The Assessment of the Risk Ranking and Mobility Potential Associated with Environmental Resistomes in Wastewater Using Metagenomic Assembly

• Published in: Sustainability 2022-11, Vol.14 (21), p.14292
• Main Authors: Ali, Osama S, Hozayen, Walaa G, Almutairi, Abdulwahab S, Edris, Sherif, Karkashan, Alaa, Abulfaraj, Aala A, Attar, Roba, Ouf, Amged A, Abbas, Basma, Mahmoud, Hamada M
• Format: Article
• Language: English
• Subjects: Annotations; Antibiotic resistance; Antibiotics; Bacteria; Bioinformatics; Contamination; Datasets; Drug resistance in microorganisms; Effluents; Environmental aspects; Gene transfer; Genes; Genetic aspects; Genomes; Health aspects; Health hazards; Health risk assessment; Health risks; Horizontal transfer; Hospital wastes; Medical wastes; Metagenomics; Mobility; Pathogenicity; Pathogens; Plasmids; Public health; Ranking; Raw sewage; Risk assessment; Risk levels; Sewage; Software; Sustainability; Wastewater; Wastewater pollution; Wastewater treatment; Wastewater treatment plants; Water treatment
• ISSN: 2071-1050; 2071-1050
• DOI: 10.3390/su142114292

The environmental pollution of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) is a growing public health concern. In the current study, de novo metagenomic assembly and bioinformatics analysis approaches were utilized to estimate the quantitative risk index of the environmental resistomes in wastewater influent (INF) and effluent (EFF) of a conventional wastewater treatment plant (WWTP) in Egypt. Furthermore, the risk indices of the local INF and EFF resistomes were compared to those calculated for the selected publicly available wastewater datasets from eight countries worldwide. Additionally, a classification framework prioritizing the public health hazard level of the discharged non-redundant highly mobilized ARGs was introduced. This integrative outline considered the estimated mobility potential percentage, host pathogenicity, and annotation category (perfect, strict, and loose) of the detected ARGs on their assembled contigs. Moreover, high-quality metagenome-assembled genomes (MAGs) were extracted and the putative genome bins with acquired ARGs were determined. The comprehensive resistome risk scores of the local WWTP showed that INF resistome had a slightly higher risk index (47.87) compared to the average score of the other examined counterparts (41.06). However, the estimated risk value of EFF resistome (26.80) was ranked within the global average (26.06) of the selected international WWTPs. Furthermore, the determination of the samples’ risk ranking showed that most of the effluent resistomes were clustered in a lower risk rank compared to the other selected samples for raw sewage, influent, and hospital wastewater, indicating the impact of the wastewater treatment process on reducing the ARG mobilization potential in downstream environments. The evaluation of the ARGs’ genetic context in their ARG-carrying contigs (ACCs) indicated that a total of 161/648 (25%) non-redundant ARGs were co-located with sequences of mobile genetic determinants on the same ACC in both the INF and EFF assemblies. These ARGs comprised the pan mobile resistome of the studied WWTP. Of them, 111 ARGs with a mobility potential percent (M%) less than 95% were grouped at the least risk level 5. The remaining 50 highly mobilized ARGs (M% ≥ 95%) were extracted and classified into four higher risk levels. Those of risk levels 1 and 2 (39 ARGs) represented the current ARG dissemination threats for further monitoring in downstream environments, where