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bioRxiv · 10.1101/2025.09.15.676352

CARD k-mers: Unmasking the pathogen hosts and genomic contexts of antimicrobial resistance genes in metagenomic sequences

Wlodarski, M. A.·Lau, T. T. Y.·Alcock, B. P.·Raphenya, A. R.·Ta, T. E.·Maguire, F.·Beiko, R. G.·McArthur, A. G.
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Abstract

Antimicrobial resistance (AMR) is a global health crisis requiring rapid surveillance across human, agricultural, and environmental systems. A major challenge during outbreaks is not only detecting antimicrobial resistance genes (ARGs), but also unmasking their pathogen hosts and genomic context, as ARGs alone do not fully capture AMR risk. Pathogen identification is often essential for guiding effective treatment. While culture-based methods remain the diagnostic gold standard, they are slow and sometimes impractical. Faster metagenomic (mNGS) tools typically detect either ARGs, taxonomy, or genomic context, but rarely all three, resulting in fragmented surveillance. Existing k-mer classifiers like Kraken2 and CLARK, designed for general taxonomy, often perform poorly on AMR-specific sequences. We introduce CARD k-mers, the first tool built to jointly predict species-level taxonomy and genomic context (plasmid vs. chromosome) for ARGs in short metagenomic reads. Integrated with the Comprehensive Antibiotic Resistance Database (CARD), CARD k-mers enables rapid, context-aware assignment of ARGs to their likely pathogen and genomic element origin. In benchmarking with 103,456 in-silico pathogen-specific AMR alleles, CARD k-mers outperformed Kraken2 and CLARK by 10.85% and 15.2%, respectively, and correctly classified the genomic context of 4,590 chromosome- and 176 plasmid-specific ARGs. The tool operates at speeds exceeding 675,000 metagenomic reads per minute. By delivering fast, accurate, and context-rich classification of ARGs, CARD k-mers significantly advances untargeted AMR surveillance and is accessible to users with basic command-line experience for use in both clinical and environmental pipelines. CARD k-mers is available at: https://github.com/arpcard/rgi.

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Wlodarski, M. A., Lau, T. T. Y., Alcock, B. P., Raphenya, A. R., Ta, T. E., Maguire, F., Beiko, R. G., McArthur, A. G.. 2025-09-18. CARD k-mers: Unmasking the pathogen hosts and genomic contexts of antimicrobial resistance genes in metagenomic sequences. https://doi.org/10.1101/2025.09.15.676352

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