Category Archives: The Art of Microbiology

“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

“Perfect is the enemy of good (microbiology)”

The Art of Microbiology, ,

This quote attributed to Voltaire (“Le mieux est l’ennemi du bien”), rings true to me. I have never been a perfectionist, and the idealistic pursuit of perfectionism can hinder real-life achievement and progress. 

The quote came back into my conciousness during the early days of the COVID pandemic when I listened to a great speech by Dr Mike Ryan from the WHO when urging countries to act quickly in the face of the rapidly developing COVID situation.

Of course, such a concept can also apply to the microbiology laboratory.. Here are a few examples:

Protracted work-up of samples: When a sample arrives into the microbiology laboratory, the clock is ticking. In relentless pursuit of isolating that fastidious bacterium, time passes by and before you know it a week has passed… The clinical usefulness of a microbiological result is inversely proportional to the time spent to produce it. In the hospital setting, the average length of stay is 3-4 days… Excessive time spent on certain samples is not only a waste of resources, it also generally does nothing for the patient. Get a result out, even if it is not the perfect one that you are striving for.

Excessive work-up of samples: The classic example of this is identifying every bacterial isolate in a mixture of enteric flora. For the most part, such an exercise is futile, even when isolated from a sterile site. Enteric flora isolated from sterile sites usually represent a source control issue, and who knows what the pathogen might be in the mixture, if any. Such practice is generally a waste of resources, and reporting individual isolates along with individual susceptibilities is time-consuming and often leads to poor antimicrobial stewardship. Working up bacteria within a mixture of enteric flora might be “technically perfect” but does little to help the patient.

Excessive testing protocols: A good example of this is stool samples arriving into the microbiology laboratory. There are many microbiological tests that one can do with a stool sample, culture, PCR for bacterial & viral pathogens, microscopy for parasites, C. difficile testing, the list goes on. However, to perform all the available tests on every stool sample in the hope of maximising the odds of isolating a pathogen would be incredibly expensive, but in most cases would do little to change patient management. Enteric testing should very much be tailored depending on what is on the microbiology request form.

I am sure there are many other examples that one could think of. Perfection in the microbiology laboratory is very much a pipe dream, and can actually be detrimental to good patient care. We cannot possibly hope to identify all potential pathogens in every sample and do it in a timeframe that is beneficial to the patient. We need to move past our fear of missing something…

When developing testing methodologies or reviewing individual patient samples, we should always be asking ourselves “By doing what we are doing, are we providing overall value to the patient?” 

Michael

 

 

“Antimicrobial Stewardship and the Problem of Unsolicited Advice”

Antimicrobial Stewardship, The Art of Microbiology,

“I would stop that fluoroquinolone…”

A good proportion of my job as a clinical microbiologist is being an antimicrobial steward. i.e. giving antibiotic advice based on microbiology results. And a good chunk of this advice is “unsolicited”, in that nobody has specifically asked for it. One could argue that the advice is “semi-solicited” in that it is given under the auspices or framework of an Antimicrobial Stewardship Program.

Being on-call over the Christmas period has made me reflect on the difference between giving solicited and unsolicited antibiotic advice. When someone specifically asks for your advice, they are genuinely interested in what you have to say and for the most part listen and act on your recommendations. However, when the advice is unsolicited, regardless of whether it is given by phone or in-person, it may not always be welcomed with open arms…

It is not that the prescriber necessarily disagrees with your advice. They know it is generally correct in purist terms. It is just that there are (several) other agendas at play for the attending clinician.

Taking it from the clinician’s perspective, antibiotic advice from an antimicrobial steward on occasion may prevent early discharge and may create logistical issues in terms of organising outpatient antibiotics, arranging further investigations, or arranging clinic follow-up. Put in simpler terms, more work. Such factors are accentuated during the Christmas break where the (laser) focus is on getting patients out of hospital, and minimising any admin work that is required during the holiday season.

A classical example of this is advising on a Staphylococcus aureus bacteraemia. (2 weeks IV abx, Echocardiogram, repeat blood cultures, etc.) Sometimes the attending clinician just doesn’t want to know…

Of course, sometimes our advice can be beneficial to the patient workflow & pathway. For example, early oral switches, and promotion of short course antibiotic therapy. I think it is really important to focus on documenting & highlighting such “wins”, as a counterbalance for when “bad news” needs to be given.

Personally, I am a little fatalistic when it comes to whether my advice is accepted, whether it solicited or unsolicited. I believe in the principle that the final management decision always rests with the attending clinician and they can choose whether to take my advice or not. There is only so much that you can do…

Building up relationships and trust is key in getting people to listen to your unsolicited advice. Some prescribers are more receptive than others. And some specialties are more receptive than others.

So, is unsolicited advice more about the giver than the receiver? Is it essentially self-serving in nature? Or is it a necessary evil of being a good antimicrobial steward? These are difficult questions, and ones that I do not have the answers for.

The other approach is to have a more passive approach to antimicrobial stewardship, to only give advice when it is specifically asked for, or at least to issue clear guidelines as to when advice should be sought.

My children often complain when I give them unsolicited advice on how to live their lives. I hope that my clinician colleagues do not feel the same way!

Michael

Check out this interesting article on the psychology of antimicrobial stewardship, published in CID