Antibiotic use in commercial broiler chicken farming and its consequential resistance development in root colonizing bacteria of carrot grown in manure-applied soils in a middle-income country

Abstract

Broiler chicken litter (BCL) is a cheap manure for vegetable crops in developing countries. Extensive antibiotic use in poultry production could increase antibiotic resistant bacteria (ARB) in manure and eventually in crop root microbiome. We investigated the prevalence of ARB in BCL from medium- and large-scale farms (n = 33) and in carrot (Daucus carota) grown in BCL-applied soils in Sri Lanka. All the BCL samples contained aerobic bacteria resistant to 10 μg·mL−1 of oxytetracycline or enrofloxacin. The abundance of ARB determined by viable plate-count method ranged from 0.05% to 30.10% of aerobic bacterial population. Soil from two fields applied with BLC for 3 yr (short history, SH) and 10 yr (long history, LH) were treated with BCL (10%, w/w) and oxytetracycline (10 and 100 mg·kg−1) in a pot experiment alongside an unamended control. Adding BCL and oxytetracycline had a significant (P < 0.05) effect on the abundance of oxytetracycline-resistant epiphytic and endophytic bacteria (EEB) in carrot roots at harvest. Both total and oxytetracycline-resistant EEB increased significantly (P < 0.05) with the application of BCL to LH soil but not to SH soil. Carrot sold at retailed markets (n = 30) contained epiphytic bacteria resistant to 1 μg·mL−1 oxytetracycline (4.13 ± 0.207 log10CFU·g−1 dry carrot). High minimum inhibitory concentrations for oxytetracycline (≥128 μg·mL−1) were observed in 83% and 50% of ARB isolates obtained from BCL (n = 18) and carrot (n = 24), respectively. Results confirmed that BCL acts as a carrier of ARB, and continuous application of BCL to soil increased the prevalence of ARB among EEB in carrot.