Microbiology analyses - New methods for measuring environmental microorganisms

In most fields of activity concerned by microbiological contamination of the environment (pharmaceuticals, agri-food, other industries and the health sector), contamination of air, surfaces and water is measured by counting colonies on agar, or viral plaques in cell culture, after collection of micro-organisms (by impaction for air, by contact for surfaces, and by water sampling). The result is given in CFU (colony-forming units) or PFU (cell lysis plaque-forming units), per cubic meter of air, per square centimeter of surface, or per milliliter or liter of water.

The criteria for classifying isolated micro-organisms correspond to morphological aspects or chemical characteristics (coloration, metabolism, resistance to certain antimicrobials, etc.). The result is obtained, in the best of cases, within 24 to 48 h, but it can take up to several days, or even weeks, for slow-growing micro-organisms. What's more, it has been suggested that only 1-2% of all environmental bacteria are cultivable on culture media.

Since the 1980s, the development of new microbiological analysis methods, and the gradual availability of these methods in environmental microbiology laboratories or on site, have introduced new microbial identification criteria. By their very nature, these new methods are generally associated with more sensitive, more precise and more reproducible results, while being capable of confirming, or ruling out, microbial contamination very quickly. This means that effective protective measures, or disinfection where necessary, can be put in place quickly and appropriately.

Among these new methods, it is traditional to distinguish between rapid microbiology methods (methods or instruments that enable rapid detection, in comparison with traditional methods, but require microorganism growth), and alternative microbiology methods which, in addition to their speed, do not require microorganism multiplication. The classification of rapid and alternative methods generally depends on their technology, i.e. micro-organism growth, viability, presence/absence of cellular compounds, nucleic acid recognition and reading. They can provide qualitative (presence or absence of microbial contamination), quantitative (numerical results giving the number of microorganisms present) and discriminative (identification of the microbial species present) results.

The use of these new methods, as a complement to culture-based analysis, overcomes the limitations of traditional microbial identification methods, such as the detection of non-cultivable bacteria, the delays inherent in culturing micro-organisms to obtain a result, the subjectivity of colony counts or even the interpretation of staining (e.g. Gram method)