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

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 Escherichia coli (AREc). PL soil amendment impact on AREc in corn fields was evaluated in a randomized field experiment (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 to 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 (TET^r), third-generation cephalosporin-resistant (3GC^r) E. coli isolates, and extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae. PL soil amendment significantly (p < 0.05) increased the levels of generic E. coli, TET^r E. coli, and 3GC^r E. coli on days 7 and 28 compared to UC or CF. Beyond day 28, AREc did not significantly (p > 0.05) differ by fertilizer treatment and returned to baseline on day 70. ESBL-producing Enterobacteriaceae were detected from 16 samples, mostly on day 70. Cover crop significantly decreased TET^r E. coli concentration on day 28, with no significant effects on the prevalence of 3GC^r E. coli and ESBL-producing Enterobacteriaceae compared to no cover crop. All ESBL-producing Enterobacteriaceae and 79% of the 3GC^r E. coli isolates were positive for bla_CTX-M gene by polymerase chain reaction. Results show that PL soil amendment transiently increases the levels of AREc compared to mineral fertilizer.