Research and implementation of a whole-genome sequencing surveillance system for outbreak detection

Abstract

Background: Traditional infection prevention (IP) methods for outbreak detection often rely on geotemporal clustering confined to single locations. We recently developed the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT), which combines whole-genome sequencing (WGS) surveillance and machine learning of the electronic health record (EHR). Our retrospective research findings show potential transmissions averted and cost savings using EDS-HAT in real time. Here, we describe the process and initial findings from EDS-HAT real-time implementation. Methods: Real-time whole-genome sequencing surveillance began on November 1, 2021. Patient cultures positive for select bacterial pathogens who were hospitalized for ≥3 days or had a recent healthcare exposure in the prior 30-days were collected. Isolates were deemed genetically related if ≤15 single-nucleotide polymorphisms (SNPs) were identified for all organisms except Clostridioides difficile (≤2 SNPs). Clusters were manually investigated by both research and IP teams, and interventions were performed by the IP team. Data on collection, analysis, notification, and intervention dates were gathered. Results: As of January 11, 2022, 413 isolates had undergone whole-genome sequencing. Among them, 18 unique patient isolates were genetically related to ≥1 other isolate, comprising 7 clusters (range, 2–6 patients). Notable findings include a Pseudomonas aeruginosa cluster possibly related to a shared bronchoscope, a pseudo-outbreak of Serratia marcescens related to autopsy blood culture practice, and a cluster of vancomycin-resistant Enterococcus faecium on a shared transplant unit. Only 1 cluster of 2 isolates of Klebsiella pneumoniae had no known possible transmission routes. The median turnaround time from patient’s culture date to IP notification was 19 days (range, 13–28), with noted delays over the winter holiday. Concusions: Real-time WGS can identify small clusters including potentially interruptible transmission routes. Rapid turnaround time, coordination between clinical and genomic laboratories, and a robust IP team are key factors in implementing a WGS surveillance program. Real-time WGS surveillance has the potential to reduce costs for hospitals, improve patient safety, and save lives.Funding: NoneDisclosures: None