Distribution characteristics of antibiotic resistant bacteria and genes in fresh and composted manures of livestock farms

Highlights: • Chicken and swine manures have higher abundance of ARB and ARGs than cow manures. • The abundance of ARB and ARGs in fresh manures was significantly higher than that in composted manures. • Detected antibiotics and MGEs were significantly correlated with some of the target ARGs. • Acinetobacter lwoffii and Psychrobacter pulmonis are multiple resistant bacteria. -- Abstract: Livestock manure is a major reservoir of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). This study investigated the distribution characteristics of ARB, ARGs in fresh and composted manures of traditional breading industry in rural areas in China. Samples collected were naturally piled without professional composting, and will be applied to farmland. The real-time quantitative polymerase chain reaction (qPCR) results showed the presence of ten target ARGs and two mobile genetic elements (MGEs) in the tested manure samples. The relative abundance of tetracycline and sulfonamide resistance genes (TRGs and SRGs) was generally higher than that of macrolide resistance genes (MRGs), followed by quinolone resistance genes (QRGs). There were significant positive correlations between the abundance of sul1, sul2, tetW and MGEs (intl1, intl2). In addition, the distribution of target ARGs was associated with the residual concentrations of doxycycline (DOX), sulfamethazine (SM2), enrofloxacin (ENR) and tylosin (TYL). Overall, a total of 24 bacterial genera were identified. The resistance rates of ARB were 17.79%–83.70% for SM2, followed 0.40%–63.77% for TYL, 0.36%–43.90% for DOX and 0.00%–13.36% for ENR, which showed a significant dose-effect. This study also demonstrated that the abundance of clinically relevant ARB and ARGs in chicken, swine and cow fresh manures significantly greater than that in composted manures, and chicken and swine manures had higher proportion of ARB and higher abundance of ARGs than that in cow manures.