Context. Effective risk assessment and control for environmental antibiotic resistance require comprehensive information of not only the composition of antibiotic resistance genes (ARGs) but also the assembly characteristics of ARG-carriers.
Gap. Owing to the advancements in sequencing technologies and bioinformatic methods, the strategies based on metagenome-assembled contigs and genomes have been developed and used for the identification of ARG-carriers in different habitats, whereas limited by complex computational processes.
Aim & Methods. In this study, we created a new bioinformatic pipeline to screen ARG-carrying microbial community (ACMC) based on metagenomic short reads without assembly; then we applied both read- and assembly-based strategies to identify ARG-carriers from the metagenomic datasets of coastal sediments.
Findings. The major results revealed by the new strategy were validated by both metagenomic assembly strategies, which phylogeny acted as primary determinant for the distribution and spread of ARGs in the coastal sediments and ARGs were mainly carried by Gammaproteobacteria and Firmicutes, especially enriched in several potential pathogens such as Staphylococcus aureus. Due to minimizing the information loss, the new strategy further discovered that stochastic processes were dominant in the assembly of total ACMC, but the primary ARG-carriers were still shaped by deterministic processes; and conditionally rare and abundant taxa (CRAT) of ACMC played an important role in carrying ARGs. In addition, compared with the analyses using assembled contigs and genomes, the analysis using ARGs-like reads reduced computation time by 79.8% to 93.7%, respectively.
Utilization. Our new pipeline successfully screens out ARG-carriers in the environment in a direct and fast way, which will be a great help for long-term surveillance of environmental resistome in the future.
