Antimicrobial resistance in escherichia coli and enterococcal isolates from irrigation return flows in a high-desert watershed

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

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/13/2021
Publication Date: 5/12/2021
Citation: Dungan, R.S., Bjorneberg, D.L. 2021. Antimicrobial resistance in escherichia coli and enterococcal isolates from irrigation return flows in a high-desert watershed. Frontiers in Microbiology. 12. Article 660697. https://doi.org/10.3389/fmicb.2021.660697.
DOI: https://doi.org/10.3389/fmicb.2021.660697

Interpretive Summary: Escherichia coli and enterococci, commonly known as fecal indicator bacteria (FIB), are often quantified in environmental waters to determine if they have been contaminated with fecal pollution. The purpose of this study was to obtain FIB isolates from irrigation return flows (IRFs) in a high desert mixed-use watershed and determine their resistance to various antibiotics used in human medicine. The IRFs are important because they return surface and subsurface water back to the Snake River. Water samples were collected throughout 2018 from 9 different IRFs and at a canal site before irrigation water entered the watershed. About 185 E. coli or enterococci were tested for antimicrobial susceptibility. The majority (77%) of the E. coli isolates were susceptible to all of the antibiotics, while the opposite was true for enterococci (9%). For the E. coli and enterococci, 11 and 13 isolates were found to be multidrug resistant to up to 7 and 5 different drug classes, respectively. Many FIB are naturally resistant to antibiotics, even without prior exposure to drug residues in the environment; however, bacteria can become resistant by exchanging genes among themselves through a process called horizontal gene transfer. It is not known if the FIB in the present study were pathogenic, but they could potentially transfer their genes to human pathogens. Since the IRFs do discharge into the Snake River, there is a potential opportunity for human contact with resistant E. coli and enterococci when the river is used for recreational purposes. Routine monitoring of FIB in the IRFs could be a useful tool to understand the long-term trends of antibiotic resistance in mixed-use watersheds.

Technical Abstract: Irrigation return flows (IRFs) are of interest because they collect surface runoff and subsurface drainage, causing them to have elevated contaminant and bacterial levels, and making them a potential point source of pollutants. The purpose of this study was to determine antibiotic susceptibility profiles of E. coli and Enterococcus spp. that were collected from IRFs in south-central Idaho. Environmental isolates can be a potentially important source of antibiotic resistance (AR) and IRFs may be one way resistance genes are transported out of agroecosystems. Water samples were collected from nine IRFs and one background site (canal water from Snake River) on a biweekly basis during 2018. Escherichia coli and Enterococcus were enumerated via a Most Probable Number technique, then subsamples were plated on selective media to obtain isolates. About 185 of 800 unique isolates for E. coli and Enterococcus were tested for antimicrobial susceptibility using the Sensititre broth microdilution plates. For E. coli, 11% of the isolates were resistant to tetracycline, with fewer numbers being resistant to the 13 other antibiotics, with none resistant to gentamicin. While 77% of the E. coli isolates were pan-susceptible, 9 MDR patterns with resistance up to 7 drug classes (10 antibiotics) occurred in 11 isolates. For the enterococcal species, only 9% of isolates were pan-susceptible and the single highest resistance was to lincomycin (75%) followed by nitrofurantoin (31%) and tetracycline (11%). In addition, 13 enterococcal isolates were determined to be MDR to up to 5 different drug classes and it was only prevalent among E. faecalis, E. faecium, E. casseliflavus, and E. thailandicus. Due to the potential for human contact, routine monitoring of E. coli and Enterococcus in the IRFs could be a useful tool to understand the long-term trends of AR in this mixed-use watershed.