Investigation of Outbreaks of Extended-Spectrum Beta-Lactamase-Producing Klebsiella Pneumoniae in Three Neonatal Intensive Care Units Using Whole Genome Sequencing

Infections caused by extended-spectrum beta-lactamase-producing <i>Klebsiella pneumoniae</i> (ESBL-KP) are on a constant rise and are a noted cause of outbreaks in neonatal intensive care units (NICUs). We used whole genome sequencing (WGS) to investigate the epidemiology of consecutive...

Full description

Bibliographic Details
Main Authors: Sammy Frenk, Nadya Rakovitsky, Elizabeth Temkin, Vered Schechner, Regev Cohen, Bat Sheva Kloyzner, Mitchell J. Schwaber, Ester Solter, Shoshana Cohen, Sarit Stepansky, Yehuda Carmeli
Format: Article
Language:English
Published: MDPI AG 2020-10-01
Series:Antibiotics
Subjects:
Online Access:https://www.mdpi.com/2079-6382/9/10/705
Description
Summary:Infections caused by extended-spectrum beta-lactamase-producing <i>Klebsiella pneumoniae</i> (ESBL-KP) are on a constant rise and are a noted cause of outbreaks in neonatal intensive care units (NICUs). We used whole genome sequencing (WGS) to investigate the epidemiology of consecutive and overlapping outbreaks caused by ESBL-KP in NICUs in three hospitals in close proximity. Clonality of 43 ESBL-KP isolates from 40 patients was determined by BOX-PCR. Short-read sequencing was performed on representative isolates from each clone. The dominant clones from each NICU were sequenced using long-read sequencing. Bioinformatics methods were used to define multilocus sequence type (MLST), analyze plasmid content, resistomes, and virulence factors. In each NICU, we found a unique dominant clone (ST985, ST37, and ST35), each belonging to a distinct sequence type (ST), as well as satellite clones. A satellite strain in NICU-2 (ST35) was the dominant strain in NICU-3, where it was isolated four weeks later, suggesting transmission. NICU-1- and NICU-2-dominant strains had <i>bla</i><sub>CTX-M-15</sub> carried on a similar transposable element (Tn3-IS<i>Ecp1</i>) but at different locations: on a plasmid and on the chromosome, respectively. We concluded that the overlapping ESBL-KP outbreaks were a combination of clonal transmission within NICUs, possible transposable element transmission between NICUs, and repeated importation of ESBL-KP from the community.
ISSN:2079-6382