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N. gonorrhoeae PBP2 Mutations Genotype Data Use Case 2

Source: R/data.R
ngono_cro_geno_raw.Rd

Raw concatenated output from AMRFinderPlus run on Neisseria gonorrhoeae genome assemblies from multiple studies enriched for ceftriaxone decreased susceptibility and resistance (total n = 2,101 genomes). This object serves as the genotype input for import_amrfp and is used to investigate mosaic PBP2 (penA) variants associated with ceftriaxone resistance.

Usage

ngono_cro_geno_raw

Format

ngono_cro_geno_raw A data frame with 23,885 rows and 24 columns:

  • Name: Sample identifier (ENA run accession).

  • Protein id: Protein identifier (all NA).

  • Contig id: Assembly contig identifier.

  • Start, Stop: Start and stop positions of the AMR element on the contig.

  • Strand: Strand orientation (+ or -).

  • Element symbol: AMRFinderPlus element symbol (e.g. pbp2, penA_A510V).

  • Element name: Full descriptive name of the AMR element.

  • Scope: AMRFinderPlus scope (core or plus).

  • Element Type: Type of AMR element (e.g. AMR).

  • Subtype: Subtype of AMR element (e.g. POINT, AMR).

  • Class: Antibiotic class (e.g. BETA-LACTAM).

  • Subclass: Antibiotic subclass (e.g. CEPHALOSPORIN).

  • Method: Detection method (e.g. POINTX, BLASTX).

  • Target length, Reference sequence length, Alignment length: Sequence length metrics (bp).

  • % Coverage of reference, % Identity to reference: Alignment quality metrics.

  • Closest reference accession: NCBI accession of the closest reference sequence.

  • Closest reference name: Name of the closest reference sequence.

  • HMM accession, HMM description: HMM-based annotation fields (all NA).

  • Hierarchy node: Gene hierarchy node name required for import_amrfp.

Source

ENA projects PRJEB58139, PRJEB57389, PRJEB76977, PRJEB45627, PRJNA577446, PRJNA776899, PRJNA778600, PRJNA560592, PRJNA874857, PRJNA909328, PRJNA957547, PRJNA1161034, PRJNA1189294, PRJNA1067895. See also Golparian et al. (2024) https://doi.org/10.1016/S2666-5247(23)00370-1, Day et al. (2022) https://doi.org/10.2807/1560-7917.ES.2022.27.46.2200803, Fifer et al. (2024) https://doi.org/10.1093/jac/dkae369, van der Veen et al. (2026) https://doi.org/10.1093/cid/ciaf530, Unemo et al. (2024) https://doi.org/10.1093/jac/dkae176.