Antibiotic resistance genes, class 1 integrons, and IncP-1/IncQ-1 plasmids in irrigation return flows

Authors: Dungan, Robert - Rob; Bjorneberg, David - Dave

Submitted to: Environmental Pollution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/2/2019
Publication Date: 2/1/2020
Citation: Dungan, R.S., Bjorneberg, D.L. 2020. Antibiotic resistance genes, class 1 integrons, and IncP-1/IncQ-1 plasmids in irrigation return flows. Environmental Pollution. 257:1-8. https://doi.org/10.1016/j.envpol.2019.113568.
DOI: https://doi.org/10.1016/j.envpol.2019.113568

Interpretive Summary: The emergence of antibiotic resistant pathogens jeopardizes the current and future effectiveness of antibiotics to treat life-threatening infections. Antibiotic resistance is encoded by antibiotic resistance genes (ARGs) and surface waters could be a dominant route by which they are disseminated. In the present study we aimed to explore the occurrence and abundance of selected ARGs and other genes associated with the enrichment of antibiotic resistance in irrigation return flows (IRFs) in the Upper Snake Rock watershed in south-central Idaho. Irrigation return flow is water that is not used within a watershed and is ultimately returned to a water body, such as a river. The ARGs were detected at all return flow sampling sites, as well as a background canal site which provides the majority of irrigation water to the watershed. Compared to the canal site, the gene levels were higher in the return flows. This study increases knowledge that IRFs accumulate ARGs from the surrounding land base and moves them from the watershed to receiving waterbodies, further enhancing their dissemination in the environment.

Technical Abstract: Antibiotic resistance is encoded by antibiotic resistance genes (ARGs) and surface waters could be a dominant route by which they are disseminated. In the present study we aimed to explore the prevalence and abundance of ARGs [blaCTX-M-1, erm(B), sul1, tet(B), tet(M), and tet(X)], class 1 integron-integrase gene (intI1), and IncP-1 and IncQ-1 plasmids in eight irrigation return flows (IRFs) and a background site (Main Line Canal, MLC) in the Upper Snake Rock watershed in south-central Idaho. Grab samples were collected on a monthly basis for a calendar year, which were processed to extract microbial DNA, followed by droplet digital PCR to quantify the gene copies on an absolute (per 100 mL) and relative (per 16S rRNA gene copies) basis. The antibiotic resistance and intI1 genes and IncP-1/IncQ-1 plasmids were recovered at all IRF sampling sites with detections ranging from 55 to 81 out of 81 water sampling events. The blaCTX-M-1 gene was detected the least frequently (68%), while the other genes were detected more frequently (88 to 100%). All of the genes were also detected at MLC from April to October when water was present in the canal. The genes from lowest to greatest relative abundance in the IRFs were: blaCTX-M-1 < erm(B) < tet(B) < IncQ-1 < tet(M) < sul1 < intI1 = IncP-1 < tet(X). When compared to the average annual relative gene abundances in MLC water samples, they were found to be at statistically greater levels (P = 0.008) except that of the IncP-1 and IncQ-1 plasmids (P = 0.8 and 0.08, respectively). The fact that most IRFs contained higher levels than found in the canal water, indicates that IRFs can be a point source of ARGs that ultimately discharge into surface waters. It was also found that ARG levels were not strongly correlated with the intI1 gene, nor IncP-1 and IncQ-1 plasmids, suggesting that the ARGs were not enriched as a result of horizontal gene transfer among or replication within environmental bacteria.