Medical Fun Facts Episode 54: Diagnosing urinary tract infections

It’s Thursday 6 April 2017. It’s pay day and as this show drops I hope I’m out at a dinner.

Urinary Tract Infections

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The other week I had the privilege of spending a couple of hours with four scholars who are beginning their coursework for a Masters of Applied Epidemiology. One of the scholars is Kaitlyn who I’ve mentioned before and she is the inspiration for this podcast/blog.

Each MAE scholar is expected to visit a medical testing laboratory and spend some time learning what happens and how to apply that to their studies in public health epidemiology. I explained a basic layout for microbiology, showed the scholars some things down the microscope and some agar plates.

One thing I didn’t get to explain in detail though was how we diagnose urinary tract infections.

The most common urine specimen in clinical microbiology is known as a midstream urine. No, it’s not the middle of a stream of urine as it emerges from your urethra. It would be hard to separate the middle from the surrounding urine and I have no idea how we would define where the middle of a stream started and ended. No, a midstream urine is the portion of urine after the first spurt of urine and before the rest of the bladder is emptied. If you’ve seen a typical yellow topped specimen container, we just need that half to three-quarters filled. Don’t get too generous, we don’t like slopping urine over our gloved hands.

In blokes, it’s straight forward. They just need to remember if they have a droopy foreskin to pull it back. We don’t want cheesy smegma contaminating the urine thanks. Most men can let some urine out, stop the flow, pass some urine in the container and then void the rest of their bladder into a toilet bowl. It’s important you don’t pee on the outside of the container.

In women, it’s important to separate their lips or labia to reduce the amount of vaginal flora contamination in the urine. It’s often easier to let the first portion go and then catch enough in the container and then empty the rest of your bladder. Some women have a lot of trouble with specimen contamination for a whole variety of reasons, mostly anatomical. In those situations, an in and out catheter may be necessary.

The reason we want the midstream and not the first pass urine is because the first pass urine is more likely to be contaminated with skin flora and flora resident in the urethra. We take advantage of this when asking for a first void urine when testing for gonorrhoea and chlamydia by PCR. Check out episode 51 which was on genital infections. It was the show where I did my own artwork. You can’t miss it.

Once we get the urine in the laboratory, we prepare a counting chamber and inoculate agar plates. The agar plates are inoculated in such a way so that a colony count can be determined. This is important, the number of bacteria per millilitre to cause infection varies from site to site. For example, in symptomatic women with cystitis, that’s infection of the urinary bladder, the number of bacteria per millilitre to cause infection is about a thousand-fold less than the concentration needed to cause pyelonephritis, or infection of the kidney.

In the counting chamber, we use a microscope to count the number of pus cells and erythrocytes if they’re present. We also look for parasites, crystals and casts too. Check out episode 17 which was on urinary casts.

Typically, if we receive a specimen on a Monday and infection is present, we’ll know the name of the bacterium by Tuesday morning and which antimicrobials to use for treatment by Tuesday afternoon.


And so, ends another episode of Medical Fun Facts. You can find the show notes for every episode at my blog

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