Medical Fun Facts Podcast

MFF0006: What’s the difference between colonisation, infection and disease

This is a question I get asked from time to time. Most medical practitioners understand the difference but to the nonmedical person, it may be a little confusing.

Let’s be clear though that quite often people will think of infection and disease interchangeably, this is not always the case.

Let’s also throw in a few more words into our mix. Words like exposure, commensalism and latency.

If you read enough pathology reports, you may come across the quaint phrase “normal flora”. This harks back to the days when bacteria were likened to plants, hence, flora. The normal meaning these inhabitants were part of the normal population of microorganisms in that particular anatomical site.


In my mind exposure means real contact or potential contact with a microorganism. For example, you are sitting in a classroom and someone with a head cold sneezes and you feel snot on your face. That’s exposure.


Colonisation means a microorganism can be recovered from a nonsterile site without evidence of any damage to the host. For example, we may find methicillin-resistant golden staph on the skin of your groin. Such a bacterium would generally be regarded as a pathogen if found say in an abscess on your arm, but just recovering it from the skin of your groin means you’re colonised. I would bet if we found it there we’d also find it in your armpits and maybe in your nose.


A commensal organism is a microorganism that forms part of the normal microflora of a particular anatomical site. For example, did you know we can find borrelial and treponemal species of spirochaetal bacteria in your mouth?


Infection occurs when there is the acquisition of a microorganism by the host. For example, if your partner has syphilis and you have unprotected sex with your partner, you will acquire the pathogen Treponema pallidum. If the infection occurs in your mouth and you develop a chancre, then unlike the commensal Treponema species in your mouth, you have the syphilis infection active in your mouth.


Latency occurs when the host, that’s you, acquires a pathogenic microorganism but it doesn’t cause disease. This can also be called dormancy. A good example is one of my favourite bacteria, namely, Burkholderia pseudomallei. I’ve even written about it on another blog. You can find the URL in the show notes.

Burkholderia pseudomallei can remain dormant or latent in lung tissue for years until the host becomes immunocompromised. The classical description is melioidosis in Vietnam veterans decades after leaving Vietnam. Burkholderia pseudomallei is an environmental bacterium that lives in the soil and becomes a problem when the water table rises. You can imagine the jungles of Vietnam during monsoon season. It’s thought that when helicopters came along to extract warfighters the rotors would kick up Burkholderia pseudomallei laden water and mud which would aerosolise the bacterium and it would get inhaled (breathed in). Burkholderia pseudomallei is an intracellular pathogen and it would sit comfortably and wait for an opportunity to overcome the host’s immune system. I apologise for anthropomorphising a bacterium but it’s the easiest way to explain what happens.


The disease stage occurs when the microorganism causes damage to the host’s tissues. If you have an abscess that is a disease process. If you have a carbuncle you have a slightly more serious disease process. I think one of the best ways to describe the difference between infection and disease is tuberculosis. I have been infected with Mycobacterium tuberculosis. I know I’ve been exposed to many patients and to open cultures in the laboratory. It wasn’t a surprise when I learnt I was infected. At the moment I don’t have tuberculosis disease. That may happen when I’m older and then I’ll get what used to be called consumption.

So there you have it. I hope this helps explain the difference between colonisation, infection and disease.

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