Tag Archives: sequencing

“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…


“A Game-Changer…”

Every so often a piece of research comes out that significantly affects our practice. It is refreshing to see that such research is still occasionally published, amidst the plethora of commerce sponsored papers that can be useful, but more often than not, are simply adverts.

Diverse Sources of C. difficile Infection Identified on Whole-Genome Sequencing. David W. Eyre et al.N Engl J Med 2013; 369:1195-1205.

This paper involves sequencing Clostridium difficile isolates from symptomatic patients over a 4 year period between 2007 and 2011 in Oxford Hospitals. 45% of the isolates were genetically distinct enough to suggest that their source was not from other patients symptomatic from Clostridium difficile infection.

The bottom line of this research is that it suggests that the epidemiology of Clostridium difficile is multi-factorial and that Infection Control measures will only go so far in controlling Clostridium difficile rates in hospitals. We also need to take such research into account when setting realistic targets for Infection Control teams to attain when addressing organisms such as Clostridium difficile.

These findings should not really surprise us that much… We know from previous carriage studies that approximately 10% of the population carry Clostridium difficile, so there are bound to be significant reservoirs in the hospital, peri-hospital and community settings. It may even be that some patients become infected with their own endemic Clostridium difficile strains, which are allowed to proliferate and produce significant amounts of toxin when the patient is challenged with broad spectrum antibiotics, thus creating an ecological niche for the Clostridium difficile bacteria. 

This study and another recent one on the laboratory diagnosis of Clostridium difficile have real implications from both a clinical and laboratory point of view on how we think about Clostridium difficile. As both these papers challenge established thought, they may not be readily accepted. From a lab point of view there may be a few grumbles because we may have to change and possibly increase our testing in light of these findings.

Both these papers need to be discussed in detail at departmental journal clubs, and not the interesting but highly isoteric environmental bacterium isolated on the blood culture bench for the first time in 10 years…