Monthly Archives: January 2016

“Open and Closed”


Will Staphylococcus aureus ever become completely resistant to penicillin?

At present about 10% of Staphylococcus aureus isolates worldwide retain susceptibility to penicillin. It has been like this for many years. The reason for this is probably two-fold.

  1. Bacterial populations do not exist in a closed system. Therefore they can “escape” to places where there is no selection pressure.
  2. The acquisition of resistant determinants by a bacterium almost always (if not always) comes with a fitness cost. Thus in the absence of any selection pressure, the resistant strain is unlikely to become dominant in such a hypothetical setting.

I would be very worried if Staphylococcus aureus as a population became completely resistant to penicillin, but I don’t think it will happen, not in “real time” anyway. On a population basis, I am not aware of any bacterial species which has variable resistance to an antibiotic, which has then become completely resistant to an antibiotic due to the use of that antibiotic in the population.

People worry about individual bacterial isolates being resistant to all known antibiotic classes, and label it as “The end of the antibiotic era”, which of course it is in a sense, and obviously terrible for the individual patients involved. But as microbiologists, I believe we need to be thinking about resistance much more in terms of bacterial populations, because this is where the answers to future resistance rates and the evolution of resistance really lie….


“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…. 


“Finding a niche”


When we were at school we were usually taught to be all-rounders, to be passable at everything, to be a “Jack of all Trades”. If we happened to be deficient in a subject we were often given remedial teaching to bring us up to “standard”.

A school report with 6 Bs was seen as a better report than one with 1 A+ and 5 Cs, and still is to a large extent.

Not any more, in my opinion anyway.

In the world of work, whether it is in the microbiology lab, or on the wards, it is really important to find yourself a niche. Something that you are better that than everybody else in the workplace. An area where if there is a problem, then you get sought out to find the solution.

It is critical that you find a niche for yourself in an area that you are passionate about. Work colleagues tend to notice when you are passionate about something and they generally respect and defer to this passion.

Examples of niches in the clinical microbiology lab include knowing how to type isolates on a MALDI-TOF analyser, being an expert on culture media, knowing a biohazard cabinet inside out. But to be honest, it doesn’t really matter what your niche is, as long as you have one.

Work is a more hostile environment than school, and it is well worthwhile finding yourself a niche area. Otherwise someone else will find a niche for you, and often one you didn’t want in the first place….


Check out this nice article on finding a career niche. (about a 5 min read)