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From a practical viewpoint, clinical bacteriology can be subdivided into three main activities. First and foremost is detection, isolation, and identification of pathogens. This is usually achieved by culture of specimens on specific media in defined conditions, accompanied by microscopy and tests of biochemical activity of an isolate. Second is the determination of antibiotic susceptibility, and occasionally, strain markers of clinical relevance—for example, serotypes, toxins, and so on. The third activity is epidemiological identification or comparison of isolates of the same species for infection control or population analysis. This has, until recently, been the preserve of the reference laboratory but devolution of increasingly complex techniques to diagnostic settings is gathering pace. In this article we review some areas in which molecular techniques are being applied for laboratory diagnosis and we examine developments in two basic strategies for test development and the technology required for their delivery to the laboratory bench.
Detection, isolation, and identification of pathogens
It can be argued that for acute bacterial infections, the clinical laboratory provides solely confirmation or denial of a clinical diagnosis, because in many cases treatment of the patient will already have begun. Most bacteriological reports are generated at least 48 hours after the receipt of the specimen. This delay largely reflects the staining and microscopy of the specimen and the growth of the organism in pure culture. The limitations of microscopy and culture include poor sensitivity of staining methods; uncultivable, slow growing, or fastidious bacteria; and the potential hazard to staff of handling highly dangerous pathogens. Other conventional methods such as antibody or antigen detection may suffer from false positive or false negative reactions, cross reactions, background titres, and non-specificity. Despite these drawbacks, conventional methods continue to serve the diagnosis of infectious diseases well, but there is considerable room for novel molecular approaches.
Nucleic acid techniques for detection and …
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