Microbiological quality of irrigation water on highly diverse fresh produce smallholder farms: elucidating environmental routes of contamination

To evaluate the microbiological safety, potential multidrug resistant bacterial presence and genetic relatedness (DNA fingerprints) of Escherichia coli isolated from the water-soil-plant nexus on highly diverse fresh produce smallholder farms. Irrigation water (n = 44), soil (n = 85), and fresh produce (n = 95) samples, from six smallholder farms with different production systems, were analysed for hygiene indicator bacterial counts and the presence of shigatoxigenic E. coli and Salmonella spp., using standard microbiological methods. Identities of isolates were confirmed using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and the genetic relatedness of the E. coli isolates determined using enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) analysis. Irrigation water E. coli levels ranged between 0-3.45 log MPN.100 mL-1 with five farms having acceptable levels according to the World Health Organization limit (3 log MPN.100 mL-1). Fresh produce samples on four farms (n = 65) harboured E. coli at low levels (90%), with all phenotypically characterised as multidrug resistant. The clustering of E. coli isolated throughout the water-soil-plant nexus, implicated irrigation water in fresh produce contamination. Highlighting the importance of complying with irrigation water microbiological quality guidelines to limit the spread of potential foodborne pathogens throughout the fresh produce supply chain.