A prospective bacterial whole-genome-sequencing-based surveillance programme for comprehensive early detection of healthcare-associated infection transmission in paediatric oncology patients

H Hakim; H L Glasgow; J N Brazelton; C H Gilliam; L Richards; R T Hayden

doi:10.1016/j.jhin.2023.10.015

A prospective bacterial whole-genome-sequencing-based surveillance programme for comprehensive early detection of healthcare-associated infection transmission in paediatric oncology patients

J Hosp Infect. 2024 Jan:143:53-63. doi: 10.1016/j.jhin.2023.10.015. Epub 2023 Nov 7.

Authors

H Hakim¹, H L Glasgow², J N Brazelton², C H Gilliam³, L Richards³, R T Hayden²

Affiliations

¹ Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA; Infection Prevention and Control, St. Jude Children's Research Hospital, Memphis, TN, USA. Electronic address: Hana.Hakim@stjude.org.
² Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
³ Infection Prevention and Control, St. Jude Children's Research Hospital, Memphis, TN, USA.

PMID: 37939882
DOI: 10.1016/j.jhin.2023.10.015

Abstract

Background: Bacterial whole-genome sequencing (WGS) and determination of genetic relatedness is an important tool for investigation of epidemiologically suspected outbreaks.

Aim: This prospective cohort study evaluated a comprehensive, prospective bacterial WGS-based surveillance programme for early detection of transmission of most bacterial pathogens among patients at a paediatric oncology hospital.

Methods: Cultured bacterial isolates from clinical diagnostic specimens collected prospectively from both inpatient and outpatient encounters between January 2019 and December 2021 underwent routine WGS and core genome multi-locus sequence typing to determine isolates' relatedness. Previously collected isolates from January to December 2018 were retrospectively analysed for identification of prior or ongoing transmission. Multi-patient clusters were investigated to identify potential transmission events based on temporal and spatial epidemiological links and interventions were introduced.

Findings: A total of 1497 bacterial isolates from 1025 patients underwent WGS. A total of 259 genetically related clusters were detected, of which 18 (6.9%) multi-patient clusters involving 38 (3.7%) patients were identified. Sixteen clusters involved two patients each, and two clusters involved three patients. Following investigation, epidemiologically plausible transmission links were identified in five (27.8%) multi-patient clusters. None of the multi-patient clusters were suspected by conventional epidemiological surveillance.

Conclusion: Bacterial WGS-based surveillance for early detection of hospital transmission detected several limited multi-patient clusters that were unrecognized by conventional epidemiological methods. Genomic surveillance helped efficiently focus interventions while reducing unnecessary investigations.

Keywords: Genomic surveillance; Healthcare-associated infections; Oncology; Prospective; Whole-genome sequencing.

MeSH terms

Child
Cross Infection* / microbiology
Delivery of Health Care
Disease Outbreaks*
Genome, Bacterial
Humans
Multilocus Sequence Typing
Prospective Studies
Retrospective Studies
Whole Genome Sequencing / methods