The present study investigated the impact of on-farm anaerobic digestion on the abundance of enteric bacteria, antibiotic resistance-associated gene targets and the horizontal transfer potential of extended-spectrum β-lactamase (ESBL) genes. Samples of raw and digested manure were obtained from six commercial dairy farms in Ontario, Canada. Digestion significantly abated populations of viable coliforms in all six farms. Conjugative transfer of plasmids carrying β-lactamase genes from manure bacteria enriched overnight with buffered peptone containing 4 mg/l cefotaxime into a β-lactam sensitive gfp-labelled E. coli as a recipient strain was evaluated in patch matings. Digestion significantly decreased the frequency of the horizontal transfer potential of ESBL genes. Twenty-five transconjugants were sequenced revealing six distinct plasmids with a size range of 40 – 180kb. A variety of ESBL genes were identified: blaCTX-M-1, blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, blaPER-1. The blaCTX-M-15 was the most prevalent ESBL gene detected on plasmids harboured by transconjugants. Various mobile genetic elements were found located proximal to resistance genes. Ten gene targets including sul1, strA, strB, ermB, ermF, intI1, aadA, incW, blaPSE and blaOXA-20 were quantified by quantitative PCR on a subset of 18 raw and 18 digested samples. Most targets were significantly more abundant in raw manure, however ermB and ermF targets were more abundant in digested samples. Overall, on-farm digestion of dairy manure abated coliform bacteria, a number of antibiotic resistance-associated gene targets, and the potential for in vitro conjugation of plasmids conferring resistance to extended-spectrum β-lactams and other classes of antibiotics into E. coli CV601.
IMPORTANCE
Using livestock manure for fertilization can entrain antibiotic resistant bacteria into soil. Manure on some dairy farms is anaerobically digested before being land applied. Recommending the widespread implementation of the practice should be founded on understanding the impact of this treatment on various endpoints of human health concern. Although lab-scale anaerobic treatments have showed potential of reducing antibiotic resistance genes, there are very few data from commercial farms. Anaerobic digestion of manure on six dairy farms efficiently abated coliform bacteria and E. coli and a majority of antibiotic resistance-associated gene targets. In addition, the conjugation potential of plasmids carrying ESBL genes into introduced E. coli CV601 was reduced. Overall, anaerobic digestion abated coliform bacteria, the genes that they carry and the potential for ESBL-carrying plasmid transfer.