Tracking nosocomial Klebsiella pneumoniae infections and outbreaks by whole-genome analysis: Small-scale Italian scenario within a single hospital

Raffaella Onori, Stefano Gaiarsa, Francesco Comandatore, Stefano Pongolini, Sylvain Brisse, Alberto Colombo, Gianluca Cassani, Piero Marone, Paolo Grossi, Giulio Minoja, Claudio Bandi, Davide Sassera, Antonio Toniolo

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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.

Original languageEnglish
Pages (from-to)2861-2868
Number of pages8
JournalJournal of Clinical Microbiology
Volume53
Issue number9
DOIs
Publication statusPublished - Sep 1 2015

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ASJC Scopus subject areas

  • Microbiology (medical)

Cite this

Onori, R., Gaiarsa, S., Comandatore, F., Pongolini, S., Brisse, S., Colombo, A., Cassani, G., Marone, P., Grossi, P., Minoja, G., Bandi, C., Sassera, D., & Toniolo, A. (2015). Tracking nosocomial Klebsiella pneumoniae infections and outbreaks by whole-genome analysis: Small-scale Italian scenario within a single hospital. Journal of Clinical Microbiology, 53(9), 2861-2868. https://doi.org/10.1128/JCM.00545-15