A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant <i>Klebsiella pneumoniae</i> Nosocomial Strains Isolated during an MDR Surveillance Program
Bernardina Gentile,
Antonella Grottola,
Gabriella Orlando,
Giulia Fregni Serpini,
Claudia Venturelli,
Marianna Meschiari,
Anna Anselmo,
Silvia Fillo,
Antonella Fortunato,
Florigio Lista,
Monica Pecorari,
Cristina Mussini
Affiliations
Bernardina Gentile
Scientific Department, Army Medical Center, Via Santo Stefano Rotondo 4, 00184 Rome, Italy
Antonella Grottola
Molecular Microbiology and Virology Unit, University Hospital Policlinico Modena, Via Del Pozzo, 71, 41124 Modena, Italy
Gabriella Orlando
Infectious Disease Clinic, University Hospital Policlinico Modena, Via Del Pozzo 71, 41124 Modena, Italy
Giulia Fregni Serpini
Molecular Microbiology and Virology Unit, University Hospital Policlinico Modena, Via Del Pozzo, 71, 41124 Modena, Italy
Claudia Venturelli
Clinical Microbiology Unit, University Hospital Policlinico Modena, Via Del Pozzo, 71, 41124 Modena, Italy
Marianna Meschiari
Infectious Disease Clinic, University Hospital Policlinico Modena, Via Del Pozzo 71, 41124 Modena, Italy
Anna Anselmo
Scientific Department, Army Medical Center, Via Santo Stefano Rotondo 4, 00184 Rome, Italy
Silvia Fillo
Scientific Department, Army Medical Center, Via Santo Stefano Rotondo 4, 00184 Rome, Italy
Antonella Fortunato
Scientific Department, Army Medical Center, Via Santo Stefano Rotondo 4, 00184 Rome, Italy
Florigio Lista
Scientific Department, Army Medical Center, Via Santo Stefano Rotondo 4, 00184 Rome, Italy
Monica Pecorari
Molecular Microbiology and Virology Unit, University Hospital Policlinico Modena, Via Del Pozzo, 71, 41124 Modena, Italy
Cristina Mussini
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
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.
