Table 1.
Methods used to type and characterize NG isolates.
| Typing method | Category | Descriptiona |
|---|---|---|
| Antimicrobial susceptibility testing | Phenotypic | Analysis based on the antimicrobial susceptibility profiles of strains, allowing the identification of AMR phenotypes. |
| Auxotyping | Phenotypic | Analysis based on the specific nutrient requirements of strains (i.e. growth or lack of growth), allowing strain differentiation when used in combination with serological methods. |
| Serology | Phenotypic | Analysis based on the antigenic properties of PorB (an outer membrane porin), allowing strain differentiation when used in combination with auxotyping methods. |
| RFLP | Non-sequence-based | Analysis based on the digestion of the bacterial genome by restriction endonucleases followed by fragment separation via electrophoresis (e.g. polyacrylamide or pulse-field gel electrophoresis), allowing strain differentiation and characterization. |
| Ribotyping | Non-sequence-based | Analysis based on the digestion of chromosomal DNA by restriction endonucleases followed by the hybridization of rRNA fragments to specific probes, allowing strain differentiation and characterization. |
| PFGE | Non-sequence-based | Analysis based on the digestion of the bacterial genome by restriction endonucleases followed by fragment separation via pulse-field gel electrophoresis, allowing the identification and characterization of AMR clusters. |
| MLST | Sequence-based | Analysis based on the detection of variation between the sequences of seven conserved housekeeping genes, allowing the identification and characterization of AMR clusters and associated transmission patterns. |
| NG-MAST | Sequence-based | Analysis based on the detection of variation between internal fragments of the highly polymorphic porB and tbpB genes, allowing the identification and characterization of AMR clusters and associated transmission patterns. |
| WGS | Sequence-based | Analysis based on the detection of variation throughout the bacterial genome (using genomic, transcriptomic, and/or epigenomic analyses), allowing the identification and characterization of AMR clusters and associated transmission patterns and resistance determinants. |
RFLP: restriction fragment length polymorphism; PFGE: pulse-field gel electrophoresis; MLST: multilocus sequence typing; NG-MAST: NG multiantigen sequence typing; WGS: whole-genome sequencing.
a
See Unemo and Dillon (2011) for a thorough review of NG-typing methods.