Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae

Abstract

The study describes the transmission of a CTX-M-15-producing ST15 Klebsiella pneumoniae between patients treated in a single center and the subsequent inter-institutional spread by patient referral occurring between May 2012 and September 2013. A suspected epidemiological link between clinical K. pneumoniae isolates was supported by patient contact tracing and genomic phylogenetic analysis from May to November 2012. By May 2013, a patient treated in three institutions in two cities was involved in an expanding cluster caused by this high-risk clone (HiRiC) (local expansion, CTX-M-15 producing, and containing hypervirulence factors). A clone-specific multiplex PCR was developed for patient screening by which another patient was identified in September 2013. Genomic phylogenetic analysis including published ST15 genomes revealed a close homology with isolates previously found in the USA. Environmental contamination and lack of consistent patient screening were identified as being responsible for the clone dissemination. The investigation addresses the advantages of whole-genome sequencing in the early detection of HiRiC with a high propensity of nosocomial transmission and prolonged circulation in the regional patient population. Our study suggests the necessity for inter-institutional/regional collaboration for infection/outbreak management of K. pneumoniae HiRiCs.

Expanding theKlebsiella pneumoniaevolatile metabolome using advanced analytical instrumentation for the detection of novel metabolites

“…; Zhou et al . ), as well as the epidemiology of K. pneumoniae infections (Munoz‐Price et al . ; Doi and Paterson ), there has been little attention paid to this pathogen's metabolism.…”

Identification ofKlebsiellacapsule synthesis loci from whole genome data

“…Furthermore, we present a curated reference database and a new tool for the identification of K-loci from genome sequences, which will greatly assist epidemiological surveillance for K. pneumoniae, and other bacterial pathogens for which capsule epidemiology has been shown to be important. adopted, although the single gene wzi and wzc typing schemes are gaining traction in the high-throughput sequencing era Bowers et al, 2016;Zhou et al, 2016). Within the wzi scheme, unique alleles are associated with specific K-types (Brisse et al, 2013).…”

Long-lasting outbreak due to CTX-M-15-producing Klebsiella pneumoniae ST336 in a rehabilitation ward: report and literature review

“…K. pneumoniae ST336 is a single locus variant of ST17 in the clonal complex 17, whose major clones are ST16, ST17 and ST20 [27][28][29][30]. K. pneumoniae isolates of clonal complex 17 are well recognized contributors to the spread of CTX-M-15 worldwide [31] and ST336 is among the less prevalent yet international clones that have been associated with the spread of various ESBL enzymes, including CTX-M-15, and even carbapenemase resistance [23,32,33]. K. pneumoniae ST336 has been reported in blood, urine, stool, exudate, intraabdominal and respiratory tract specimens and an unknown specimen from 45 patients in North America, Europe and Asia [27,28,[31][32][33][34][35][36].…”

“…Nine reports described outbreak clones that produced various ESBLs or carbapenemases including SHV-4 [17], SHV-2 [8], an unidentified ESBL [2], the AmpC beta-lactamase ACC-1 [18], KPC-2 carbapenemase and SHV-5 [19], NDM carbapenemase [20], NDM-1 carbapenemase, CTX-M-15 and OXA-1 [21], KPC carbapenemases [22], and CTX-M-15 and OXA-1 [23]. Four reports distinguished between colonized and infected patients; the infection rate ranged from none to almost 60% [2,18,20,23]. …”