Genomic Investigation Reveals Contaminated Detergent as the Source of an Extended-Spectrum-β-Lactamase-Producing Klebsiella michiganensis Outbreak in a Neonatal Unit

Abstract

Klebsiella species are problematic pathogens in neonatal units and may cause outbreaks, for which the sources of transmission may be challenging to elucidate. We describe the use of whole-genome sequencing (WGS) to investigate environmental sources of transmission during an outbreak of extended-spectrum-β-lactamase (ESBL)-producing Klebsiella michiganensis colonizing neonates. Ceftriaxone-resistant Klebsiella spp. isolated from neonates (or their mothers) and the hospital environment were included. Short-read sequencing (Illumina) and long-read sequencing (MinION; Oxford Nanopore Technologies) were used to confirm species taxonomy, to identify antimicrobial resistance genes, and to determine phylogenetic relationships using single-nucleotide polymorphism profiling. A total of 21 organisms (10 patient-derived isolates and 11 environmental isolates) were sequenced. Standard laboratory methods identified the outbreak strain as an ESBL-producing Klebsiella oxytoca, but taxonomic assignment from WGS data suggested closer identity to Klebsiella michiganensis. Strains isolated from multiple detergent-dispensing bottles were either identical or closely related by single-nucleotide polymorphism comparison. Detergent bottles contaminated by K. michiganensis had been used for washing milk expression equipment. No new cases were identified once the detergent bottles were removed. Environmental reservoirs may be an important source in outbreaks of multidrug-resistant organisms. WGS, in conjunction with traditional epidemiological investigation, can be instrumental in revealing routes of transmission and guiding infection control responses.

Genotypic Characterization of Clinical Klebsiella spp. Isolates Collected From Patients With Suspected Community-Onset Sepsis, Sweden

“…In addition to the misidentification of members of the K. pneumoniae complex, the species for five of 21 isolates initially reported as K. oxytoca with MALDI-TOF MS (DB-4110) were corrected when using ANI on the Illumina short-read data (Figure 1). Four isolates were genotypically identified as the closely related K. michiganensis as reported previously (Founou et al, 2019;Chapman et al, 2020), and one isolate as E. coli.…”

Variation in Accessory Genes Within the Klebsiella oxytoca Species Complex Delineates Monophyletic Members and Simplifies Coherent Genotyping

“…Members of the KoSC are versatile pathogens and have been isolated from wound-, intra-abdominal-, urinary-, and lower respiratory tract infections (Herzog et al, 2014;Singh et al, 2016). Outbreaks have environmental sources (Hendrik et al, 2015) and subsequent dissemination of phylogroup members in healthcare settings is a major problem -especially in neonatal intensive care units (Rønning et al, 2019;Chapman et al, 2020;Chen et al, 2020). Outbreaks involve strains with extended-spectrum beta-lactamases (Lowe et al, 2012;Vasaikar et al, 2017), extended-spectrum activity of the chromosomal beta-lactamase (Fournier et al, 1995;Decré et al, 2004) and carbapenemases (Validi et al, 2016).…”

Budget impact analysis of routinely using whole-genomic sequencing of six multidrug-resistant bacterial pathogens in Queensland, Australia

“…Identifying SNP differences, through WGS, to investigate MRO outbreaks has become instrumental in revealing the routes of transmission and guiding the infection control response strategy. 16 17 The number of isolates in a cluster required to begin a response differs with each MRO. Based on current clinical practice, a cluster was acted on when two related isolates of an MRO were identified, except for MRSA and ESBL E. coli , where three related isolates were required.…”