Category Archives: The Science of Microbiology

“Kiestra TLA and the impending Artificial Intelligence revolution”

Future of Microbiology, The Science of Microbiology, , , ,

We are now into our 10th year of having Kiestra TLA at the laboratory where I work in New Zealand. I think it is fair to say that once you have worked in a laboratory with bacterial culture automation (i.e. Kiestra TLA, WASPLab) in place, you would never go back! We certainly don’t intend to.

I am a firm believer in optimising the quality of results generated by the microbiology lab. From a quality perspective, the advantages of automated bacterial culture systems over traditional manual-based methodologies are very impressive.

Here are ten important benefits in terms of quality that result from having a Kiestra TLA in place:

  • Improved Standardization – Automates streaking, incubation, and imaging, reducing variability between technicians and ensuring consistent results.
  • Enhanced Sample Traceability – Uses barcoding and digital tracking to prevent sample mix-ups and ensure a complete audit trail.
  • Optimized Culture Conditions – Automated incubation ensures optimal temperature and humidity, leading to better microbial growth and more reliable colony morphology.
  • Higher Reproducibility – Robotics ensure that plating and streaking techniques are performed identically every time, minimizing human error.
  • Faster Turnaround Times – Automation accelerates the workflow by processing and incubating samples continuously, leading to earlier pathogen detection and reporting.
  • Advanced Digital Imaging – High-resolution imaging captures colony growth at multiple time points, allowing for early detection and remote review without disturbing culture plates.
  • Reduced Contamination Risk – Minimizes human handling of samples, lowering the risk of cross-contamination and false-positive results.
  • Integration with LIS (Laboratory Information System) – Enables seamless data transfer, reducing transcription errors and improving result accuracy.
  • Enhanced Quality Control – Automated processes ensure that each step is performed according to predefined parameters, improving compliance with laboratory standards (e.g., ISO, CLSI).
  • Improved Staff Efficiency and Safety – Reduces manual labor, decreases repetitive strain injuries, and allows microbiologists to focus on complex tasks like interpretation and antimicrobial susceptibility testing.

It is important to note that the list above is Artificial Intelligence (AI) generated. It would take me much, much longer to generate such a list myself! I have however reviewed it and agree with all the points mentioned.

And it is due to the impending AI revolution, that systems such as Kiestra TLA are really going to come into their own over the next 10 years.

The Kiestra TLA system generates thousands of images of cultured agar plates each day, which are ripe for machine learning approaches. AI assisted applications, such as for MRSA identification and identification of urine pathogens are already available on the BD Kiestra platform.

I have no idea what the researchers at BD Kiestra are currently up to (!), but one could envisage that there is a lot of development work going on to further extend these AI-assisted apps into pathogen identification for general wound swabs, sputum samples, etc.

I observe with interest what the Kiestra TLA will be capable of by 2035. One would think that a lot of the routine microbiology culture results will be generated with very little human intervention, leaving the laboratory scientists to focus on the more complex (and interesting) samples.

Undoubtedly, by 2035, we will have new Kiestra TLA hardware in place in our laboratory, but it is in the AI-assisted software where the real revolution is coming…

Michael

 

“Trying to escape microbiology”

Confessions of a Microbiologist, The Science of Microbiology, The Wandering Microbiologist, , ,

“You can take the microbiologist out of the lab, but you can’t take the lab out of the microbiologist”

I was fortunate enough to attend the Olympics in Paris last month, the first time I have ever been to the Olympics. It was a fantastic experience, and we managed to see several events, including football, tennis, athletics, cycling, Rugby 7s and triathlon. Moreover, Paris is my favourite city, so I take every opportunity to visit!

I was hoping to forget all about all things microbiological for a month, and to a large extent this happened, until I was watching the triathletes swimming in the Seine!

You are probably aware of the story, but it was a big thing, and something of a propaganda stunt, allowing the Olympic athletes to swim in the River Seine, and the French Government invested heavily in cleaning up the Seine in order to facilitate this. 

In the end it was touch and go. Heavy rain before the Olympics put the E.coli counts up in the river, and at least one of the training sessions and the men’s individual event had to be postponed due to levels exceeding the acceptable limits.

A few athletes got sick after swimming in the Seine but of course it was virtually impossible to prove that the river swimming caused the illnesses.

Which got me thinking. “What are the acceptable faecal contamination limits for swimming in rivers, and is the risk any different for elite athletes in the Olympics?

There are safety standards set by World Triathlon, which indicate that colony-forming units (CFU) of E. coli per 100 milliliters of water should not exceed 1,000 and enterococci levels should be below 400 CFU/100ml. As one can see from this report, levels were acceptable on the day of the race, but not on several other days.

