Category Archives: “One world” Microbiology

Back to Basics

Working on the urine bench always brings to the front of my mind the lack of understanding that some clinical staff have of the basics of microbiology and the commonly used abbreviations – Note that I said some and not all.

We frequently see request forms with statements such as “MSU Bag urine” – which one is it? A MSU or a Paediatric Bag collect? or “MSU” but with clinical details that the patient has a “permanent SPC” – again is it an MSU or a Catheter specimen? or most commonly “MSU” written under tests required which in my opinion is being mixed up with the abbreviation MC&S (short for microscopy, culture and sensitivities). MSU is not a test but a specimen type. It is an abbreviation of Midstream Urine as opposed to other urine types such as CSU or Catheter spec urine, EMU or early morning urine, Aspirated urine or just a random collect or clean catch collect.

This may seem to be a bit pedantic but the type of specimen we receive in the laboratory has a bearing on what and how we report out to the clinician and whether or not we deem it relevant to report sensitivities. For example, a true MSU should have less chance of having cellular and/or bacterial contamination as opposed to a clean catch urine which often has larger numbers of epithelial cells present and often vaginal contamination if collected from female patients. Also, growth from a catheter specimen is less likely to get sensitivities reported due to the fact that the presence of bacteria and/or cells is often reflective of colonisation rather than infection and changing the catheter, if in situ for a longer term, will often be more effective than antibiotic treatment. Again this is where it is important for the laboratory to be given relevant clinical details so we know if the patient is showing signs of systemic involvement in which case antibiotics will be reported, or if the catheter is merely an in/out catheter for collection purposes as opposed to a long-term solution for a tetraplegic.

It is also important that the correct urine type be collected for the right purpose. If a clinician is wanting testing for TB then an MSU is not going to be sufficient and will be rejected by the laboratory. They will need to ensure a full early morning collect is sent through to the lab so that it can be further concentrated to optimise the chances of isolating any Mycobacteria present. Likewise, random urine collects, although adequate for screening purposes is not the preferred specimen for accurate biochemical dipstick testing or bacterial isolation due to the fact that the potential exists for dilution if the patient has recently consumed fluids.

All this information assists us as laboratory workers to perform our job to the best of our ability and to put out results that are relevant to patient treatment so it is important for clinical staff to understand the differences and to ask themselves what they are wanting to achieve from their request from the laboratory and then together we can maximise the outcomes for patients.

 

“Money….”

I have long ago dismissed any notion of becoming wealthy, having realised the many other things that are far more important in life. I will earn what I need to earn and spend it as well as I can102px-Mcol_money_bag_svg. After what I hope to be a hedonistic old age!, I will leave what little is left to the family.

So what about microbiology labs? How does money affect them? We like to claim that we work in impoverished laboratories, and certainly some labs work to tight budgets. However in New Zealand where I currently work, it is difficult to imagine that any lab is desperately short of money relative to some of the laboratories in the developing world.

Of more interest to me is the microbiology lab that has too much money. What are the signs and effects of this? Here are a few suggestions based on a few of the many labs I have experienced throughout my career:

  • Too many managers, leading to excess bureaucracy and difficulty getting decisions made.
  • Too many unnecessary or superfluous tests being performed.
  • Inefficient processing methods, overuse of antimicrobial susceptibility testing.
  • Avoidance of making difficult decisions.
  • Lack of hunger to modernise the service.

I have been in labs that are clearly playing to a tight budget, and also in labs that have been “dripping with money”. What is interesting however is how little difference there is in terms of performance between them….

Microbiology matters, money less so….

Michael

“Comparing Apples with Oranges.”

Apple_and_Orange_-_they_do_not_compareIn NZ (as with several other parts of the world) there is currently a significant outbreak of pertussis in the population.

In the acute phase of pertussis/whooping cough, some NZ labs offer culture for Bordetella pertussis (with an overall sensitivity of 60-70%) and some offer PCR (with a sensitivity of approx. 90%).

So which is the better test? Purely in terms of efficacy, there is no comparison. (I know which test I would want…)

However the cost of a Bordetella pertussis culture is a few dollars, that of PCR 50-100 dollars. So which one is best now? I guess it depends to some extent on your agenda.

The point I am trying to make here is that the overall value of a test to the health service should not only be considered in terms of performance but also in its cost-effectiveness. There is only a fixed amount of money in the pot with a lot of different hands dipping in.

I am always intrigued by the amount of times I have sat in a conference listening to a speaker discuss a new assay or a new technology. Yet, most of the time, very little is said about the cost, skills required, and the other practicalities of implementing the test in a routine diagnostic lab. To omit such details is essentially only giving half the story and for me indicates somewhat of a detachment from the real world.

I think cost should always be considered when discussing any test. I like to think that microbiology scientists and clinical microbiologists know as much about money as managers do about microbiology.

Michael

p.s. For those that are interested I have added a short tutorial to the website on Hepatitis B serological markers, something that always confused me somewhat as a student!