Tag Archives: electronic ordering

“The Microbiology Lab in 2050….”

Future of Microbiology, , ,

What will you be doing in 2050?

I will be 77. Fingers crossed I will still be alive. If so, I will probably still be working, as by then the retirement age will likely have gone up to 80!

Have you thought about how clinical microbiology laboratories in general might look in 2050?

Here are my thoughts:

  • They will be highly automated. Much more like the biochemistry and haematology departments of today.
  • They will generally be big. Because of the above, laboratory “capacity” will often be far in excess of (local) demand.
  • They will be virtually paperless. Accreditation agencies will insist on electronic audit trails and fully interfaced hardware, and rightly so.
  • Electronic ordering will be the norm. …and with it the ability to reject tests due to insufficient details or because a similar test was done a couple of days ago.
  • For bacteria, culture will still be around, but in a hands off mode. I suspect genital and enteric bacteriology will have gone completely molecular. Testing of general wound swabs, respiratory samples, urines and sterile site samples will probably still be culture based in part, but culture inspection will almost certainly be of a digital image, as part of an automated processing system.
  • Antimicrobial Resistance Testing will remain controversial. Likely to remain a combination of phenotype, genotype, and increasingly proteotype.
  • Maldi-TOF will have evolved. ID of filamentous fungi and mycobacteria will be routine on Malditof. Several different resistance determinants will be identifiable by mass spectrometry. The hardware will be more sophisticated than currently.
  • Sequencing will be common. More common than nowadays, but I suspect their main role will still be in roles outwith routine diagnostic microbiology, eg genetic tumour markers, HLA typing, outbreak typing etc.
  • Microscopes will be very different. Will be completely digital, with viewing and manipulation done on a large screen. Looking “down” a microscope will be a thing of the past.
  • Training will be very different. Training will be more focused on troubleshooting automated systems and quality control processes as opposed to learning about the individual micro-organisms.
  • There will be a lot less microbiologists about. Microbiology scientists and technical staff, as well as Clinical Microbiologists will all be reduced in number due to both the automation and also the cost.

I look forward to checking back on this post in 33 years time to see how accurate these predictions turned out to be…..!

Michael

“The devil is in the (clinical) details”

Confessions of a Microbiologist, , ,

Lack of clinical details on the request forms must affect thousands of microbiology laboratories worldwide.

"Very high temperature, query cause?"
“Very high temperature, query cause?”

Clinical details are important for the following reasons along with a few examples, of which there are many more:

  • In deciding what different tests to carry out on the sample. Particularly important in enteric samples, where travel history and duration of symptoms can lead to more efficient testing.
  • In deciding what antimicrobial susceptibilities to report. For example if the patient is pregnant, has a history of antibiotic allergy, has a history of an MDRO etc.
  • It also ensures that the requestor has thought about why he/she is ordering the test. If the requestor understands why they are ordering the test, it is likely to make inappropriate ordering less likely in the future.

As mentioned before, I think the introduction of electronic ordering will alleviate this problem to some extent. With electronic ordering one can simply prevent the request being completed unless some clinical details are submitted.

Laboratories have traditionally taken a very passive approach to this problem, processing everything that arrives at reception. I think this will change with time, as laboratories gradually become their own gatekeepers and the technologies to facilitate this come into play.

I would love to one day be part of a laboratory set-up where short but pertinent clinical details are mandatory on the request form for a microbiological sample.

I would not be looking for an essay, just a rationale for the test and any other pertinent clinical details as necessary….

I am interested in whether anyone else makes clinical details mandatory for microbiology samples, and what their experiences are of this?

Michael

p.s. You may be interested in this website on pharmaceutical microbiology. http://www.pharmamicroresources.com/

“All samples are equal but some are more equal than others…”

The Art of Microbiology, , , ,

Most samples that arrive into the microbiology laboratory are processed. However there are some where the clinical usefulness of the result must be almost negligible.

Let me give you a few examples…

Swabs of boils that have just been lanced. It is the lancing (draining of pus) which will almost certainly lead to the infection being cured. Much the same applies for peri-anal abscesses.

Swabs of chronic ulcers, including pressure sores. These will almost certainly be colonised by bacteria. Even if a “pathogenic” organism is isolated, it is impossible to say what it means in this setting.

Culturing drain fluids from drainage bags where the drain has been in for more than 5 days. Whatever bacteria are growing in the drainage bag will bear little relation what is growing in the collection that the fluid has come from.

Swabs from ears where the history is of a straightforward otitis externa. Outer ear canals grow all sorts of junk which rarely means much in this clinical setting.

Samples from long term urinary catheters where urine has become cloudy or smelly. This demonstrates that urine has become colonised with bacteria which will always happen eventually when a catheter is in situ. Usually an indication to change the catheter.

Follow up urines after a urinary tract infection has been treated. Rarely indicated, except in pregnancy, pre-urological surgery and in transplant patients. Treat the patient, not the laboratory result.

and the list goes on….

I suspect samples from the above list make up a good 20% of the daily workload of a microbiology laboratory.

But how do you police it?

Not easily. Probably needs a combination of the following:

  • Education of Laboratory Users: Grand Rounds, Clinical Updates etc etc
  • Feedback in the form of a comment added to the test report where the test looks to be unjustified.
  • An insistence on clinical details supporting a rationale for the test.

Regarding the last point, I think the establishment of electronic ordering, which is now starting to come into many labs, may facilitate this, effectively making it impossible to complete test ordering without a supporting clinical rationale for the test.

We process most microbiology samples that come into the lab because it has always been done this way. However with the health budget becoming ever tighter, it is time for the laboratory to move from being the passive recipient and start becoming the gatekeeper for what should be done and what should not.

Think how much time it would free up with at least 20% of the workload gone, and also with the knowledge that the vast majority of specimens that you were working on were genuinely important….

Michael

On another topic altogether, click here for an interesting article on looking for anti-microbial substances on the seabed, a good place to look in my opinion.