Monthly Archives: April 2017

“Too soft, too generous, too nice, and too slow…”

Antimicrobial Resistance, Confessions of a Microbiologist, The Art of Microbiology, , ,

Guidelines for antimicrobial stewardship often include only a cursory mention of the role of the clinical microbiology laboratory, which is a shame, because in my opinion it is one of the key areas where real change to anti-microbial stewardship can be effected. (The other key area is in the writing of sensible narrow spectrum empiric antibiotic policies.)

But we don’t help ourselves…. Speaking generally, I think clinical microbiology laboratories are notoriously bad at antimicrobial stewardship.

Why?

Several reasons actually.

Because we are too soft: We often release antimicrobial susceptibilities from the laboratory even when we have no idea what is going on with the patient. I.e. no clinical details have been provided. Therefore we think nothing of releasing a range of antibiotics to the clinician when we don’t actually know what is wrong with the patient, whether they have an infection, and how severe it is.

Antibiotic susceptibilities should not be released unless the laboratory has reasonable evidence that they are required.

Because we are too generous: We are happy to test a whole range of antibiotics (often up to 20 for the one isolate!), “just in case” one of them might need to be used. This range often includes both narrow spectrum and broad spectrum agents. Probably over 95% of all the susceptibilities that we test and report are never utilised.

We need to dramatically reduce the range of antibiotics that we test for and we need to focus our reporting to the narrowest spectrum antibiotics that we can get away with.

Because we are too nice: We have a low threshold for releasing antibiotic susceptibilities on “putative pathogens“. By doing this, we have just given the green light for the clinician to classify a putative pathogen as an actual pathogen, and therefore start/continue antibiotics.

If we have isolated a putative pathogen, let’s keep it putative. Report the organism, and ask the clinician to make a clinical assessment, and then to get back to the laboratory if susceptibilities are required.

Because we are too slow: We are certainly quicker than we used to be, thanks to MALDI-TOF, smart incubators, and increasingly rapid PCR platforms, but we need to be quicker still… We need to get rid of self-congratulatory, retrospective infectious serology testing and channel our test budgets into real-time diagnosis with PCR or similar, and on patients who fulfil well defined clinical criteria for testing. We need to get rapid molecular platforms for STDs into Sexual Health clinics so they are not required to prescribe an antibiotic for everybody who walks through the door. We need to increase Influenza and RSV testing during the winter season to try and reduce unnecessary antibiotic prescribing for viral infections.

Not only do we need to be quicker, we also need to be smarter…

The clinical microbiology laboratory doesn’t score very well in the antimicrobial stewardship report card. We need to be bold and innovative to change things for the better.

But it is entirely up to us…

Michael

“Dead Certs and Long Shots”

The Science of Microbiology, , ,

The more uncertain the result will be, the more useful the laboratory test generally is…

Sounds a little paradoxical, but it is absolutely true.

If we are looking to confirm something that is almost certain before the lab test is performed, then we need a “super-sensitive” test to fulfil this task. Otherwise we run the risk of giving false negative results.

For example, if we have a teenager with a sore throat and lymphadenopathy, a lymphocytosis and atypical lymphocytes on blood film, then the probability of this being EBV infection is about 90%. There is little point then in doing a confirmatory Monospot test with a sensitivity of 80-85%. This will only lead to giving negative results on patients who actually have EBV infection.

And if we are looking to diagnose a long shot (aka a very unlikely diagnosis) then we had better be sure our laboratory test is “super-specific”, otherwise we will run the risk of giving false positive results.

For example if we want to diagnose dengue fever in a patient with “flu like” symptoms returning from Mexico (an area of relatively low Dengue endemicity), then we need to think twice about performing Dengue serology testing which has a specificity rate of about 95%. You are just as likely to report a positive test in someone who doesn’t actually have Dengue.

What we are doing in actual practice here is taking our pre-test probability, and using it to give a prevalence rate (by proxy) in our tested population. Once we know this, then we can use our test sensitivity and specificity to calculate positive and negative predictive values, not always with the results we would like…

Laboratory specialists tend to be more aware of testing limitations such as these. Clinicians, in general,  tend to just take the laboratory results as gospel.

But I believe it is ultimately the laboratory’s responsibility to stress the limitations of using laboratory testing for “Dead Certs or Long Shots”, and either prevent such testing taking place, or put big disclaimers on the results.

Michael

 

“My cubicle”

Confessions of a Microbiologist,

Here is my cubicle, where I live.

There is just room enough for me, as I have boxes of old files stacked up in the space where one could potentially squeeze an extra seat in. I have no great desire to sort through and clear them all. Any meetings with colleagues or visitors can take place at nearby cafes, which is probably not a bad thing…

I spend at least 4 hours a day in my cubicle and it is the nerve centre of my working life.  It is where all the “execution” happens, where policies are drafted, where presentations are written, where results are processed. It is not however where I generate my ideas. That seems to happen elsewhere,  in the car, in the shower, in bed.

Sitting in front of a computer is simply not conducive to deep thinking and idea generation.

It is quite a cluttered cubicle, with a fair amount of paper floating about. So much for a paperless workplace! Sometimes I don’t always practice what I preach…

I never was one for tidying up before guests arrive.

The same 4 walls (or 3 walls and a glass partition), day after day, week after week, month after month. “The daily grind”, ad infinitum.  It is quite comforting in a way, protecting me from whatever dangers the outside world might hold. It is easy to become trapped inside, metaphorically if not physically speaking.

I have become quite attached to my cubicle. However there is always the danger of staying too long… One more email to write, one more paper to read, one more phone call to make. It is very difficult to make personal connections when you are cocooned inside your cubicle. I suspect our most important work is done when we finally manage to escape from our cubicles.

I guess I have become a little institutionalised in a way, in my cubicle. It is my comfort zone. Sometimes it’s nice just to sit comfortably. No standing office for me!

I will miss it when I go…

Michael