pathogenic E. coli genomes isolated from italian biosolids
Biowastes of anthropogenic and animal origin, known as “biosolids”, represent useful sources of water, inorganic and organic compounds for agriculture. However, their regular and intense use as Top Soil Improvers (TSIs) may originate potential food safety non-compliance. The characterization of the hazards and risks associated with the use of municipal and livestock waste, including the spread of pathogens and AMR genes, has not yet been framed in a comprehensive and combined assessment. In this work, biosolids (n=31) of different origin (municipal sludge-derived compost; manure and compost from intensive animal farming systems; compost from green and household wastes) were analysed, before and after enrichment in a non-selective medium, to detect virulence genes of different pathogenic E. coli (Shiga toxin producing - E. coli – STEC; Enteropathogenic E. coli – EPEC; Enteroaggregative E. coli – EAEC; Enteroinvasive E. coli – EIEC; Enterotoxigenic E. coli – ETEC) and Salmonella spp. Virulence genes characteristic of all E. coli pathogroups were detected in all the samples analysed. Before enrichment, most of the samples showed positive signals for the presence of stx1, stx2 and eae genes, few samples showed positive signals for aggR, aaiC, ipaH, lt, stp, sth genes and no signal was detected for Salmonella spp. Positive signals related to the presence of all the E. coli pathogroups were detected in the majority of the enriched samples, including those showing negative signals before enrichment. Three pathogenic E. coli strains were successful isolated from the enriched cultures, including one STEC strain isolated from bovine slurry, showing the presence of the ETEC heat stabile enterotoxin (stx1+, sta1+), one EPEC (eae+) and one ETEC (stp+) strain isolated from the same pig slurry sample.   The detection of viable pathogens in TSI samples suggests that the fermentation treatments used for the stabilization of biosolids may be not fully effective in eliminating pathogenic E. coli strains and underlines the risk that these pathogens may be introduced into the agri-food supply chain and possibly pose a risk to consumers. Moreover, the concomitant presence of virulence genes associated to different E. coli pathogroups can lead to the emergence of new hybrid strains with shuffled virulence features, that can be highly virulent to human, representing a serious issue in public health