Approach Category Technique Common Acronym Most Common Means of Discrimination Select Publications Review Articles and/or Descriptions Hybridization Size fractionated nucleic acids Short Tandem Repeat STR labeled probe [13, 14]   Ribotyping - with rRNA probes   labeled probe [15-17] [18, 19] Restriction Fragment Length Polymorphisms RFLP labeled probe [20-22] [23, 24] Insertion Sequence Typing IS-Typing labeled probe [25, 26] [27] Size independent nucleic acid arrays Dot Blot Analysis and macroarrays   labeled probe [28-31] [32] PCR and Oligo-based microarrays   labeled probe [33-35] [36, 37] Comparative Genomic Hybridization microarrays CGH labeled probe [38-40] [36, 41-43] Microbead Array   various [44-46] [47-50] Direct Analysis of the Target (without amplification or immobilization) Plasmid Analysis Size & number analysis   agarose gel electrophoresis,  (AGE) [51-53] [54-56] Restriction Fragment Length Polymorphisms RFLP AGE [57-60] [61, 56] Restriction Analysis & Mapping Pulsed-Field Gel Electrophoresis PFGE AGE [62-64] [65-67] DNA Sequencing 16S rRNA reverse transcriptase   labeled DNA [68-74] [75-77] Target Amplification   PCR Rolling Circle Replication PCR-Restriction Fragment Length Polymorphisms PCR-RFLP  AGE [78-80] [81] Multiplex PCR mu-PCR AGE, or capillary electrophoresis (CE) with fluorescent detection [82-84] [85, 86] Real-Time PCR & Multiplex Real-Time PCR RT-PCR & mu-RT-PCR Real-time thermocycler with optical reader [87-92] [93, 94] Random Amplified Polymorphic DNA-PCR  & Arbitrary Primed-PCR RAPD-PCR & AP-PCR AGE [95-98] [97, 99, 100] Amplified Fragment Length Polymorphism  & fluorescent-AFLP AFLP & fAFLP AGE, or capillary electrophoresis (CE) with fluorescent detection [101, 102] [103-105] Repetitive Extragenic Palindromic sequence-PCR & Enterobacterial Repetitive Intergenic Consensus sequence-PCR; and others REP-PCR ERIC-PCR & others AGE [106-111] [112-116] Variable Number Tandem Repeat Multi-Locus VNTR Analysis VNTR MLVA AGE or CE with or without fluorescent detection [117-121] [122-124] Single Nucleotide Polymorphism Multi-Locus Sequence Typing SNP MLST various [125-132] [133-138] Combination Methods PCR and DNA Sequencing DNA sequencing with amplification; Whole Genome Sequencing; Next Generation Sequencing WGS 454-Seq’ing various systems [139-144] [145] Ribosomal RNA Sequencing   various [146-148] [149] Ribosomal Intergenic Spacer Analysis RISA various [150-152] [153, 154] Single Nucleotide Repeat Sequencing or Mononucleotide Repeat SNR MNR various [155-157] [158, 159] Sequence-Based Typing SBT various [160-162] [163, 164] Repetitive Element PCR & Hybridization Spacer Oligonucleotide Typing Spoligo-typing labeled probe [165-168] [169, 170] Table 1: List of common methods and techniques used for the molecular typing and molecular epidemiology of bacterial pathogens Goto home»