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Whole-genome sequencing enables molecular characterization of non-clonal group 258 high-risk clones (ST13, ST17, ST147 and ST307) among carbapenem-resistant Klebsiella pneumoniae from a tertiary university hospital centre in Portugal

2022-02Contribution to journal Open access
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datacite.subject.fosCiências Médicas
datacite.subject.sdg03:Saúde de Qualidade
dc.contributor.authorMendes, Gabriel
dc.contributor.authorRamalho, João F.
dc.contributor.authorBruschy-Fonseca, Ana
dc.contributor.authorLito, Luís
dc.contributor.authorDuarte, Aida
dc.contributor.authorMelo-Cristino, José
dc.contributor.authorCaneiras, Cátia
dc.date.accessioned2025-12-03T12:22:58Z
dc.date.available2025-12-03T12:22:58Z
dc.date.issued2022-02
dc.description.abstractThe carbapenem-resistant Enterobacterales (CRE) strains have been identified by the World Health Organization as critical priority pathogens in research and development of diagnostics, treatments, and vaccines. However, recent molecular information about carbapenem-resistant K. pneumoniae (CRK) epidemiology in Portugal is still scarce. Thus, this study aimed to provide the molecular epidemiology, resistome, and virulome of CRK clinical strains recovered from a tertiary care hospital centre (2019–2021) using polymerase chain reaction (PCR) and the advanced molecular technique whole-genome sequencing (WGS). PCR amplification of carbapenemase genes was performed in 437 carbapenem-resistant K. pneumoniae strains. The most frequent carbapenemases were: KPC-3 (42%), followed by OXA-181 (20%), GES-5 (0.2%), and NDM-1 (0.2%). Additionally, 10 strains (2%) coproduced KPC-3 and OXA-181, and 1 strain coproduced KPC-3 and OXA-48 (0.2%). The genomic population structure of 68 strains characterized by WGS demonstrated the ongoing dissemination of four main high-risk clones: ST13, ST17, ST147, and ST307, while no clones belonging to the European predominant clonal groups (CG15 and CG258) were found. Moreover, we describe one K. pneumoniae ST39-KL62 that coproduced the NDM-1 carbapenemase and the extended-spectrum beta-lactamase CTX-M-15, and one K. pneumoniae ST29-KL54 GES-5 and BEL-1 coproducer. Furthermore, a high prevalence of iron siderophores were present in all CRK strains, with several strains presenting both colibactin and the hypermucoviscosity phenotype. Thus, the data presented here highlight an uncommon molecular epidemiology pattern in Portugal when compared with most European countries, further supporting the emergence and dissemination of nonclonal group 258 hypervirulent multidrug high-risk clones and the need to promote in-depth hospital molecular surveillance studies.eng
dc.identifier.citationMendes G, Ramalho JF, Bruschy-Fonseca A, Lito L, Duarte A, Melo-Cristino J, Caneiras C. Whole-Genome Sequencing Enables Molecular Characterization of Non-Clonal Group 258 High-Risk Clones (ST13, ST17, ST147 and ST307) among Carbapenem-Resistant Klebsiella pneumoniae from a Tertiary University Hospital Centre in Portugal. Microorganisms. 2022; 10(2):416. https://doi.org/10.3390/microorganisms10020416
dc.identifier.doi10.3390/microorganisms10020416
dc.identifier.issn2076-2607
dc.identifier.urihttp://hdl.handle.net/10400.26/60185
dc.language.isoeng
dc.peerreviewedyes
dc.publisherMDPI
dc.relation.hasversionhttps://doi.org/10.3390/microorganisms10020416
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectKlebsiella pneumoniae
dc.subjectKPC-3
dc.subjectOXA-181
dc.subjectNDM-1
dc.subjectwhole-genome sequencing (WGS)
dc.subjectcarbapenem-resistance
dc.subjectmolecular epidemiology
dc.subjecthypermucoviscosity (HMV)
dc.subjecthypervirulent
dc.subjectST13
dc.subjectST17
dc.subjectST307
dc.subjectST147
dc.subjectST39-KL62
dc.subjectPortugal
dc.titleWhole-genome sequencing enables molecular characterization of non-clonal group 258 high-risk clones (ST13, ST17, ST147 and ST307) among carbapenem-resistant Klebsiella pneumoniae from a tertiary university hospital centre in Portugaleng
dc.typecontribution to journal
dspace.entity.typePublication
oaire.citation.issue2
oaire.citation.startPage416
oaire.citation.titleMicroorganisms
oaire.citation.volume10
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85

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