Differential analysis of longitudinal methicillin-resistant Staphylococcus aureus colonization in relation to microbial shifts in the nasal microbiome of neonatal piglets

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dc.contributor.authorPatel, Shriram
dc.contributor.authorVlasblom, Abel A.
dc.contributor.authorVerstappen, Koen M
dc.contributor.authorZomer, Aldert
dc.contributor.authorFluit, Ad C.
dc.contributor.authorRogers, Malbert R. C.
dc.contributor.authorWagenaar, Jaap A.
dc.contributor.authorClaesson, Marcus J.
dc.contributor.authorDuim, Birgitta
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderHealth Research Boarden
dc.contributor.funderZonMwen
dc.contributor.funderHorizon 2020en
dc.date.accessioned2022-11-09T10:36:44Z
dc.date.available2022-11-09T10:36:44Z
dc.date.issued2021-07
dc.date.updated2022-11-09T09:37:54Z
dc.description.abstractMethicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen and often colonizes pigs. To lower the risk of MRSA transmission to humans, a reduction of MRSA prevalence and/or load in pig farms is needed. The nasal microbiome contains commensal species that may protect against MRSA colonization and may be used to develop competitive exclusion strategies. To obtain a comprehensive understanding of the species that compete with MRSA in the developing porcine nasal microbiome, and the moment of MRSA colonization, we analyzed nasal swabs from piglets in two litters. The swabs were taken longitudinally, starting directly after birth until 6 weeks. Both 16S rRNA and tuf gene sequencing data with different phylogenetic resolutions and complementary culture-based and quantitative real-time PCR (qPCR)-based MRSA quantification data were collected. We employed a compositionally aware bioinformatics approach (CoDaSeq - rmcorr) for analysis of longitudinal measurements of the nasal microbiota. The richness and diversity in the developing nasal microbiota increased over time, albeit with a reduction of Firmicutes and Actinobacteria, and an increase of Proteobacteria. Coabundant groups (CAGs) of species showing strong positive and negative correlation with colonization of MRSA and S. aureus were identified. Combining 16S rRNA and tuf gene sequencing provided greater Staphylococcus species resolution, which is necessary to inform strategies with potential protective effects against MRSA colonization in pigs.IMPORTANCE The large reservoir of methicillin-resistant Staphylococcus aureus (MRSA) in pig farms imposes a significant zoonotic risk. An effective strategy to reduce MRSA colonization in pig farms is competitive exclusion whereby MRSA colonization can be reduced by the action of competing bacterial species. We complemented 16S rRNA gene sequencing with Staphylococcus-specific tuf gene sequencing to identify species anticorrelating with MRSA colonization. This approach allowed us to elucidate microbiome dynamics and identify species that are negatively and positively associated with MRSA, potentially suggesting a route for its competitive exclusion.en
dc.description.sponsorshipDutch ZonMw (JPIAMR-2017-1-B grant no. 50-52900-98-043)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationPatel, S., Vlasblom, A. A., Verstappen, K. M, Zomer, A., Fluit, A. C., Rogers, M. R. C., Wagenaar, J. A., Claesson, M. J. and Duim, Birgitta (2021) 'Differential analysis of longitudinal methicillin-resistant Staphylococcus aureus colonization in relation to microbial shifts in the nasal microbiome of neonatal piglets', Msystems, 6 (4), (15 pp). doi: 10.1128/mSystems.00152-21en
dc.identifier.doi10.1128/mSystems.00152-21en
dc.identifier.endpage15en
dc.identifier.issn2379-5077
dc.identifier.issued4en
dc.identifier.journaltitleMsystemsen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/13839
dc.identifier.volume6en
dc.language.isoenen
dc.publisherAmerican Society for Microbiologyen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/en
dc.relation.projectinfo:eu-repo/grantAgreement/EC/H2020::MSCA-COFUND-FP/754535/EU/APC Postdoctoral EXcellence Programme/APEXen
dc.rights© 2021 Patel et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectBacterial interferenceen
dc.subjectIdentificationen
dc.subjectAssayen
dc.subjectMRSAen
dc.subjectPCRen
dc.titleDifferential analysis of longitudinal methicillin-resistant Staphylococcus aureus colonization in relation to microbial shifts in the nasal microbiome of neonatal pigletsen
dc.typeArticle (peer-reviewed)en
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