Of course, the cut-offs for E. coli and enterococci are completely arbitrary… The higher the counts, the higher the level of faecal contamination, and thus the higher the risk. E. coli and enterococci are of course only indicators, as most E. coli and enterococci do not cause gastrointestinal illness. There are a whole range of infections that one can acquire by swimming in faecally contaminated river water, including bacteria, viruses, & spirochaetes. Gastroenteritis is likely the highest risk but ear infections and skin infections can also occur.

There are several other factors that may affect the overall risk. The risk will depend on the range of gastrointestinal pathogens present in the water. I.e. swimming in a river in India might carry a different risk to swimming in a river in Paris even if the E. coli levels are equivalent. The amount of water ingested will also be a factor. I imagine an elite athlete going hell for leather in the Olympic triathlon will be intaking a lot more water whilst swimming than if President Macron goes for a leisurely dip in the Seine, if he ever does. The exposure time will also be a factor. The athletes competing in the 10km distance swimming event will have a lot more cumulative exposure than the triathletes swimming 1500m. Finally, the “host” needs to be taken into account. The cohort swimming in the Olympics will be overwhelmingly young, fit and immunocompetent thus potentially at less risk than the general population.

So clearly it is not as simple as just saying >1000 E. coli per 100ml of water is unsafe and less than that is safe. It is far more nuanced than that.

For elite athletes, whose livelihoods depend on competing in such events, they really have little choice in the matter. For myself however, who is definitely not an elite athlete, I like looking at the Seine, and it certainly appears cleaner than in years gone by, but I will pass on the swimming just for now.

Michael

 

 

 

“When the bugs take their time…”

The Science of Microbiology, ,

You are probably familiar with the scenario… A blood culture takes a couple of days to become positive. A Gram stain shows Gram negative rods. The plates are subbed but after another couple of days there is still no growth on the plates. The clinicians are getting impatient and are phoning the lab looking for an identification…

It is certainly a frustrating situation but one that occurs not infrequently.

Is there anything that can be done to help the clinician, and more importantly the patient, whilst we are waiting for the organism to grow?

There are several organisms to consider in this sort of scenario. We should be thinking about HACEK organisms, anaerobes, Pasteurella spp., oxidative non-fermentors like Burkholderia spp., Capnocytophaga spp. Consider micro-aerophilic bacteria such as Campylobacter spp. and Helicobacter spp.  And don’t forget about exotic organisms such as Brucella spp.  Even then, this list is by no means exhaustive, and I am sure there are others that you have come across that I have forgotten about!

What can the lab/clinical microbiologist do to narrow the differential down and manage accordingly pending plate growth?

A few things come to mind:

Aerobic or anaerobic bottle positive?: If the aerobic bottle only is positive it can point to non-fermentors like Burkholderia spp. If the anaerobic bottle only is positive, then one must think about anaerobes (e.g. Bacteroides spp. Fusobacterium spp. )

Gram stain appearance: A cocco-bacillary appearance should make one think of Haemophilus and Brucella. Longish, pleomorphic spindle-shaped organism on Gram point towards Capnocytophaga. “Seagulls” or “squiggles” should send you in the direction of Campylobacter/Helicobacter

Patient History: A history of dog bites/exposure should make one think of Capnocytophaga. A prosthetic valve or other valve disease, or clinical stigmata of endocarditis can indicate a HACEK organism. A history of injecting drug use makes one suspicious of Burkholderia cepacia. A travel history to an endemic area could make one think of Brucella spp. or Burkholderia pseudomallei. In a patient with neck pain and swelling, you don’t want to miss a Fusobacterium necrophorum. If the patient is frankly septic, you want to make sure they are getting covered for Capnocytophaga and Pasteurella.

Of course, all this is speculation, and our educated guesses may be completely wrong in the end. It is however important speculation… We want to make sure that the patient is being covered for the most likely and the most serious possibilities.

Taking another, but no less important angle, from a lab point of view it is essential that any slow growing Gram-negative organisms are worked up in a biohazard cabinet. Laboratory exposure incidents for organisms such as Brucella spp.  and Burkholderia pseudomallei are resource-intensive, stressful for the staff, and for the most part avoidable.

And sometimes the bugs just like to mock us, even make fools of us. Just recently, I was convinced a wavy Gram negative rod in (multiple) positive blood cultures from a patient was going to turn out to be a Campylobacter, only for it to finally be identified as a Helicobacter cinaedi… Wrong again!

Michael