Tag Archives: genotype

“The Transition”

Genotype_Plus_EnvironmentAt present, routine anti-microbial susceptibility testing is still dominated by phenotype, with genotypic testing occasionally getting a look in for MDROs.

I doubt this is likely to be the case forever…

As our knowledge of genotypic resistance determinants increases, and the cost continues to decrease, I see a time when first line testing will be the resistance genotype and not the phenotype. I believe this is more likely to be a resistance genotype determined by sequencing as opposed to PCR or other molecular methods.

There will always be some difference between the genotype and phenotype as far as susceptibility results are concerned (Think about the behaviour of identical twins. It’s similar but not identical!). The environment that the bacteria lives in will see to that. However as our understanding of the genotype increases we will be able to more accurately predict the phenotype.

But the correlation will never be perfect. There will still be a role for confirming the phenotype, with phenotypic susceptibility testing indicated in the sick patient who is not responding as expected.

I can see this transition happening within my working lifetime, i.e. within the next 25 years.

However having said all this, it is important to be aware that the genotype is not always the perfect answer, and has its own set of problems (the following is an excerpt from my book, The Art of Clinical Microbiology)…

  • Genotypic resistance testing may well be over-calling antimicrobial resistance in some cases, and thus pushing patients unnecessarily towards broader spectrum antibiotics, thus starting a vicious circle of resistance. This is not something however, that is often brought up in the antimicrobial stewardship committee setting.
  • Genotypic testing will (currently) miss some resistance that is demonstrated phenotypically and due to multiple combined mechanisms e.g. carbapenem resistance in some Pseudomonas aeruginosa due to hyper-production of AmpC plus porin loss and/or efflux pump.
  • Genotypic testing will (currently) only pick up the resistance genes we know about. We need phenotypic methods to detect new resistance as it appears and then use genotypic testing to find the genetic ‘code’ for it.
  • Genotypic testing may be over-sensitive when used to screen for MDROs in the setting of Infection Control. This can lead to patient isolation or non-use of an antibiotic because of a positive result, but the burden present or organism carrying the resistance gene(s) does not pose a significant clinical risk to the patient, and possibly no Infection Control rise to the institution.

However I don’t think this will stop the transition from phenotypic to genotypic susceptibility testing happening, when the price is right…

And when this transition does occur that might spell the end for large volume, culture based diagnostic bacteriology…


“Anti-microbial Resistance Testing: Phenotype, Genotype and ?Proteotype”

There has long been a debate over whether the microbial genotype or phenotype is a better determinant of clinical response when looking at antimicrobial resistance testing. The genotype for antimicrobial susceptibility testing identifies genes within the microbe that have the potential to cause resistance. However it does not provide information on whether the gene is “switched on”. The phenotype is how the microbe responds to the antimicrobial in the laboratory setting, but would not pick up resistance potential, and in particular resistance genes that may code for “inducible” resistance.  There has been a trend in recent years for a move towards calling results from genotypic testing the “gold standard”. This is probably due to two factors:

  • Increased range of molecular assays for resistance determinants available.
  • Fear of not knowing the genotype and thus missing the potential for resistance.

My worry would be that genotypic resistance testing may well be over-calling anti-microbial resistance in some cases, and thus pushing patients unnecessarily towards broader spectrum antibiotics, thus starting a vicious circle of resistance. This is not something however, that is often brought up in the anti-microbial stewardship committee setting.

In addition to this confused picture, if Maldi-tof techniques start reliably detecting resistance determinants, then we will have another category to deal with. Maldi-tof in it’s current form in the diagnostic laboratory looks mainly at proteins, so we will therefore have the PROTEOTYPE. This is different from both genotype and phenotype. Although it provides information on gene expression, it still does not necessarily predict the phenotypic response.

Thus, as the process of anti-microbial susceptibility testing gets ever more complex, the number of people who fully understand it, (if anyone) diminishes further.

It may also be that as more and more genes are discovered that have the “potential” to cause resistance, the “gap” between the resistance genotype and phenotype, which is currently quite small, will continue to widen.

It’s an interesting topic, and I am sure debate on the above points will continue for generations yet.


p.s. I have downloaded some software which facilitates viewing of the website on I-phones etc.