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Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing.
Raphenya AR, Robertson J, Jamin C, de Oliveira Martins L, Maguire F, McArthur AG, Hays JP. Raphenya AR, et al. Sci Data. 2022 Jun 15;9(1):341. doi: 10.1038/s41597-022-01463-7. Sci Data. 2022. PMID: 35705638 Free PMC article.
One increasingly common use of genomic and metagenomic sequencing is in identifying the type and range of antimicrobial resistance (AMR) genes present in bacterial isolates in order to make predictions regarding their AMR phenotype. ...These dat …
One increasingly common use of genomic and metagenomic sequencing is in identifying the type and range of antimicrobial res …
Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data.
Clausen PT, Zankari E, Aarestrup FM, Lund O. Clausen PT, et al. J Antimicrob Chemother. 2016 Sep;71(9):2484-8. doi: 10.1093/jac/dkw184. Epub 2016 Jun 30. J Antimicrob Chemother. 2016. PMID: 27365186
OBJECTIVES: Next generation sequencing (NGS) may be an alternative to phenotypic susceptibility testing for surveillance and clinical diagnosis. However, current bioinformatics methods may be associated with false positives and negatives. In this study, a novel mapping …
OBJECTIVES: Next generation sequencing (NGS) may be an alternative to phenotypic susceptibility testing for surveillance and clinical diagno …
Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae.
Foster-Nyarko E, Cottingham H, Wick RR, Judd LM, Lam MMC, Wyres KL, Stanton TD, Tsang KK, David S, Aanensen DM, Brisse S, Holt KE. Foster-Nyarko E, et al. Microb Genom. 2023 Feb;9(2):mgen000936. doi: 10.1099/mgen.0.000936. Microb Genom. 2023. PMID: 36752781 Free PMC article.
However, low base-call accuracy has limited the reliability of ONT data for critical tasks such as antimicrobial resistance (AMR) and virulence gene detection and typing, serotype prediction, and cluster identification. Thus, Illumina sequencing …
However, low base-call accuracy has limited the reliability of ONT data for critical tasks such as antimicrobial resistance …