Metagenomics insights into the profiles of antibiotic resistome in combined sewage overflows from reads to metagenome assembly genomes

Combined sewage overflows (CSOs) have become an important source of antibiotic resistance genes (ARGs) in the environment, while the distribution and dynamics of antibiotic resistome in the CSOs events have not been well understood. This study deciphered the profiles of antibiotic resitome in the CSOs based on metagenomics analysis from reads to metagenome assembly genomes (MAGs), and the dynamical changes of ARGs were clarified through continuous monitoring of the CSO event. Results showed that antibiotic inactivation was the dominant resistance mechanism, and sulfonamide, aminoglycoside along with multidrug resistance were the dominant antibiotic resistance types. It was speculated that the antibiotic resistome were generally determined by sewer sediment flushed out along with the CSOs not domestic sewage in the pipes. The host range and mobility of the antibiotic resistome were determined at contigs level, and the hosts mainly belonged to the Proteobacteria with the genus of Pseudomonas, Escherichia, Enterobacter and Aeromonas being dominant. The transposase (tnpA), 1591 and integmns were mobile genetic elements (MGEs) located together with ARGs, and a MAG carrying 32 ARGs and 140 VFGs was assembled. Although microbial community contributed most to the changes of antibiotic resistome in the CSOs directly, the risks caused by the MGEs should be paid more attention.

Automated summary

This study explored the profiles and dynamic changes of antibiotic resistome in combined sewage overflows (CSOs) through metagenomics analysis. The dominant resistance mechanism was found to be antibiotic inactivation, and sulfonamide, aminoglycoside, and multidrug resistance were the main types of antibiotic resistance. The hosts of antibiotic resistome were mainly Proteobacteria, including Pseudomonas, Escherichia, Enterobacter, and Aeromonas. Mobile genetic elements (MGEs) such as transposase (tnpA), 1591, and integmns were associated with the ARGs.