Tag Archives: sputum

“The Sputum Factory”

Confessions of a Microbiologist, ,

It is the peak of the (Southern Hemisphere) influenza season here in New Zealand. Influenza has come early this year, and the season has been relatively busy to date, with a fairly even mix of Influenza A&B.

And it is not just influenza, there is plenty of circulating RSV, rhinoviruses and all those other less well known respiratory viruses that we know best by their appearance on extended respiratory viral panel menus.

However it is not just GPs and Emergency departments that feel the effects of the wave of respiratory viruses during the winter season. Microbiology departments get a surge in sputum samples arriving at the laboratory. Recently it has felt like my laboratory is simply a sputum processing factory!

And this is because any microorganism which infects the respiratory epithelial cells (bacteria or viruses) will inflame the respiratory epithelial cells and increase the production of “purulent” sputum. It doesn’t matter whether it is a bacterium or virus. Can the sputum colour discriminate between the two?? Only in the textbooks…

Sputum for bacterial culture is one of my least favourite microbiology samples! This is not just because of its appearance, but more because it suffers from appalling sensitivity and specificity when diagnosing bacterial pathogens, even when a pre-screening Gram stain is performed, as many labs do nowadays.

If sputum culture was subject to to FDA approval as a “diagnostic assay”, it wouldn’t have a prayer…

During the winter season when respiratory viruses abound, the prevalence of bacterial infection in the tested population will be relatively lower, with a consequent further deterioration in positive predictive value.

There are many guidelines that show the extremely limited value of sputum culture, particularly from the community setting, for the management of non-specific cough symptoms, acute bronchitis, and COPD. The most common clinical details we receive on sputum samples are things like “Cough”, “cough with purulent sputum”, “COPD”, or simply nothing at all. Yet we still accept these samples without question.

As a profession, sometimes I think we are too soft…

My lab is planning to introduce restrictions on what sputum samples are acceptable from the community setting, according to the published guidelines, so hopefully by next winter, we will be a haven of tranquility as opposed to a sputum processing factory.

Michael

Apologies for the picture, but it had to be done!

 

“A paradigm shift…”

Confessions of a Microbiologist, ,

At the moment most antibiotics are initiated without waiting for the microbiological result, if they are thought to be clinically necessary.

Quite right too.

This is so called “empirical therapy”.

There is a good reason for this. Traditionally, microbiology tests have neither been good enough nor fast enough to make the antibiotic prescription dependent on the result.

Take for example the patient who sees his GP with a productive cough and fevers. The GP is not going to say to the patient “Let’s just wait a few days until we get the sputum culture result back. By the way there is a good chance it will be negative even if you do happen to have a pneumonia. And on the flipside, if it does grow something it might just represent the bacteria in your throat.”

No chance…, the GP will simply prescribe an antibiotic based on the most likely pathogens, and also the local antibiotic susceptibility patterns.

Along the same lines, the GP is not going to say to the patient a couple of days later. “Your sputum sample has come back negative, so let’s stop your antibiotic.” Sputum cultures are nowhere near sensitive enough to allow this approach.

On the very odd occasion, the treatment will actually change as a consequence of the microbiology result, if there happens to be an unusual or resistant organism.

And sputa are only one sample type. Ear swabs, peri-anal swabs, & ulcer swabs probably have even less impact on patient management…

In fact for the vast majority of  samples (probably > 95%) that get processed by the microbiology laboratory, the impact on patient management is rather small indeed.

However change is coming on to the horizon. The newer microbiological tests, and in particular the polymerase chain reaction (PCR) assays, are both fast enough and sensitive enough to start genuinely impacting on patient management right at the time of prescribing.

Take the following potential examples:

  • Macrolide antibiotics could be witheld in a patient with suspected whooping cough until the Bordetella pertussis PCR is back.
  • Patients with urethral discharge and suspected gonorrhoea would only be treated if the Neisseria gonorrhoeae PCR result comes back positive.
  • Patients with meningo-encephalitis could have acyclovir to cover HSV, dependent on the CSF viral panel result.
  • Legionella cover in a patient with moderate to severe community acquired pneumonia could be dependent on the result of the Legionella PCR in a sputum sample.

These are all tests which, if performed quickly enough, can significantly reduce the amount of antibiotics given to the tested cohort, so they all have potential to play a big part in any antimicrobial stewardship program.

So we need to get such assays into our microbiology laboratories, whatever it takes.

Microbiology matters, but we need to ensure that we utilise new tests and technology to make it matter even more…

Michael

 

“Thresholds”

The Art of Microbiology, ,

 

I have noticed while authorising sputum culture reports, that some people have high thresholds for working up suspect colonies from plate cultures, only proceeding when the potential pathogen is dominant amongst the upper respiratory tract flora that is also inevitably present.

Other people have very low thresholds for working up suspect colonies, painstakingly trying to pick out potential pathogens even when there only a few of the same colony type present in the milieu.

Depending on what your threshold is, it clearly has the potential to produce a different result for the clinician.

But who is right and who is wrong? Is it that sometimes we just try a bit too hard?

My gut instinct is that a few colonies of a respiratory pathogen (e.g. Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis) nestling amongst a mass of mixed upper respiratory tract flora is unlikely to be significant, but I am not aware of any literature that supports such an assertion.

I tend not to get too excited by sputum cultures as a rule… Clinicians don’t hang around waiting for the patient to firstly produce a sputum sample, and then wait another 2 or 3 days whilst the microbiology laboratory processes it. They treat the patient empirically, according to guidelines that are hopefully formulated by laboratory data outlining the expected pathogens and antibiograms in the local area.

Only on rare occasions does a sputum culture result actually change patient management.

If “sputum culture” were a new immunoassay, and therefore subject to FDA approval before being released to the market, it wouldn’t have a prayer of being accepted. The sub-optimal sensitivity and specificity (even with prior filtering of samples using macroscopic appearance and Gram stain) would simply not cut it from a regulatory point of view.

So we will continue to grapple with the vagaries of sputum culture, but I suspect it will be around for many years yet.

But we should not lose any sleep over it, whatever your threshold is…

Michael