As we know antibiotiic resistance is a dire clinical problem with important ecological dimensions. It is in human pathogens continues to rise at alarming rates.
I am searching for antibiotic resistance genes classification systems. Is it possible to classificate them. If it is possible, which way should i choice or which algorithm should i use for ?
Hi, I am not sure about classification systems. My guess is that it would be a very hard task, given that most of the antibiotic resistant strains come from mutations (often point mutations) in "regular" genes. However, there are databases that you can query about known antibiotic resistance genes, and therefore you can access to annotated information of such genes. Some of these resources:
There are also tools developed that query more than one database. One has been described in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910750/.
Hope this is of help,
Sergio
It really depends upon what you are referring to specifically. Resistance genes can of course be classified according to what resistance they confer. But there are also subcategories within some of the resistance families. For example there are many subgroupings of B-lactamase genes as well as others. Generally these categorizations are based either on biochemical properties of the enzyme or transporter, or based on some sequence differences.
Hi Büşra Aktaş,
I think there is no specific classification system for antibiotic resistance genes because of the diversity of antibiotic classes and there are a large number of genes for each class and for each bacteria, may be you can classify the genes according to the classes of antibiotics for the different species of bacteria, as the following article
http://www.sciencedirect.com/science/article/pii/S1319562X14000941
and you can use the database of antibiotic resistance for this classification
http://aac.asm.org/content/57/7/3348.full
BEST REGARDS
Dear
I recommend you this paper: Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data. J. Antimicrob. Chemother. (2016) 71 (9): 2484-2488. http://jac.oxfordjournals.org/content/71/9/2484.full.pdf+html
Hoping to be helpful
Marius
I would like to add few points to this discussion. I do not think such a classifier is devised so far, as there are various mechanisms how drug resistance evolve in organisms, namely, 1. modification in the target molecule (by point mutation etc.), 2.expression of drug degrading enzymes, 3. drug inactivating enzymes/or small molecules, 4. it may be also due to drug efflux pumps. There may be many more discovered/undiscovered reasons. So, it is difficult to tell whether such a classifier tool could be made in near future?
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