The effects of environmental factors on the prevalence and diversity of bacteriophages lytic against the top six non-O157 Shiga toxin-producing Escherichia coli on an organic farm

Bacteriophages (or phages) specific to Shiga toxin-producing Escherichia coli (STEC) strains are frequently isolated from animal-associated environments primarily because ruminant animals are the natural reservoir of STEC. However, little is known about these phages in produce-growing environments. The objective of this study was to determine the effects of environmental factors on the prevalence of the phages lytic against O157 and the top six non-O157 STEC on an organic farm. A total of 370 samples were collected from an organic farm, containing animal-active and produce-growing areas, for 1 year. A bacterial cocktail, including nonpathogenic and pathogenic E. coli strains, was used for phage isolation. Meanwhile, culture methods and PCR were used to isolate STEC strains. Weather information was also collected for each sampling trip. Twenty-eight samples contained phages lytic against STEC (or STEC-infecting phages), of which 26 were collected from the animal-active area. Moreover, the winter season had a higher phage prevalence than other seasons, likely due to high rain precipitation. The phages belonging to the Myoviridae family and those lytic against STEC O103 were the most prevalent. One E. coli O103:H2 was isolated from a water sample where no STEC O103-infecting phages were found. Additionally, no STEC O103 was present in the samples containing STEC O103-infecting phages. The findings indicate that animal is the primary factor contributing to the prevalence of the STEC-infecting phages in the surrounding environment of the organic farm, and the presence of these phages contributes to a negative correlation with their STEC hosts.