Investigation of outbreaks of extended-spectrum beta-lactamase-producing klebsiella pneumoniae in three neonatal intensive care units using whole genome sequencing

Sammy Frenk*, Nadya Rakovitsky, Elizabeth Temkin, Vered Schechner, Regev Cohen, Bat Sheva Kloyzner, Mitchell J. Schwaber, Ester Solter, Shoshana Cohen, Sarit Stepansky, Yehuda Carmeli

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Infections caused by extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (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 blaCTX-M-15 carried on a similar transposable element (Tn3-ISEcp1) 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.

Original languageEnglish
Article number705
Pages (from-to)1-10
Number of pages10
JournalAntibiotics
Volume9
Issue number10
DOIs
StatePublished - Oct 2020

Keywords

  • Dual technology WGS
  • ESBL-KP
  • Neonatal ICU
  • Outbreak

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