Whole genome sequencing of carbapenem-resistant Klebsiella pneumoniae : evolutionary analysis for outbreak investigation

Carbapenemase-resistant represents a major concern in hospital setting. The evolutionary history of carbapenem-resistant strains was analyzed by core genome multilocus sequence typing and Bayesian phylogenesis by whole genomes sequencing. A great increase carbapenem-resistant causing blood stream in...

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Bibliographic Details
Published in:Future microbiology 2020-02, Vol.15 (3), p.203-212
Main Authors: Fontana, Carla, Angeletti, Silvia, Mirandola, Walter, Cella, Eleonora, Alessia, Lai, Zehender, Gianguglielmo, Favaro, Marco, Leoni, Davide, Rose, Diego Delle, Gherardi, Giovanni, Florio, Lucia De, Salemi, Marco, Andreoni, Massimo, Sarmati, Loredana, Ciccozzi, Massimo
Format: Article
Language:English
Subjects:
Antibiotics
Bayesian analysis
Carbapenemase
Deoxyribonucleic acid
DNA
Enzymes
Epidemiology
Genes
Genomes
Identification
Klebsiella pneumoniae
Mass spectrometry
Medical records
Mortality
Multilocus sequence typing
Nucleotide sequence
Outbreaks
Patients
Phylogenetics
Phylogeny
Phylogeography
Plasmids
Scientific imaging
Software
Strains (organisms)
Whole genome sequencing
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Summary:Carbapenemase-resistant represents a major concern in hospital setting. The evolutionary history of carbapenem-resistant strains was analyzed by core genome multilocus sequence typing and Bayesian phylogenesis by whole genomes sequencing. A great increase carbapenem-resistant causing blood stream infection was observed in the years 2015-2016. At multilocus sequence typing (MLST), they were prevalently ST512 and ST101. ST512 were core genome (cg)MLST 53, while ST101 mainly cgMLST453. The minimum-spanning tree, based on cgMLST, showed strains clustering based on the different STs. By Bayesian phylogenetic analysis, maximum clade credibility tree showed that strains were introduced in the year 2005 with the most probable location in the ICU ward. Two outbreaks by ST101 and ST512 strains with Tower T8 as the probable location were evidenced. Molecular epidemiology is a powerful tool to track the way of transmission of resistant bacteria within the hospital setting.
ISSN:1746-0913
1746-0921
DOI:10.2217/fmb-2019-0074