Wednesday, March 01, 2017

BtB# 12- Why is ID a Requirement in Clinical Microbiology

I have been recently on a very tight schedule with regards to my work and hence have not been able to post for past couple of weeks. In this post, I want to talk about a very basic clinical microbiology question. A clinical microbiologist often encounters several different types of microbes in the clinical samples. For bacterial isolates, antibiotic resistance profile is tested and the treatment is decided based on the profile obtained.

So the question, why do you actually need to identify the pathogen? If you have a colony growing there, wouldn't it be sufficient to test antibiogram and then start treatment based on that? Why devote resources to go ahead and identify the pathogen? Sounds a trivial question. I have asked this question myself as an undergrad (Yeah, I know!!! The typical undergrad who keeps asking boring questions). But, if you consider that most of the times it is desirable to not only identify the species but also go ahead and identify its serotype or pathotype identity (Not in all cases), the question doesn't look so trivial.

If you can distill all the reasons, there are following essential reasons of why a clinical microbiologist like to identify the pathogen.

1. Predict the likely outcome of the infection.
2. Predict likely sensitivity to antimicrobials.
3. Obtain research information on a new disease.

There is a great depth of clinical research that has been done and thus the most likely outcomes of a given infection are almost predictable. For example, identification of E coli or Shigella dystentriae has different meanings for the expected clinical outcome when isolated from the stool sample. The treatment strategy varies accordingly and mere antibiotic sensitivity is not enough for the treating physician.

International and local data are available regarding antibiotic resistance pattern for a good number of pathogens. Certain pathogens are inertly resistant to different antibiotics. For example, Pseudomonas aeruginosa is inherently resistant to tigecycline and I will not even consider testing for tigecycline if my presumptive identification of the pathogen is P aeruginosa. The same is the case for colistin in the case of E meningoseptica. If the pathogen is known, treatment can be started more accurately even though the actual resistance profile is not known.

The third reason is that fishing can be a good research in itself. Thanks to an increasing ability conferred by genetic diagnostics, many different infections have been attributed to agents that otherwise were previously not attributed to being pathogenic. The knowledge of different species that can cause infection has significantly expanded. Interestingly, it has been the opinion that in many cases the species identification has been wrong (Shown using genetic tests) and they are in reality a different species.

The immediate next question is when is it desirable to identify upto a species level and when is it necessary to go beyond?

For most cases speciation is sufficient except for those situations where sub species has a different clinical effect. For example, it is sufficient to know for treating physician that the skin infection is caused by S aureus and is not a MRSA to treat. Knowing its clonal type and further wouldn't be of immediate patient interest, though it maybe pursued to study molecular epidemiology. For Salmonella enterica, identified from a stool sample, it is desirable to further identify it as Typhi/Paratyphi/Cholerasuis etc. It is also advisable to go further down the line, if something unusual is noticed. For example, If a particular type of resistance pattern is constantly observed from same ward it indicates a possible outbreak which should be investigated by typing.

I should end with a note. There are situations where the identification hasn't been yet done but resistance profile is available. For example, in cases of meningitis where most probably there is a single species involved, organism can be plated and on other hand a heavy inolculation can be made on MHA and antibiotics put directly. This has been shown to effective by some studies in reducing the time for reporting. In such cases, the ID is not yet available but the probable resistance profile is available to aid physician. It should be noted that this is not a confirmatory situation. This is usually followed up with routine culture, identification and sensitivity testing.

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