Pig manure treatment strategies for mitigating the spread of antibiotic resistance
One of the most important public health challenges facing the world today is that posed by antibiotic resistance. Many pathogenic antibiotic-resistant bacteria and their antibiotic resistance genes, usually located on mobile genetic elements, are frequently present in the faeces of farm animals. To prevent the possibility of antimicrobial resistance transfer to the environment, these faeces should undergo treatment before being used as natural fertilizer. The two strategies for processing pig manure proposed in this study, viz. storage (most commonly used for livestock manure today) and composting, are cheap and do not require special tools or technologies. The present study examines the changes in the physicochemical properties of treated manure, in the microbiome, through metagenomic sequencing, and in the resistome, using the SmartChip Real-time PCR system compared to raw manure. This is the first such comprehensive analysis performed on the same batch of manure. Our results suggest that while none of the processes completely eliminates the environmental risk, composting results in a faster and more pronounced reduction of mobile genetic elements harbouring antibiotic resistance genes, including those responsible for multi-drug resistance. The physicochemical parameters of the treated manure are comparable after both processes; however, composting resulted in significantly higher organic matter. Overall, it appears that the composting process can be an efficient strategy for mitigating the spread of antibiotic resistance in the environment and reducing the risk of its transfer to agricultural crops and hence, the food chain. It also provides the organic matter necessary for humus formation, and increases the sorption properties of the soil and the micro and macro elements necessary for plant growth, which in turn translates into increased soil productivity. HighlightsO_LIThe changes in microbial population composition correlate with changes in specific antibiotic-resistance genes and mobile genetic elements in the studied populations. C_LIO_LIPositive correlations have been demonstrated between microbial phyla and genes coding the multi-drug resistance mechanism C_LIO_LICo-occurrence networks showed positive correlations between antibiotic-resistance genes and mobile genetic elements C_LIO_LIThe composting strategy was most efficient at reducing microbial loads, antibiotic resistance genes and mobile genetic elements. C_LIO_LIComposted manure can be part of a natural, safe soil fertilization strategy. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/492273v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@155a284org.highwire.dtl.DTLVardef@1209100org.highwire.dtl.DTLVardef@10f9dbborg.highwire.dtl.DTLVardef@3c8b9d_HPS_FORMAT_FIGEXP M_FIG C_FIG