Comparison of Environmental Microbiomes in an Antibiotic Resistance-Polluted Urban River Highlights Periphyton and Fish Gut Communities as Reservoirs of Concern

Abstract

Natural waterways near urban areas are heavily impacted by anthropogenic activities, including their microbial communities.  A contaminant of growing public health concern in rivers is antibiotic resistant genes (ARGs), which can spread between neighboring bacteria and increase the potential for transmission of AR bacteria to animals and humans.  In order to identify the matrices of most concern for AR, we compared ARG burdens and microbial community structures between sample types from the Scioto River Watershed, Ohio, United States from 2017-2018.  Five environmental matrices (water, sediment, periphyton, detritus, and fish gut) were collected from 26 river sites.  Due to our focus on clinically relevant ARGs, three carbapenem resistance genes (blaKPC, blaNDM, and blaOXA-48) were quantified via DropletDigitalTM PCR.  At a subset of nine urbanized sites, we conducted16S rRNA gene sequencing and functional gene predictions.  Carbapenem resistance genes were quantified from all matrices, with blaKPC being the most detected (88% of samples), followed by blaNDM (64%), and blaOXA-48 (23%).  Fish gut samples showed higher concentrations of blaKPC and blaNDM than any other matrix, indicating potential bioaccumulation of ARGs, and risk of broader dissemination through aquatic and nearshore food webs.  Periphyton had higher concentrations of blaNDM than water, sediment, or detritus.  Microbial community analysis identified differences by sample type in community diversity and structure.  Sediment samples had the most diverse microbial communities, and detritus, the least.  Spearman correlations did not reveal significant relationships between the concentrations of the monitored ARGs and microbial community diversity.  However, several differentially abundant taxa and microbial functions were identified by sample type that are definitive of these matrices’ roles in the river ecosystem and habitat type.  In summary, the fish gut and periphyton are a concern as AR reservoirs due to their relatively high concentration of carbapenem resistance genes, diverse microbial communities, and natural functions that promote AR.

Keywords: Carbapenem resistance, periphyton, fish gut microbiome, One Health, river ecosystem, Sediment