Tag Archives: in vitro

“When the patient and the microbiology lab don’t agree”

I am signing out blood culture results. A patient has an E. coli resistant to amoxycillin clavulanate (augmentin) in both their blood culture and urine specimen. I ring up the patient’s doctor to see how the patient is doing. The patient is currently on augmentin but is nevertheless feeling much better, has been switched to oral augmentin and is ready to be discharged home. Hmm… What should I do? Should I change the antibiotic or am I just treating myself rather than the patient…?

Or the patient who develops a post-operative wound infection and they get treated empirically with flucloxacillin, to which they “respond” well, becoming afebrile and the wound discharge dries up. A swab of the wound then grows an MRSA. Should they complete their course of flucloxacillin or should they switch to an antibiotic to which the MRSA is susceptible to?

The joys of being a clinical microbiologist!

These scenarios have a few possible explanations:

  • Some patients will get better from infections, even bacteraemias and septicaemias, whatever you have used to treat them. Not all patients who contracted infections in the pre-antibiotic era succumbed to them.
  • Just because an antibiotic has tested resistant in the lab does not mean there will be no clinical response. Lots of other factors come into play here, e.g. dosage and pharmacokinetics, penetration into site of infection, host immunity, etc.
  • The isolated pathogen is not actually the cause of infection.

Clinical microbiologists are often left in a difficult situation here. Do they listen to the laboratory telling them that the isolate is resistant to an antibiotic, or do they listen to the clinician telling them that the patient is better. And what happens if they listen to the clinician and then the patient takes a turn for the worse…

It is almost a no-win situation. Is it any wonder that older, more experienced clinical microbiologists like myself end up becoming slightly insane!

These scenarios, or something similar happens to me every few weeks. It is not often discussed how to approach this situation, and it is probably glossed over somewhat in clinical microbiologist training. I was certainly never trained how to deal with it. In fact it could even be regarded as something of a taboo subject…

I think the answer lies in a case by case approach, taking into account the type of infection, the pathogenicity of the organism, the degree of resistance to the antibiotic, the reserves of the patient and how unwell they were on presentation, and a multitude of other factors that cannot possibly be learned from a textbook.

There is a lot of science in microbiology, but sometimes experience, intuition and common sense count even more than knowledge. Antimicrobial susceptibility results are important, but they are not the whole story by any stretch of the imagination.


Apologies for the paucity of posts recently, a combination of busyness and laziness!


“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…


“From the Laboratory to the Patient.”

Antimicrobial Resistance Testing: From the lab to the patient.

Question: What do the following have in common?

Antibiotic Dose

Tissue Penetration

Site of Infection

Patient Immunity

Pharmacokinetics of drug in patient

Extent of Infection

Wrong pathogen isolated

Polymicrobial Infection


……and probably many more.


Yes, these are all factors which dictate why even though a lab says a bacterium is resistant to an antimicrobial, the patient nevertheless gets better on that antimicrobial, and vice versa.


We are entering the murky world of in-vitro versus in-vivo response.


I often get queries from GPs wondering why MRSA infections improve on Flucloxacillin, etc etc. “How can this happen?”


The reasons are above. In the pre-antibiotic era, lots of people, particularly with minor soft tissue infections, got better without the help of antimicrobials.


Because of the myriad of different factors involved, I cannot see in-vitro susceptibility testing ever being anything more than a “best guess” at clinical response. For this reason alone, it actually makes me wonder whether we may overdo susceptibility testing and whether it should be more often reserved for the more serious infections.



MIC Breakpoints.


In-vitro susceptibility testing is based on MIC (minimum inhibitory concentration) breakpoints. Above a certain breakpoint, the bacterium is deemed resistant to the antimicrobial, and vice versa.

The MIC breakpoint is set using an ill-defined mix of epidemiological, pharmacokinetic and occasionally, clinical data.


To make matters worse, there are different organisations involved with setting standards for laboratory antimicrobial susceptibility testing. Sometimes these organisations struggle to agree on the MIC Breakpoints for different organism/antimicrobial combinations. For example look up Cefipime breakpoints for E. coli in both the CLSI and EUCAST guidelines. (What must the clinicians think of us!)


What is important to note however is that giving an MIC is better than just calling an organism susceptible or resistant. At least with an MIC value you can get an idea of the degree of in-vitro resistance or susceptibility. If the antibiotic is just reported as susceptible or resistant, then it gives the clinician no idea of how close it is to the breakpoint (from an in-vitro point of view).


I think the debate around in-vitro testing and in-vivo response will continue unabated for the rest of my lifetime…