Browsing by Subject "Culture-Independent"

The use of antimicrobials in livestock production has shown to increase the abundance of antibiotic resistance genes (ARGs) in animal microbiomes. The use of manure as a fertilizer is essential in animal agriculture, however, manure application disseminates ARGs to the farm environment. In soil, the ARGs could be horizontally transferred to the environmental bacteria. Antimicrobial resistance is currently mitigated by limiting the use of antimicrobials for animals; thus, it is important to examine the ARG dynamics in countries where antimicrobial use is restricted. In addition to the antimicrobial use, also manure application rates are tightly regulated in Finnish dairy farming, offering suitable sites for examining the transmissions of ARGs in response to agricultural practices. The main aim of this study was to determine the host range of three antibiotic resistance genes by culture-independent epicPCR to understand the fate of antimicrobial resistance in agricultural environments. The cells were extracted from manure and soil samples taken from two Finnish dairy farms. Aminoglycoside (strB), beta-lactam (blaOXA-58) and tetracycline (tetM) resistance genes were linked with a phylogenetic marker gene to determine the host bacteria using epicPCR. Results were compared to the total bacterial community. In total, 664 OTU’s were linked to ARGs. Antibiotic resistance genes strB and tetM shared six host genera and three genera were found to carry all the studied genes. The most common host genera for tetM were Escherichia-Shigella, Sedimentibacter and Fibrobacter. For blaOXA-58, the most common hosts were Sphingobacterium and Acinetobacter. Acinetobacter, Pseudomonas and Psychrobacter carried strB genes in all studied samples. For the first time the host range of ARGs in manure and soil communities were determined by epicPCR, providing also valuable information for further improving comparatively new method.