Distribution of antibiotic-resistant bacteria in aerobic composting of swine manure with different antibiotics

Abstract

Background Livestock manure is an important reservoir of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs). The bacterial community structure and diversity are usually studied using high-throughput sequencing that cannot provide direct evidence for ARB changes. Thus, little is known about the distribution of ARB, especially in the presence of different antibiotics in composting process. In this study, the fate of ARB was investigated in aerobic composting of swine manure, using chlortetracycline, sulfamethoxazole, lincomycin, and ciprofloxacin as typical antibiotics. The abundance and species of ARB were analyzed systematically to evaluate their ecological risk at different stages of composting. Results The absolute abundance of total ARB decreased, while the relative abundance increased on day 2. The relative abundance of lincomycin-resistant bacteria was higher than other ARBs during the whole composting process. The absolute abundance of four ARBs was 9.42 × 106–2.51 × 102 CFU/g (lincomycin- > chlortetracycline- > sulfamethoxazole- > ciprofloxacin- > multiple antibiotic-resistant bacteria), and they were not completely inactivated at the end of composting. Antibiotics led to a partial proliferation of ARBs including Corynebacterium, Sporosarcina, Solibacillus, and Acinetobacter. Especially, Corynebacterium, a pathogenic genus, was observed in chlortetracycline and lincomycin treatments. Conclusion Among the antibiotics studied, lincomycin showed the highest ecological risk, due to it expanded the range of lincomycin-resistant bacteria at the phyla level (Firmicutes, Actinobacteria, and Proteobacteria). The principal co-ordinates analysis indicated that the bacterial community structure was primarily associated with the composting stages rather than antibiotic types. Possible potential hosts and the related to the decrease of ARGs abundance were indicated based on the network analysis. The decrease of culturable Proteobacteria and the increase of culturable Firmicutes (Solibacillus, Bacillus) partially explained the high degradation rate of various ARGs with the progress of composting in this study. These results provided important information for the control of antibiotic resistance in composting.

Commercial farmed swine harbour a variety of pathogenic bacteria and antimicrobial resistance genes

“…The Corynebacterium genus was the most common on farm A and is commonly found in animal manure and fertilizer used in agriculture, which can spread to cause human nosocomial infections [48]. Furthermore, high prevalence of antimicrobial resistance are also observed in Corynebacterium, potentially correlated with the use of antibiotics in livestock [49,50]. Reports in Europe have helped characterize transmission events between farm workers and swine of specific livestock-associated lineages of Staphylococcus aureus [51][52][53][54].…”

Distribution of antibiotic resistant bacteria in different soil types following manure application

“…The extraction of CTC was performed according to a previous study (Ho et al, 2012). The manure used in this study was obtained from previous composting experiments in our laboratory (Song et al, 2020;Song et al, 2021a). The basic physical and chemical properties of the soils and manure are shown in Table 1.…”

“…Finally, 0.1 mL of this bacterial suspension was inoculated onto beef paste peptone solid medium plates. CRB were cultured with a medium containing 16 mg L −1 CTC (Song et al, 2021a). All bacteria were incubated at 35°C for 48 h. Each sample was replicated three times.…”

“…All bacteria were incubated at 35°C for 48 h. Each sample was replicated three times. We adopted this method of bacterial pre-treatment before sequencing with reference to previous studies (Yang et al, 2014;Song et al, 2021a;Sardar et al, 2021b). Taxonomic identification of the bacterial community was performed using 16S rRNA sequence analysis.…”

“…The most prevalent CRB genera found in the manure were Sporosarcina (56.70%), Lysinibacillus (26.39%), Bacillus (3.32%), unclassified_f_Planococcaceae (10.79%) and Solibacillus (1.29%) (Fig. S2) (Song et al, 2021a). The bacterial communities in livestock manure and soil are very different, with soil indigenous microorganisms being more adaptive and competitive than those in manure (Peng et al, 2016).…”