Monthly Archives: March 2016

“On second thoughts…”

I love fallacies, old wives tales, and urban myths…

You are probably familiar with the dogma that you should never use cotrimoxazole to treat infections due to Streptococcus pyogenes.

In the laboratory setting we have traditionally never been much good at in-vitro susceptibility testing for cotrimoxazole against Streptococcus pyogenes…


In vitro susceptibility testing of Streptococcus pyogenes against cotrimoxazole is dependent on/vulnerable to the amount of thymidine in the susceptibility media. Thymidine allows Streptococcus pyogenes to bypass sulphonamide mediated inhibition of folate metabolism.

In the past, media contained unregulated (and often high) levels of thymidine, particularly those media that contained blood. As a consequence Streptococcus pyogenes survived quite happily on such media, even in the presence of sulphonamides and thus showed in-vitro resistance.

However modern media such as Mueller-Hinton agar (MHA) are now regulated as to their thymidine content. A study in the Journal of Clinical Microbiology in 2012 using such agar showed at least 99% in-vitro susceptibility of Streptococcus pyogenes to cotrimoxazole.

It is likely that our poor laboratory practice in the past has led to cotrimoxazole being labelled a ”No-No” for infections due to Streptococcus pyogenes.

However this information above only refers to in-vitro susceptibility testing. Whether this translates into in-vivo susceptibility/clinical response is another question altogether, and in the modern day, will likely  need clinical trials to answer. (See this article for a bit about in-vitro and in-vivo susceptibility)

All the textbooks in my lab say that Streptococcus pyogenes is resistant to cotrimoxazole. That’s because they are all 10-20 years old!

It is difficult to change people’s minds at the best of times. Old habits die hard…


“Think twice”

What have the following got in common?

  • E.coli resistant to nitrofurantoin
  • E.coli resistant to fosfomycin
  • Haemophilus influenzae resistant to ciprofloxacin
  • Group B streptococcus resistant to penicillin.
  • Coagulase negative staphylococci resistant to vancomycin
  • Candida albicans resistant to fluconazole

In my area of the world anyway (New Zealand), the percentage resistance rates of the above micro-organism/antimicrobial combinations is less than 1%. i.e. the prevalence is very low.

And because the prevalence is very low, unless your susceptibility testing methods are very specific, the positive predictive value of the result will also be very low. Thus , there will generally be a large number of false positives amongst such results.

Such a result should therefore automatically trigger a double check of everything, with a close look at the audit trail leading to the result. In some circumstances, repeating the test or sending the isolate to a reference laboratory may be the best option even if the result looks genuine.

We always need to be very careful when reporting low prevalence results, because even though we would like them to be, our tests are generally not perfect…




“Publish or Perish”

You will probably have heard this saying before, the idea being that if you don’t regularly write articles for ‘research’ journals then your career will start to go backwards.

I think there may be a modicum of truth to this, particularly if you are planning to climb up the greasy (and slightly corporatised) academic pole of a tertiary university hospital.

Having said that, when I look around at my colleagues in microbiology, some publish profusely and others completely ignore this avenue. Fortunately none, as far as I am aware, have ‘perished’ due to failing to publish.

It is also worthwhile noting, just how commercialised the whole business of publishing research articles has become… With the advent of ‘Open Access’ journals, where the contributor pays, and not the user, the ease with which one can get something published has changed dramatically. I will not comment on the quality of the articles…

I would get an average of two emails a day in my Inbox asking/pestering me to publish an article in some (Open Access) journal or other, no doubt at significant expense to myself!

So from a personal point of view I have been fairly quiet on the publication front recently. However, always wanting to be a little bit different from my colleagues, and never being one to conform to what is traditionally expected, I have opted to bring out my own publication, “The Art of Clinical Microbiology”.


This is a book which draws on content from this website, presented in a nicely ordered format and with some other bits and pieces included.

The manuscript goes to the printers in the next few days so I will keep you posted on how to get hold of a copy in due course.

And the nicest part of the whole process was getting the ISBN (publication) number for the book. That’s when the reality (and satisfaction) of writing your own book hits home!