Establishing and characterising the genetic diversity profile of bacteria colonising fresh produce sold in open-air markets in Juja

Abstract

Increase in the consumption of fresh produce and changes in their production/distribution chains, coupled with the complex biology of bacterial pathogens, limit the usefulness of conventional processing and chemical sanitising methods used in preventing foodborne outbreaks. The microbial quality of nine types of fresh produce obtained from the two selected open markets was determined by both standard quantitative and 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 faecal 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 was 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.