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Studying bacterial infections through culture-independent approaches

Molecular Microbiology Research Laboratory, Pharmaceutical Science Division, Franklin-Wilkins Building, King's College London, 150 Stamford Street, London SE1 9NH, UK.
Journal of Medical Microbiology (Impact Factor: 2.27). 06/2009; 58(Pt 11):1401-18. DOI: 10.1099/jmm.0.013334-0
Source: PubMed

ABSTRACT The ability to characterize accurately the cause of infection is fundamental to effective treatment. The impact of any antimicrobial agents used to treat infection will, however, always be constrained by both the appropriateness of their use and our ability to determine their effectiveness. Traditional culture-based diagnostic microbiology is, in many cases, unable to provide this information. Molecular microbiological approaches that assess the content of clinical samples in a culture-independent manner promise to change dramatically the types of data that are obtained routinely from clinical samples. We argue that, in addition to the technical advance that these methodologies offer, a conceptual advance in the way that we reflect on the information generated is also required. Through the development of both of these advances, our understanding of infection, as well as the ways in which infections can be treated, may be improved. In the analysis of the microbiological content of certain clinical samples, such as blood, cerebrospinal fluid, brain and bone biopsy, culture-independent approaches have been well documented. Herein, we discuss how extensions to such studies can shape our understanding of infection at the many sites of the human body where a mixed flora, or in more ecological terms, a community of microbes, is present. To do this, we consider the underlying principles that underpin diagnostic systems, describe the ways in which these systems can be applied to community characterization, and discuss the significance of the data generated. We propose that at all locations within the human body where infection is routinely initiated within the context of a community of microbes, the same principles will apply. To consider this further, we take insights from areas such as the gut, oral cavity and skin. The main focus here is understanding respiratory tract infection, and specifically the infections of the cystic fibrosis lung. The impact that the use of culture-independent, molecular analyses will have on the way we approach the treatment of infections is also considered.

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    • "This is because the largest portion of microorganisms (generally more that 99%) cannot be cultivated under standard laboratory conditions (Amann et al. 1995). Well studied environments that display viable but not culturable microorganisms include soil (Torsvik et al. 1990); the activated-sludge process for waste-water treatment (Wagner et al. 1993); clinical samples exhibiting mixed communities of biofilm-forming bacteria resistant to antibiotics (Rogers et al. 2009); and foods and beverages (Mamlouk et al. 2009). For these reasons, a combination of culture-dependent and independent methods can maximize the estimation of microbial richness in complex ecosystems, as well as the detection of non-cultivable but functional microbes. "
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