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Assessing the presence and genetic basis of ESBL-producing bacteria in pre-boil wort, dairy cattle manure and dog faeces

Antimicrobial resistance (AMR) is becoming the biggest problem facing human and animal health care, with a predicted 10 million deaths per year due to antibiotic resistance by 2050 (Review on Antimicrobial resistance, 2014). The focus of many AMR studies is on problems inside clinical settings, such as hospitals and veterinary practices, yet, as this study shows, often the most diverse sources of resistance genes are found in relatively unexplored areas of the environment; in particular dog faeces and dairy cattle manure. Chromogenic media analysis showed dog faeces had the greatest number and diversity of ESBL-producing bacteria. Multiplex PCR showed inconclusive evidence of what the resistance genes were in both dairy cattle manure and dog faeces. Phylogenetic analysis of the 16S rRNA showed Flavobacteriaceae-like bacteria in dairy cattle manure but the presence of Enterobacteriaceae-like bacteria, most similar to Escherichia coli, in dog faeces. The major conclusion of this study is that ESBL-producing bacteria are present in high abundance in both dog faeces and dairy cattle manure and that ESBL-producing bacterial species in dog faeces showed higher diversity than first expected while pre-boil wort had no ESBL-producing bacteria. The results of this study have crucial significance for future studies and the wider community. The statistical, microbiological and phylogenetic data collected provide strong evidence of the role of the environment in the spread of antibiotic resistance. Secondly, the study utilises a holistic visual model to map the spread of resistance and inform the wider community of the issue of AMR in the environment.