Category Archives: Future of Microbiology

“Indole positive or negative?”

If you asked me whether E. coli was indole positive or negative, I wouldn’t have a clue.

Despite being told the answer many times over the years, the answer just doesn’t stick. I simply don’t care..

My colleagues must despair of me.

It is a wonder that I managed to pass any exams at all…

Which brings me to college microbiology exams and my increasing disillusionment with them.

Formal exams in general have not changed much in style over the past few hundred years. They essentially test knowledge that can be held in the head. (I hold very little in my head..)

But most young people have an I-Phone in their back pocket…

The skills that young microbiologists need nowadays are not related to hoarding large amounts of microbiological facts. This is becoming increasingly irrelevant. They need to be able to problem-solve and troubleshoot. They need to be computer savvy and innovative. They need to be observant and be able to spot the unusual. They need to have the patience to tolerate a degree of repetitive work, and they need to be able to get on with their colleagues and build a rapport with lab users.

Do the microbiology exams of today really test these skills?

If it were up to me, I would get the students into the microbiology lab on day 1 of their training (so they can see if they really enjoy it) and keep them there as much as possible. I would pay them part-time for doing some simple tasks in the laboratory (so they don’t finish their degree in lots of debt). The academic part of the course would be primarily online, with occasional small group tutorials. I would ban large group didactic lectures altogether. I would focus on the diagnostic microbiology of today and tomorrow, not of yesterday. I would not have a formal written exam at the end, but rather continuous assessment throughout the training period. I would however advocate an oral examination at the end to ensure the student has a good understanding of the basic concepts of microbiology and has good safety awareness in the laboratory. I would be brutally honest with them in terms of future job prospects and where I see future work opportunities within clinical microbiology.

There are too many people within academic institutions who have too much of a self-interest in keeping things the way they are at the moment.

This has got to change…

Modern microbiology degrees are needed for modern microbiologists.


I see that most E. coli are “indole positive”. I have just checked Google on my smartphone…

“Reinventing yourself”

In the next generation (20-25 years), the diagnostic microbiology laboratory workforce will be decimated worldwide.

If you are a student, they don’t tell you that at the careers fair…

“You sound like exactly the sort of person we are looking for. Come and “train” for four years in a lecture theatre, and then work in a clinical microbiology laboratory, that is if you are lucky enough to get a job. Unless your Mum and Dad are well off, you will accrue a hefty debt which will likely take you a couple of decades to pay off. However in 20 years time your job will probably not even exist…”

Am I being too harsh?

In terms of general culture based bacteriology, most of it will have gone molecular. Whatever is left of it will be automated, not just partially automated as with the current Kiestra TLA system, but completely automated to include plate interpretation, colony picking, identification, antibiotic susceptibility testing and rule based signout. The whole works…

Most microbiology samples will never touch a laboratory worker’s hands.

Molecular testing will have increased, but on highly automated platforms, processing high volumes of work, with minimum manual input.

Our work will be reduced to oddities and troubleshooting. I would even chance to say that there will be just as many engineers as microbiologists on the laboratory floor.

And then I look at the core components of my own job as a clinical microbiologist…

  • Authorising important results:- This will be done automatically using sophisticated rules based computer algorithms. And they will do it much better than I can.
  • Giving antibiotic advice:- Decision support apps downloaded on clinicians’ smartphones will do this more sensibly than me.
  • Laboratory Management:- I fear there will be nobody left in the lab to manage…
  • Demand management:- Although the process of demand management will be performed by software algorithms, there might still be a little work left for me regarding the initiation and governance of such projects.
  • Anti-microbial stewardship:- Anti-microbial resistance is not going away anytime soon so there may be a continuing role in the governance of such programmes. But the nuts and bolts will be highly automated and app-based.

So I am not overly optimistic about my own long term future. No one is immune…

It is no accident that during conferences I heavily focus  on presentations in molecular diagnostics and demand management. That should help in the short term at least in securing my usefulness. However it is entirely possible I will need to retrain in something completely different before I am done.

I know my job description as a clinical microbiologist will change out of all recognition before I retire. It is not impossible that clinical microbiology as a career entity will cease to exist altogether.

We need to be constantly looking at what we do today, then imagining what we will potentially be doing tomorrow, and preparing for it as best we can…


“Molecular diagnosis of wound infections: The Holy Grail.”

The slice of pie taken by the molecular department in the microbiology laboratory is increasing, slowly but surely.

On the contrary, the proportion of culture based microbiology is inexorably declining.

Many clinical microbiology laboratories are now switching, or looking at switching over to molecular diagnosis of enteric pathogens.

Molecular diagnosis of pathogens causing vaginitis and pharyngitis will not be far behind, and a few labs have already moved in this direction.

However diagnosis of wound infections remains firmly culture based. There is not even much in the literature with regards to molecular diagnosis of wound infections…

Is it even possible?

So what are the difficulties?:

  • Potential number of pathogens: There are several pathogens or putative pathogens that are able to cause wound infections. This makes PCR based molecular diagnosis more difficult. However, on the flip side, 95% of wound infections in a general clinical setting are caused by two pathogens, Staphylococcus aureus and Streptococcus pyogenes (Group A streptococcus).
  • Lack of susceptibility information: Molecular diagnosis of resistance determinants is still a little behind phenotypic culture based testing. However with regards to the two main pathogens as above, PCR analysis can easily differentiate between MSSA and MRSA, and susceptibility data for Streptococcus pyogenes is only required for a small proportion of patients who have anaphylactic reactions to penicillin.
  • “Over-sensitivity”: It is always nice to know which are the dominant organisms within a wound. Culture is relatively good at this. However molecular methods are starting to be able to quantify to some extent (e.g by playing with the cycle threshold cut-off).
  • Cost: The culture of a standard wound swab might cost $10 or so, even when overheads are included. In my experience molecular tests have to be performed in very large volumes to even get close to this kind of price. However wound swabs do arrive into the laboratory in very large volumes!

If it was easy it would have been done by now… I suspect it is the 4 things above acting together as a “bundle”, as opposed to any one insurmountable barrier which has contributed to the lack of progress up until now.

However it will come in some form or other, you can be sure of that…

Here is a potential solution I have thought of:

  • Any wound swab accompanied with clinical details suggesting an unusual pathogen e.g. animal bites (Pasteurella), water exposure (vibrios, aeromonas), immunocompromise,  would still undergo routine “catch-all” bacterial culture.
  • The rest (the vast majority) would be subjected to a multiplex PCR for the detection of MSSA, MRSA and Streptococcus pyogenes (and possibly Group G streptococcus also). A positive result would be reported routinely. A  negative result would have an accompanying comment to suggest contacting the laboratory if the patient’s symptoms were persisting, or if further susceptibilities are required, so that culture could be set up if necessary.

In this way molecular diagnostics could be performed on (a good proportion of) wound swabs at a relatively low cost.

In addition multiplex PCRs could be developed specifically for infections in specific clinical situations, e.g. post animal bite,  etc., etc.

Automated bacteriology culture systems like Kiestra TLA would not have happened if the industry didn’t think that there was at least another 20 years or so of culture based bacteriology left, and they are probably right. But I don’t think it will be too long before commercial laboratory diagnostics companies start looking closely at “wholesale” molecular options as above.

And who knows, whole genome sequencing might come in and completely disrupt PCR based molecular diagnostics, and the picture might change again…

The future’s uncertain and the end is alway near