Monthly Archives: October 2017

“Ageing methodology”

The laboratory detection of verotoxin/shigatoxin producing E. coli (sometimes called enterohaemorrhagic E. coli) has caused much grief for diagnostic microbiology laboratories over the decades. It is a relatively nasty infection, and it can cause bloody diarrhoea in a good proportion of patients. In a small minority it can cause severe complications such as Haemolytic Uraemic Syndrome (HUS) or Thrombotic Thrombocytopenic Purpura (TTP).

Diagnosis was initially centred on the culture of E. coli 0157 which can produce verotoxin/shiga toxin.

SMAC (Sorbitol MacConkey) agar plates were all the rage in the 1990s, taking advantage of the fact that E. coli 0157 does not ferment sorbitol. 

How lucky is that?

These were soon replaced by the more selective CTSMAC (Cefixime Tellurite Sorbitol MacConkey), with the cefixime and tellurite inhibiting other annoying non-sorbitol fermenters such as Proteus Spp.

The only problem is that E. coli 0157 is not the only E. coli serotype that can produce verotoxins. Lots of other E. coli serotypes are capable of doing this as well, e.g. 0111, 026, 045, 0145, etc.. As time passed, and our understanding of the infection improved, it became very apparent that a very significant proportion of VTEC induced diarrhoea was actually not due to E. coli 0157.

How inconvenient…

Nevertheless, CTSMAC plates were now entrenched in laboratories. And it was better than nothing.

As the years passed,  alternative methods came onto the scene.

ELISAs used for “direct” VTEC toxin detection in stool were employed in some labs in the early 2000s. At least they detected non-0157 associated disease, but sensitivity remained an issue when used directly on samples. They were not widely adopted by diagnostic laboratories.

Chromagar plates have also been developed to pick up the main VTEC serotypes. A little pricey however, and still need follow-up work for confirmation.

Then came PCR, and more recently multi-plex PCR, not only detecting (the toxins of) VTEC, but all the other common gastrointestinal pathogens as well.

In the molecular age, CTSMAC plates are starting to look a bit dated. What was seen as  modern methodology a generation ago no longer cuts the mustard.

As we move through this transition period for VTEC detection there is a real mish-mash of different VTEC methodologies used in laboratories worldwide. I don’t think this messy situation will last. In a decade or so I suspect 90% or more of microbiology laboratories will be using molecular methods for VTEC detection (and everything else stool related).

However at the moment, there are still plenty of CTSMAC plates being manufactured worldiwde. We still (guiltily) use them at our lab, as we continue to work out how to afford molecular testing for enteric pathogens…

But now they are used in the knowledge that they will clearly not pick up all VTEC strains in the patient samples, or anywhere close.

CTSMAC plates are getting old, and I for one can’t wait to see the back of them…


Note that the Infectious Diseases Society of America has just brought out updated guidelines on Infectious Diarrhoea, including quite a bit of detail on VTEC/STEC. Apart from the incorrect spelling of diarrhoea, they are very good!

I will add them to the guidelines section of this website also.

“Modern Plague: Learning from the Past”

I have had a passing interest in the recent Plague outbreak in Madagascar. Living and working in provincial New Zealand, I don’t come across many cases of Plague. In fact I can safely say, I have never seen a case, and may well never do so. But as a microbiologist, I need to know something about the plague, just in case somebody asks…

The causative agent of Plague is Yersinia pestis. The other two main pathogenic bacteria in the Yersinia genus are Yersinia enterocolitica and Yersinia pseudotuberculosis

And I am bored to tears already… Rote learning is no way whatsoever to learn about bacteria, and especially ones like Y. pestis which most people will only encounter very rarely in real life.

When I think of plague, my mind turns to medieval London, Ring-a-ring-of-roses, Samuel Pepys, etc.

But most of all I think of the discoverer of the causative organism, Alexandre Yersin (picture above), a Swiss-French bacteriologist who has a fascinating life history. 

Born in Switzerland in 1863, he went to medical school in Lausanne, before ending up in Paris at Louis Pasteur’s research institute. There he was involved in the development of anti-rabies serum with Emile Roux. He joined the Pasteur Insitute in 1889 and again with Roux, discovered diptheria toxin.

He then worked as a doctor for a shipping company in South East Asia and it was during a secondment to Hong Kong in 1894 to investigate an outbreak of plague, that he discovered the pathogen responsible for causing plague. It was originally named Pasteurella pestis, but this has since been changed to Yersinia pestis in 1944.

As is often the case, there was a degree of controversy as to who was the first to make the discovery of Y. pestis. A fellow scientist, Kitasato Shibasaburo, made very similar findings to Yersin, but over the years, Yersin took most of the credit for the discovery due to the greater accuracy of his microbiological findings.

He then settled in and spent most of his life in Nha Trang, now in Vietnam.

He also directed a medical school in Hanoi, and was involved in establishing rubber trees and Cinchona trees (used for making quinine) in the region.

Alexandre Yersin died in Nha Trang in 1943, during World War II. A museum was set up in his former house and to this day, he is venerated by the Vietnamese people.

When you read about the history of a disease, it contextualises it, and thus the associated facts get remembered better.

So if you get asked to learn about Yersinia pestis, then go and read about Alexandre Yersin, go and read about The Great Plague of London, read about the living conditions, the rats, and the fleas… All you need to know about Yersinia pestis will be in such texts, and you will remember the stories.

And it is also far more interesting than reading a textbook


“The Introverted Microbiologist”

I am quite far to the left on the introversion/extroversion scale.

And maybe that is why I am a microbiologist…

I have always been a bit of a loner, a dreamer, a wanderer, and most days I need and crave a lot of time by myself. I guess I am a little anti-social, and much prefer talking to people one on one, as opposed to being part of a group conversation.

On occasion my introversion borders on misanthropism, but don’t take it personally. Such feelings never last long.

I hate the idea of networking with strangers at conferences. That is anathema to me! On the contrary I thrive on the amount of time I can get to myself during conference leave. Maybe that is why I am attracted to large “anonymous” conferences such as ECCMID, where I can disappear unknown into the crowd…

You can get away with being an introvert as a microbiologist, regardless of whether you are a scientist, a technician or a clinical microbiologist. Our jobs mean we do not necessarily need to be face to face with other people for large parts of the day. Obviously you need to be able to communicate, but there must be a lot of other professions where a degree of extroversion would be more useful than in microbiology…

I don’t think I am the only microbiologist that is introverted. I look at my colleagues and I can see similar characteristics in many of them, just maybe not to the same extent as myself. It reassures me that I am not the only one!

Sometimes I can override my tendency towards introversion. My desire to have my opinion heard can often conquer my natural reluctance to speak out, particularly when I am in familiar company. I am also not afraid to take risks and try new things out in the microbiology laboratory. My low boredom threshold and innate need for change often overrule the introvert’s need for a “quiet life”. An introvert is not the same thing as a luddite.

However my displays of extroversion are often forced, and short lived in nature. I always end up veering back towards introversion.

So I embrace my introvert personality. I am supremely confident in my ability to be a competent and influential microbiologist in spite of my introvert tendencies.

I might be quiet, but underestimate me at your peril…