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Table 2 Current applications of high-throughput genome sequencing in clinical microbiology

From: Clinical detection and characterization of bacterial pathogens in the genomics era

Objective Methods Applicationsa Examples [references]
Pathogen detection Identification of target fragments and PCR primer design   Mycobacterium paratuberculosis[15]
Streptococcus pyogenes[17]
Syndrome-based detection RT-PCR Febrile illness [20]
  Multiplex RT-PCR Tuberculosis [8]
  Microarray Pneumonia [22]
Highly sensitive molecular detection PCR targeting multi-copy targets Whipple’s disease [23]
Suicide PCR Rickettsioses [24]
Genotyping DNA banding methods Pulsed-field gel electrophoresis, PCR-RFLP Yersinia pestis[9]
Presence/absence of genes RT-PCR Acinetobacter baumannii[29]
Presence/absence of repeats MLVA Mycobacterium tuberculosis[32]
Presence/absence of point mutations SNP detection Bacillus anthracis[35]
Whole-genome typing Microarray Escherichia coli[44]
  Genome sequencing Staphylococcus aureus[61]
Multiple gene sequencing MLST Escherichia coli[49]
Multiple non-coding fragment sequencing MST Rickettsia species [56]
Detection of virulence markers Comparison of virulent/avirulent strains   Yersinia pestis[10]
Identification of lateral gene transfer   Salmonella Enterica[73]
Search for known virulence factors in public databases   Campylobacter species [77]
Detection of antibiotic resistance Comparison of resistant/susceptible strains   Streptococcus pneumoniae[96]
Detection of antibiotic resistance markers in clinical isolates and specimens RT-PCR Staphylococcus aureus[100]
Culture medium design Detection of defective metabolic pathways Design of specific culture media Tropheryma whipplei[12]
Outbreak investigation Genome comparison WGS Escherichia coli[118]
  1. aAbbreviations: bp, base pair; Mb, megabase; MLST, multi-locus sequence typing; MLVA, multiple variable number tandem repeat analysis; MST, multi-spacer typing; RFLP, restriction fragment length polymorphism; RT-PCR, real-time polymerase chain reaction; SNP, single nucleotide polymorphism; WGS, whole-genome sequencing.