Illustration on Phenotypic and Genotypic Characteristics of Typical Multi-Antibiotic Resistant Bacteria in Aquatic Environments Through Complete Genomes and Comparative Genomics

Abstract

Pathogenic multi-antibiotic resistant bacteria (MARB) possess the ability to multiply and spread drug-resistant genes and become a type of special dangerous pollutant in the water environment. In this study, under the selective pressures from ampicillin, kanamycin and tetracycline, a multi-resistant superbug (named TR3) was screened. The results from metagenomic technology showed that TR3 was ubiquitous in the sludge of the wastewater treatment plants (WWTPs) with different geographical and climatic characteristics and the abundances of TR3 were between 0.0019% and 0.018%. The complete genome of TR3 strain (Aeromonas media) was obtained by Single Molecule Real-Time Sequencing and de novo assembly for the first time. The cell contained a genome (4521851 bp in length) and a plasmid (9182 bp in length). In terms of the genotype, the multi-antibiotic resistance mechanism of the TR3 was confirmed and the antibiotics resistance genes (ARGs) were located in the core genome possessing genetic stability. As for the phenotype, under 1×MIC conditions, the strain TR3 showed resistance to all 5 types of antibiotics (ciprofloxacin, tetracycline, ampicillin, clarithromycin, and kanamycin), and the survival rates of the strain were 12.85%, 71.22%, 67.84%, 78.44% and 91.74%, respectively. The TR3 was most resistant to kanamycin (belonging to aminoglycoside) and still had a survival rate of 67.77% at 10×MIC. In addition, chlorine and ultraviolet (UV) sterilization on TR3 strain showed that UV was ineffective at low intensity, and it was easy to be revived by light. Low concentration of hypochlorous acid was effective for sterilization, but it can cause the release of DNA, which might become a potential source of ARGs discharged from WWTPs to environmental water bodies.

Keywords: Activated sludge, Multi-antibiotic resistant bacteria (MARB), Complete genome sequence, Genotypes and phenotypes, Disinfection