Full-assembly screening reveals mobile antibiotic-resistance cargo missed by chromosome-only genomes

Authors

Saniya, S., Khan, A. A.

Abstract

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.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 12 Jun 2026.

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