Determining the Presence of Escherichia coli and Salmonella sp. as Indicator Organisms of Contamination from Fresh Produce Sold in Open-Air Markets in Juja

Abstract

The aim of this study was to determine the presence of Escherichia coli and Salmonella sp. as indicator organisms of contamination from fresh produce sold in open-air markets in Juja, Kenya. The microbial quality of nine types of fresh produce was  obtained from the two selected open markets and was determined by both standard quantitative and Next-Generation Sequencing (NGS) techniques. Purposive sampling technique was used in this cross-sectional study design to collect fresh produce items based on their tendency to be consumed raw or with minimal processing from the two selected open markets. Standard laboratory microbe culturing techniques were used to detect the presence of fecal coliform E. coli and foodborne pathogen Salmonella paratyphi. DNA was extracted from the surfaces of samples and 16S rDNA sequences were used to analyse the diversity of microbiomes found on the fresh produce using QIIME II software. Members of the Enterobacteriaceae family were in high proportional abundances, and pathogens belonging to this family were detected in the fresh produce. Bla-TEM is one of the most important genes encoding ESBLs, predominantly in the Enterobacteriaceae family, and it is prevalent in the fresh produce resistome. Findings of this study provided the much-needed genomic information about pathogenic bacteria contaminating fresh produce sold in the open market that will guide the development and deployment of reliable control/management strategies against foodborne outbreaks.