Tracking Nosocomial Klebsiella pneumoniae Infections and Outbreaks by Whole-Genome Analysis: Small-Scale Italian Scenario within a Single Hospital

Abstract

f 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.

Multidrug‐resistant Klebsiella pneumoniae in hospital‐acquired infections: Concomitant analysis of antimicrobial resistant strains

“…The rapid spread of K pneumoniae all over the world in the hospital settings is mostly because of the common occurrence of MDR strains. 21 The present study showed that K pneumoniae isolates were recovered from 42/250 (16.8%) of HAI cases. Similar findings were reported by other researchers.…”

Biofilm formation and antibiotic resistance inKlebsiella pneumoniaeurinary strains

“…; Onori et al . ). In a study performed in 2012 in the north‐west of Italy, among all the isolates of K. pneumoniae , 17·5% were KPC‐producing strains, more frequently isolated in tertiary care referral hospitals and from urine samples (50%) (De Rosa et al .…”

“…Later on the circulation of ESBL strains at the end of the last century, the spread of isolates resistant also to the 'last line of defence' antibiotics, that is, carbapenems, has drastically reduced treatment options and diffusion containment. Particularly, carbapenem-resistant K. pneumoniae strains belonging to the clonal group 258 (CG258), comprising ST258 and ST512, have rapidly disseminated and are frequently isolated (Chmelnitsky et al 2013;Pulcrano et al 2014;Angeletti et al 2015;Onori et al 2015). In a study performed in 2012 in the northwest of Italy, among all the isolates of K. pneumoniae, 17Á5% were KPC-producing strains, more frequently isolated in tertiary care referral hospitals and from urine Quantitative biofilm production assay 7·5 7·2 6·9 6·6 6·3 6·0 5·7 5·4 5·1 4·8 4·5 4·2 3·9 3·6 3·3 3·0 2·7 2·4 2·1 1·8 1·5 1·2 0·9 0·6 0·3 0·0 0 3 6 9 1 2 1 5 1 8 2 1 2 4 2 7 3 0 3 3 3 6 3 9 4 2 4 5 4 8 5 1 5 4 5 7 6 0 6 3 6 6 6 9 7 2 7 5 7 8 8 1 8 4 8 7 9 0 9 3 9 6 9 9 1 0 2 1 0 5 1 0 8 1 1 1 1 1 4 1 1 7 1 2 0 samples (50%) (De Rosa et al 2015).…”

The Changing Role of the Clinical Microbiology Laboratory in Defining Resistance in Gram-negatives

“…Genomic data are usually used to determine overall antibiotic resistance and virulence backgrounds, 96,97 evolution/adaptation under antibiotic selective conditions or diverse environments, 98,99 and clonal relationship of bacteria in different settings or geographic regions. 87,100 For instance, Wright and colleagues, 101 characterizing 49 Acinetobacter baumannii isolates from 1 US integrated hospital system with the Illumina method, observed wide variations in gene content, even among strains that were almost identical phylogenetically. Transfer of mobile genetic elements, mobilization of insertion sequences, and genome-wide homologous recombination contributed to this diversity.…”