Wastewater treatment plants (WWTPs) are known environments for the presence and transfer of antibiotic resistant genes (ARGs), an evolving environmental pollutant. This study aimed to explore the prevalence of ARGs and resistant bacteria in a conventional, and a membrane bioreactor (MBR) WWTP in Michigan (USA). A sequence-based metagenomic approach was implemented to detect the profile of ARGs in the activated sludge (AS), before disinfection (BD), and after disinfection (AD) treatment stages in each WWTP. Metagenomic alignment detected genes resistant to sulfonamide, tetracycline, macrolide, elfamycin, aminoglycoside, and β-lactam classes of antibiotics to be prevalent ARGs in both WWTPs. Effluent samples yielded the highest presence of ARGs in each plant compared to AS and BD samples. Quantitative analysis found that 56.25% and 53.33% of a total of 23 ARGs, which were detected at ≥ 90% gene similarity among all samples, were not detected until after disinfection samples for the conventional and MBR WWTPs, respectively. To our knowledge, this study is the first to report the prevalence of elfamycin resistant genes in WWTPs. In addition to this, Acinetobacter baumannii, Pseudomonas aeruginosa, and Pasteurella multocida were found to be predominant resistant bacteria in AD samples from each WWTP. The occurrence of ARGs increased in both WWTPs as treatment progressed further suggesting that increased wastewater treatment selects for antimicrobial resistance.
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