Diversity of Escherichia coli isolates from milk obtained along the Nairobi dairy value chain by DNA fingerprint analysis

Abstract

Background The Nairobi dairy food system is highly complex and involves informal and formal dairy production and marketing channels. The sector comprises numerous small-scale interlinked actors characterized by diverse food handling practices that may affect product safety. This cross-sectional study sought to analyze the diversity of Escherichia coli, which contaminates cow milk, in material obtained from the supply chain serving Nairobi's rapidly urbanizing city in Kenya. The GTG5 fingerprinting method was used to determine the diversity of 107 E. coli isolates obtained from milk. Dendrograms were used to display E. coli genetic diversity patterns within and between farms from different types of samples. These included raw, pasteurized, processed fermented, and home-made fermented milk sourced from various nodes, including farms, milk bars, milk vending machines, roadside milk vendors and shops. Results Analysis of the first dendrogram with 46 E. coli isolates recovered from various milk types from different nodes showed three major clusters based on bacterial banding patterns. A large proportion of the subsequent sub-clusters in these phylogenies revealed a similarity matrix of between 50 – 70 % among isolates from the same location. Dendrograms derived from analysis of E. coli at farm level showed that most isolates from milk samples obtained from the same farms did not cluster together which strongly suggests variation in the recovered E. coli strains and in the populations of E. coli in those farms. These findings indicate distinct bacterial milk contamination sources and not as a result of the clonal spread of certain strains. Conclusions These results show that the source of milk contamination is diverse and occurs at several points along the value chain. Therefore, policy on the management of food safety (including control of milk-borne diseases) should not only focus on activities at few nodes but along the entire value chain to ensure milk safety