Characterizing microbial diversity and resistome in urban sewage using shotgun metagenomics in Kampala, Uganda

Abstract

Introduction: Recently, antimicrobial resistant (AMR) infections have shown up as the leading threat to human health, having 700,000 directly attributed estimated deaths per year worldwide. For Africa, AMR data is still not available for 42.6% – quite a big number, of the countries. In absence of a collaborative and joint global response, the figure is approximated to rise to 10 million annual deaths worldwide by 2050. Therefore, there is a need for availing AMR surveillance information and urban sewage is attractive because it is rich in sampling material from large and mostly healthy populations. In this study we sought to; identify and characterize the microbes in urban sewage in Kampala, determine the urban sewage resistome i.e., the set of resistant genes in Kampala’s sewage, and determine the country-wise differences of microbial diversity and resistome versus the sewage of East Africa Methods: Samples were collected from 2 wastewater treatment plants during the wet and dry seasons to account for the population’s behaviour during both seasons. DNA was then extracted and subjected to shotgun metagenomics sequencing. The resultant fastq files were subjected to a customized metagenomics workflow to profile the microbes, antibiotic resistant genes, and virulence factors. Samples from Kenya and Tanzania were also downloaded from NCBI to perform a country wise comparison of the wastewater composition between the countries. Results: From the pathobiome, Pseudomonas psychrophila – a fish pathogen, was the most abundant and Klebsiella pneumonia the least abundant. 23 resistant genes were found and most of them conferred resistance against tetracyclines. 29 virulence factors were detected and from their functional classification, most of them were related to the bacterial motility. Interestingly, all of these virulence factors were distributed within Pseudomonas aeruginosa PAO1. From the country wise comparison between the three East African countries; Uganda, Tanzania, and Kenya, it is evident that there are significant differences in the microbial community structure and composition of the wastewater across the countries. Conclusion: Application of shotgun metagenomics to sewage is essential in regular surveillance of microbial diversity and antimicrobial resistance. It reveals details that would be much too difficult or expensive with the use of the conventional methods such as the PCR and culture-based methods