Often, we talk about epidemics, infection outbreaks etc. The technology has advanced sufficient enough in past 10 years for us to efficiently track and come up with epidemiological pattern in a matter of days. Organisms are seldom talked in terms of species. Rather we prefer, to talk in terms of strains, sub-types, genotypes etc. With the ability to sequence an entire bacterial genome in less than a day, molecular epidemiology is a simple thing (Not really!! But compared to what was something a decade ago, it really is simple). Often you would read publications on genotypic epidemiology with fancy graphs and pictures. But how many of us have given thought on how to type? Basic question.
|Fig 1: Typing methods.|
|Fig 2: Criteria|
1. The target which is to be typed is sufficiently variable. That means, if all the E coli is expressing the same antigenic "O", then it is not of potential target.
|Fig 3: Delicate balance between variability|
3. If there are 2 targets it should be resolvable. That means there are no confusing reactions. in other words technique should be able to discriminate between two different types even when they appear to superficially related.
There are a set of strains called as "Untypable strains". There will occasionally be a strain that cannot be typed by one method. Such strains are called as untypable. For example, there are Spa-untypable S auerus strains. But they can be typed by other genetic methods.
That means you have to select a target that has sufficient chance to vary but doesn't vary so often (Or lets simply call it stable). With genetic methods, there is an additional advantage of estimating evolutionary pattern and hence we can cluster the types and follow lineages. There is a very detailed discussion about the epidemiological typing methods in Microrao and recommend you have a look at it (Link).
One more question. What is the point of typing. Isn't it enough to know the pathogen.
There are several answers to this question. The first important point is, different strains have different pathogenic ability despite being the same species. For example, USA 300 which is a particular clone type in S aurues has higher pathogenic ability than some of its other counterparts. 0157 H7 strains of E coli are known to be notoriously pathogenic causing complications in comparison to other types. The second point is tracking. When there is a sudden increase in number of a particular case typing helps to track down the source of infection and also the pattern in which it is moving. By knowing these parameters it is possible to control these issue and thus reduce the spread of such an infection.
van Belkum A, Tassios PT, Dijkshoorn L, Haeggman S, Cookson B, Fry NK, Fussing V, Green J, Feil E, Gerner-Smidt P, Brisse S, Struelens M, & European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group on Epidemiological Markers (ESGEM) (2007). Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clinical microbiology and infection, 13 Suppl 3, 1-46 PMID: 17716294
Struelens MJ (1996). Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems. Clinical microbiology and infection, 2 (1), 2-11 PMID: 11866804