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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

2022Journal article Open access
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dc.contributor.authorMendes, Gabriel
dc.contributor.authorRamalho, João Francisco
dc.contributor.authorBruschy Fonseca, Ana
dc.contributor.authorLito, Luís
dc.contributor.authorDuarte, Aida
dc.contributor.authorCristino, José Melo
dc.contributor.authorCaneiras, Catia
dc.date.accessioned2022-02-18T16:01:38Z
dc.date.available2022-02-18T16:01:38Z
dc.date.issued2022
dc.description© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).pt_PT
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.pt_PT
dc.description.sponsorshipThis research was partially funded by Fundação para a Ciência e a Tecnologia (FCT), under grant numbers UIDB/04295/2020 and UIDP/04295/2020. Moreover, Cátia Caneiras (C.C.) acknowledges the funding provided by the “Research Award in Healthcare Associated Infections” granted by Escola Superior de Saúde Norte da Cruz Vermelha Portuguesa (2019) and by “BInov award”, an innovation award granted by the Southern Regional Section and Autonomous Regions of the Portuguese Pharmaceutical Society (2021). Gabriel Mendes (G.M.) was supported by Fundação para a Ciência e Tecnologia (FCT), Portugal, through a PhD Research Studentship Contract (Contrato de Bolsa de Investigação para Doutoramento 2020.07736.BD).pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationMicroorganisms 2022, 10, 416pt_PT
dc.identifier.doi10.3390/microorganisms10020416pt_PT
dc.identifier.eissn2076-2607
dc.identifier.urihttp://hdl.handle.net/10451/51422
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherMDPIpt_PT
dc.relationEnvironmental Health Institute
dc.relationEnvironmental Health Institute
dc.relationInterplay between resistance and virulence markers in Enterobacteriales carbapenemase producers
dc.relation.publisherversionhttps://www.mdpi.com/journal/microorganismspt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectKlebsiella pneumoniaept_PT
dc.subjectKPC-3pt_PT
dc.subjectOXA-181pt_PT
dc.subjectNDM-1pt_PT
dc.subjectWhole-genome sequencing (WGS)pt_PT
dc.subjectCarbapenem-resistancept_PT
dc.subjectMolecular epidemiologypt_PT
dc.subjectHypermucoviscosity (HMV)pt_PT
dc.subjectHypervirulentpt_PT
dc.subjectST13pt_PT
dc.subjectST17pt_PT
dc.subjectST307pt_PT
dc.subjectST147pt_PT
dc.subjectST39-KL62pt_PT
dc.subjectPortugalpt_PT
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 Portugalpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleEnvironmental Health Institute
oaire.awardTitleEnvironmental Health Institute
oaire.awardTitleInterplay between resistance and virulence markers in Enterobacteriales carbapenemase producers
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F04295%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDP%2F04295%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//2020.07736.BD/PT
oaire.citation.issue2pt_PT
oaire.citation.titleMicroorganismspt_PT
oaire.citation.volume10pt_PT
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream6817 - DCRRNI ID
person.familyNameFernandes Mendes
person.familyNameMarmelo Ramalho
person.familyNameDuarte
person.familyNameMelo Cristino
person.familyNameCaneiras
person.givenNameGabriel
person.givenNameJoão Francisco
person.givenNameAida
person.givenNameJosé
person.givenNameCatia
person.identifier2030815
person.identifier2524696
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person.identifier.ciencia-id5217-449F-3B4F
person.identifier.orcid0000-0003-2610-8522
person.identifier.orcid0000-0002-2312-225X
person.identifier.orcid0000-0002-0616-4650
person.identifier.orcid0000-0001-8643-1722
person.identifier.orcid0000-0002-3735-8554
person.identifier.ridM-5272-2013
person.identifier.ridH-3726-2013
person.identifier.scopus-author-id35495748300
person.identifier.scopus-author-id7004053640
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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