Utilizing Metagenomic Data and Bioinformatic Tools for Elucidating Antibiotic Resistance Genes in Environment

Abstract

Antibiotics resistance genes (ARGs) are mainly caused by the extensive use and abuse of antibiotics and have become a global public health concern. Owing to the development of high-throughput sequencing, metagenomic sequencing has been widely applied to profile the composition of ARGs, investigate their distribution pattern, and track their sources in diverse environments. However, the lack of a detailed transmission mechanism of ARGs limits the management of its pollution. Hence, it’s essential to introduce how to utilize the metagenomic data to obtain an in-depth understanding of the distribution pattern and transmission of ARGs. This review provides an assessment of metagenomic data utilization in ARG studies and summarizes current bioinformatic tools and databases, including ARGs-OAP, ARG analyzer, DeepARG, CARD, and SARG, for profiling the composition of ARGs and tracking the source of ARGs. Several bioinformatic tools and databases were then benchmarked. Our results showed that although SARG is a good database, the application of two or more bioinformatic tools and databases could provide a comprehensive view of ARG profiles in diverse environmental samples. Finally, several perspectives were proposed for future studies to obtain an in-depth understanding of ARGs based on metagenomic data. Our review of the utilization of metagenomic data together with bioinformatic tools and databases in ARG studies could provide insights on exploring the profiles and transmission mechanism of ARG in different environments that mitigate the spread of ARGs and manage the ARGs pollution.