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 | Â | Mycobacterium paratuberculosis[15] |
Streptococcus pyogenes[17] | |||
Syndrome-based detection | RT-PCR | Febrile illness [20] | |
| Â | Multiplex RT-PCR | Tuberculosis [8] | |
| Â | 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] | |
| Â | 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 | Â | Yersinia pestis[10] |
Identification of lateral gene transfer | Â | Salmonella Enterica[73] | |
Search for known virulence factors in public databases | Â | Campylobacter species [77] | |
Detection of antibiotic resistance | Comparison of resistant/susceptible strains | Â | 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] |