Antimicrobial resistance is an emerging threat for the whole humankind and it is known that human impacted environments are reservoirs of bacterial antibiotic resistance genes that are more and more considered as environmental contaminants. Interestingly, also the natural environment is known to harbor a pool of antibiotic resistance genes. Human activities, such as animal husbandry and agriculture, might cause transferring of genetic material from environmental bacteria to bacteria capable of causing infections. Restricting the use of antibiotics in agriculture is presented as one of the requirements for winning the battle against “superbugs”. However, there is a lack of data on the environmental effects of low agricultural antibiotic use. Our latest study contributes to the battle by providing data of the effects of regulated antibiotic use that would be beneficial for global surveillance.
In this work, we followed four Finnish production animal farms during the growing season 2014. We used a sampling strategy that allows us to see the direct effect of the manure application and the recovery of the situation after land application of manure until the first harvesting. We think that combination of the sampling strategy with High Throughput Quantitative PCR makes our study unique in the whole world. Samples were taken from fresh and stored manure, crop field soils before and after manure application until the harvesting time, and from ditches receiving run-off from the fields. With the help of High Throughput Quantitative PCR, we were able to measure the relative abundances of 363 genes related antibiotic resistance and transfer of genetic elements and we could detect 182 genes.
Our results show that the soil ecosystem in the studied farms was able to resist the manure load since the abundance and diversity of manure-associated resistance genes clearly decreased only six weeks after the manure application. Therefore we suggest that adopting similar agricultural practices than in Finland with restricted use of antibiotics might help in decreasing the dissemination of antibiotic resistance genes to the environment. Still, we also confirmed our previous observation that the resistance genes carried by bacteria prevalent in manure disseminated to soil due to land application, despite the low use of mainly narrow spectrum antibiotics. The dissemination was linked to enrichment of ARGs during winter storage of manure, which was seen irrespective of the farm or production animal. This kind of enrichment might cause a considerable threat in the future, as there will be more pressure for utilization of solid by-products from e.g. wastewater treatment processes due to expected phosphorus depletion, and therefore further studies are urgently needed.