Monthly Archives: December 2014

“The In-Betweeners”

Confessions of a Microbiologist

Samples from bursae (olecranon, patellar, sub-acromial etc.) have always been for me in a bit of a “grey zone”, when it comes microbiological processing.

Not as critical as joint aspirates, but more important than superficial swabs.

We find it difficult to know exactly what to do with them in the microbiology lab, in terms of work-up, incubation period, and even communicating the results.

Bursa samples possibly need a section of their own within the manuals, so everyone is clear what to do with respect to them.

Michael

Best wishes for the holiday season!

“Filling in the Gaps”

Future of Microbiology, ,

If you are in any way involved with clinical microbiology labs, you will be aware of the tsunami of interest in “complete” bacteriology  culture automation. Examples of such systems are Biomeurieux FMLA, BD Kiestra TLA and Copan Wasp, along with a host of others. One of them will be at a lab near you in the near future, if not already…

A lot of these systems claim “total” lab automation. They certainly represent progress, and there are a lot of quality benefits which I will go into in another post.

So where do the new systems fall short of “complete”. Let’s go through the process..

  • Fetching the correct plates.
  • Barcoding the plates.
  • Uncapping the correct sample.
  • Inoculating the plates.
  • Taking the plates to the appropriate incubator.
  • Incubating the plate for a certain amount of time.
  • Imaging the plates.
  • Interpreting the plates.
  • Picking colonies off the plates for ID and susceptibility.
  • Interfacing results to LIS.
  • Validating the results.

The three areas highlighted in red are where these systems are not quite there yet….

Interpreting the plates: There is rapid development in software to aid scientists in interpreting agar plates. Good progress has been made in reading negative plates, reading chromogenic plates, and reading and interpreting susceptibilities. However there are still a lot of plates for which humans are still better than computers for reading. In 5 years time however, I would expect that the majority of plates will be read automatically.

Picking colonies off the plates for ID and susceptibility. At present these newer systems tend to return appropriate plates from the incubators to benches in order for the follow up work to be done. However colony pickers are being developed which will automatically pick marked colonies off plates. These picked colonies will then be used to automatically inoculate plates /broths for susceptibility testing and also a MALDI-TOF plate for identification. It is difficult to say when this technology will be commercialised, but I would guess within 5-10 years.

Validating the results: As information technology improves and the application of “logic” rules to the results becomes ever easier, I would anticipate that the vast majority of bacteriolgy culture results will eventually be released automatically, without human checking. Again I would anticipate this to happen in the next 5 years.

So there you have it. I think it is a little disingenuous for companies to claim that they already have “complete” bacteriology culture automation. Not yet, but it’s coming. I would predict by 2020 at least some samples will go through the whole bacterial culture process without being seen or touched by humans. It is a scary thought, but there is no point in denying that it is going to happen. Instead, embrace it and involve yourself with it. It is what the biochemists and haematologists have already been through in the past couple of decades….

Michael

 

“Excuses”

The Art of Microbiology,

You might belong to one of the many labs/institutions that still routinely performs susceptibility testing on beta- haemolytic streptococci. 

Beta-haemolytic streptococci are invariably susceptible to penicillin, so unless there is a clinical history of allergy to penicillin, why bother?

Here are a few potential reasons:

  • Just in case the patient develops an allergy to penicillin, or the allergy was not mentioned on the request form.
  • That is the way we have always done it.
  • People might complain or be upset if we change.
  • It is easy to do it so we might as well.
  • It gives us epidemiological information (even though we are a diagnostic lab)
  • We might be the first lab to detect penicillin resistance.

All of the above can be potentially argued, but not very strongly, and in the meantime, someone foots the bill for virtually meaningless testing. I see the above more as excuses than reasons.

Sometimes we think the sky might fall if we change a method that is engrained in our psyche, but in my experience the sky rarely falls. In contrast such changes usually makes things brighter….

Michael

…A few labs might do it because they get paid for it (fee for service funding). However in a financially constricted Health Sector this is difficult to justify morally and demonstrates one of the main weaknesses of such a funding model.