A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant Klebsiella Pneumoniae Nosocomial Strains Isolated during an MDR Surveillance Program

Multidrug-resistant (MDR ), in particular carbapenem-resistant (CR- ), has become endemic in Italy, where alarming data have been reported on the spread of colistin-resistant CR- (CRCR- ). During the period 2013-2014, 27 CRCR- nosocomial strains were isolated within the Modena University Hospital Po...

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Published inAntibiotics (Basel) Vol. 9; no. 5; p. 246
Main Authors Gentile, Bernardina, Grottola, Antonella, Orlando, Gabriella, Fregni Serpini, Giulia, Venturelli, Claudia, Meschiari, Marianna, Anselmo, Anna, Fillo, Silvia, Fortunato, Antonella, Lista, Florigio, Pecorari, Monica, Mussini, Cristina
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 12.05.2020
MDPI
Subjects
DNA sequencing
Genetic aspects
genetic relatedness
Health aspects
Klebsiella
Klebsiella pneumoniae
MDR nosocomial spread
Methods
Nucleotide sequencing
whole-genome sequencing
Italy
whole-genome sequencing
Klebsiella pneumoniae
MDR nosocomial spread
genetic relatedness
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Abstract Multidrug-resistant (MDR ), in particular carbapenem-resistant (CR- ), has become endemic in Italy, where alarming data have been reported on the spread of colistin-resistant CR- (CRCR- ). During the period 2013-2014, 27 CRCR- nosocomial strains were isolated within the Modena University Hospital Policlinico (MUHP) multidrug resistance surveillance program. We retrospectively investigated these isolates by whole-genome sequencing (WGS) analysis of the resistome, virulome, plasmid content, and core single nucleotide polymorphisms (cSNPs) in order to gain insights into their molecular epidemiology. The in silico WGS analysis of the resistome revealed the presence of genes, such as , related to the phenotypically detected resistances to carbapenems. Concerning colistin resistance, the plasmidic genes were not detected, while known and new genetic variations in , , and were found. The virulome profile revealed the presence of type-3 fimbriae, capsular polysaccharide, and iron acquisition system genes. The detected plasmid replicons were classified as , , , , and types. The cSNPs genotyping was consistent with the multi locus sequence typing (MLST) and with the distribution of mutations related to colistin resistance genes. In a nosocomial drug resistance surveillance program, WGS proved to be a useful tool for elucidating the spread dynamics of CRCR- nosocomial strains and could help to limit their diffusion.
AbstractList Multidrug-resistant Klebsiella pneumoniae (MDR Kp ), in particular carbapenem-resistant Kp (CR- Kp ), has become endemic in Italy, where alarming data have been reported on the spread of colistin-resistant CR- Kp (CRCR- Kp ). During the period 2013–2014, 27 CRCR- Kp nosocomial strains were isolated within the Modena University Hospital Policlinico (MUHP) multidrug resistance surveillance program. We retrospectively investigated these isolates by whole-genome sequencing (WGS) analysis of the resistome, virulome, plasmid content, and core single nucleotide polymorphisms (cSNPs) in order to gain insights into their molecular epidemiology. The in silico WGS analysis of the resistome revealed the presence of genes, such as blaKPC , related to the phenotypically detected resistances to carbapenems. Concerning colistin resistance, the plasmidic genes mcr 1–9 were not detected, while known and new genetic variations in mgrB , phoQ , and pmrB were found. The virulome profile revealed the presence of type-3 fimbriae, capsular polysaccharide, and iron acquisition system genes. The detected plasmid replicons were classified as IncFIB(pQil) , IncFIB(K) , ColRNAI , IncX3 , and IncFII(K) types. The cSNPs genotyping was consistent with the multi locus sequence typing (MLST) and with the distribution of mutations related to colistin resistance genes. In a nosocomial drug resistance surveillance program, WGS proved to be a useful tool for elucidating the spread dynamics of CRCR- Kp nosocomial strains and could help to limit their diffusion.
Multidrug-resistant Klebsiella pneumoniae (MDR Kp), in particular carbapenem-resistant Kp (CR-Kp), has become endemic in Italy, where alarming data have been reported on the spread of colistin-resistant CR-Kp (CRCR-Kp). During the period 2013-2014,27 CRCR-Kp nosocomial strains were isolated within the Modena University Hospital Policlinico (MUHP) multidrug resistance surveillance program. We retrospectively investigated these isolates by whole-genome sequencing (WGS) analysis of the resistome, virulome, plasmid content, and core single nucleotide polymorphisms (cSNPs) in order to gain insights into their molecular epidemiology. The in silico WGS analysis of the resistome revealed the presence of genes, such as blaKPC, related to the phenotypically detected resistances to carbapenems. Concerning colistin resistance, the plasmidic genes mcr 1-9 were not detected, while known and new genetic variations in mgrB, phoQ, and pmrB were found. The virulome profile revealed the presence of type-3 fimbriae, capsular polysaccharide, and iron acquisition system genes. The detected plasmid replicons were classified as IncFIB(pQil), IncFIB(K), ColRNAI, IncX3, and IncFII(K) types. The cSNPs genotyping was consistent with the multi locus sequence typing (MLST) and with the distribution of mutations related to colistin resistance genes. In a nosocomial drug resistance surveillance program, WGS proved to be a useful tool for elucidating the spread dynamics of CRCR-Kp nosocomial strains and could help to limit their diffusion.
