Category Archives: The Art of Microbiology

“Testing ad infinitum”

Take for example the patient who presents with “recent weight loss”, even though their recorded weight is exactly the same as it was 6 months ago.

…or the patient who “bounds” into the surgery, looking far healthier than the doctor will ever be, and then complains of “tiredness”.

…or the patient who has diagnosed themselves with “Chronic Lyme Disease” on the internet, even though they have never travelled to an area endemic for Lyme disease.

The temptation for the clinician in such cases above is to order a whole battery of tests in order to prove to, or reassure the patient that they have no organic pathology.

The patient then leaves the clinic with a whole list of (often expensive) laboratory investigations, and thinks to themselves;

“Wow, look at how many tests I am getting. The doctor must be worried for me. I really must be sick!”

And thus the cycle goes on. The tests come back negative, but the sick role is now reinforced. The patient then often comes back for more, or goes off elsewhere to seek a second opinion…

Worse still, if enough tests are performed, then one will eventually come back falsely equivocal or positive, confusing the issue even further for the clinician. And the positive reinforcement of the sick role in the patient has just gone through the roof!

Everyone is scared of missing something, of not diagnosing that long shot… But sometimes it is best just to trust good clinical acumen, and appreciate that laboratory testing can occasionally cause more harm than good…

Michael

“The Requesting Pyramid”

In many laboratories, clinical details on request forms can be structured into a pyramid shape as below.

Let’s take the example of otitis externa.

A good proportion of request forms will be at the bottom of the pyramid, where there are no clinical details present to suggest that otitis externa is the clinical suspicion (as opposed to otitis media, cellulitis of the pinna, or some other condition). Also included in this category are cases where clinical details have been included but are unrelated to sample type, e.g. an ear swab sent with clinical details of “sore throat”. This scenario happens in all sample types with disturbing frequency… (e.g. mid-stream urine sent for a patient with clinical details of chest pain!)

The next level up in the pyramid is where clinical details are present but are insufficient to justify the sample being sent to the laboratory. For example the clinical details might state “Otitis externa“. However most patients with straightforward otitis externa do not need an ear swab sent to the laboratory. Laboratory culture of an ear swab in clinically suspected otitis externa should be the exception as opposed to the rule…

The top level of the pyramid is where clinical details are not only present, but they also give a sound rationale as to why the laboratory is receiving a sample. e.g. “Recalcitrant otitis externa not responding to topical treatment.” or “Diabetic with painful inner ear and fever, clinical suspicion of malignant otitis externa“.

This requesting pyramid applies to most different sample types and clinical scenarios.

At my laboratory, we are doing our utmost to turn this pyramid on it’s head. We have made significant progress to date. In fact our pyramid is starting to look more like a rectangle.

By the end of the year we hope to have removed the base of the pyramid altogether by adopting a policy of having accompanying clinical details pre-requisite for all microbiology tests. I.e. No clinical details, no test.

And that is the way it should be…

Michael

“Bacteriology Automation: Warts and all…”

Whether you are a microbiology student undertaking exams, a lab manager considering a business case, or a scientist wondering just what exactly the future holds, you need to know something about bacteriology automation.

We have now had the Kiestra TLA in place for 18 months at the lab where I work. It would be foolish to say it has all been plain sailing. Far from it. There have been breakdowns, computer malfunctions, and interfacing problems, particularly in the early days.

The learning curve is very steep.

But would I ever go back to traditional “manual” bacteriology processing? No way! In fact, I would go as far as to say that I would be very reluctant to ever work in a microbiology lab in the future that didn’t have automation of the bacterial culture process.

It would simply be a backward step…

With some great feedback from staff members (and expanding on a previous post), I have listed below an honest account as to what I think are the advantages and disadvantages of a bacterial automation system like Kiestra:

 

ADVANTAGES

  • Standardised incubation times: Personally I think this is one of the strongest advantages of the system. No matter when the plate was inoculated, the system will image the plate after a pre-set incubation time, and thus allow plate reading. This in turn will allow reduction in turnaround times for specimens. The old concept of Day 1, Day 2, etc. plate reading should disappear and be replaced by 1st reading, 2nd reading….
  • Plate Tracking: Each plate has a  comprehensive electronic audit trail attached to it, including when it was inoculated, incubated, imaged and read, and by whom. The audit trail is encyclopaedic, if not a little complex in nature.
  • Less menial tasks: Gets rid of finding appropriate plates for each sample, carrying the plates to and from the incubator, “putting up” of specimens, and other repetitive, manual tasks.
  • Better plate spreading: Automated spreading performed by machine will almost always succeed in better use of the whole agar plate and improved isolation of single colonies. It will also be a standardised procedure. Kiestra TLA uses the magnetic rolling bead method. It occasionally needs a bit of tweaking, but when it works, it is beautiful!
  • Less plate contamination: As the plate has less manual handling and less time spent with its lid off, the risk of plate contamination is almost certainly much reduced, which is very important for those “sterile site” specimens. A study in this area would make a nice research project for someone.
  • Storage of digital images of plates: Plates eventually deteriorate, images do not, and images can be stored to be viewed again at any stage in the future depending on how long you want to store them for. Great for presentations!
  • Less time out of the incubator: The plate goes straight into the incubator when it is inoculated, and essentially stays in the incubator whilst it is being examined. No hanging around and very little downtime. The advantage is twofold; shortened turnaround times, and a decreased chance of “losing” fastidious organisms.
  • Remote plate reading: The system should allow you to view the plate images from anywhere, including home. The possibility of microbiology scientists working from home in the near future is a real one.
  • Plate interpretation: This is still in the developmental stage but software is now available allowing rapid detection of plates with no growth, and (chromogenic)plates with colonies of a particular colour. Further development in such software will eventually lead to massive gains in efficiency.

 

DISADVANTAGES

  • Redundancy of staff: Whether staff members are made redundant or not due to the implementation of a system like Kiestra TLA, the simple fact is that this type of automation will get through (far) more specimens with less labour. Some (managers) might see this as an advantage, but from a people point of view it is a big downside. I personally find this aspect of automation very difficult to deal with.
  • Dependency on the automation: What happens if it breaks down? Because of the above, and because it is a complex operation, the consequences can be potentially serious if the system goes down. Fortunately as the Kiestra TLA is modular in nature, it is very unusual for the whole system to go down at once. We are also fortunate to have excellent engineering support at our lab.
  • Loss of ownership: Because the majority of the culture process is automated, staff members are less involved with the clinical sample from start to finish. This can lead to a loss of “ownership” of the sample.
  • Loss of continuity: Even with Kiestra TLA, there are still a few steps in the process that are still to be automated. Those steps are batched together in lists (e.g. MALDI-TOF spotting, susceptibility testing). Staff members are often only involved with one step in the whole culture process for any one patient sample. Continuity, which I regard as important, can therefore be lost…
  • More knowledge required: Not only do the staff now need to know about microbiology, they also need to know about Kiestra, how the system works, and how to troubleshoot any issues. Therefore a lot of new learning is required, as well as keeping up core knowledge in microbiology.

 

Change always comes with downsides as well as upsides.

But having said that, change is utterly inevitable, and I believe that Kiestra TLA or similar systems ( Biomeurieux, Copan Wasp) will be as ubiquitous as MALDI-TOFs in our clinical microbiology laboratories in 10 years time.

And if you understand both the pros and the cons of such systems before you start, it makes that change just a little bit easier…

Michael

A couple more posts coming on microbiology automation over the next week!