Antibiotic resistant superbugs of hospital acquired infections are increasing to dangerous level so that mechanism of antibiotic resistance should be studied.
Honestly, this is whole genome sequencing. WGS provides all the information you need about resistance mechanism and epidemiology (MLST, sequence type, etc.) of the strains. However, it is not a routine technology at this time.
Just take it, in case of Staphylococcus aureus MRSA strains which mecA cassette gene is involved, there is reports shown even single nucleotide mutation comes with susceptibility to methicillin therefore presence of mec isn't enough to say having MRSA.
Using Random Amplified Polymorphic DNA (RAPD) analysis for resistance detection is a good method. The development of new molecular techniques, e.g., PCR using molecular beacons and DNA chips, expands the possibilities for monitoring resistance. Please go through these documents. https://cmr.asm.org/content/14/4/836 https://pdfs.semanticscholar.org/ef81/cc5c41776c16de8981cc9ca1b8a28772478b.pdf. Article Diagnostic accuracy of molecular methods for detecting marke...
The advanced methods are described in detail in the one below.
Article Recent Advances in the Studies of Molecular Mechanisms Regul...