Hidden Resistome: Enrichment Reveals the Presence of Clinically Relevant Antibiotic Resistance Determinants in Treated Wastewater-Irrigated Soils

Abstract

Treated-wastewater (TW) irrigation transfers antibiotic-resistant bacteria (ARB) to soil, but persistence of these bacteria is generally low due to resilience of the soil microbiome. Nonetheless, wastewater-derived bacteria and associated antibiotic resistance genes (ARGs) may persist below detection levels and potentially proliferate under copiotrophic conditions. To test this hypothesis, we exposed soils from microcosm, lysimeter, and field experiments to short-term enrichment in copiotroph-stimulating media. In microcosms, enrichment stimulated growth of multidrug-resistant Escherichia coli up to 2 weeks after falling below detection limits. Lysimeter and orchard soils irrigated in-tandem with either freshwater or TW were subjected to culture-based, qPCR and shotgun metagenomic analyses prior, and subsequent, to enrichment. Although native TW- and freshwater-irrigated soil microbiomes and resistomes were similar to each other, enrichment resulted in higher abundances of cephalosporin- and carbapenem-resistant Enterobacteriaceae and in substantial differences in the composition of microbial communities and ARGs. Enrichment stimulated ARG-harboring Bacillaceae in the freshwater-irrigated soils, whereas in TWW-irrigated soils, ARG-harboring γ-proteobacterial families Enterobacteriaceae and Moraxellaceae were more profuse. We demonstrate that TW-derived ARB and associated ARGs can persist at below detection levels in irrigated soils and believe that similar short-term enrichment strategies can be applied for environmental antimicrobial risk assessment in the future.

Effects of dog ownership on the gut microbiota of elderly owners

“…Therefore, the increase in the abundance of Ruminococcaceae is considered a marker of the intervention effect [ 28 , 29 ]. In addition, a high abundance of Moraxellaceae is thought to be associated with a variety of diseases, such as drug resistance, cancer, and asthma [ 30 – 32 ]. 16S rRNA sequencing analysis showed that Actinobacteria , Bifidobacteriaceae , and Ruminococcaceae were significantly increased, while Moraxellaceae was significantly reduced in elderly dog owners.…”

Enrichment of antibiotic resistance genes within bacteriophage populations in saliva samples from individuals undergoing oral antibiotic treatments

“…Indeed, a notorious hotspot for transduction events is wastewater treatment plants, where high concentrations of microorganisms can be found together with several stressors ( Rizzo et al, 2013 ; Lood et al, 2017 ). In such milieus, bacteriophage induction is a potent mechanism for horizontal gene transfer and organic material from WWTPs has been demonstrated to facilitate resistance spread through bacteriophages in soil ( Gatica and Cytryn, 2013 ; Marano et al, 2021 ). Most wastewater treatment plants have only been designed for the removal of resistant bacteria, not specifically resistant genes encapsulated within bacteriophages, hence allowing for such resistance spread even within developed countries.…”

Microbial Journey: Mount Everest to Mars

“…Horizontal gene transfer, mutation, and genetic recombination mediate the proliferation of these ARGs into soil microbiota [70]. Marano et. al.…”

“…(2021) recently highlighted that the soil copiotrophosome and the wastewater used for irrigating the soil act as a hotspot that has the potential to transmit novel ARGs from the environmental microbiome to pathogenic microbial strains. The compounding assembly of ARGs in soil poses dire consequences on human health via the food chain [71]. Necessary actions are required to mitigate the transmission of antibiotic-resistant bacteria (ARB) through improved surveillance, reduced dependence and over-prescription of antibiotics, sanitation, animal husbandry, and finding alternatives to antibiotics for long-term sustainability [72,73].…”