Wastewater treatment plants (WWTP) receive the effluents from various sources (communities, industrial, and hospital effluents) and are recognized as reservoir for antibiotic-resistance genes (ARGs) that are associated with clinical pathogens. The aquatic environment is considered a hot-spot for horizontal gene transfer, and lake sediments offer the opportunity for reconstructing the pollution history and evaluating the impacts. In this context, variation with depth and time of the total bacterial load, the abundance of faecal indicator bacteria (FIB; E. coli and Enterococcus spp. (ENT)), Pseudomonas spp., and ARGs (blaTEM, blaSHV, blaCTX-M, blaNDM, and aadA) were quantified in sediment profiles of different parts of Lake Geneva using quantitative PCR. The abundance of bacterial marker genes was identified in sediments contaminated by WWTP following eutrophication of the lake. Additionally, ARGs, including the extended-spectrum ß-lactam- and aminoglycoside-resistance genes, were identified in the surface sediments. The ARG and FIB abundance strongly correlated (r ≥ 0.403, p < 0.05, n = 34) with organic matter and metal concentrations in the sediments, indicating a common and contemporary source of contamination. The contamination of sediments by untreated or partially treated effluent water can affect the quality of ecosystem. Therefore, the reduction of contaminants from the source is recommended for further improvement of water quality.

The occurrence of emerging biological contaminants including antibiotic resistance genes (ARGs) and Faecal Indicator Bacteria (FIB) is still little investigated in developing countries under tropical conditions. In this study, the total bacterial load, the abundance of FIB (E. coli and Enterococcus spp. (ENT)), Pseudomonas spp. and ARGs (blaTEM, blaCTX-M, blaSHV, blaNDM and aadA) were quantified using quantitative PCR in the total DNA extracted from the sediments recovered from hospital outlet pipes (HOP) and the Cauvery River Basin (CRB), Tiruchirappalli, Tamil Nadu, India. The abundance of bacterial marker genes were 120, 104 and 89 fold higher for the E. coli, Enterococcus spp. and Pseudomonas spp., respectively at HOP when compared with CRB. The ARGs aadA and blaTEM were most frequently detected in higher concentration than other ARGs at all the sampling sites. The ARGs blaSHV and blaNDM were identified in CRB sediments contaminated by hospital and urban wastewaters. The ARGs abundance strongly correlated (r ≥ 0.36, p < 0.05, n = 45) with total bacterial load and E. coli in the sediments, indicating a common origin and extant source of contamination. Tropical aquatic ecosystems receiving wastewaters can act as reservoir of ARGs, which could potentially be transferred to susceptible bacterial pathogens at these sites.

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The increasing contamination of fresh water resource by toxic metals and Persistence Organic Pollutants (POPs) is a major environmental concern globally. In the present investigation, surface sediments collected from three main rivers named, Makelele, Kalamu and Nsanga, draining through the city of Kinshasa, Democratic Republic of the Congo, were characterized for grain size, organic matter, toxic metals, POPs (including organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs)), and polycyclic aromatic hydrocarbons (PAHs). Furthermore, enrichment factor (EF) and geoaccumulation index (Igeo) were performed to determine metal source and pollution status. The results highlighted high concentration of toxic metals in all sediment samples, reaching the values (mg kg) of 325 (Cu), 549 (Zn), 165 (Pb) and 1.5 (Cd). High values of PCBs and OCPs were detected in sediment samples, e.g. in Makelele river, PCB values ranged from 0.9 to 10.9 with total PCBs (∑7 PCBs × 4.3): 169.3 μg kg; OCPs from 21.6 to 146.8 with ∑OCPs: 270.6 μg kg. The PBDEs concentrations were higher in investigated rivers comparatively with values detected in many rivers from Sub-Saharan Africa. The ΣPAHs value ranged from 22.6 to 1011.9 μg kg. River contamination may be explained by local intense domestic activities, urban and agricultural runoff, industrial and hospital wastewaters discharge into the rivers without prior treatment. This research provides not only a first baseline information on the extent of contamination in this tropical ecosystem but also represents useful tools incorporated to evaluate sediment quality in the river receiving systems which can be applied to similar aquatic environments.

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