Tag Archives: agar plates

“Bias in the diagnostic microbiology laboratory”

The Art of Microbiology, ,

We are all fundamentally flawed as humans. We just have to do the best we can given our limitations.

I attended an interesting clinical Grand Round at my local hospital last week. Whilst the case presented was intriguing, it was the presenters’ focus on the different types of cognitive bias which are seen in clinical medicine which really caught my attention. 

It got me thinking… Do the same types of bias apply when reading and interpreting microbial cultures on agar plates?

The answer is of course yes.

Below are examples of the main types of cognitive bias one might be subject to when reading agar plates:

  • Confirmation Bias – Scientists may interpret bacterial growth in a way that confirms their expectations or prior hypotheses. For example, if they expect a certain antibiotic to inhibit growth, they might unconsciously downplay colonies that appear resistant.

  • Anchoring Bias – The first observation or previous experience can heavily influence interpretation. If a scientist has seen a particular growth pattern before, such as satellitism of Haemophilus influenzae around Staphylococcus aureus they might assume it’s the same species or reaction without fully considering other possibilities. 

  • Availability Heuristic – The tendency to rely on readily available examples in memory. If a scientist recently encountered an unusual bacterial isolate, they might overestimate its likelihood when analysing new plates, leading to misidentification.

  • Observer-Expectancy Effect – The scientist’s expectations may subtly influence how they interpret ambiguous results. For instance, if they believe a sample contains Streptococcus pneumoniae, they might unconsciously interpret the MALDI-TOF result as such, and ignore the possibility of Streptococcus mitis.

  • Hindsight Bias – After identifying bacterial species via additional testing, e.g. MALDI-TOF, scientists might believe the identification was more obvious than it actually was when first observing the plate, leading to overconfidence in future interpretations.

…and then of course there is the classical clinical judgement bias, that of “Premature Closure” where an “easy” or quick diagnosis is made, and further investigations into a more challenging/important secondary diagnosis are withheld because of this. It happens not infrequently in clinical medicine. An example of this in the microbiology laboratory might be a patient with crystals in a synovial fluid sample leading to a diagnosis of gout, where sufficient duration of culture was not performed to pick up the secondary diagnosis of septic arthritis!

Now that we can simply google the key biochemical reactions of E. coli, maybe cognitive bias is the sort of thing we should be teaching microbiology students, so that they are aware of the sub-conscious ways we can slip up when reading agar plates, no matter how good our intentions… A nice exam question perhaps!

Michael

 

 

“Three is a crowd….”

The Art of Microbiology, ,

I have a personal rule with regards to bacteriology cultures. This is the “three species rule”. If there are more than three different bacterial species on a plate then I do not support each individual species being identified and reported.

The reasons for this are as follows:

  • When multiple bacterial species are found on one plate, the end result hardly ever affects patient management.
  • Who knows which bacterial species, if any on the plate is causing the problem?
  • Multiple bacterial species on one plate often indicates contamination of one sort or another.
  • Releasing antimicrobial susceptiblities on multiple different bacteria is likely to lead to overtreatment and select out for bacterial resistance.

Far better to group them together and report as mixed skin flora, mixed enteric flora, mixed environmental organisms, or whatever is most appropriate. This applies for sterile site samples also. It saves a huge amount of laboratory time and consumables and simplifies the report for the clinician.

It is only a rule, and rules can of course be broken occasionally, as I am well used to doing myself…..

The one routine exception I would have for this rule is for sputum cultures from cystic fibrosis patients. In this rather unique cohort it is important to detail all the potential pathogens, regardless of number. When interpreting CF sputum cultures, it is just as important to look at previous culture results, to see what organisms have appeared and what has disappeared.

It is always good to step back, have a look at the culture result you are putting out and think to yourself, “What clinical impact is this result going to have for the patient?” or put more simply “Am I helping the patient here?”

 Michael