Clinical detection and characterization of bacterial pathogens in the genomics era

Abstract

The availability of genome sequences obtained using next-generation sequencing (NGS) has revolutionized the field of infectious diseases. Indeed, more than 38,000 bacterial and 5,000 viral genomes have been sequenced to date, including representatives of all significant human pathogens. These tremendous amounts of data have not only enabled advances in fundamental biology, helping to understand the pathogenesis of microorganisms and their genomic evolution, but have also had implications for clinical microbiology. Here, we first review the current achievements of genomics in the development of improved diagnostic tools, including those that are now available in the clinic, such as the design of PCR assays for the detection of microbial pathogens, virulence factors or antibiotic-resistance determinants, or the design of optimized culture media for 'unculturable' pathogens. We then review the applications of genomics to the investigation of outbreaks, either through the design of genotyping assays or the direct sequencing of the causative strains. Finally, we discuss how genomics might change clinical microbiology in the future.

Figure 1

Applications of bacterial genomics to the management of infectious diseases. Genome sequence analysis has enabled the development of various clinical-microbiology tools for pathogen detection, identification or genotyping by identification of sequence fragments specific at distinct taxonomic levels (genus, species, strain, clone), for the detection of genes associated with antibiotic resistance or virulence and for the identification of deficient metabolisms to aid the development of optimized culture media. However, whole-genome sequencing, by giving access to the full genetic repertoire of an isolate, has demonstrated an undisputed discriminatory power for deciphering outbreaks of infectious diseases.

Figure 2

Principles of genome-based genotyping methods. By genomic comparison, investigators can identify specific sequence signatures that can be used in non-sequence-based methods (DNA banding-pattern-, PCR- or hybridization-based methods) or sequence-based methods (partial or complete genome sequencing). MLST, multi-locus sequence typing; MLVA, multiple locus variable number tandem repeat analysis; MST, muti-spacer sequence typing; PCR-RFLP, PCR-restriction fragment length polymorphism; PFGE, pulsed-field gel electrophoresis; RFLP, restriction fragment length polymorphism; SNP, single nucleotide polymorphism.