Category Archives: Confessions of a Microbiologist

“Communication Breakdown”

We conducted a brief audit recently on blood culture identification, and in particular how long it took for a definitive identification result (by MALDI-TOF) to be relayed to the hospital clinicians.

Audits are great at demonstrating that you are not half as good as you think you are…

Our audit showed that it was taking anywhere (depending on which cohort was studied) between 8 and 16 hours from when the identification was released by the laboratory into the “result repository”, until the result was actually viewed by a clinician.

And at the weekends the time delay was even longer, up to a day.


You can have the most sophisticated equipment in your laboratory, and we do…

You can have highly skilled and motivated staff members, and sure enough, we have them.

And you can also have one of the most progressive provincial microbiology laboratories in the world, and I like to think we have that as well.

But it all counts for nothing if we can’t communicate our results in a timely fashion.

Audit can be painful to perform, but highly informative in implementing best practice.

So back to the drawing board for us. Time to sit down and talk with the clinicians and work out a way to communicate results more quickly in order to optimise patient outcomes.

It’s good to talk.

Pre-analytical, peri-analytical and post-analytical phases. They all matter, and they all need to be addressed…



“Separating the wheat from the chaff”

For every two or three genuine positive blood cultures, there is usually one which represents skin contamination (in my laboratory at least). As laboratory microbiologists, we often need to make an assessment about the likelihood of this fact, in order to guide the clinicians.

The “offending” microbes are usually coagulase negative staphylococci, corynebacterium species, propionibacterium species, and bacillus species.

However the isolates listed above do not always represent contamination. How can we assess the likelihood of such an isolate being genuine?

The following factors should be considered:

  • Time to Positivity: A blood culture signalling positive after 10 hours is more likely to be significant than one which signals positive after 30 hours. Bear in mind though that some organisms, such as propionibacterium species, are going to take a long time to become positive whether they are contaminants or not.
  • Number of bottles positive: If both bottles in the set are positive for the same isolate, then this increases the chance of the isolate being genuine. However remember that sometimes there will only be one bottle in the set (paediatric blood culture), and some organisms will often only grow in one bottle (bacillus-aerobic bottle, propionibacterium-anaerobic bottle)
  • Other BC sets taken and whether they are positive: If 6/6 bottles from 3 sets are positive with a coagulase negative staphylococcus then start looking hard for a geuine infection. On the other hand if only 1 bottle out of 6 is positive, then chances of this being a contaminant are high.
  • Clinical details- Prosthetic material on board: Coagulase negative staphylococci, corynebacterium species, and propionibacterium species all love clinging to and infecting prosthetic material. Has the patient got a prosthetic joint, a pacemaker, orthopaedic metalware, a venous or arterial line, etc, etc. if they do then think twice before dismissing blood culture isolates as skin contaminants.
  • Clinical details- Immunocompromise: I was “stung” once with a Bacillus species in a blood culture, which turned out to be genuine, as the patient was immunocompromised. The clue was in the fact that the isolate was present in two separate blood cultures…

All of these points above are just pieces of evidence in the puzzle. I advocate a systematic approach to assessing the potential significance/insignificance of blood culture isolates. Even if takes a couple of minutes per blood culture, it can be potentially very rewarding.

Even better is to look at ways of reducing the contamination rate of blood cultures. This new device looks very promising, essentially reducing the contamination rate by “discarding” the first part of the collection (the blood culture equivalent of an MSU!). I would have thought that such a device could potentially save both time and money on both the clinical and laboratory side. If those funding silos could only be broken down, I would love to try it!



“Hand holding and Chinese whispers..”

As part of my job as a clinical microbiologist, I am usually on the telephone 20-30 times per day.

That is a lot of telephone time for a man…

With regards to outgoing calls, a lot of these are simply information gathering. For example, is this patient with Gram negative bacteraemia on appropriate Gram negative cover? Has this patient with Clostridium difficile infection been isolated and treated? Has this patient with Staphylococcus aureus bacteraemia been investigated properly?

Gathering this information by telephone is of course always a little fraught with difficulty. Trying to get hold of the right person to speak to can take up a lot of valuable coffee drinking time. There is also no guarantee that the information you are given is accurate, and has not evolved along a chain of “Chinese whispers”. Sometimes you finish the phone call no more enlightened than when you started…

Many of these calls would not be necessary if the hospital/health network had a live, real time “Electronic Health Record”, along with an electronic/digital drug chart for each patient. These innovations simply cannot come soon enough to my neck of the woods. Objective, readily accessible clinical information is what microbiologists crave.

Incoming calls are generally from clinicians looking for advice on antibiotics, infection control, optimal samples, etc. Much of the information that I give out could easily be accessed from published clinical guidelines. There is often an element of “hand holding” here, of sharing the responsibility for the decision made, and sharing the blame if something goes wrong..

Personally I was never very good at hand-holding…

And then, once or twice a day, an interesting phone call comes along, one which stimulates the mind, and prompts further thought and reading, and reminds me that I do after all work in a microbiology laboratory, and not a call centre…