Metagenomics of Wastewater from the sewerage system of Nairobi, Kenya.

Wastewater based genomic surveillance study using shotgun metagenomics to reveal bacterial composition, abundance and associated resistome in Nairobi-Kenya sewerage system. Wastewater samples were collected in Nairobi between July and October 2021 for epidemiological surveillance. The approaches used involved extraction of total nucleic acid (TNA) and sequencing on Illumina NextSeq 550. 125 samples were sequenced and the sequence data was subjected to taxonomic classification to profile pathogens (and other organisms) detected within the samples. Also identified were antibiotic resistance genes. The sample sites were regions within Nairobi which in our analysis were classified into low, middle and high income neighborhoods based on socio-economic factors captured in the 2019 Kenyan census. The main goal of the study was to evaluate the utility of wastewater as a means of rabid detection of disease outbreaks for public health awareness. Further, in our analysis we try to assess the dynamics of different pathogens endemic to the region, profile the antibiotic resistance genes and the responsible drugs.