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Genomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistance

2022-08-13Journal article Open access
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dc.contributor.authorSpadar, Anton
dc.contributor.authorPhelan, Jody
dc.contributor.authorElias, Rita
dc.contributor.authorModesto, Ana
dc.contributor.authorCaneiras, Cátia
dc.contributor.authorMarques, Cátia
dc.contributor.authorLito, Luís
dc.contributor.authorPinto, Margarida
dc.contributor.authorCavaco‑Silva, Patrícia
dc.contributor.authorFerreira, Helena
dc.contributor.authorPomba, Constança
dc.contributor.authorSilva, Gabriela J. Da
dc.contributor.authorSaavedra, Maria José
dc.contributor.authorMelo‑Cristino, José
dc.contributor.authorDuarte, Aida
dc.contributor.authorCampino, Susana
dc.contributor.authorPerdigão, João
dc.date.accessioned2023-08-17T17:32:02Z
dc.date.available2023-08-17T17:32:02Z
dc.date.issued2022-08-13
dc.date.updated2023-01-02T16:45:50Z
dc.description.abstractKlebsiella pneumoniae (Kp) bacteria are an increasing threat to public health and represent one of the most concerning pathogens involved in life-threatening infections and antimicrobial resistance (AMR). To understand the epidemiology of AMR of Kp in Portugal, we analysed whole genome sequencing, susceptibility testing and other meta data on 509 isolates collected nationwide from 16 hospitals and environmental settings between years 1980 and 2019. Predominant sequence types (STs) included ST15 (n = 161, 32%), ST147 (n = 36, 7%), ST14 (n = 26, 5%) or ST13 (n = 26, 5%), while 31% of isolates belonged to STs with fewer than 10 isolates. AMR testing revealed widespread resistance to aminoglycosides, fluoroquinolones, cephalosporins and carbapenems. The most common carbapenemase gene was blaKPC-3. Whilst the distribution of AMR linked plasmids appears uncorrelated with ST, their frequency has changed over time. Before year 2010, the dominant plasmid group was associated with the extended spectrum beta-lactamase gene blaCTX-M-15, but this group appears to have been displaced by another carrying the blaKPC-3 gene. Co-carriage of blaCTX-M and blaKPC-3 was uncommon. Our results from the largest genomics study of Kp in Portugal highlight the active transmission of strains with AMR genes and provide a baseline set of variants for future resistance monitoring and epidemiological studies.pt_PT
dc.description.sponsorshipSC is funded by the Medical Research Council UK (Grant no. MR/M01360X/1) and BBSRC UK (BB/R013063/1). TGC is supported by the Medical Research Council UK (Grant no. MR/K000551/1, MR/M01360X/1, MR/N010469/1, MR/R020973/1) and BBSRC (BB/R013063/1). JPe is supported by Fundação para a Ciência e Tecnologia (ref. CEECIND/00394/2017 and UID/DTP/04138/2019). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationSpadar A, Phelan J, Elias R, Modesto A, Caneiras C, Marques C, et al. Genomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistance. Sci Rep [Internet]. 13 de agosto de 2022;12(1):13791. Disponível em: https://www.nature.com/articles/s41598-022-17996-1pt_PT
dc.identifier.doi10.1038/s41598-022-17996-1pt_PT
dc.identifier.issn2045-2322
dc.identifier.slugcv-prod-3107714
dc.identifier.urihttp://hdl.handle.net/10451/58918
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherSpringer Naturept_PT
dc.relationNot Available
dc.relationResearch Institute for Medicines
dc.relation.publisherversionhttps://www.nature.com/articles/s41598-022-17996-1pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.titleGenomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistancept_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleNot Available
oaire.awardTitleResearch Institute for Medicines
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/CEEC IND 2017/CEECIND%2F00394%2F2017%2FCP1476%2FCT0001/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UID%2FDTP%2F04138%2F2019/PT
oaire.citation.issue1pt_PT
oaire.citation.startPage13791pt_PT
oaire.citation.titleScientific Reportspt_PT
oaire.citation.volume12pt_PT
oaire.fundingStreamCEEC IND 2017
oaire.fundingStream6817 - DCRRNI ID
person.familyNameSpadar
person.familyNameElias
person.familyNameDuarte
person.familyNameLucas Mota Perdigão
person.givenNameAnton
person.givenNameRita
person.givenNameAida
person.givenNameJoão Ruben
person.identifier2524696
person.identifier.ciencia-id4F17-84D2-B49E
person.identifier.ciencia-idD517-F4DB-17C1
person.identifier.ciencia-id991C-F26A-9843
person.identifier.orcid0000-0002-1548-1121
person.identifier.orcid0000-0001-6959-9005
person.identifier.orcid0000-0002-0616-4650
person.identifier.orcid0000-0002-0339-1305
person.identifier.ridM-5272-2013
person.identifier.scopus-author-id57220858605
person.identifier.scopus-author-id35495748300
person.identifier.scopus-author-id24723211800
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
rcaap.cv.cienciaid991C-F26A-9843 | João Ruben Lucas Mota Perdigão
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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