Molecular Diversity of Bacteria from a Municipal Dumpsite: Implications to Public Health

Abstract

Despite known risks of inappropriate disposal of solid wastes; most cities in developing countries dispose waste in open dumpsite where humans, animals and microbes interact. This study was done in Arusha municipal dumpsite, Tanzania to investigate the abundance and diversity of bacteria, compare the faecal microbiota of pigs scavenging on dumpsite and indoor reared pigs, and also determine the resistance profile of enteric bacteria from the dumpsite. Domestic wastes, solid biomedical wastes, sludge from the river near the dumpsite and faecal materials of pigs were sampled. Total DNA was extracted and the variable region four (v4) of the 16S rRNA gene was sequenced using high throughput Illumina MiSeq platform. The quality control of sequences and the statistical analyses was performed using Mothur platform. A total of 8,469,294 quality sequences were generated. The mean of bacterial species per sample was 8,243. Diversity was high with an average InvSimpson index of 44.2. Thirty-five bacterial phyla dominated by Firmicutes (38%), Proteobacteria (35%), Bacteroidetes (13%) and Actinobacteria (3%) were found. Overall, 76,862 operational taxonomic units (OTUs) dominated by Acinetobacter (12.1%), Clostridium sensu stricto (4.8%), Proteinclasticum and Lactobacillus (each 3.4%), Enterococcus (2.9%) and Escherichia/Shigella (1.7%) were revealed. There was a significant difference in faecal microbiota between scavenging and indoor reared pigs. Pathogenic genera like Brucella, Rickettsia and Listeria were exclusive to scavenging pigs. In solid biomedical waste, 36.2% of OTUs were related to dehalogenation, 11.6% degraders of aromatic hydrocarbons, 8.5% chlorophenol degradation and Atrazine metabolism 8.3%, and bacteria related to pathogens were 34%. Escherichia/ Shigella, Bacilli and Proteiniclasticum were predominant enteric bacteria. Some bacteria in scavenging pigs had 99% sequence similarity to pathogenic Escherichia furgosonii, Shigella sonnei, Enterococcus faecium and Escherichia coli O154:H4. Over 50% of the isolates were multidrug resistant. The study provides a comprehensive report on diversity of bacteria in Arusha municipal dumpsite. The high species richness shows the complexity of this man-made ecosystem, and calls for further research to assess for a link between human diseases and the dumpsite. This would provide insight into proper disposal of the waste, as well as, limit the risks to human health associated with the dumpsites.