113. Upstream with the Paddle: Wastewater-Based Genomic Surveillance and Near-Source Detection of Vancomycin-Resistant Enterococcus Prior to Case Identification

TL;DR

Wastewater surveillance detected vancomycin-resistant enterococci in a hospital before clinical cases were identified, enabling early alerts and infection control.

Contribution

Demonstrates the first use of building-level wastewater genomic surveillance to detect antimicrobial resistance before clinical recognition in an oncology setting.

Findings

Wastewater surveillance detected a vancomycin-resistant enterococci (VRE) cluster one week before clinical cases were reported.

Genomic analysis of wastewater samples confirmed the presence of VRE and vanA gene before patient cultures confirmed infection.

The study highlights how wastewater surveillance can complement clinical genomic data to improve infection control and antimicrobial stewardship.

Abstract

Wastewater surveillance (WWS) is a public health tool complementing traditional case reporting when deployed to near-source sites. Presented here is a cluster event involving oncology patients experiencing vancomycin-resistant enterococci (VRE) infection where active WWS protocols served as a leading detection tool for an antimicrobial resistant (AMR) pathogen of significant clinical impact to immunocompromised patients.Plots Depicting Longitudinal Normalized Abundance of VRE and AMR genes (vanA, vanB) in Wastewater from Hospital Buildings.* VRE positive cultures patient 1;† VRE positive cultures patient 2;RPKM: Reads Per Kilobase Per Million Mapped Reads; VRE: Vancomycin Resistant Enterococcus; AMR: Antimicrobial Resistance; Med-Surg: Medical-Surgical Inpatient Wards; MICU: Medical Intensive Care Unit; SICU: Surgical Intensive Care Unit; PICU: Pediatric Intensive Care UnitBuilding Level Wastewater and Clinical Event TimelinesWWS: Wastewater Surveillance; ED: Emergency Department; SICU: Surgical Intensive Care Unit; Med-Surg: Medical Surgical Ward/Building; OR: Operating Room (location or building); PACU: Post Anesthesia Care Unit

Plots Depicting Longitudinal Normalized Abundance of VRE and AMR genes (vanA, vanB) in Wastewater from Hospital Buildings.

* VRE positive cultures patient 1;

† VRE positive cultures patient 2;

RPKM: Reads Per Kilobase Per Million Mapped Reads; VRE: Vancomycin Resistant Enterococcus; AMR: Antimicrobial Resistance; Med-Surg: Medical-Surgical Inpatient Wards; MICU: Medical Intensive Care Unit; SICU: Surgical Intensive Care Unit; PICU: Pediatric Intensive Care Unit

Building Level Wastewater and Clinical Event Timelines

WWS: Wastewater Surveillance; ED: Emergency Department; SICU: Surgical Intensive Care Unit; Med-Surg: Medical Surgical Ward/Building; OR: Operating Room (location or building); PACU: Post Anesthesia Care Unit

WWS sampling was conducted 3-times weekly from October 2024 through April 2025 at 8 outpatient, inpatient, and MEDEVAC housing effluent points. Samples were concentrated, nucleic acid was extracted, and over 180 bacterial pathogens and 1200 AMR gene markers were analyzed using specialized bioinformatic pipelines. Clinical isolates underwent whole genome sequencing (WGS) as part of the Department of Defense Multidrug-resistant organism Repository and Surveillance Network (MRSN).

Building-level WWS inclusive of the oncology ward identified a spike in VRE one week before two clinical cases were reported in inpatient oncology patients (Figure 1). An alert (time 0) was registered to the facility. A positive urine culture from patient 1 corresponded with a 4-fold increase in Enterococcus faecium and vanA gene detection in wastewater (week 1). Patient 2 tested positive by urine culture for the same pathogen (week 2) (Figure 2). MRSN WGS analysis of the patients’ clinical isolates obtained during week 3 and 4 confirmed the case cluster, while genomic fragments of the clinically relevant organisms detected by WWS during the outbreak indicated a detection in the weeks prior. The Infection Prevention and Control Team (IPaC) investigation suspected shared care teams contributed to the cluster event. Patient 2, admitted from a nursing facility earlier in the month, is the suspected reservoir.

Demonstrating the operational value of our unique, building-level, near-source WWS protocol to detect pathogen hot spots before clinical recognition, the study team provided early awareness as designed. Furthermore, this study exemplifies how WWS can complement genomic analysis of clinical isolates as part of a layered IPaC and antimicrobial stewardship effort to improve antimicrobial prescribing practices, patient safety, and outcomes.

All Authors: No reported disclosures

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