Effect of poultry litter soil amendment on antibiotic-resistant Escherichia coli

Authors: Agga, Getahun; Durso, Lisa; Sistani, Karamat

Submitted to: Journal of Environmental Quality
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/14/2024
Publication Date: 4/4/2024
Citation: Agga, G.E., Durso, L.M., Sistani, K.R. 2024. Effect of poultry litter soil amendment on antibiotic-resistant Escherichia coli. Journal of Environmental Quality. https://doi.org/10.1002/jeq2.20560.
DOI: https://doi.org/10.1002/jeq2.20560

Interpretive Summary: Poultry litter is land applied, usually untreated, for the purpose of its removal from the poultry houses and for use as fertilizer for plant growth. However, it can introduce antibiotic resistant bacteria such as Escherichia coli into the soil which can further disseminate into the environment through runoff from crop fields. Therefore, it is essential to evaluate the impact of poultry litter soil amendment on the levels and persistence of antibiotic resistant bacteria in agronomic soils. Plots of a corn field amended with poultry litter, chemical fertilizer or left unamended were longitudinally monitored for total bacteria and bacteria resistant to antibiotics commonly used to treat bacterial infections in humans. Specifically, we targeted total E. coli and strains resistant to tetracycline, cephalosporins, and extended spectrum beta-lactamase producing bacteria, the enzyme that confers resistance to broader range of beta-lactam antibiotics. Poultry litter soil amendment significantly increased the total concentrations and prevalence of E. coli and tetracycline and third generation cephalosporin resistant strains one week after amendment, compared to chemical fertilizer or unamended soil. However, this increase was transient, and the levels returned to their baseline values by day 28 post amendment. Extended spectrum beta-lactamase enzyme producing bacteria were also detected at a lower prevalence. Majority of the beta-lactam antibiotic resistant bacteria carried the widely disseminated gene that confers resistance to a broader range of beta-lactam antibiotics. Third generation cephalosporin resistant and extended spectrum beta-lactamase producing E. coli isolates were multidrug resistant. We showed that poultry litter soil amendment for crop production enriches total and resistant E. coli populations more than chemical fertilizer, but the effects are transient. Understanding the factors responsible for the reductions in the levels of total and resistant E. coli populations after the initial increase requires further investigations.

Technical Abstract: Given the high cost and non-renewability of mineral-based fertilizers, there is increasing interest in the innovative use of manure-based materials, such as poultry litter (PL). However, manure-based fertilizers add both nutrients and microbes to the soil, including antibiotic resistant E. coli (AREc). PL soil amendment impact on AREc in corn fields was evaluated in a longitudinal field-study (May-October 2017). Two winter cropping systems (fallow and cover crop) were assigned to whole plots with three spring-applied fertilizer treatments (untreated control [UC], PL, and commercial fertilizer [CF]) assigned to subplots. Soil was collected from 0-15 cm on days 0, 7, 28, 70, 98, and 172 post treatment applications. Samples were cultured for the enumeration and prevalence of generic-, tetracycline resistant (TETr)-, 3rd generation cephalosporin resistant (3GCr)-E. coli isolates, and extended spectrum beta-lactamase (ESBL) producing Enterobacteriaceae. PL soil amendment significantly (P<0.05) increased the levels of generic-, TETr- and 3GCr-E. coli on days 7 and 28 compared to UC or CF. Beyond d 28, AREc did not significantly (P>0.05) differ by fertilizer treatment and returned to baseline on d 70. ESBLs were detected from 16 samples, mostly on d 70. Cover crop was significantly associated with lowered TETr E. coli concentration on d 28 but showed no significant effects on the prevalence of 3GCr E. coli and ESBL-producing Enterobacteriaceae. All ESBL-producing Enterobacteriaceae and 79% of the 3GCr E. coli isolates were positive for blaCTX-M gene by PCR. Results show that PL soil amendment transiently increases the levels of AREc compared to mineral fertilizer.