“Should anaerobic culture be performed on superficial swabs ??”

This is a (version of) a post I published a couple of years ago, and I am still toying with the idea. Any thoughts or experience with this topic would be much appreciated, before I take the plunge!

Anaerobic culture has always been difficult in a diagnostic bacteriology laboratory. In the early days  of bacteriology labs anaerobic culture was very difficult if not impossible, so it just wasn’t done.

Then came along anaerobic jars and anaerobic cabinets where the oxygen could be removed from the environment surrounding the agar plate. This led to an “explosion” in anaerobic culture in many different types of samples.

Now the reality is starting to sink home… We are still not that good at recovering anaerobes. This is not particularly the laboratory’s fault. It is just very difficult to mimic the anaerobic conditions of certain parts of the body right from when the bacteria are taken from the patient until they are growing in an anaerobic environment in the laboratory. 

In addition there are areas of the body such as the GI tract, vagina, oropharynx which contain lots of anaerobes anyway, so culturing anaerobes from these areas means nothing at all in terms of pathogenicity.

So back to the question: Should superficial swabs be cultured for anaerobes?

My gut (excuse the pun) feeling here is that we are not helping the patient by culturing superficial swabs for anaerobes because:

  • Superficial areas are exposed to oxygen, so although anaerobes may exist in deeper areas of a wound, getting a good sample of such with a swab is very difficult.
  •  A clinician’s  decision whether to include anaerobic  cover should very much be decided by the clinical presentation, not the microbiological results. Eg bite wounds, infected diabetic foot ulcers, aspiration pneumonias, dental infections are all clinical conditions where anaerobic cover should generally be routine. Not culturing anaerobes from such specimens should not prompt discontinuation of anaerobic cover.
  • The growth of anaerobes or mixed anaerobes from superficial wound is of dubious value. If isolated, are the anaerobes really causing the problem? My experience is that when anaerobes are found in superficial swab culture, they are often found with other colonising enteric flora, so are of doubtful significance. Other anaerobic isolates may co-exist with other pathogens such as Staphylococcus aureus, and treatment of the Staph aureus alone often sorts out the infection. 

There is no question that anaerobic culture is of more importance when the sample is taken from a sterile site. In these cases it can have a real impact on both the diagnosis and subsequent management of the patient. E.g. Fusobacterium necrophorum in a blood culture suggests the possibility of a Lemierre’s syndrome. Isolating Bacteroides in a blood culture suggests intra-abdominal pathology, often a collection of some sort.

Lots of laboratories still culture for anaerobes from at least some superficial swabs, because that is the way it has always been, or that is what is expected of the lab, or because we do isolate anaerobes from superficial swabs.

However I think that when we decide to culture a superficial swab for anaerobes, we don’t really think about how poor both the sensitivity and specificity of the result is. Although we are trying to be helpful, the truth is that we may not be helping at all…. 


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