AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data.

Autor: Marini S; Department of Computer and Information Science and Engineering, University of Florida, 2004 Mowry Road Gainesville, FL 32610, USA., Oliva M; Department of Computer and Information Science and Engineering, University of Florida, 432 Newell Dr, Gainesville, FL 32611, USA., Slizovskiy IB; Department of Veterinary Population Medicine, University of Minnesota, 1365 Gortner Avenue 225, St. Paul, MN 55108, USA., Das RA; Department of Computer and Information Science and Engineering, University of Florida, 2004 Mowry Road Gainesville, FL 32610, USA., Noyes NR; Department of Veterinary Population Medicine, University of Minnesota, 1365 Gortner Avenue 225, St. Paul, MN 55108, USA., Kahveci T; Department of Computer and Information Science and Engineering, University of Florida, 432 Newell Dr, Gainesville, FL 32611, USA., Boucher C; Department of Computer and Information Science and Engineering, University of Florida, 432 Newell Dr, Gainesville, FL 32611, USA., Prosperi M; Department of Computer and Information Science and Engineering, University of Florida, 2004 Mowry Road Gainesville, FL 32610, USA.
Jazyk: angličtina
Zdroj: GigaScience [Gigascience] 2022 May 18; Vol. 11.
DOI: 10.1093/gigascience/giac029
Abstrakt: Background: Antimicrobial resistance (AMR) is a global health concern. High-throughput metagenomic sequencing of microbial samples enables profiling of AMR genes through comparison with curated AMR databases. However, the performance of current methods is often hampered by database incompleteness and the presence of homology/homoplasy with other non-AMR genes in sequenced samples.
Results: We present AMR-meta, a database-free and alignment-free approach, based on k-mers, which combines algebraic matrix factorization into metafeatures with regularized regression. Metafeatures capture multi-level gene diversity across the main antibiotic classes. AMR-meta takes in reads from metagenomic shotgun sequencing and outputs predictions about whether those reads contribute to resistance against specific classes of antibiotics. In addition, AMR-meta uses an augmented training strategy that joins an AMR gene database with non-AMR genes (used as negative examples). We compare AMR-meta with AMRPlusPlus, DeepARG, and Meta-MARC, further testing their ensemble via a voting system. In cross-validation, AMR-meta has a median f-score of 0.7 (interquartile range, 0.2-0.9). On semi-synthetic metagenomic data-external test-on average AMR-meta yields a 1.3-fold hit rate increase over existing methods. In terms of run-time, AMR-meta is 3 times faster than DeepARG, 30 times faster than Meta-MARC, and as fast as AMRPlusPlus. Finally, we note that differences in AMR ontologies and observed variance of all tools in classification outputs call for further development on standardization of benchmarking data and protocols.
Conclusions: AMR-meta is a fast, accurate classifier that exploits non-AMR negative sets to improve sensitivity and specificity. The differences in AMR ontologies and the high variance of all tools in classification outputs call for the deployment of standard benchmarking data and protocols, to fairly compare AMR prediction tools.
(© The Author(s) 2022. Published by Oxford University Press GigaScience.)
Databáze: MEDLINE
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