Monthly Archives: October 2017

“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…


“Nothing is perfect..”

Apologies for the paucity of posts recently. I have had an unwell child.

MALDI-TOF (Matrix Assisted Laser Desorption & Ionisation- Time Of Flight) has revolutionised microrganism identification in the past decade, and in particular bacterial identification in the microbiology laboratory. It will continue to evolve into fields such as filamentous fungi, mycobacteria, antimicrobial resistance etc.

Rarely has such an innovation been so rapidly and comprehensively adopted by the laboratory community. And you can see why. It’s quick, it’s easy, it’s cheap (the consumables are anyway) and it’s reliable.

But it’s not perfect….

Some well known identification limitations are listed below where MALDI-TOF struggles to give the microbe a label, or at least one which fits in with our pre-defined beliefs.

Take the following well known, and not so well known examples…

  • E. coli and Shigella species
  • Streptococcus pneumoniae and Streptococcus mitis
  • Bordetella pertussis and Bordetella bronchiseptica
  • Klebsiella oxytoca and Raoultella ornitholytica
  • Shewanella putrifaciens and Shewanella algae
  • Proteus vulgaris and Proteus penneri
  • Klebsiella pneumoniae and Klebsiella variicola
  • Haemophilus haemolyticus and Haemophilus influenzae
  • Serratia ureilytica and Serratia marcescens

There are many more. Please feel free to suggest others that you have come across. There will be even be differences between different MALDI-TOF platforms, e.g. Bruker and VITEK MS.

Most of the time it does not matter too much from a clinical point of view. Some of the time, it does, and we need to try and clarify with molecular or biochemical means.

It shouldn’t surprise us however that the identification is not perfect. All identification systems are essentially typing systems in disguise, and they all have databases or libraries at the core of their function..

  • “APIs” are a typing system based on biochemical reactions.
  • MALDI-TOF is a typing system based on proteonomics.
  • 16SRNA sequencing is a typing system based on nucleic acid sequences.

Identification systems therefore suffer from the inherent problems of all typing systems. No typing system can be matched exactly against any other typing system.

For all typing systems the ability to group isolates and the ability to discriminate them is a trade-off of sorts. For MALDI-TOF, the bigger the databases get, the more the system can discriminate, and thus the more it can potentially differ from the original (textbook) identification.

So no system is perfect, including MALDI-TOF.

But it’s very, very good….