Profiling of emerging pathogens, antibiotic resistance genes and mobile genetic elements in different biological wastewater treatment plants

The emergence and spread of antibiotic resistance through insufficiently treated effluents from wastewater treatment systems are detrimental to the receiving environment and human health. Metagenomic and transcriptomic approaches were employed to assess the diversity and the removal of bacterial pathogens, antibiotic-resistant genes (ARGs) and mobile genetic elements (MGEs) in three wastewater treatment plants (WWTPs) in Durban, South Africa. In total, 23 pathogenic bacterial genera, including enteric and emerging opportunistic pathogens, were found abundant in the samples. Aeromonas and Acinetobacter spp were the most dominant pathogens detected in the influent metagenomes, while the influent transcripts showed Escherichia and Acinetobacter spp as the most dominant pathogens. Shannon-Wiener indices showed that the bacterial diversity increased from influents to final effluents in two selected treatment plants. ARG types, including those conferring resistance to aminoglycosides, beta-lactamases, tetracycline and sulfonamide were abundant in both influent and effluent samples. Results further exposed that MGE-ARGs associations were the main drivers of ARG persistence into final effluents. This included 5 plasmids: R338-R151 (sulI), pRH-1238 (strB), pPM91 (aadA), pRH-1238 (aadA4–5), pRH-1238 (sulII); two class 1 integrons (aadA and arr) and 1 transposon Tn4351(tetX). In transcripts, MGE-ARG association showed two plasmids: pRH-1238 (aadA) and pPM91(aadA) and one hybrid plasmid R338-R151 (sulI). It was apparent across all the WWTPs that chlorination had little or no effect on MGE-ARG association . Combined, this study has highlighted the presence of bacterial pathogens, ARGs and MGEs in treated effluents, which can encourage the propagation of antibiotic resistance and potential sharing of genes in the downstream environments.