Price, Vivien 
ORCID: 0000-0003-3573-5106, Dunn, Steven J, Moran, Robert A, Swindells, Jonathan and McNally, Alan
(2022)
Whole-genome sequencing enhances existing pathogen and antimicrobial-resistance surveillance schemes within a neonatal unit.
Microbial genomics, 8 (6).
mgen000841-.
Abstract
In some neonatal units, the screening of isolates for antimicrobial-resistant organisms is a matter of routine, with theoretical benefits including the prevention or early detection of outbreaks. This study sought to use whole-genome sequencing (WGS) retrospectively to characterize the genomic epidemiology of Gram-negative organisms obtained from a screening programme in a 32-bed unit providing intensive, high-dependency and special care at City Hospital, Birmingham, UK, identifying occult transmission events and clinically important antimicrobial-resistance (AMR) genes. WGS was performed for 155 isolates collected from rectal and umbilical screening swabs over a 2 month period from 44 individual neonates. Genomic epidemiological analysis showed possible transmission events involving <i>Escherichia coli</i>, <i>Enterobacter cloacae</i>, <i>Klebsiella oxytoca</i> and <i>Klebsiella pneumoniae</i> not detected by routine screening, with eight putative clusters involving different individuals identified. Within phylogenetic clusters, the relatedness of organisms - as determined by the abundance of SNPs - varied widely, indicating that a variety of transmission routes may be implicated. While clinically important AMR genes were not present in the putative transmission clusters, our observation of suspected interspecies horizontal transfer of <i>bla</i><sub>CTX-M-15</sub> within individuals highlights the potential for their spread between organisms as well as individuals in this environment, with implications for surveillance. Our data show that WGS may reveal occult Gram-negative transmission events, demonstrating the potential of sequencing-based surveillance systems for nosocomial pathogens. Challenges remain in understanding how to utilize WGS surveillance to maximum effect in real-world settings.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | Humans, Klebsiella pneumoniae, beta-Lactamases, Anti-Bacterial Agents, Retrospective Studies, Phylogeny, Drug Resistance, Microbial, Genome, Bacterial, Infant, Newborn |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 02 Feb 2024 11:39 |
| Last Modified: | 15 Mar 2024 18:25 |
| DOI: | 10.1099/mgen.0.000841 |
| Open Access URL: | https://doi.org/10.1099/mgen.0.000841 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3178350 |
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