Category Archives: Future of Microbiology

“The Requesting Pyramid”

In many laboratories, clinical details on request forms can be structured into a pyramid shape as below.

Let’s take the example of otitis externa.

A good proportion of request forms will be at the bottom of the pyramid, where there are no clinical details present to suggest that otitis externa is the clinical suspicion (as opposed to otitis media, cellulitis of the pinna, or some other condition). Also included in this category are cases where clinical details have been included but are unrelated to sample type, e.g. an ear swab sent with clinical details of “sore throat”. This scenario happens in all sample types with disturbing frequency… (e.g. mid-stream urine sent for a patient with clinical details of chest pain!)

The next level up in the pyramid is where clinical details are present but are insufficient to justify the sample being sent to the laboratory. For example the clinical details might state “Otitis externa“. However most patients with straightforward otitis externa do not need an ear swab sent to the laboratory. Laboratory culture of an ear swab in clinically suspected otitis externa should be the exception as opposed to the rule…

The top level of the pyramid is where clinical details are not only present, but they also give a sound rationale as to why the laboratory is receiving a sample. e.g. “Recalcitrant otitis externa not responding to topical treatment.” or “Diabetic with painful inner ear and fever, clinical suspicion of malignant otitis externa“.

This requesting pyramid applies to most different sample types and clinical scenarios.

At my laboratory, we are doing our utmost to turn this pyramid on it’s head. We have made significant progress to date. In fact our pyramid is starting to look more like a rectangle.

By the end of the year we hope to have removed the base of the pyramid altogether by adopting a policy of having accompanying clinical details pre-requisite for all microbiology tests. I.e. No clinical details, no test.

And that is the way it should be…


“Bringing the patient into the laboratory…”

Photo courtesy of Cabalari

Sometimes we can process a wound swab from start to finish without ever knowing why it has been taken. It could literally be anything from a “burst pimple”, to a burns patient with a severely infected skin graft.

Insisting on clinical details goes some way to solving this problem, but even then, the details provided may not accurately convey the type or severity of the infection.

Wouldn’t it be great if we had each patient right in front of us whilst processing the wound swab? Obviously this is not practical. However  if we could view a photographic image of the infection, it would immediately contextualise the wound swab that we are processing.

With the current advances in electronic requesting, such a facility is not out of the question. Dermatologists use a lot of digital imaging these days. So why not microbiologists?

Pictures are often better than words…

And when validating the report, I could then have even more information at hand:- The result, the Kiestra digital plate images, the request form and a digital image of the infection site on the patient.

Quality assurance by using all the evidence.

… And requestors might also think twice about sending in swabs of burst pimples  if they also needed to provide a picture of the infection as well!


p.s. There are many dubious reasons for taking microbiological samples, as there are often multiple agendas at play…

“Indole positive or negative?”

If you asked me whether E. coli was indole positive or negative, I wouldn’t have a clue.

Despite being told the answer many times over the years, the answer just doesn’t stick. I simply don’t care..

My colleagues must despair of me.

It is a wonder that I managed to pass any exams at all…

Which brings me to college microbiology exams and my increasing disillusionment with them.

Formal exams in general have not changed much in style over the past few hundred years. They essentially test knowledge that can be held in the head. (I hold very little in my head..)

But most young people have an I-Phone in their back pocket…

The skills that young microbiologists need nowadays are not related to hoarding large amounts of microbiological facts. This is becoming increasingly irrelevant. They need to be able to problem-solve and troubleshoot. They need to be computer savvy and innovative. They need to be observant and be able to spot the unusual. They need to have the patience to tolerate a degree of repetitive work, and they need to be able to get on with their colleagues and build a rapport with lab users.

Do the microbiology exams of today really test these skills?

If it were up to me, I would get the students into the microbiology lab on day 1 of their training (so they can see if they really enjoy it) and keep them there as much as possible. I would pay them part-time for doing some simple tasks in the laboratory (so they don’t finish their degree in lots of debt). The academic part of the course would be primarily online, with occasional small group tutorials. I would ban large group didactic lectures altogether. I would focus on the diagnostic microbiology of today and tomorrow, not of yesterday. I would not have a formal written exam at the end, but rather continuous assessment throughout the training period. I would however advocate an oral examination at the end to ensure the student has a good understanding of the basic concepts of microbiology and has good safety awareness in the laboratory. I would be brutally honest with them in terms of future job prospects and where I see future work opportunities within clinical microbiology.

There are too many people within academic institutions who have too much of a self-interest in keeping things the way they are at the moment.

This has got to change…

Modern microbiology degrees are needed for modern microbiologists.


I see that most E. coli are “indole positive”. I have just checked Google on my smartphone…