Purpose: An organic farming system was examined for prevalence and genetic relatedness of Escherichia coli O157 and Salmonella spp. over two years, including two types of compost, surface irrigation water, soil, pastured animals and produce.
Methods: E. coli O157 and Salmonella spp. were isolated using standard techniques and latex agglutination; isolation of E. coli O157 utilized immunomagnetic separation. Confirmation involved serotyping and conventional PCR (E. coli O157- stx1, stx2, hlyA, eaeA, rfbO157, fliC; Salmonella- invA, iroB, rfbJ). Genetic relatedness (≥90% similarity) was determined using pulsed-field gel electrophoresis (PFGE).
Results: Pathogens were observed at low levels in agricultural inputs, but were not detected in crops. Salmonella spp. were isolated during composting (15 positive/423 total samples), from surface irrigation water (2/148) and soil (5/234). E. coli O157:H7 were isolated during composting (18/423) and after turned pile (6/70) and aerated static pile (1/147) compost met time-temperature requirements for the process to further reduce pathogens, as well as in surface irrigation water (1/148), sheep manure (5/10) and soil (7/234). E. coli O157 isolates (two H-, one H+, four H1, eight H12 and five H42) were detected. A lettuce isolate (E. coli O157:H12) was genetically similar to a soil isolate (E. coli O157:H12). Five E. coli O157:H7 sheep manure isolates displayed similarity to three E. coli O157:H7 isolates recovered from soil plots where sheep were pastured. Some soil isolates (E. coli O157:H7) were genetically similar to a turned pile compost isolate (E. coli O157:H7). A soil isolate (E. coli O157:H42) was genetically similar to an irrigation water isolate (E. coli O157:H42) collected on the same date.
Significance: Although pathogens were detected at low levels in agricultural inputs, genetic relationships indicated potential bacterial transmission from irrigation water to soil, compost to soil, pastured animals to soil and soil to produce.