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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-014-0114-2) contains supplementary material, which is available to authorized users.
Highlights
The availability of genome sequences obtained using next-generation sequencing (NGS) has revolutionized the field of infectious diseases
Microbial genomics, enabling a rational design of most molecular assays by selecting molecular targets according to their objective, has had a major impact on the diagnosis and prevention of infectious diseases, with detection and identification of pathogens being directly performed within specimens without the need for culture [5]
We review the most relevant applications of genomics to the fields of molecular detection, identification and genotyping of infectious-disease agents, detection of virulence and antibiotic-resistance markers, design of culture media and investigation of outbreaks (Table 2; Figure 1), including those that are already available in clinical microbiology laboratories, and we offer our thoughts on how genomics might change clinical microbiology in the future
Summary
Comparison of virulent/avirulent strains Identification of lateral gene transfer. 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. 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 This method, based on point-nucleotide changes between strains of a given species, has enabled the genotyping of several bacterial pathogens [9,34-39], including Coxiella burnetii [40]. Real-time genomics for the diagnosis of infections or the investigation of outbreaks The development of NGS bench-top sequencers such as the MiSeq (Illumina) and Ion Torrent Personal Genome Sequencer (PGM; Life Technologies) has made genome sequencing compatible with the routine clinicalmicrobiology workflow [6] Such a strategy enables, within a few hours, exhaustive access to the genotype [39], virulence markers and antibiotic-resistance repertoire. This implies a constant update and curation of public databases as well as the development of systems-biology-based softwares that will enable prediction of virulence and antibiotic resistance from genome sequences
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