Klebsiella pneumoniae blaKPC-3 nosocomial epidemic: Bayesian and evolutionary analysis.
K. pneumoniae isolates carrying blaKPC-3 gene were collected to perform Bayesian phylogenetic and selective pressure analysis and to apply homology modeling to the KPC-3 protein. A dataset of 44 blakpc-3 gene sequences from clinical isolates of K. pneumoniae was used for Bayesian phylogenetic, selective pressure analysis and homology modeling. The mean evolutionary rate for blakpc-3 gene was 2.67×10-3substitution/site/year (95% HPD: 3.4×10-4-5.59×10-3). The root of the Bayesian tree dated back to the year 2011 (95% HPD: 2007-2012). Two main clades (I and II) were identified. The population dynamics analysis showed an exponential growth from 2011 to 2013 and the reaching of a plateau. The phylogeographic reconstruction showed that the root of the tree had a probable common ancestor in the general surgery ward. Selective pressure analysis revealed twelve positively selected sites. Structural analysis of KPC-3 protein predicted that the amino acid mutations are destabilizing for the protein and could alter the substrate specificity. Phylogenetic analysis and homology modeling of blaKPC-3 gene could represent a useful tool to follow KPC spread in nosocomial setting and to evidence amino acid substitutions altering the substrate specificity.
Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Italy. Electronic address: s.angeletti@unicampus.it.
Silvia
S
Angeletti
Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy.
Alessandra
A
Lo Presti
Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy; Public Health and Infectious Diseases, Sapienza University, Rome, Italy.
Eleonora
E
Cella
Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Italy.
Marta
M
Fogolari
Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Italy.
Lucia
L
De Florio
Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Italy.
Etleva
E
Dedej
Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Italy.
Aletheia
A
Blasi
Department of Biochemical Science "A. Rossi Fanelli", Sapienza University, Rome, Italy.
Teresa
T
Milano
Department of Biochemical Science "A. Rossi Fanelli", Sapienza University, Rome, Italy.
Stefano
S
Pascarella
Unit of Geriatrics, Department of Medicine, University Campus Bio-Medico of Rome, Italy.
Raffaele Antonelli
RA
Incalzi
Department of Surgery, University Campus Bio-Medico of Rome, Italy.
Roberto
R
Coppola
Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Italy.
Giordano
G
Dicuonzo
Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Italy; Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy.
Massimo
M
Ciccozzi
D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics*; D001499:Bayes Theorem; D003428:Cross Infection / Q000453:epidemiology / Q000382:microbiology*; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D058872:Epidemics / Q000706:statistics & numerical data*; D019143:Evolution, Molecular; D006801:Humans; D007558:Italy / Q000453:epidemiology; D007710:Klebsiella Infections / Q000453:epidemiology / Q000382:microbiology*; D007711:Klebsiella pneumoniae / Q000145:classification / Q000235:genetics*; D017720:Molecular Epidemiology; D010802:Phylogeny; D001618:beta-Lactamases / Q000145:classification / Q000235:genetics*
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D001618:beta-Lactamases; C495220:beta-lactamase KPC-3, Klebsiella pneumoniae
Bayesian analysis; Evolutionary analysis; K. pneumoniae; blaKPC-3 gene