Category Archives: Future of Microbiology

“The Annual Ritual”

A lot of diagnostic clinical microbiology laboratories create an annual antibiogram at the start of each year in order to inform laboratory users of local susceptibility rates for common microbe/antibiotic combinations. Here is a link to the one for my own laboratory.

It is a time honoured tradition, a ritual of sorts… There would be uproar from the clinicians if we didn’t produce it.

And yet such antibiograms are fundamentally flawed…

They are overly simplistic because resistance rates can vary markedly in different patient cohorts and different sample types.

Take the following examples (based on my local data searches):

  • Antibiotic resistance rates for urinary isolates differ markedly according to age and sex. Urinary isolates from young women have much lower resistance rates to uropathogens than old men, with the difference being up to 25% depending on what microbe/antibiotic is being tested. This has very obvious implications for empirical antibiotic choices for UTI in different population cohorts.
  • Staphylococcus aureus resistance rates to mupirocin are much higher in young people with recurrent skin infections than in the (elderly) cohort about to go elective  joint replacement.
  • MRSA rate as a percentage of total Staphylococcus aureus isolates is significantly higher in superficial wound swabs than it is in blood cultures.

These are just a few examples of many, but the common theme here is that different exposure rates to particular antibiotics in different population cohorts lead to different resistance rates.

So I suspect the days are numbered of static antibiograms shown in table form on an A4 sheet of paper.

So last year!

I see the future being an electronic interactive antibiogram, possibly in the form of a smartphone “app”. The clinician enters a few important variables, such as patient age, sex, sampling site, and community/hospital patient, along with the microbe isolated. The app then calculates a more accurate antibiogram based on the particular cohort that this patient falls into.

This is the future, I am sure of it.

The only downside to such an approach is by splitting the total susceptibility data available into different cohorts, the sample size for analysis goes down, which can then lead to bigger margins of error in the results for less common microbe/antimicrobial combinations. This however could be addressed in the app by adding a disclaimer to resistance rates calculated from small sample numbers.

And maybe an interactive electronic antibiogram is in existence already, in an ultra-progressive laboratory somewhere… If so, please let me know!

I had better get started on creating that app!

Michael

“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…

Michael

“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!

Michael

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