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Chapter 20 : Emerging Tools for Microbial Diagnosis, Surveillance, and Discovery
Category: Clinical Microbiology
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This chapter provides a review of methods and perspectives for pathogen surveillance and discovery, and discusses the challenges in proving a causal relationship between the presence of a candidate organism and disease. To illustrate the complexity of pursuing pathogen discovery research, examples from the authors' own work that are intended to provide insights into the process that leads to the selection of particular strategies have been included. Although this chapter focuses on molecular methods for pathogen surveillance and discovery, the importance of clinicians, for both humans and animals, as well as experimentalists with expertise in pathology, serology, and culture techniques is emphasized. Mass spectrometry is an intriguing approach to pathogen discovery; however, potential problems include mutations in flora that alter spectra without clinical correlation, the requirement for establishment of large libraries of spectra representing flora of thousands of organisms propagated in vitro and isolated in vivo, and the difficulties associated with extending this technology to viruses, where disease may occur without robust protein expression and pathogenicity may be correlated with single base substitutions. Colony collapse disorder (CCD) is a syndrome wherein honeybee (Apis mellifera) colonies inexplicably lose the majority of their adult workers. The observation that CCD is transmissible through reuse of equipment from affected colonies, and that such transmission can be broken by irradiation of the equipment before use, is consistent with a role for an infectious agent in the pathogenesis of CCD.
Staged strategy for pathogen detection and discovery.
Method of MassTag PCR. MS, mass spectrometer; A and B indicate mass tags.
Composition of the Greene Pathogen Database.
Analysis of high-throughput sequencing (HTS) data. BLASTN, basic local alignment sequence tool (nucleotide queries); BLASTX, basic local alignment sequence tool (deduced amino acid queries).