Prevalence and Antimicrobial Resistance Phenotype of Enteric Bacteria from a Municipal Dumpsite

Abstract

The objective of the study was to determine the prevalence and antibiotic resistance phenotype of enteric bacteria from the municipal dumpsite. A qualitative survey of the dumpsite was conducted to identify types of solid wastes and nature of interaction on the dumpsite. Samples were collected from different type of solid waste, including domestic waste (Dom), solid biomedical waste (Biom), river sludge near the dumpsite (Riv) and faecal material of pigs scavenging on the dumpsite (FecD). A control sample was collected from faecal material of pigs initially reared indoor (FecI) and shifted to scavenging on the dumpsite (FecIF). Total genomic DNA was extracted, and the 16S rRNA gene was amplified, sequenced and used to study prevalence of enteric bacteria. The same sample was used to isolate enteric bacteria that were later tested to 8 different antibiotics for their susceptibility phenotype. Solid wastes are not sorted in Arusha municipal. There was high interaction between animals and humans on the dumpsite. A total of 219 enteric bacteria from 75 genera were identified. Escherichia sp and Shigella sp (12%), Bacillus sp (11%) and Proteiniclasticum (4%) were the predominant genera. Most of the Escherichia sp, Shigella sp and Bacillus were from FecD, while Proteiniclasticum spp was from Biom. Some isolates from FecD had 99% sequence similarity to pathogenic Escherichia furgosonii, Shigella sonnei, Enterococcus faecium and Escherichia coli O154:H4. Over 50% of the isolates were resistant to Penicillin G, Ceftazidime and Nalidixic Acid. Ciprofloxacin and Gentamycin were the most effective antibiotics with 81% and 79% susceptible isolates, respectively. Of all the isolates, 56% (45/80) were multidrug resistant. Escherichia sp and Bacillus sp (12 isolates each) constituted a large group of multidrug resistant bacteria. All Pseudomonas sp from Biom and FecD were multidrug resistant. There is high prevalence of antibiotic resistant enteric bacteria on the dumpsite. We report possible risks of spreading antibiotic resistant bacteria/genes from the dumpsite to clinical settings through animals and humans interacting on the dumpsite. This finding calls for a comprehensive research to study the shared resistome in bacteria from the environment, humans and animals using PCR and metagenomic based approaches to identify prevalence of known and capture new resistant genes.