Quantitative PCR versus metagenomics

The widespread occurrence of clinically relevant antibiotic resistance within humans, animals and environment continuum considered in the One Health approach, motivates the development of sensitive and accurate detection and quantification methods. Metagenomics and quantitative PCR (qPCR) are amongst the most used approaches, and often employed for distinct purposes. In this study, we aimed to evaluate and compare the performance of metagenomics and qPCR analyses to screen antibiotic resistance genes in animal faecal, wastewater and water samples. Water and wastewater samples were from hospital effluent, from two treatment plants at different treatment stages, and from the receiving river up- and downstream the discharge point. The animal faecal samples were from varying mixture of pig and chicken faeces. Antibiotic resistance gene coverage, sensitivity, and usefulness of the quantitative information produced were analysed and discussed. While both methods were able to distinguish the distinct resistome profiles and detect the gradient stepwise mixture of pig and chicken faeces, qPCR presented higher sensitivity for the detection of a number of antibiotic resistance genes in water/wastewater. In addition, qPCR had higher accuracy when predicted and observed antibiotic resistance gene quantification values were compared. Metagenomics analyses, while less sensitive, were able to provide a markedly higher coverage of antibiotic resistance genes compared to qPCR in all samples. The results highlight the complementarity of both methods and show the importance of the selecting the best method according to the study purpose.