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On-line orders - Molecular detection of microorganisms

Molecular detection of pathogens (molecular microbiology) is a new, dynamic and progressive arm of the classic, cultivation-based microbiology. It plays an important role in clinical situations when standard microbiology (relying on the successful cultivation of potential pathogens) produces suboptimal results or completely fails.

Classic, cultivation – based microbiology

Classic, cultivation-based microbiology is a diagnostic mainstay that deals with cultivation requirements of individual microorganisms (bacteria, fungi, viruses) and their biochemical properties. The absolute requirement for the identification of a microorganism is its successful cultivation in supportive cultivation media, followed by the identification itself (morphology, biochemistry, MALDI-TOF). If the microorganism is cultivatable, classic microbiology can also detect its antibiotic/antimycotic resistance. Nevertheless, in cases of uncultivatable agents (for example Ehrlichia, Borrelia, Chlamydia), fastidious pathogens (viruses, strictly anaerobic microorganisms), or microbes with compromised fitness (sub-optimally sampled specimens, long or sub-optimal transport conditions), the classic cultivation-based microbiology might completely fail.

Molecular microbiology

Molecular microbiology does not deal with cultivation requirements of individual microorganisms. Molecular microbiology relies on the precise quantitative identification of unique DNA/RNA spectra of the agents in any biological material. Using this approach, microorganisms are not only accurately identified, but the technology also allows for their precise quantitation. The quantitative finding is of high clinical relevance for the assessment of the causality of the agents identified; especially if primarily non-sterile biological material is investigated (mixed-microbial flora specimens). If more than one pathogen is present is the biological sample, the quantitative analysis can address their potential clinical importance.

Advantages of molecular microbiology

  • Molecular microbiology does not depend on cultivation criteria of individual microorganisms. The cultivation requirements might often be highly specific and demanding. Molecular microbiology deals exclusively with unique DNA/RNA profiles of the individual microorganisms.
  • Molecular microbiology does not have any limitations, in respect to the biological material investigated. Any biological specimen is suitable for molecular analysis.
  • Molecular microbiology works within hours (targeted quantitative detection using pathogen-specific probes) or in a few days (qualitative or quantitative pandetection of bacteria and fungi using Sanger sequencing or NGS - Next Generation Sequencing, respectively). Molecular microbiology is a method of choice for clinical cases when the result from classic microbiology (cultivation) is negative or dubious (successfully cultivated microbe does not seem to be the causative one), the patient suffers from a hyperacute infectious clinical condition (sepsis, meningitis etc), or the sampled specimen is limited in size (molecular microbiology is based on amplification techniques) or limited in fitness (suboptimal sampling or transport conditions).
  • Molecular microbiology, per se, is not able to address susceptibility to antibiotics/antimycotics in its full complexity. Resistance of microbes to antibiotics is a phenotypic feature and no genetic test is able to evaluate it in full extent. Nevertheless, the absolute majority of bacteria or fungi (except for polyresistant nosocomial agents) have their specific and naturally occurring antibiotic/antifungal profiles and can be eradicated purely based on the knowledge of their species identity. Moreover, as mentioned above, many microorganisms are a priori uncultivatable or fastidious so that assessment of their antibiotic/antifungal profile is impossible anyway.

Diagnostic role of Molecular microbiology

Molecular microbiology plays an important diagnostic role in clinical situations when classic microbiology, based on the cultivation of microbial agents fails due to its technical limitations (uncultivatable or fastidious agents) or its often-sub-optimal speed (several days/weeks needed to successfully cultivate and identify the causative microorganism).

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