crAssphage: the sentinel of phages carrying antimicrobial resistance genes in water systems

Abstract

The global rise of antibiotic resistance (AR) is driven by clinical misuse and complex ecological dynamics within the environmental resistome. In addition to bacteria and free DNA, bacteriophages play a critical role in disseminating antibiotic resistance genes (ARGs) via transduction. Anthropogenically impacted matrices—such as wastewater, sludge, and agricultural effluents—act as major hotspots where dense microbial communities and selective pressures promote ARG persistence. However, monitoring these environments remains challenging due to ARG diversity and the lack of standardized surveillance frameworks. The discovery of crAssphage, a highly abundant and human-specific gut virus, offers a promising solution. Because the best indicator for a phage is another phage, crAss-like phages are ideal fecal indicators due to their high persistence and environmental stability. Notably, the isolation of new crAssBcn phages has enabled the functional characterization of their infectivity, confirming their robustness against environmental stressors and disinfection. Furthermore, crAss-like phages show exceptional human specificity and strongly correlate with ARG abundance in fecally contaminated matrices, often outperforming traditional bacterial indicators. Comparative analyses across wastewater, sludge, and food matrices demonstrate that crAssphage mirrors ARG trends, remaining detectable even when conventional bacteria decline. These findings support integrating crAss-like phages as functional indicators in environmental surveillance frameworks. This approach simplifies monitoring human-derived ARGs and provides insight into phage-mediated mobilization. While geographic variability must be considered, their performance as fecal and ARG-associated markers underscores their value for One Health-oriented strategies to track antibiotic resistance dissemination in aquatic systems.