Genomic Epidemiology of an Endoscope-Associated Outbreak of Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae

Abstract

Increased incidence of infections due to Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-Kp) was noted among patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) at a single hospital. An epidemiologic investigation identified KPC-Kp and non-KPC-producing, extended-spectrum β-lactamase (ESBL)-producing Kp in cultures from 2 endoscopes. Genotyping was performed on patient and endoscope isolates to characterize the microbial genomics of the outbreak. Genetic similarity of 51 Kp isolates from 37 patients and 3 endoscopes was assessed by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Five patient and 2 endoscope isolates underwent whole genome sequencing (WGS). Two KPC-encoding plasmids were characterized by single molecule, real-time sequencing. Plasmid diversity was assessed by endonuclease digestion. Genomic and epidemiologic data were used in conjunction to investigate the outbreak source. Two clusters of Kp patient isolates were genetically related to endoscope isolates by PFGE. A subset of patient isolates were collected post-ERCP, suggesting ERCP endoscopes as a possible source. A phylogeny of 7 Kp genomes from patient and endoscope isolates supported ERCP as a potential source of transmission. Differences in gene content defined 5 ST258 subclades and identified 2 of the subclades as outbreak-associated. A novel KPC-encoding plasmid, pKp28 helped define and track one endoscope-associated ST258 subclade. WGS demonstrated high genetic relatedness of patient and ERCP endoscope isolates suggesting ERCP-associated transmission of ST258 KPC-Kp. Gene and plasmid content discriminated the outbreak from endemic ST258 populations and assisted with the molecular epidemiologic investigation of an extended KPC-Kp outbreak.

Nosocomial infection and its molecular mechanisms of antibiotic resistance

“…The carbapenemases group of class A contains members of the KPC, NMC, IMI, SME, and GES families. Among these families, the KPC carbapenemases are the most predominant, usually existing on plasmids in Klebsiella pneumoniae (43,44). The carbapenemases group of class D contains OXA β-lactamases usually found in Acinetobacter baumannii.…”

Phenotypic and Genotypic Methods for Determination of Carbapenemase Producing Enterobacteriaceae Isolates

“…Yüksek riskli suşların analizlerinin yapılması, potansiyel salgın ve yayılımların tespiti, klonal ilişkilerin araştırıl-ması, salgın suşu ve sporadik suşların karşılaştı-rılması gibi sürveyans için gerekli çalışmalarda kullanılmaktadır (11,33) . "Pulsed field gel electrophoresis" (PFGE) bu amaçla sık kullanılan yöntem-lerdendir.…”

“…Bu yöntemde spesifik restriksiyon enzimleri ile bakteriyel genom belirli yerlerinden kesilir. Periyodik elektriksel alan uygulaması ile oluşan DNA fragmentlerinin oluşturduğu patern, belli kriterlere göre yorumlanıp klonal ilişkiler ve yakınlık dereceleri incelenir (11,33,59) . Cubero ve ark.…”

“…Diğer bir çalışma-da Marsh ve ark. (33) KPC pozitif suşlarla gelişen endoskop ilişkili bir salgının genomik epidemiyolojisini PFGE ile incelemişlerdir. Sekans analiz yöntemlerinden multilokus sekans tipleme (MLST), moleküler epidemiyolojide kullanımı yaygınlaşan yöntemlerdendir (22) .…”

Carbapenem-Resistant Enterobacteriaceae Transmission in Health Care Facilities — Wisconsin, February–May 2015

“…WSLH's use of WGS to detect single nucleotide polymorphisms (SNPs) of enteric bacterial pathogens and subsequent expansion of WGS to nonenteric bacteria has further enhanced the capability of WSLH to make genetic comparisons of CRE isolates of interest (3).…”