Monthly Archives: August 2016

“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…

Michael

“The Road to Hell”

road to hell

“The road to Hell is paved with good intentions” (ancient proverb)

  • A laboratory might culture only 50 samples in a year for mycobacteria and look forward to getting a positive culture for Mycobacterium tuberculosis once in a ‘blue moon’.
  • A scientist might be happy to report “No microfilariae seen” on a blood sample despite having last seen a positive case of filariasis 25 years ago.
  • A clinical microbiologist might be willing to give advice on the significance of a rare filamentous fungus that they have only read about in the textbooks.

If I am doing a lab inspection/accreditation for another microbiology laboratory, one of the first things I do is find out is what tests/procedures are being done in low volume. (the other is to spend as much time as possible with the staff on the benches, to find out what really happens in the lab…)

We all have good intentions, but the cold reality is that if we only encounter something very occasionally, the chances of us getting it wrong are much increased.

Quality and knowing your/the lab’s limitations are necessarily entwined.

There is no shame in referring low volume tests on to another bigger laboratory, nor is there shame in seeking advice about something you don’t encounter very often, from someone who does.

I work in an affluent area of provincial New Zealand. Throw me into a microbiology laboratory in Sub-Saharan Africa and I would absolutely be a fish out of water.

Despite our best intentions, we can end up doing more harm to our patients if we think we are as good at doing the things we only do occasionally, as opposed to the things we do often… 

Michael

“Tricky Trichomonas”

trichomoniasis

I have always found the diagnosis of trichomoniasis a difficult one to deal with.

Not personally of course! I am more thinking about the best approach to this issue in the laboratory…

Up until now we have been looking for Trichomonas vaginalis in every single one of the 50,000+ vaginal swabs we get into our laboratory per year.

The vaginal swabs more often than not land on our doorstep with no (clinical) indication as to why they have been sent to us. 

To me this is old style medical/laboratory practice… We need to move away from diagnosing the swab per se, just as clinicians need to move away from treating the lab result on its own , without thinking about the patient.

There are essentially three main ways to diagnose Trichomonas vaginalis:

  • Wet film or other related direct microscopy method: Cheap but very insensitive
  • Culture: usually in micro-titre plates: More sensitive but still not great. Still cheap though
  • Nucleic acid amplification, e.g. PCR: Very sensitive, but also expensive.

More and more laboratories are moving towards the molecular methods, but we (and others) simply cannot afford to test 50,000 vaginal swabs for Trichomonas vaginalis by PCR. 

Nor would it be a good use of financial resources…

So, out of necessity, the laboratory needs to move towards targeted testing; e.g. high risk age groups, sexual health clinics, on specific request, appropriate clinical details, etc.

And therein lies the dilemma – You will pick up more cases because you are using a more sensitive test, but the overall number of diagnoses might be similar because you are testing less patients.

But my gut instinct tells me that the latter approach of targeted testing (based on patient symptoms and risk factors) using the optimal test is the way of the future. Not to mention it also allows the capability to test men as well! (Trying to diagnose trichomoniasis in men using traditional microscopy and culture is virtually impossible.)

Sometimes you just have to throw the old rule book out the window and start again…

Michael

Picture courtesy of GiantMicrobes.com !