Bacterial Identification: How do they do it?

Magic. 

Magic is far from getting a correct identification of bacteria. 

I am pretty sure 90% of medical doctor do not know what is going on with the blood culture they have taken from a patient. They would only expect that some result will be handed to them stating the name of the bacteria and what antibiotic that is susceptible to it. It is just like magic. They must be some magical machine that we use by entering a certain amount of blood and it magically processes until a piece of paper came out at a different port as a culture result. 

The process however are more complicated than that. With the help of technology ,however, we were moving ahead quickly to the future where magic could really happen like what I had described above. 

Microbiologist used to culture the blood specimen everyday. Once it reaches the lab, a drop of blood will be streaked on to a culture plate and put into an incubator. One day later, the culture plate will be reviewed. One day later also, if the culture did not grow, another drop of blood from the bottle send will be streaked again on a culture plate and incubated. This process happen everyday until they grew something out of it. If it does not, at day 5, the last process of streaking on a culture plate will be done and it will be incubated at least for 2 days. In total, they will be seven days before official result will be out. The process is labour intensive and imagine how many culture plate were needed to culture the blood everyday.

Technology change everything. A bactec system were created a few years back. This system really change everything. With this system, a special bottle were used to collect the blood (aerobic and anaerobic bottle) containing enriched medium or ‘food’ for bacteria to grow. The system incubate and automatically detect whether bacteria are presence or not inside the bottle by measuring CO2 produced by bacteria (a common sense, if there are living thing inside, it must produce CO2). This process took 5 days and if the there were no bacterial growth detected, official result will be out after 5 days. This cut 2 days compare to manual technique used previously. Basically you don’t have to do anything for that 5 days if bacteria were not presence. 

If the system detected presence of bacteria, then the blood will be streaked onto a culture plate and incubated for 24 hours. After 24 hours, the colony of bacteria is ready to be identified. If it does not grow, it will be reincubated. If it still no growth, the culture will be incubated in an anaerobic condition to see whether it could be an anaerobic organisms ( bacteria that could not live with oxygen). 

If we imagined how a microbiologist identified a bacteria, one thing will came to our imagination that is a microscope- a person with white coat looking at microscope and start giving name for a bacteria. That is only a small part of it. That process of looking at bacteria that was stained with a different stain specific for a certain bacteria could give a presumptive identification, only presumed…. 

To be certain, biochemical test will be used. There were a lot of biochemical test and it reaction can give a certainty for the identification. A microbiologist will choose which test to be done, if it was chosen wrongly, none or wrong identification will be made. That is dangerously harmful to patient. Thus, a microbiologist must be certain on which test to be done. 

A few commercial kit already available today ( eg: Analytical profile index, ID 32, etc…). This kit test multiple biochemical reaction on a single test strip. The reaction were notes and a combination of reaction will be calculated by an online server to gave an automatic identification for the bacteria. This remove human error elements. Safe to assume that no wrong test would be chosen because generally test everything. Microbiologist or technologist however need to choose which kit to be used. Instead of remembering 100 if not thousand biochemical test, now we only need to remember a few test kit to be used. There were more advanced technology such as Vitek system,MALDI TOF, or molecular technique such as rt PCR and etc, which make identification much more accurate and specific. 

Technology is the magic in microbiology. The flaw is, technology can’t correlate with clinical presentation of a patient. It just process whatever you put inside them and provide the most accurate identification, but our life were full of bacteria. It was like shooting a flock of birds. You want the bird with the red beak among hundreds with other beak colour… no matter how advanced your sniper rifle is, you need to aim it in a right direction.. Same as the technology in microbiology, it must be aimed to a right direction for identification. 

In the future, they might be a technology that can correlate with patient clinical presentation, and identify the bacteria accordingly. Will it replace human in the field of microbiology? Possible. It could be a good thing so that we can focus on other part of the field, and open up more possibility for the benefit of mankind.