Tag Archives: textbooks

“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


Sterile Pyuria: Horses for Courses

Open most microbiology textbooks (particularly the older ones) and you will find tuberculosis high on the differential diagnosis of sterile pyuria.

This might be true in some parts of the world, but I suspect in a lot of places, and certainly where I work in New Zealand, renal tuberculosis is an extremely rare cause of sterile pyuria.


I would estimate about 1 in 1000 cases of sterile pyuria are due to TB here in NZ. There are much more common causes such as recently treated UTI, contamination with vaginal leucocytes secondary to chlamydia, candida infection, infection due to fastidious organisms etc etc.

GPs often reflexively order 3 Early Morning Urines for mycobacterial culture when they see a report suggesting sterile pyuria (because of those textbooks). In some areas of the world this might be appropriate, but in our lab in New Zealand, we like to see either repeated sterile pyuria results on the same patient or strong supporting clinical information before even accepting urines for TB culture.

Along the same lines if you have a young sexually active adult with sterile pyuria with no obvious cause, then excluding chlamydia should be at the forefront of your mind, and an appropriate comment to suggest this should always be added to such reports.

Horses for Courses….


I am away at a virus conference for the next few days…..

“The Smiling Executioner”

I have done many exams in the past, several of them microbiological. They have been consistent both in their lack of originality and also their focus on knowledge base, often requiring regurgitation of factual knowledge learnt from textbooks.


The primary focus of any professional exam should first and foremost be to ensure that the candidate has a good understanding of the subject, is safe, trustworthy, and knows when to ask for help. These are difficult enough attributes to assess.

However in addition, I think exams should also at least attempt to assess candidates on their ability to think on their feet, to innovate, to adapt and to lead. These are attributes I would certainly also be looking for in a prospective employee.

Here are a few examples of exam questions I have thought of that at least try to assess these additional attributes:

  • Summarise your prototype design for a “perfect” incubator?
  • You have been asked to put together a multiplex PCR for enteric bacteria. What micro-organisms would you include and why?
  • You have been asked to restrict to eight the number of different types of agar plates that the laboratory orders in. Which agar plates would you choose in this sub-set of eight and why?
  • You happen to notice that very few agar plates are growing Staphylococcus aureus in the morning plate read. Give reasons for this and what further investigations are required?
  • The Laboratory Biohazard cabinet will be out of action for two days. How will this affect your laboratory service and how will you cope?
  • A sales rep meets with you, presenting a new Enyme Immuno Assay which he/she proclaims to have 100% sensitivity, 100% specificity and 100% positive predictive value. What questions would you want to ask him/her in order to get the real story?

Most importantly, these are the sort of questions that cannot be answered straight from a textbook, although obviously a good deal of knowledge and understanding is required for all the issues involved.

I suspect not all microbiology students would like these types of questions. Maybe it is just as well I am not an examiner. Otherwise I would probably be known as the “Smiling Executioner”!