Fertilization with Poultry Litter Increases the Abundance of Antibiotic-Resistant Bacteria in Tropical Soil: a Microcosm Study

Various antimicrobial agents are used in the poultry industry to treat microbial infections and prevent disease or as growth promoters. As a result, poultry litter (PL) can contain antibiotic residues (AR), antibiotic-resistant bacteria (ARB), and antibiotic resistance genes. Still, PL is used in many countries as a fertilizer and feed supplement for cattle. To evaluate whether usage of PL in agriculture leads to the accumulation of AR and ARB accumulate in the soil, we (i) measured the concentration of monensin, tylosin, ciprofloxacin, oxytetracycline, and chlortetracycline and the abundance of culturable monensin-, tylosin-, and ciprofloxacin-resistant bacteria in 15 commercial PL samples and (ii) exposed soil microcosms to two PL regimes and followed the persistence of PL-associated ARB for 128 days through cultivation on media containing antibiotics. The PL samples analyzed contained high concentrations of monensin (27–95 mg kg⁻¹), tylosin (152–450 mg kg⁻¹), ciprofloxacin (29–101 mg kg⁻¹), and (oxy/chlor)tetracycline (13–87 mg kg⁻¹). Congruently, they included large absolute and relative numbers of bacteria capable of growing on agar plates supplemented with 5 to 50 μg mL⁻¹ monensin (medians, 10⁷–10⁹ CFU g⁻¹, 0.6–45%) or 25 to 50 μg mL⁻¹ tylosin (median, 10⁸ CFU g⁻¹, 14–26%). By contrast, the abundance of bacteria resistant to 25–250 μg mL⁻¹ CP in the PL samples was much lower (median values ranging from 10⁶ to less than 10² CFU g⁻¹, relative abundances, < 0.13%). We observed rapid increments of 1–3 logs in the amount of culturable tylosin- and CP-resistant bacteria in most microcosms upon fertilization (n = 3/4 and n = 5/8, respectively, p < 0.01). Half of these increments were sustained across the experiment (p < 0.05), demonstrating that the introduced ARB can thrive in soil. These results show that fertilization with PL can increase the basal amount of tylosin- and CP-resistant bacteria in the soil. The environmental and sanitary consequences of this finding justify changes in PL’s manufacturing process and a debate on its approved uses in agricultural systems.