Category Archives: Future of Microbiology

Creating Microbiology Presentations Using AI

Confessions of a Microbiologist, Future of Microbiology, , ,

I have been using AI to help create a couple of microbiology-related educational presentations over the past few weeks, for the first time in a couple of years.

I shouldn’t have left it so long…

Things have clearly improved. AI technology is now evolving at an incredible rate. Pause for breath and you will be left behind. It is not perfect by any means but starting to become functional in the professional setting in many different facets, including presentations.

Here are a couple of my personal comments on using AI to generate microbiology presentations for teaching purposes.

  • I used Co-Pilot to generate the presentations: Because I am old and stuck in my ways, I still use PowerPoint for all my presentations. As a result, it makes sense for me to use Co-Pilot, as this is also a Microsoft product and is thus designed to generate PowerPoint presentations. 
  • Prompting is everything: A good initial “prompt ” is key in producing a good AI-generated presentation. How many slides do you want it to produce? Who is the target audience? What areas do you want it to focus on? Do you want it to reference the evidence for its statements? Do you want it to be humorous? Do you want it to include pictures/graphs/tables. Do you want it to include hypothetical case studies. Do you want it to produce MCQs on the topic at the end. And that is just for starters… I think in future I am going to develop a template prompt for presentations which I can then amend for each topic I need to teach on.
  • It still has a tendency to produce generic presentations: My experience so far is that AI has a tendency to produce generic presentations. As I get better at prompting, hopefully I will get better at getting AI to include interesting details in the presentations and not “genericise” so much.
  • Editing is key: The presentation it produces for you will never be exactly the way you want it, even with optimal prompting. Therefore, you will need to dedicate a significant amount of time to editing and polishing it, and indeed giving it a personal touch.
  • Watch out for Hallucinations: In the AI age, hallucinations now have a very different meaning than back in my student days! Large Language Model (LLM) AI systems still have a tendency to make things up if they don’t know the answer. This flaw is becoming less common with more sophisticated software but watch out for it nevertheless. Bias can be another issue. My AI generated presentations did not have any evidence of hallucinations, but there were a couple of clear instances of bias which required editing.
  • It is more difficult to present an AI generated presentation: Because you have not actually written the presentation yourself, it is more difficult to actually present it to an audience. So rehearsal is key. Usually, I would spend 3-4 hours writing a presentation then 1/2 hour rehearsing it. With AI, I would recommend 1/2 hour on the prompt, an hour editing and an hour rehearsing your presentation. AI does save time, but not as much as you might think.

Despite my amateurish initial attempts, I am going to persist with using AI for presentations. The technology can only continue to improve, and very quickly at that. The presentations that it can produce now are light years ahead of what it could do a couple of years ago. I am keen to get tips from anyone else experimenting with giving microbiology presentations by AI. I would also encourage all my colleagues to give it a go.

Several of my children have already been “pinged” at school for using AI in their assignments. Being the bad parent that I am, I ignore the teachers’ frustrations and let the kids embrace the technology as much as they are able. This is the future whether the teachers like it or not…

Michael

 

“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

 

“A Smorgasbord of Microbiology”

Future of Microbiology, The Art of Microbiology, The Wandering Microbiologist,

I was fortunate enough to have attended the ECCMID conference in Barcelona a couple of weeks ago, the so-called “Glastonbury” of microbiology conferences. (it is just the drugs that are different…). In general, the conference venue wasn’t great, but the industry exhibition was very impressive, a massive well-lit hall with a true smorgasbord of microbiology tests & platforms available. There were literally hundreds of stands offering a vast array of products. Some of the stands were very flashy affairs, demonstrating fully functioning microbiology platforms. Most importantly, some were even offering free coffee!, although we all know there is no such thing as a “free lunch”. Microbiology is big business now. It can’t have been cheap to hire the floor space at ECCMID, so it must be worth their while.

Healthcare in general is becoming ever more expensive to fund. There are good reasons for this. There is so much more that we can do now than even a generation ago. Stem cell transplants, CAR-T therapy, new anti-cancer drugs, minimally invasive cardiac procedures (e.g. TAVI) to name but a few. In addition, we have a lot more elderly people. Good healthcare and its associated cost will keep a patient alive, who will then inevitably present later in life with further health issues to manage. Spending on healthcare undoubtedly improves life expectancy, but there is a ceiling on life expectancy and there is a law of diminishing returns which eventually kicks in…

With regards to microbiology, there is no difference really. There are so many more things we can offer in a microbiology lab which we could not offer even 20 years ago. Multi-plex & rapid turnaround PCRs, 16s RNA sequencing, metagenomics are a few examples. There are more antibiotics to perform susceptibilities on, and we can now perform both phenotypic and genotypic susceptibility testing. There are a lot more infectious conditions we can now effectively diagnose, usually with PCR based methods. We are also required to spend a lot more money on good quality assurance frameworks, and rightly so, it’s critically important! The landscape has changed out of all recognition in the microbiology lab. A generation ago, it was mainly culture-based bacteriology. Times have changed…

All of this means that diagnostic stewardship plays an increasingly important role in the microbiology laboratory, if we are to have any hope of limiting costs whilst providing good value to the clinicians and patients. What tests and platforms should we have in the laboratory, and which patients should we perform these tests on? Personally, I think diagnostic stewardship should be a key component and focus of the jobs of both clinical microbiologists and laboratory managers alike.

“Diagnostic Stewardship is a never-ending process…”

When wandering around the industry exhibition hall, it is easy to get caught up in the euphoria and hype; “I’ll have one of those, and I’ll take that as well”, but there is now an almost infinite array of things that a microbiology lab can have… The key is to listen to what the industry reps have to offer, and then work out what is going to give most value to your particular patient cohort. Will that 24-plex respiratory PCR improve patient management over and above the incumbent 16-plex? Will this assay which gives me susceptibility results from positive blood cultures in 2 hours instead of 6 hours decrease patient mortality? 

Diagnostic stewardship is a fascinating area. Industry presents us with all these options. It takes an effective team working together in the lab to make the right decisions.

Michael