In which truths are revealed

There are many things I love passionately about science, but one aspect has got to be right up there in the top ten: the transformation of a deep unknown into perfect clarity.

I find it amazing that using simple lab techniques, we can start from something as obscure and inscrutable as this:

Infected urine sample

and with a few manipulations, arrive at its precise essence:

Bacterial urine culture

The upper image is, as you’ve probably guessed, a fresh urine specimen from a person with an acute urinary tract infection. The lower image shows what you get when you spin down the urine and take a closer look. The centrifugation collects the heavy sediment, which is enriched for bladder cells that have been shed from the afflicted organ as a sort of bodily defense mechanism – and these tend to be loaded with a cargo of bacteria clinging to their outsides or packed within. Once plated on chromogenic agar, various species of bacteria can take root, grow to macroscopic colonies and be identified by their colors – all based on the agar being spiked with various chemical substrates that interact in different ways with different bacterial metabolism systems.

The plate above shows that the culprits in this patient are largely E. coli (brownish colonies), with a smattering of Enterococcus (blue). Depending on what’s in the urine, these plates can reveal a rainbow of possible microbes. And by performing dilutions and doing a little back-calculation, you can work out the exact concentration of each species.

None of this is Large Hardron Collider-style stuff; the color tricks may be fancy and newfangled, but the rest of the general procedure is ancient by modern science standards. Still, I think that that sometimes the classic tricks are the most satisfying. Sure, from here we’ll use PCR and sequencing to identify strains from their ribosomal RNA content, and eventually fluorescence in situ hibridization to work out precisely which bugs are getting inside cells, but for me, this initial discovery step will be a lot more magical.

About Jennifer Rohn

Scientist, novelist, rock chick
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10 Responses to In which truths are revealed

  1. Cath@VWXYNot? says:

    That’s quite the photo to see when checking out the OT home page! I’d ask if you’re taking the piss, but the joke’s far too obvious.

    Chromogenic agar… who’d have thought… I love the future!

  2. That chromogenic agar is wonderful stuff. Colourful, informative, and (reasonably) immediate. 🙂

    I recall using some kind of “dipstick” affair lo these many moons ago in undergrad… some kind of thing with different substrates on it that gives you a kind of rainbow pattern to identify different bugs. Do those still exist?

    And… I’d never thought of using FISH for that purpose. Would love to see some of those micrographs once you get to them. 🙂

  3. Winty, I think you’re referring to API strips. They do use these in the lab but I haven’t tried it yet. But I’m really enjoying doing Gram stains again…there is something truly satisfying about it, and it *always* works. Good party trick!

    Cath…would I take the piss? Even a wee bit?

  4. Ah yes, thanks, those are the things. API Strips.

    As for your other comment – urine violation of the anti-pun standards, you know.

  5. Ian the EM guy says:

    I’m afraid there can be no mention of urine, or particularly the phrase taking the piss without me posting a link to my minute or so of fame, appearing in my lab coat no less and in the lab to tell the delightful Victoria Coren my theory on the etymology of the phrase “taking the micky” for the BBC2 programme “Balderdash and Piffle” about 4 or 5 years ago (in my pre EM guy incarnation). Jenny, now our resident wee expert, will obviously spot that it isn’t actually urine that I’m pipetting, but tv people being who they are wanted it to look like I was. They brought some fake options themselves, including some apple juice but seeing as they looked more like the sample Jenny has shown above, I told them that if that was what their urine looked like, they should go and see their GP!

    Enjoy my cringeworthy performance at this link, I do my bit at about 1 min 20 seconds in.

  6. rpg says:

    “Is that your idea or did you read it somewhere?”

    Awesome. So extracting the Michael.

  7. Cath@VWXYNot? says:

    “urine violation of the anti-pun standards”

    Have those standards been pee-er reviewed?

  8. Cath@VWXYNot? says:

    (I’m assuming that Jenny predicted and was ready for this kind of response, btw)

  9. Cath – I’m not interested in these piddling little details.

    Jenny – sorry.

  10. Cath, Winty, I’ll come up with a good riposte in just a tinkle.

    Ian, that TV spot is hilarious! They must have been wetting themselves (heh heh) when a scientist wrote in and they realized they could shoot some silly lab scenes. I love the way Coren totally loses it at the end.

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