AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence - PubMed (original) (raw)

. 2021 Jun 16;11(1):12728.

doi: 10.1038/s41598-021-91456-0.

Vyacheslav Brover 2, Narjol Gonzalez-Escalona 3, Jonathan G Frye 4, Julie Haendiges 3, Daniel H Haft 2, Maria Hoffmann 3, James B Pettengill 3, Arjun B Prasad 2, Glenn E Tillman 5, Gregory H Tyson 6, William Klimke 2

Affiliations

Michael Feldgarden et al. Sci Rep. 2021.

Abstract

Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable whole genome sequencing, in silico approaches to assessing AMR gene content can be used to detect known resistance mechanisms and potentially identify novel mechanisms. To enable accurate assessment of AMR gene content, as part of a multi-agency collaboration, NCBI developed a comprehensive AMR gene database, the Bacterial Antimicrobial Resistance Reference Gene Database and the AMR gene detection tool AMRFinder. Here, we describe the expansion of the Reference Gene Database, now called the Reference Gene Catalog, to include putative acid, biocide, metal, stress resistance genes, in addition to virulence genes and species-specific point mutations. Genes and point mutations are classified by broad functions, as well as more detailed functions. As we have expanded both the functional repertoire of identified genes and functionality, NCBI released a new version of AMRFinder, known as AMRFinderPlus. This new tool allows users the option to utilize only the core set of AMR elements, or include stress response and virulence genes, too. AMRFinderPlus can detect acquired genes and point mutations in both protein and nucleotide sequence. In addition, the evidence used to identify the gene has been expanded to include whether nucleotide or protein sequence was used, its location in the contig, and presence of an internal stop codon. These database improvements and functional expansions will enable increased precision in identifying AMR genes, linking AMR genotypes and phenotypes, and determining possible relationships between AMR, virulence, and stress response.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1

Figure 1

Overview of AMRFinderPlus gene identification method using protein and nucleotide sequences. When AMRFinderPlus is run in protein-only or nucleotide-only modes only the relevant side of the flowchart above is utilized. Note that HMMs are not used with nucleotide-only data which results in reduced sensitivity for some families. "Ignored" matches are not used, however an alternative method may still report the protein (e.g., an ignored HMM match will not suppress reporting based on BLASTP or BLASTX hit). *Details are simplified in this diagram; a more detailed description is included in the methods text.

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References

    1. Allard MW, et al. Genomics of foodborne pathogens for microbial food safety. Curr. Opin. Biotechnol. 2018;49:224–229. doi: 10.1016/j.copbio.2017.11.002. - DOI - PubMed
    1. Jackson BR, et al. Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation. Clin. Infect. Dis. 2016;63:380–386. doi: 10.1093/cid/ciw242. - DOI - PMC - PubMed
    1. Do Nascimento, V. et al. Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of enteroaggregative Escherichia coli isolated from cases of diarrhoeal disease in England, 2015–16. J. Antimicrob. Chemother.72, 3288–3297. 10.1093/jac/dkx301 (2017). - PubMed
    1. Day MR, et al. Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Salmonella enterica serovars Typhi and Paratyphi. J. Antimicrob. Chemother. 2018;73:365–372. doi: 10.1093/jac/dkx379. - DOI - PubMed
    1. Rehman MA, Yin X, Persaud-Lachhman MG, Diarra MS. First Detection of a Fosfomycin Resistance Gene, fosA7, in Salmonella enterica Serovar Heidelberg Isolated from Broiler Chickens. Antimicrob. Agents Chemother. 2017 doi: 10.1128/aac.00410-17. - DOI - PMC - PubMed

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