There is little information about environmental contamination with antibiotic resistance genes (ARG) in Sub-Saharan Africa, home to about 1 billion people. In this study we measured the abundance of three genes (sul1, sul2, and intI1) used as indicators of environmental contamination with ARGs in the sediments of four urban wetlands in southwestern Nigeria by qPCR. In addition, we characterised the variable regions of class 1 integrons in sulfamethoxazole/trimethoprim (SMX/TRI)-resistant bacteria isolated from the wetlands by PCR and DNA sequencing. The indicator ARGs were present in all wetlands with mean absolute copy numbers/gram of sediment ranging between 4.7x10 6 and 1.2x10 8 for sul1, 1.1x10 7 and 1x10 8 for sul2, and 5.3x10 5 and 1.9x10 7 for intI1. The relative abundances (ARG/16S rRNA copy number) ranged from about 10 −3 to 10 −1. These levels of ARG contamination were similar to those previously reported for polluted environments in other parts of the world. The integrase genes intI1 and intI2 were detected in 72% and 11.4% SMX/TRIresistant isolates, respectively. Five different cassette array types (dfrA7; aadA2; aadA1| dfrA1; acc(6')lb-cr|arr3|dfrA27; arr3|acc(6')lb-cr|dfrA27) were detected among 34 (59.6%) intI1-positive isolates. No gene cassettes were found in the nine intI2-positive isolates. These results show that African urban ecosystems impacted by anthropogenic activities are reservoirs of bacteria harbouring transferable ARG.

In many countries, emission of insufficiently treated wastewater into water bodies appears to be an important factor in spreading clinically relevant antimicrobial resistant bacteria. In this study, we looked for the presence of Enterobacteriaceae strains with resistance to 3 rd generation cephalosporin antibiotics in four urban wetlands in southwestern Nigeria by isolation, whole genome sequencing and qPCR enumeration of marker genes. Genome analysis of multi-drug resistant and potentially pathogenic Escherichia coli isolates (members of the widely distributed ST10 complex) revealed the presence of the extended spectrum beta-lactamase gene bla CTX-M-15 on self-transmissible IncF plasmids. The gene was also present together with a bla TEM-1B gene on self-transmissible IncH plasmids in multi-drug resistant Enterobacter cloacae isolates. A Citrobacter freundii isolate carried bla TEM-1B on an IncRtype plasmid without discernable conjugation apparatus. All strains were isolated from a wetland for which previous qPCR enumeration of marker genes, in particular the ratio of intI1 to 16S rRNA gene copy numbers, had indicated a strong anthropogenic impact. Consistent with the isolation origin, qPCR analysis in this study showed that the bla CTX-M gene was present at an abundance of 1x10 -4 relative to bacterial 16S rRNA gene copy numbers.The results indicate that contamination of these urban aquatic ecosystems with clinically relevant antibiotic resistant bacteria is substantial in some areas. Measures should therefore be put in place to mitigate the propagation of clinically relevant antimicrobial resistance within the Nigerian aquatic ecosystems. PLOS ONEPLOS ONE | https://doi.org/10.

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