By Datuk Dr M Jegathesan Clinical Consultant (Microbiology)
Amongst the disciplines available in a clinical pathology laboratory, microbiology appears to be the least used and sought after by practicing clinicians. An exception perhaps is the serological tests for diseases such as HIV and hepatitis, which by virtue of automation have now entered the realms of biochemical methodology. Even under these circumstances there are issues of interpretation and results that may not be always easy to manage.
There are a number of reasons why microbiology is not used as extensively as it should be:
- The expected outputs are not as exact or precise as in biochemistry as we are dealing with living things and on many occasions the causative agents are difficult to isolate.
- Even if organisms are isolated in culture one is not always able to ascribe a pathogenic role as the organisms could merely be commensals or contaminants.
- Being living organisms, microorganisms take time to grow and identify and are also affected by extraneous factors such as antibiotic therapy and even natural anti bacterial substances in the patient's body fluids.
To offset some of the above shortcomings, rapid methods have been suggested as a possible alternative, but rapid methods themselves have their own constraints. For instance, in general a positive result while indicating evidence of the presence of the organism will not clarify whether the organism identified is still viable and alive. Furthermore rapid methods do not deliver a live culture on which further characterising work including antibiotic sensitivity testing can be done. Whilst all these constraints may not be solved immediately or with ease a number of things can be done to minimize some of them and improve the outputs from a microbiology laboratory.
- Improving the quality (viability) and representativeness (reflective of the lesion) of the sample submitted to the laboratory. The enhanced value of a stool sample vs rectal swab in the isolation of gastrointestinal pathogens is a case in point for the former and the demonstration of cellular elements as an indicator of the integrity of sputum for the latter.
- Improving the quality of transport of the specimen (including where indicated refrigeration) to ensure that it retains its viability. The use of appropriate transport media may facilitate this.
- The incorporation of methods in routine work up to enhance viability or representativeness e.g. the use of urine dip sticks instead of 'mid stream' urine as a method to overcome overgrowth of bacteria due to prolonged delay in processing.
- Ensuring that specimens for bacteriology are taken before any antibiotic is administered to the patient
- On receipt of the specimen in the laboratory not omitting to do the simple microscopy, both unstained and stained, where indicated before processing specimens. Such examination would give valuable clues as to likely presence as well as type of bacteria, and the most appropriate media to use under the circumstances. Examinations of unstained specimens will enable motility of organism present to be observed which on occasion can be pathognomonic.
Not withstanding the shortfalls, the importance and impact of proper microbiology on both the suffering individual for whom the appropriate antibiotic can be prescribed as well as the community at large cannot be overemphasised. In empirical therapy, where treatment is given without the benefit of microbiological testing the decision should be made on the basis of an intimate knowledge of the prevailing epidemiology, an insight of which can only be obtained through accumulation of laboratory based evidence involving both causative agents and their antibiotic sensitivity patterns in particular settings.
In the outbreak situation the ability to rapidly identify the causative agent will make a significant difference to the control measures to be implemented based on the predicted behavior of the implicated pathogen, the best treatment for it and the most likely method for its eradication. The expertise of the microbiology laboratory to utilize a series of epidemiological markers (antibiograms, serotyping, biotyping, phagetyping, genotyping and molecular typing) will further complement the control personnel's efforts in tracing sources of the outbreak and hence facilitate its eradication.
While traditional microbiological methods of culture and identification will continue for a while as the mainstay of laboratory support in the diagnosis, treatment and control of infectious diseases, the role of the more modern rapid techniques including molecular biological methods as well as the increased use of automation has potential to grow in anticipation of its improved efficacy, reliability, user friendliness and reduced cost.