title: Tracking Nosocomial Klebsiella pneumoniae Infections and Outbreaks by Whole-Genome Analysis: Small-Scale Italian Scenario within a Single Hospital.
abstract: Multidrug-resistant (MDR) Klebsiella pneumoniae is one of the most important causes of nosocomial infections worldwide. After the spread of strains resistant to beta-lactams at the end of the previous century, the diffusion of isolates resistant to carbapenems and colistin is now reducing treatment options and the containment of infections. Carbapenem-resistant K. pneumoniae strains have spread rapidly among Italian hospitals, with four subclades of pandemic clonal group 258 (CG258). Here we show that a single Italian hospital has been invaded by three of these subclades within 27 months, thus replicating on a small scale the "Italian scenario." We identified a single clone responsible for an epidemic outbreak involving seven patients, and we reconstructed its star-like pattern of diffusion within the intensive care unit. This epidemiological picture was obtained through phylogenomic analysis of 16 carbapenem-resistant K. pneumoniae isolates collected in the hospital during a 27-month period, which were added to a database of 319 genomes representing the available global diversity of K. pneumoniae strains. Phenotypic and molecular assays did not reveal virulence or resistance determinants specific for the outbreak isolates. Other factors, rather than selective advantages, might have caused the outbreak. Finally, analyses allowed us to identify a major subclade of CG258 composed of strains bearing the yersiniabactin virulence factor. Our work demonstrates how the use of combined phenotypic, molecular, and whole-genome sequencing techniques can help to identify quickly and to characterize accurately the spread of MDR pathogens.
authors.affiliation: University of Insubria and Ospedale di Circolo e Fondazione Macchi, Varese, Italy.
authors.forename: Raffaella
authors.initials: R
authors.lastname: Onori
authors.affiliation: Fondazione IRCCS Policlinico S. Matteo, Pavia, Italy Università degli Studi di Milano, Milan, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Gaiarsa
authors.affiliation: Università degli Studi di Milano, Milan, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Comandatore
authors.affiliation: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy.
authors.forename: Stefano
authors.identifier: http://orcid.org/0000-0002-4823-3562
authors.initials: S
authors.lastname: Pongolini
authors.affiliation: Institut Pasteur and CNRS, UMR 3525, Paris, France.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Brisse
authors.affiliation: University of Insubria and Ospedale di Circolo e Fondazione Macchi, Varese, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Colombo
authors.affiliation: University of Insubria and Ospedale di Circolo e Fondazione Macchi, Varese, Italy.
authors.forename: Gianluca
authors.initials: G
authors.lastname: Cassani
authors.affiliation: Fondazione IRCCS Policlinico S. Matteo, Pavia, Italy.
authors.forename: Piero
authors.initials: P
authors.lastname: Marone
authors.affiliation: University of Insubria and Ospedale di Circolo e Fondazione Macchi, Varese, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Grossi
authors.affiliation: University of Insubria and Ospedale di Circolo e Fondazione Macchi, Varese, Italy.
authors.forename: Giulio
authors.initials: G
authors.lastname: Minoja
authors.affiliation: Università degli Studi di Milano, Milan, Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Bandi
authors.affiliation: Università degli Studi di Pavia, Pavia, Italy davide.sassera@unipv.it.
authors.forename: Davide
authors.initials: D
authors.lastname: Sassera
authors.affiliation: University of Insubria and Ospedale di Circolo e Fondazione Macchi, Varese, Italy.
authors.forename: Antonio
authors.initials: A
authors.lastname: Toniolo
mesh_terms: D000368:Aged; D001431:Bacteriological Techniques / Q000379:methods; D003428:Cross Infection / Q000453:epidemiology* / Q000382:microbiology; D004196:Disease Outbreaks; D016680:Genome, Bacterial; D005838:Genotype; D006761:Hospitals; D006801:Humans; D007558:Italy; D007710:Klebsiella Infections / Q000453:epidemiology* / Q000382:microbiology; D007711:Klebsiella pneumoniae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000502:physiology; D008297:Male; D017720:Molecular Epidemiology / Q000379:methods; D010641:Phenotype; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*