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Antibiotic resistant bacteria and genes which confer resistance to antibiotics from human/animal sources are currently considered a serious environmental and a public health concern. This problem is still little investigated in aquatic environment of developing countries according to the different climatic conditions. In this research, the total bacterial load, the abundance of relevant bacteria ( Escherichia coli (E .  coli) ,  Enterococcus  (Ent), and  Pseudomonas ), and antibiotic resistance genes (ARGs:  bla  OXA-48 ,  bla  CTX-M ,  sul1 ,  sul2 ,  sul3 , and  tet(B) ) were quantified using Quantitative Polymerase Chain Reaction (qPCR) in sediments from two rivers receiving animal farming wastewaters under tropical conditions in Kinshasa, capital city of the Democratic Republic of the Congo. Human and pig host-specific markers were exploited to examine the sources of contamination. The total bacterial load correlated with relevant bacteria and genes  bla  OXA-48 ,  sul3 , and  tet(B)  (P value < 0.01).  E .  coli  strongly correlated with 16s rDNA,  Enterococcus ,  Pseudomonas  spp.,  bla  OXA-48 ,  sul3 , and  tet(B)  (P value < 0.01) and with  bla  CTX-M ,  sul1 , and  sul2  at a lower magnitude (P value < 0.05). The most abundant and most commonly detected ARGs were  sul1 , and  sul2 . Our findings confirmed at least two sources of contamination originating from pigs and anthropogenic activities and that animal farm wastewaters didn’t exclusively contribute to antibiotic resistance profile. Moreover, our analysis sheds the light on developing countries where less than adequate infrastructure or lack of it adds to the complexity of antibiotic resistance proliferation with potential risks to the human exposure and aquatic living organisms. This research presents useful tools for the evaluation of emerging microbial contaminants in aquatic ecosystems which can be applied in the similar environment.

Occurrence of Bacterial Markers and Antibiotic Resistance Genes in Sub-Saharan Rivers Receiving Animal Farm Wastewaters