Background. Probiotic bacteria occupy the same gut niches as enteric pathogens, prompting concern that probiotic strains might carry or contribute mobile antibiotic-resistance genes (ARGs). Genome-based screening is routinely used to assess this risk, but many screens use chromosome-level assemblies that may omit plasmid-borne, high-mobility cargo. We quantified this effect and compared the mobile context resistomes of probiotic-associated and pathogen reference genomes. Methods. We screened 50 bacterial reference genomes (25 probiotic-associated, 25 pathogen/comparator) using a reproducible workflow with the CARD nucleotide catalog, PlasmidFinder replicons, and ISfinder insertion sequences. Each ARG was assigned a four-tier in silico mobile-context risk category from plasmid co-localization and insertion sequence (IS) flanking. The identical strain panel was screened in matched full-assembly and chromosome-only modes. Acquired calls were curated against intrinsic/efflux/biocide determinants and cross-checked with AMRFinderPlus, ResFinder, and targeted BLAST, with MOB-suite as a plasmid/mobility overlay. Results. Full-assembly screening detected 373 ARG loci versus 338 in chromosome-only mode on the same strains, increasing High-risk calls from 4 to 15 and recovering 32 plasmid replicons (chromosome-only: 0). All 15 High-risk mobile-context loci occurred in pathogen/comparator genomes and none in probiotic-associated genomes; no ARG was shared across groups at >=95% nucleotide identity (0/175 edges). Per-strain ARG burden was higher in pathogen genomes (mean 12.32 versus 0.52 loci; Mann-Whitney U = 606.5, P < 0.001). Most priority High-risk loci were corroborated by one or more external tools, with discordant calls retained explicitly as flagged records. Conclusions. Chromosome-only screening materially undercounts mobile ARG cargo. In this reference-genome panel, high-risk mobile-context loci were concentrated in pathogen/comparator genomes; this is an in silico reference-genome-level safety signal rather than evidence for commercial products or genetic transfer.
Saniya, S., Khan, A. A.
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