“Why you should not buy a microbiology textbook…”


If you are doing under or postgraduate exams in microbiology, I would advise you not to buy a microbiology textbook, even if you have been given a reading list full of them!

I attended the ASM conference in Boston recently and was blown away by how many book stands there were dotted around the industry hall.

I didn’t realise there were so many microbiology textbooks out there.

So someone must be buying them…

But not me… I haven’t bought a textbook of any description whatsoever in almost 20 years. That doesn’t mean however I don’t study. Far from it.

Here are the reasons why I don’t buy microbiology textbooks, in no particular order:

  • They are too expensive. I am a self-confessed academic skinflint, who prefers spending his disposable income on nice wine and travel.
  • They are too heavy. I have too many bad memories of lugging around a large satchel full of books at school.
  • They teach you a very standardised set of microbiology facts. i.e. they stick to the syllabus. I think syllabuses are much over used, over detailed, and over-rated.
  • They teach you stuff that everyone else knows/is supposed to know. There is a finite resource of information in a textbook, so it leaves little room for exploring an area in more detail, or one that is of particular interest to you.
  • They become out of date very quickly. My own laboratory contains a whole shelf of historical textbooks, none less than 10 years old.

I use the Internet instead. I stay away from patient websites, commercial websites, and chat forums, but most of the rest is reasonably reliable.

By using the internet I can (metaphorically speaking) wander around, get second opinions, and look for stuff on a particular topic that other people are not likely to know. I ask myself a few specific questions, then search for the answers. To learn stuff in more detail, I occasionally source out a journal article or two. I know it sounds stupid, but I make a point of never learning stuff that I know already. I know lots of people that do. I am much more of a gap filler.

Some people might argue that there is stuff in the textbook that is not online. I don’t buy that. Everything is online.

Don’t feel compelled to read a microbiology textbook, just because someone from the establishment has told you to read it. Set your own learning agenda…


“Four more years…”


Four years is the time period between Olympic Games. It is the time period of an American presidency.

It is also the time required to train as a microbiology scientist in New Zealand.

Four years is a long, long time…

Four years sitting in a lecture theatre or mock laboratory, amassing debt, and learning (increasingly irrelevant) microbiology facts.

Would you recommend it to your children..?

This is an outdated model of training. If there was ever a profession that lent itself to an online, problem based learning course, combined with laboratory attachments from day 1, it is medical laboratory science, and especially microbiology.

Medical laboratory scientists in NZ (in all disciplines) do not get into a “real laboratory” until Year 4 of their training. What about if you enter the laboratory in year 4 and decide that spending day after day in a laboratory environment is just not for you.

Wasted years…

Microbiology laboratories are changing fast. The technology is changing, the skill requirements are changing, the manpower requirements are changing.

The training (and the exams) needs to change as well in order to keep up…


“The Transition”

Genotype_Plus_EnvironmentAt present, routine anti-microbial susceptibility testing is still dominated by phenotype, with genotypic testing occasionally getting a look in for MDROs.

I doubt this is likely to be the case forever…

As our knowledge of genotypic resistance determinants increases, and the cost continues to decrease, I see a time when first line testing will be the resistance genotype and not the phenotype. I believe this is more likely to be a resistance genotype determined by sequencing as opposed to PCR or other molecular methods.

There will always be some difference between the genotype and phenotype as far as susceptibility results are concerned (Think about the behaviour of identical twins. It’s similar but not identical!). The environment that the bacteria lives in will see to that. However as our understanding of the genotype increases we will be able to more accurately predict the phenotype.

But the correlation will never be perfect. There will still be a role for confirming the phenotype, with phenotypic susceptibility testing indicated in the sick patient who is not responding as expected.

I can see this transition happening within my working lifetime, i.e. within the next 25 years.

