Category Archives: History of Microbiology

“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!

“Old rules for old tests”

800px-Mantoux_tuberculin_skin_test

I have been looking recently at the various merits of Mantoux testing versus the newer Interferon Gamma Release Assays (IGRAs) for the diagnosis of latent TB infection. Whilst the IGRAs (such as T -spot and Quantiferon Gold) are not perfect by any stretch of the imagination they still seem to have difficulty replacing the long entrenched Mantoux test.

The Mantoux test, which has been in existence for well over a hundred years suffers from various problems. False negatives due to immunocompromise, false positives after BCG, inter-observer variability in measuring the results, and the logistics of administration, just for starters.

One wonders if Mantoux were a new test invented today, whether a test with so many deficiencies and subjectivity would get anywhere near the commercial market. The validation requirements for new tests as stipulated by accreditation agencies are much stricter now than they were 100 years ago, 50 years ago, or even 20 years ago.

I think we are applying old rules for old tests to a certain extent. Mantoux testing is an institution, a tradition, and is what a lot of us are used to. However because it was acceptable testing in previous generations does not mean it is acceptable by today’s standards.

I don’t think IGRAs will need to improve too much more before Mantoux testing ends up as a historical test, and PPD is kept in museums and not laboratories….

Michael

TB or not TB – that is the question?

As usual my delving into family history has prompted a post … I’ve been researching my Great-great-Uncle who was killed in action at Somme, France whilst serving as a WW1 ANZAC and discovered that his father, my great-great-grandfather died from (and I shall quote from the Marlborough newspaper that it was printed in) … “that dread disease consumption“.

Now you may consider TB to be a third world, old-fashioned type of disease and to a degree you would be right however TB remains the second greatest killer globally (HIV/AIDS is number one) due to a single infectious agent.  In 2013, 9 million people fell ill with tuberculosis and 1.5 million died as a result – 480,000 of these cases were MDR-TB (multi drug resistant).  There is an upside to all this in that 37 million lives were saved due to effective diagnosis and treatment between 2000-2013 and the number falling ill to the disease each year is declining albeit slowly.  New Zealand statistics show 305 cases nationwide during 2014 and this number has been relatively stable over the past five years.

MDR-TB is defined as those strains that are resistant to at least Isoniazid and Rifampicin (the two most powerful and standard first line drugs for treatment of TB).   XDR-TB are strains that are extensively drug resistant and are defined as MDR-TB with additional resistance to any fluoroquinolone and at least one of the second line agents (Amikacin, Capreomycin or Kanamycin).  Of the 480,000 MDR-TB cases in 2013 about 9.0% of these were determined to be XDR-TB.  Within New Zealand the rate of resistance is much lower, on average only 1-2% of isolates each year showing this level of resistance.  In the past 10 years there have been 33 cases of MDR-TB in good ol’ NZ and all but two of these cases were born overseas where it has been assumed they contracted it – 29 of these 31 cases were born in an Asian country.  Only one case of XDR-TB has ever been identified in New Zealand, this was in 2010.  I think this is one time were our geographical isolation from a large part of the world is to our benefit.

Tuberculosis was a disease that the WHO considered dropping from their watchlist in the 1960’s/1970’s due to it’s decline however it made a huge resurgence in the 1990’s with the number of HIV/AIDS cases increasing and is certainly a disease which we cannot afford to ignore.

You can view a copy of the 2014 WHO global TB report here.