Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms

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dc.contributor.authorRamos, Pablo Ivan Pereira
dc.contributor.authorPicao, Renata Christina
dc.contributor.authorAlmeida, Luiz Gonzaga Paula de
dc.contributor.authorLima, Nicholas Costa B.
dc.contributor.authorGirardello, Raquel [UNIFESP]
dc.contributor.authorVivan, Ana Carolina P.
dc.contributor.authorXavier, Danilo Elias [UNIFESP]
dc.contributor.authorBarcellos, Fernando G.
dc.contributor.authorPelisson, Marsileni
dc.contributor.authorVespero, Eliana Carolina
dc.contributor.authorMedigue, Claudine
dc.contributor.authorVasconcelos, Ana Tereza Ribeiro de
dc.contributor.authorGales, Ana Cristina [UNIFESP]
dc.contributor.authorNicolas, Marisa Fabiana
dc.contributor.institutionLab Nacl Computacao Cient
dc.contributor.institutionUniversidade Federal do Rio de Janeiro (UFRJ)
dc.contributor.institutionUniversidade Estadual de Londrina (UEL)
dc.contributor.institutionUniversidade Federal de São Paulo (UNIFESP)
dc.contributor.institutionGenoscope
dc.date.accessioned2016-01-24T14:35:09Z
dc.date.available2016-01-24T14:35:09Z
dc.date.issued2014-01-22
dc.description.abstractBackground: Klebsiella pneumoniae is an important opportunistic pathogen associated with nosocomial and community-acquired infections. A wide repertoire of virulence and antimicrobial resistance genes is present in K. pneumoniae genomes, which can constitute extra challenges in the treatment of infections caused by some strains. K. pneumoniae Kp13 is a multidrug-resistant strain responsible for causing a large nosocomial outbreak in a teaching hospital located in Southern Brazil. Kp13 produces K. pneumoniae carbapenemase (KPC-2) but is unrelated to isolates belonging to ST 258 and ST 11, the main clusters associated with the worldwide dissemination of KPC-producing K. pneumoniae. in this report, we perform a genomic comparison between Kp13 and each of the following three K. pneumoniae genomes: MGH 78578, NTUH-K2044 and 342.Results: We have completely determined the genome of K. pneumoniae Kp13, which comprises one chromosome (5.3 Mbp) and six plasmids (0.43 Mbp). Several virulence and resistance determinants were identified in strain Kp13. Specifically, we detected genes coding for six beta-lactamases (SHV-12, OXA-9, TEM-1, CTX-M-2, SHV-110 and KPC-2), eight adhesin-related gene clusters, including regions coding for types 1 (fim) and 3 (mrk) fimbrial adhesins. the rmtG plasmidial 16S rRNA methyltransferase gene was also detected, as well as efflux pumps belonging to five different families. Mutations upstream the OmpK35 porin-encoding gene were evidenced, possibly affecting its expression. SNPs analysis relative to the compared strains revealed 141 mutations falling within CDSs related to drug resistance which could also influence the Kp13 lifestyle. Finally, the genetic apparatus for synthesis of the yersiniabactin siderophore was identified within a plasticity region. Chromosomal architectural analysis allowed for the detection of 13 regions of difference in Kp13 relative to the compared strains.Conclusions: Our results indicate that the plasticity occurring at many hierarchical levels (from whole genomic segments to individual nucleotide bases) may play a role on the lifestyle of K. pneumoniae Kp13 and underlie the importance of whole-genome sequencing to study bacterial pathogens. the general chromosomal structure was somewhat conserved among the compared bacteria, and recombination events with consequent gain/ loss of genomic segments appears to be driving the evolution of these strains.en
dc.description.affiliationLab Nacl Computacao Cient, Petropolis, RJ, Brazil
dc.description.affiliationUniv Fed Rio de Janeiro, Inst Microbiol Paulo de Goes, Rio de Janeiro, Brazil
dc.description.affiliationUniv Estadual Londrina, Dept Biol Geral, Londrina, Parana, Brazil
dc.description.affiliationUniversidade Federal de São Paulo, Disciplina Infectol, São Paulo, Brazil
dc.description.affiliationUniversidade Federal de São Paulo, Dept Patol Clin Anal Clin & Toxicol, São Paulo, Brazil
dc.description.affiliationGenoscope, CEA, CNRS UMR 8030, Lab Anal Bioinformat Genom & Metab,Inst Genom, Evry, France
dc.description.affiliationUnifespUniversidade Federal de São Paulo, Disciplina Infectol, São Paulo, Brazil
dc.description.affiliationUnifespUniversidade Federal de São Paulo, Dept Patol Clin Anal Clin & Toxicol, São Paulo, Brazil
dc.description.sourceWeb of Science
dc.description.sponsorshipCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
dc.format.extent16
dc.identifierhttp://dx.doi.org/10.1186/1471-2164-15-54
dc.identifier.citationBmc Genomics. London: Biomed Central Ltd, v. 15, 16 p., 2014.
dc.identifier.doi10.1186/1471-2164-15-54
dc.identifier.fileWOS000331114400003.pdf
dc.identifier.issn1471-2164
dc.identifier.urihttp://repositorio.unifesp.br/handle/11600/37321
dc.identifier.wosWOS:000331114400003
dc.language.isoeng
dc.publisherBiomed Central Ltd
dc.relation.ispartofBmc Genomics
dc.rightsAcesso aberto
dc.subjectCarbapenemaseen
dc.subjectComparative genomicsen
dc.subjectEnterobacteriaceaeen
dc.subjectGram-negativeen
dc.subjectNosocomial pathogensen
dc.subjectPathogenic bacteriaen
dc.subjectSNPsen
dc.titleComparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanismsen
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