DISCLOSING THE PHAGE-MEDIATED ANTIBIOTIC RESISTANCES IN THE FOOD CHAIN

The aim of this PhD project is to evaluate the presence and the role of viruses in food related environment with particular attention on the mobilization of antibiotic resistance genes (ARGs). During the last three years it has been investigated samples from different food related environments in order to fully characterize the respective microbial and viral communities with a focus on the identification of ARGs in virome and microbiomes. Water from aquaculture was the first sample analyzed (i) being a matrix that has a strong direct contact with the respective food; secondly, it has been analyzed water from Lambro river (ii) since it is used in the field’s irrigation so it directly came in contact with cereals and vegetables. Last project involved the analysis of air surrounding different moment of cheesemaking production (iii). Once again the viruses present in the air could deposit on the surface of the food and they can be ingested by humans. Shotgun metagenomic sequencing was used to study both microbes and viruses, while 16S rRNA profiling analysis completed the characterization of the bacterial community. The three different projects showed how antibiotic resistance genes are wide spread in the viromes of different environments irrespective of the presence of associated anthropic activities. In this context, we hypothesize that the release of antibiotics molecules in the environment by the microbiota is a driving force able to maintain ARGs in the microbiome and, consequently, mobilize them in the virome. In addition, we should consider the effect of the intense environmental release of antibiotics by humans activities. For these reasons this novel approach even if really useful to collect a high amount of information on the sample, is insufficient to discriminate how ARGs have mobilized to the virome and from the virome to the microbiome. In this context, the development of mesocosms can be the turning point since this system let us to work with complex environmental samples but focusing the attention only at one variable at time as, for example, the supplementation of defined amount of antibiotics.