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• Harvested fruits from wastewater-irrigated tree are exempt of fecal-borne pathogens. • Heavy metals did not accumulate in fruit and leaves of wastewater-irrigated trees. • Endophytic bacteria increased in shoot irrigated with wastewater. • No E. coli was found neither in apple nor in nectarine shoot/fruit. • E. coli internalized but did not migrate to the epigeal part of plants (shoot). The use of secondary treated wastewater (STW) for irrigation is considered as a strategy to mitigate water shortage in summer periods. Unfortunately, the utilization of STW in agriculture is not exempt from environmental and health risks, being a potential source of toxic chemicals (e.g. heavy metals) and human pathogens (e.g. Salmonella spp. and Escherichia coli). The aim of this work is to verify whether irrigation of apple and nectarine trees with STW may lead to heavy metal and microbial contamination in shoot, leaf and fruit tissues. Three-year old trees were grown in pots and drip irrigated separately, for one season, using either tap water (TW) or STW. STW irrigation did not affect heavy metal and trace element concentration (e.g. B, Na, Zn) both in leaves and fruits. Heavy metal concentrations in fruit tissues were lower than international limits for human consumption in both species. Independently from the species, the total bacterial count (TBC) on shoot was almost the double in STW irrigated plants compared to the TW-irrigated ones. No E. coli was found in shoot and fruit; few coliforms (TC) were detected in shoot tissues and in nectarine fruits, far below European microbiological limits for foodstuff. Finally, a laboratory trial, aimed at evaluating possible mechanisms of E. coli translocation inside plants, was carried out on 3-month old peach rootstock plants (i.e. GF 677), artificially inoculated with two E. coli strains, characterized by a different level of pathogenicity (disarmed DH5α and E. coli 1576). Populations of both E. coli strains were isolated as epiphytic and as endophytic only at root level. Nonetheless, the endophytic population of the E. coli 1576 was generally higher than the DH5α strain. Colonization of the epigeal part was never observed. These results are promising for the use of STW, especially for drip irrigated orchards, since water does not wet the canopy and consequently the final product. [ABSTRACT FROM AUTHOR]