Background: The microorganisms that inhabit food processing environments (FPE) can strongly influence the
associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant
microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat
processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a
detailed analysis of a newly opened pork cutting plant over 1.5 years of activity.
Results: We identified a relatively restricted principal microbiota dominated by Pseudomonas during the first 2
months, while a higher taxonomic diversity, an increased representation of other taxa (e.g., Acinetobacter,
Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An
increase in total abundance, alpha diversity, and β-dispersion of ARGs, which were predominantly assigned to
Acinetobacter and associated with resistance to certain antimicrobials frequently used on pig farms of the region,
was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum β-lactamase-
producing Enterobacteriaceae and vancomycin-resistant Enterococcaceae was observed when cutting activities
started. ARGs associated with resistance to β-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently
co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly
detected at the later sampling times in drains.
Conclusions: The observations made suggest that pig carcasses were a source of resistant bacteria that then
colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces,
represented a reservoir for the spread of ARGs in the meat processing facility.
