Fecal Microbiome and Resistome in the Long-Term Care of an Apennine Wolf (Canis lupus italicus)

The Apennine wolf (Canis lupus italicus) increasingly inhabits human-modified land-scapes, where exposure to anthropogenic environments may influence pathogen cir-culation and antimicrobial resistance (AMR). Despite this relevance, no shotgun met-agenomic data are available for this subspecies during rehabilitation. A juvenile male wolf admitted to a Wildlife Rehabilitation Center (WRC) after traumatic injury and treated with multiple antibiotics was sampled at admission (T0) and after 11 months of rehabilitation (T1). Shotgun metagenomic sequencing (Illumina NovaSeq) was used to characterize fecal microbial communities, potential pathogens, and antimicrobial resistance genes (ARGs) using Kraken2 and CARD-RGI. Bacterial diversity increased from T0 to T1. Microbial composition shifted from Enterobacterales-dominated pro-files to more diverse communities. Reads associated with animal and human patho-gens were detected at both time points, together with human-associated taxa and viral reads at T1. ARGs were abundant (444 at T0; 417 at T1), mainly involving efflux pumps and β-lactamases. Genes related to Highest Priority Critically Important Anti-microbials—including mcr variants, van clusters, and oxazolidinone resistance deter-minants—were identified. Shotgun metagenomics revealed marked microbiome changes and high ARG diversity in an Apennine wolf during rehabilitation. These findings highlight wolves as potential sentinels of environmental AMR and emphasize the importance of biosecurity measures in WRCs.