“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!

“Weighing up the evidence…”

  • There are some microbiology results which point so strongly towards a particular clinical diagnosis, that even counter-evidence should not put you off the scent without investigating further…

For example:

  • An Enterococcus faecalis growing in 6/6 blood culture bottles in a patient with a prosthetic valve suggests infective endocarditis, even if the trans-thoracic echo is “normal”.
  • A Streptococcus gallolyticus growing from a blood culture is suggestive of a colorectal adenoma or adenocarcinoma, even if the patient has no symptoms or colorectal history. (this bacterium was formerly called Streptococcus bovis)
  • A Bacteroides fragilis isolated from a blood culture is suggestive of an intra-abdominal collection or intestinal micro/macro perforation, even if the abdominal examination is unremarkable.
  • A Fusobacterium necrophorum isolated from the blood cultures of a young adult is suggestive of Lemierre’s syndrome, even if the patient is not complaining of neck pain.
  • 2 or more different enterobacteraciae isolated from a CAPD fluid is suggestive of a bowel perforation, even if the patient is not systemically unwell.
  • An Aspergillus species isolated from 2 or more sputum samples is suggestive of architectural lung disease, even if the patient has no history of such.

Sometimes microbiological evidence is ignored by clinicians. 

What are the reasons for this?

Sometimes the result is thought to represent contamination. Sometimes the result is ignored due to lack of knowledge. And occasionally it is just plain denial.

Part of our job as microbiologists is to make clinicians aware of the strength of the microbiological evidence, so that a prospective diagnosis is not dismissed lightly….

Michael

“To err is human”

Those that know me, will be aware that I am a passionate believer in having clinical rationale and clinical context as pre-requisite for all microbiology samples that are processed by the laboratory.

Exactly the same principles should apply for antibiotic prescriptions…

There are various reasons why a clinician might prescribe an antibiotic:

  • Fear: That if an antibiotic is not prescribed, then any suspected infection might increase in severity or even be potentially life threatening.
  • Pressure: Pressure to prescribe an antibiotic from the patient or their relatives.
  • Action: To be seen to be doing something positive for the patient.
  • Justification: That prescribing an antibiotic justifies the cost or time of the consultation.
  • Loyalty: If an antibiotic is not prescribed then the patient may go elsewhere to get what they want.
  • Bacterial infection: That there is a genuine suspicion of a bacterial infection where the evidence shows that antibiotics are indicated in that particular clinical scenario.

It would be foolish to think that the real prescribing reason is always the last one on this list.

Humans are subject to all sorts of internal biases, and external pressures. We are in essence, fundamentally flawed. It is therefore wrong to expect us to always prescribe antibiotics for the right reasons as opposed to the “not so right” ones.

In other words we need tight controls on our decision making behaviours.

At the moment a clinician can write a prescription for most antibiotics without including any indication as to why the antibiotic was prescribed.

This needs to change.

It is my belief that all antibiotic prescriptions should have the clinical indication for prescribing included on the prescription form as a pre-requisite for dispensing, in both community and hospital settings.

Otherwise the pharmacist is essentially dispensing blindly.

Once such a system is in place, then specific criteria can start to be applied for certain infections in order for an antibiotic prescription to be valid/approved.

Then we can start getting some real controls in place for the purposes of antibiotic stewardship.

The days of clinicians being able to request laboratory tests and prescribe antibiotics without providing a clinical rationale are numbered.

I hope…

Michael