Multidrug-resistant (MDR ), in particular carbapenem-resistant (CR- ), has become endemic in Italy, where alarming data have been reported on the spread of colistin-resistant CR- (CRCR- ). During the period 2013-2014, 27 CRCR- nosocomial strains were isolated within the Modena University Hospital Policlinico (MUHP) multidrug resistance surveillance program. We retrospectively investigated these isolates by whole-genome sequencing (WGS) analysis of the resistome, virulome, plasmid content, and core single nucleotide polymorphisms (cSNPs) in order to gain insights into their molecular epidemiology. The in silico WGS analysis of the resistome revealed the presence of genes, such as , related to the phenotypically detected resistances to carbapenems. Concerning colistin resistance, the plasmidic genes were not detected, while known and new genetic variations in , , and were found. The virulome profile revealed the presence of type-3 fimbriae, capsular polysaccharide, and iron acquisition system genes. The detected plasmid replicons were classified as , , , , and types. The cSNPs genotyping was consistent with the multi locus sequence typing (MLST) and with the distribution of mutations related to colistin resistance genes. In a nosocomial drug resistance surveillance program, WGS proved to be a useful tool for elucidating the spread dynamics of CRCR- nosocomial strains and could help to limit their diffusion.
Audience Academic
Author Orlando, Gabriella
Fregni Serpini, Giulia
Pecorari, Monica
Grottola, Antonella
Fillo, Silvia
Lista, Florigio
Venturelli, Claudia
Gentile, Bernardina
Anselmo, Anna
Fortunato, Antonella
Meschiari, Marianna
Mussini, Cristina
AuthorAffiliation 5 Clinical Microbiology Unit, University Hospital Policlinico Modena, Via Del Pozzo, 71, 41124 Modena, Italy; venturelli.claudia@policlinico.mo.it
1 Scientific Department, Army Medical Center, Via Santo Stefano Rotondo 4, 00184 Rome, Italy; dinagentile629@gmail.com (B.G.); annanselm@gmail.com (A.A.); silviafillo@gmail.com (S.F.); antonellafortunato75@gmail.com (A.F.); romano.lista@gmail.com (F.L.)
3 Department of Surgery, Medicine, Dentistry, and Morphological Sciences with Transplant Surgery, Oncology, and Regenerative Medicine Relevance, University of Modena and Reggio Emilia, Via Del Pozzo 71, 41124 Modena, Italy; cristina.mussini@unimore.it
2 Molecular Microbiology and Virology Unit, University Hospital Policlinico Modena, Via Del Pozzo, 71, 41124 Modena, Italy; grottola.antonella@policlinico.mo.it (A.G.); fregniserpini.giulia@policlinico.mo.it (G.F.S.); pecorari.monica@policlinico.mo.it (M.P.)
4 Infectious Disease Clinic, University Hospital Policlinico Modena, Via Del Pozzo 71, 41124
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– name: 3 Department of Surgery, Medicine, Dentistry, and Morphological Sciences with Transplant Surgery, Oncology, and Regenerative Medicine Relevance, University of Modena and Reggio Emilia, Via Del Pozzo 71, 41124 Modena, Italy; cristina.mussini@unimore.it
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Issue 5
Keywords whole-genome sequencing
Klebsiella pneumoniae
MDR nosocomial spread
genetic relatedness
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Snippet Multidrug-resistant (MDR ), in particular carbapenem-resistant (CR- ), has become endemic in Italy, where alarming data have been reported on the spread of...
Multidrug-resistant Klebsiella pneumoniae (MDR Kp), in particular carbapenem-resistant Kp (CR-Kp), has become endemic in Italy, where alarming data have been...
Multidrug-resistant Klebsiella pneumoniae (MDR Kp ), in particular carbapenem-resistant Kp (CR- Kp ), has become endemic in Italy, where alarming data have...
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StartPage 246
SubjectTerms DNA sequencing
Genetic aspects
genetic relatedness
Health aspects
Klebsiella
Klebsiella pneumoniae
MDR nosocomial spread
Methods
Nucleotide sequencing
whole-genome sequencing
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Title A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant Klebsiella Pneumoniae Nosocomial Strains Isolated during an MDR Surveillance Program
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