The global groundwater resistome: core antibiotic resistance genes, their dynamics and drivers

Abstract

Despite the importance of groundwater environments as drinking water resources, there is currently no comprehensive picture of the global levels of antibiotic resistance genes in groundwater. Moreover, the biotic and abiotic factors that might shape the groundwater resistome remain to be explored on a global scale. Herein, we attempted to fill this knowledge gap by in silico re-analysis of publicly available global groundwater metagenomes. We first investigated the occurrence of antibiotic resistance genes (ARGs) to define the core groundwater resistome. We further tested whether the ARG dissemination in the pristine groundwater environments could be explained by natural ecological processes such as competition between fungal and bacterial taxa. Six ARGs encoding resistance to aminoglycosides (aph3'), aph3''), sulfonamides (sul1, sul2), and beta-lactams (blaOXA, blaTEM) occurred in at least 50% of samples at high abundance, thereby constituting the core groundwater resistome. ARG abundances differed significantly between countries and only weakly correlated with bacterial community composition. While only limited effects of anthropogenic impacts could be observed, ecological interactions played a significant role in shaping the abundance patterns of at least a number of the core ARGs. Fungal abundance positively correlated with blaTEM and blaOXA abundance, ARGs that confer resistance to beta-lactams, regularly produced by fungi. However, no direct correlation was determined for the remainder of the core ARGs. Still, using co-occurrence network analysis we identified that the fungal abundance acted as a hub-node that included blaOXA and blaTEM, but also indirectly contributed to the abundance of aminoglycoside ARG aph3'). Hence, interactions between bacteria and fungi including potential antibiotic production can contribute to the dissemination of ARGs in groundwater environments. Consequently, fungal/bacterial SSU ratio could serve as an indicator for the abundance of certain ARGs in the pristine groundwater environments.

On composite sampling for monitoring generic and antibiotic-resistant coliforms in irrigation ponds

“…The general abundance of cultured E. coli has been shown to correlate with levels of antibiotic-resistant E. coli in riverine (Somerville et al, 2007;Ram and Kumar, 2020;Ott et al, 2021;Givens et al, 2023) and lacustrine (Stocker et al, 2023) systems however the ratios between the two groups is dependent on the local resistance in the human and animal populations (Huijbers et al, 2020;Givens et al, 2023). For example, no associations between anthropogenic markers and ARGs were found in a study using multi-nation sequencing data from pristine environments (Kampouris et al, 2022) whereas these associations are common in agriculture or anthropogenically affected ecosystems (Larsson and Flach, 2022;Bengtsson-Palme et al, 2023). The possibility of relationships between fecal pollution and antibiotic resistance has led to the idea that measuring the general abundance of E. coli in waterbodies, which is already routinely measured, may be a reasonable starting point for surveilling potential ARB risks without any additional antibiotic resistance testing (Berendonk et al, 2015;Anjum et al, 2021;Liguori et al, 2022;Bengtsson-Palme et al, 2023).…”