However having said all this, it is important to be aware that the genotype is not always the perfect answer, and has its own set of problems (the following is an excerpt from my book, The Art of Clinical Microbiology)…

  • Genotypic resistance testing may well be over-calling antimicrobial resistance in some cases, and thus pushing patients unnecessarily towards broader spectrum antibiotics, thus starting a vicious circle of resistance. This is not something however, that is often brought up in the antimicrobial stewardship committee setting.
  • Genotypic testing will (currently) miss some resistance that is demonstrated phenotypically and due to multiple combined mechanisms e.g. carbapenem resistance in some Pseudomonas aeruginosa due to hyper-production of AmpC plus porin loss and/or efflux pump.
  • Genotypic testing will (currently) only pick up the resistance genes we know about. We need phenotypic methods to detect new resistance as it appears and then use genotypic testing to find the genetic ‘code’ for it.
  • Genotypic testing may be over-sensitive when used to screen for MDROs in the setting of Infection Control. This can lead to patient isolation or non-use of an antibiotic because of a positive result, but the burden present or organism carrying the resistance gene(s) does not pose a significant clinical risk to the patient, and possibly no Infection Control rise to the institution.

However I don’t think this will stop the transition from phenotypic to genotypic susceptibility testing happening, when the price is right…

And when this transition does occur that might spell the end for large volume, culture based diagnostic bacteriology…


“The Road to Hell”

road to hell

“The road to Hell is paved with good intentions” (ancient proverb)

  • A laboratory might culture only 50 samples in a year for mycobacteria and look forward to getting a positive culture for Mycobacterium tuberculosis once in a ‘blue moon’.
  • A scientist might be happy to report “No microfilariae seen” on a blood sample despite having last seen a positive case of filariasis 25 years ago.
  • A clinical microbiologist might be willing to give advice on the significance of a rare filamentous fungus that they have only read about in the textbooks.

If I am doing a lab inspection/accreditation for another microbiology laboratory, one of the first things I do is find out is what tests/procedures are being done in low volume. (the other is to spend as much time as possible with the staff on the benches, to find out what really happens in the lab…)

We all have good intentions, but the cold reality is that if we only encounter something very occasionally, the chances of us getting it wrong are much increased.

Quality and knowing your/the lab’s limitations are necessarily entwined.

There is no shame in referring low volume tests on to another bigger laboratory, nor is there shame in seeking advice about something you don’t encounter very often, from someone who does.

I work in an affluent area of provincial New Zealand. Throw me into a microbiology laboratory in Sub-Saharan Africa and I would absolutely be a fish out of water.

Despite our best intentions, we can end up doing more harm to our patients if we think we are as good at doing the things we only do occasionally, as opposed to the things we do often… 


“Tricky Trichomonas”


I have always found the diagnosis of trichomoniasis a difficult one to deal with.

Not personally of course! I am more thinking about the best approach to this issue in the laboratory…

Up until now we have been looking for Trichomonas vaginalis in every single one of the 50,000+ vaginal swabs we get into our laboratory per year.

The vaginal swabs more often than not land on our doorstep with no (clinical) indication as to why they have been sent to us. 

To me this is old style medical/laboratory practice… We need to move away from diagnosing the swab per se, just as clinicians need to move away from treating the lab result on its own , without thinking about the patient.

There are essentially three main ways to diagnose Trichomonas vaginalis:

  • Wet film or other related direct microscopy method: Cheap but very insensitive
  • Culture: usually in micro-titre plates: More sensitive but still not great. Still cheap though
  • Nucleic acid amplification, e.g. PCR: Very sensitive, but also expensive.

More and more laboratories are moving towards the molecular methods, but we (and others) simply cannot afford to test 50,000 vaginal swabs for Trichomonas vaginalis by PCR. 

Nor would it be a good use of financial resources…

So, out of necessity, the laboratory needs to move towards targeted testing; e.g. high risk age groups, sexual health clinics, on specific request, appropriate clinical details, etc.

And therein lies the dilemma – You will pick up more cases because you are using a more sensitive test, but the overall number of diagnoses might be similar because you are testing less patients.

But my gut instinct tells me that the latter approach of targeted testing (based on patient symptoms and risk factors) using the optimal test is the way of the future. Not to mention it also allows the capability to test men as well! (Trying to diagnose trichomoniasis in men using traditional microscopy and culture is virtually impossible.)

Sometimes you just have to throw the old rule book out the window and start again…


Picture courtesy of GiantMicrobes.com !