCmec). We initially screened 726 MRSA isolates from a single UK hospital trust by recombinase polymerase amplification (RPA), a novel, isothermal alternative to PCR. Undetected isolates were further characterised using multilocus sequence, spa typing and whole genome sequencing. 96% of our tested phenotypically MRSA isolates contained one of the six orfX-SCCmec junctions our RPA test and commercially available molecular tests target. However 30 isolates could not be detected. Sequencing of 24 of these isolates demonstrated recombinations within the SCCmec element with novel insertions that interfered with the RPA, preventing identification as MRSA. This result suggests that clinical laboratories cannot rely solely upon molecular assays to reliably detect all methicillin-resistance. The presence of significant recombinations in the SCCmec element, where the majority of assays target their primers, suggests that there will continue to be isolates that escape identification. We caution that dependence on amplification-based molecular assays will continue to result in failure to diagnose a small proportion (?4%) of MRSA isolates, unless the true level of SCCmec natural diversity is determined by whole genome sequencing of a large collection of MRSA isolates. © 2014 Hill-Cawthorne et al.<br><br><h5>Citation</h5>Hill-Cawthorne GA, Hudson LO, El Ghany MFA, Piepenburg O, Nair M, et al. (2014) Recombinations in Staphylococcal Cassette Chromosome mec Elements Compromise the Molecular Detection of Methicillin Resistance in Staphylococcus aureus. PLoS ONE 9: e101419. doi:10.1371/journal.pone.0101419.<br><br><h5>Publisher</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.publisher=Public Library of Science (PLoS),equals">Public Library of Science (PLoS)</a><br><br><h5>Journal</h5><a href="https://repository.kaust.edu.sa/search?spc.sf=dc.date.issued&spc.sd=DESC&f.journal=PLoS ONE,equals">PLoS ONE</a><br><br><h5>DOI</h5><a href="https://doi.org/10.1371/journal.pone.0101419">10.1371/journal.pone.0101419</a><br><br><h5>PubMed ID</h5><a href="https://www.ncbi.nlm.nih.gov/pubmed/24972080">24972080</a><br><br><h5>PubMed Central ID</h5><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4074205">PMC4074205</a></span>
kaust.personHill-Cawthorne, Grant A.
kaust.personNair, Mridul
kaust.personPain, Arnab
kaust.personAbd El Ghany, Moataz
orcid.authorHill-Cawthorne, Grant A.::0000-0002-3828-5473
orcid.authorHudson, Lyndsey O.
orcid.authorAbd El Ghany, Moataz
orcid.authorPiepenburg, Olaf
orcid.authorNair, Mridul
orcid.authorDodgson, Andrew
orcid.authorForrest, Matthew S.
orcid.authorClark, Taane G.::0000-0001-8985-9265
orcid.authorPain, Arnab::0000-0002-1755-2819
orcid.id0000-0002-1755-2819
orcid.id0000-0001-8985-9265
orcid.id0000-0002-3828-5473
refterms.dateFOA2018-06-13T15:14:50Z
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