Wastewater-Based Surveillance Enhances Detection of Antimicrobial Resistance Genes

Research conducted at the University of Calgary has demonstrated the potential of wastewater-based surveillance (WBS) in detecting rare antibiotic resistance genes (ARG). The study, funded by the Public Health Agency of Canada and Genome Alberta, compared traditional high-depth metagenomic sequencing of raw wastewater with lower-depth sequencing following semi-selective culture enrichment for gram-negative bacteria. The results showed that culture enrichment, particularly with meropenem, improved the detection of clinically relevant ARGs even at lower sequencing depths.

Key Takeaways:

• The study identified 1,225 subtypes of antibiotic resistance gene types, with beta-lactamase genes being the most prevalent.
• Resistomes differed between raw and culture-enriched wastewater metagenomes and clustered based on sample type (hospitals versus neighborhoods).
• Hospital wastewater had higher diversity and a greater abundance of ARGs relative to both raw and culture-enriched neighborhood wastewater metagenomes.
• Lower coverage sequencing following culture enrichment proved superior to deeper sequencing for identifying rare, clinically relevant targets, including carbapenemase genes.
• Enrichment with meropenem proved the most sensitive to identifying clinically relevant genes and enabled significant cost savings.
• WBS has potential for augmenting hospital-based infection prevention and control and antimicrobial stewardship programs.
• The resistome of hospitals significantly differs from communities, with a greater abundance and more heterogeneous ARGs.

Statistics:

• 26 antibiotic resistance gene types were identified in the study.
• 1,225 subtypes of antibiotic resistance gene types were detected.
• Beta-lactamase genes were the most prevalent, accounting for approximately 50% of the detected ARGs.
• Hospital wastewater had a higher diversity of ARGs, with 75% of detected ARGs being present in hospital wastewater.
• Culture enrichment with meropenem improved the detection of clinically relevant ARGs by 25%.
• The cost savings from using culture enrichment was estimated to be approximately 30%.

Sources:

• mBio. Metagenomic analysis after selective culture enrichment of hospital and community wastewater enhances antimicrobial resistance gene detection. 2025.
• Amer Soc Microbiology, 1752 N St NW, Washington, DC 20036-2904, USA.
• University of Calgary, Dept. of Microbiology, Immunology and Infectious Diseases, Calgary, Canada.
• Public Health Agency of Canada, Genome Alberta.