The need of bacterial identification?

IM has discussed about alternative methods for the detection of hazardous or harmful bacteria with Dr. Elias Hakalehto.

It is most important to know the pathogens which will appear in patient samples. Clinical microbiologists shall know who are the enemies of the ill people: their metabolic capabilities, antibiotic resistence patterns etc. Their overall features are easy to find from literature or internet whenever the name of the species is known. This identification can be performed by selective cultivations on agar plates or in PMEU incubator, and further tests like microscopic examinations, API ID systems, immunological tests and/or PCR can be done to confirm the basic identification.

Paper mill is definitely another challenge for microbiologist. In some (relatively rare cases) the names of microorganisms are important to know: if the product shall have high hygiene quality (like LPB and other food-grade cartonboards) or questions about bioterrorism have been arisen (spore-forming Bacillus anthracis as an example). The occurrence of Legionella pneumophila is also a risk in the waste water treatment of paper industry today. Selective cultivations, either on plates or in PMEU, are the solid solutions for continuous microbiological control in those cases. PMEU is preferred because its speed (hours, compared to days with colony count analyses).

Papermakers shall focus more on the metabolic activities than the names of bacteria which they are living with in paper mills, however. Continuous inoculation of the paper production processes by contaminants, delivered with incoming lots of starches, mineral fillers, raw water, dry pulp etc. shall be controlled to avoid spoilage (amylolytic activity as an example), biofilm and slime growth, tastes and odours, spots and colours in the product etc. Because the wide range of bacterial species and their origin from the nature itself, clinical methods do not suit very well for this monitoring. There is no time to start labourous cultivations, pure cultures and identifications when the bacterial input continues day and night, "7/24". PMEU seems to be an excellent tool to check the basic features of process populations, their biocide resistence patterns included.

One important fact must also be taken into account. There are a lot of harmful microbes which actually cannot be cultivated on agar at all. One example are certain filamentous bacteria which may cause biofilm layers into the processes. They can be cultivated in some broths, however, but the usage of the original samples as the growth medium is the best way to detect them all. This can be done with ordinary mb laboratory equipment or with PMEU incubator.

Identification of bacterial species is still needed when the mapping of contamination routes into the processes is the subject of the study. IM will discuss about the microbiological mapping in his next posts.

Statistical methods in microbiology.

IM has discussed about the evaluation of novel microbiological methods with several professionals. His knowledge of statistical methods in microbiology bases on the lessons by Prof. Seppo Niemelä, who was (and still is) a well-known specialist in this not-so-well-known area of microbiology.

Testing of microbiological data is more complicated than similar analyses in chemistry. The main reason is the model of repeat distribution: chemistry follows the ordinary normal distribution but the colony counts of microbiological analyses are featured by the Poisson distribution. The reason for this difference is easy to understand: the count of molecules is overwhelming when compared to the limited count of colonies in microbiological cultivations. The dependence of variance on the mean of the data is another problem of colony count analyses, preventing the usage of parametric methods.

Luck enough, there are some non-parametric statistical analyses for Poisson-distributed data, helping the comparisons of means and trends of colony count results.

A novel problem seems to have arisen in microbiological evaluations since 70's. Many modern, automatized instruments of microbiology are not based on the measurements of chemical concentrations or counts of colonies but on specified metabolic activities of microbes. Examples of these analytical procedures are eg. measurements of impedance, turbidity, pH or CO2 production. Because these parameters are in a close connection to the growth rates - and to a new parameter, time - , their evaluations are very challenging procedures.

- More in next posts...