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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-014-0114-2) contains supplementary material, which is available to authorized users.

Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing

“…They also are cost effective; but, they are not accurate, sensitive, specific and cost effective in the cases with huge number of specimens [16, 17, 21, 24, 25, 36, 41, 43, 46]. …”

Proteome signatures—how are they obtained and what do they teach us?

“…Consequently, the development of proteomic studies has increased exponentially due to the suggestion that the genome sequence is not sufficient to elucidate the biological functions of an organism (Aggarwal and Lee 2003). Following the advances in whole-genome sequencing, which provides information regarding pathogen detection and identification, genotyping, determination of virulence factors, and antibiotic-resistant determinants (Fournier et al 2014), transcriptomic and proteomic methodologies have been widely used to investigate microbial global expression. In order to obtain the quantitative protein expression profile, methodologies such as isobaric tags for relative and absolute quantitation (iTRAQ), stable isotope labeling by amino acids in cell culture (SILAC), area under the curve (AUC), and isotope-coded affinity tags (ICAT) are frequently employed (Abdallah et al 2012;Otto et al 2014;Roe and Griffin 2006).…”

Targeted treatment for bacterial infections: prospects for pathogen-specific antibiotics coupled with rapid diagnostics

“…55,218 After sequencing, the infective species can be identified with the highest degree of confidence by alignment to a reference genome (if available) or by multilocus sequence typing (MLST) if a member of the same species has not yet been sequenced. 55,219 In addition to species identification, WGS provides information on the presence of resistance markers and virulence factors and is an unparalleled tool for differentiating strains for epidemiological purposes.…”

“…55 Pathogen identification directly from patient samples using a metagenomics approach removes the >24 h delay required for DNA extraction from culture, 223,224 while improvements in NGS have already drastically reduced the time and price required for sequencing (a single bacterial genome with sufficient depth coverage can now be obtained in less than a day for $200 by academic core facilities, with cost-savings truly becoming significant when many bacteria are sequenced). 55,218,225 With continued advances in NGS and automated data analysis software, 223 it appears that WGS is posed to replace all other NAT diagnostics.…”