Tag Archives: enteric flora

“Perfect is the enemy of good (microbiology)”

The Art of Microbiology, ,

This quote attributed to Voltaire (“Le mieux est l’ennemi du bien”), rings true to me. I have never been a perfectionist, and the idealistic pursuit of perfectionism can hinder real-life achievement and progress. 

The quote came back into my conciousness during the early days of the COVID pandemic when I listened to a great speech by Dr Mike Ryan from the WHO when urging countries to act quickly in the face of the rapidly developing COVID situation.

Of course, such a concept can also apply to the microbiology laboratory.. Here are a few examples:

Protracted work-up of samples: When a sample arrives into the microbiology laboratory, the clock is ticking. In relentless pursuit of isolating that fastidious bacterium, time passes by and before you know it a week has passed… The clinical usefulness of a microbiological result is inversely proportional to the time spent to produce it. In the hospital setting, the average length of stay is 3-4 days… Excessive time spent on certain samples is not only a waste of resources, it also generally does nothing for the patient. Get a result out, even if it is not the perfect one that you are striving for.

Excessive work-up of samples: The classic example of this is identifying every bacterial isolate in a mixture of enteric flora. For the most part, such an exercise is futile, even when isolated from a sterile site. Enteric flora isolated from sterile sites usually represent a source control issue, and who knows what the pathogen might be in the mixture, if any. Such practice is generally a waste of resources, and reporting individual isolates along with individual susceptibilities is time-consuming and often leads to poor antimicrobial stewardship. Working up bacteria within a mixture of enteric flora might be “technically perfect” but does little to help the patient.

Excessive testing protocols: A good example of this is stool samples arriving into the microbiology laboratory. There are many microbiological tests that one can do with a stool sample, culture, PCR for bacterial & viral pathogens, microscopy for parasites, C. difficile testing, the list goes on. However, to perform all the available tests on every stool sample in the hope of maximising the odds of isolating a pathogen would be incredibly expensive, but in most cases would do little to change patient management. Enteric testing should very much be tailored depending on what is on the microbiology request form.

I am sure there are many other examples that one could think of. Perfection in the microbiology laboratory is very much a pipe dream, and can actually be detrimental to good patient care. We cannot possibly hope to identify all potential pathogens in every sample and do it in a timeframe that is beneficial to the patient. We need to move past our fear of missing something…

When developing testing methodologies or reviewing individual patient samples, we should always be asking ourselves “By doing what we are doing, are we providing overall value to the patient?” 

Michael

 

 

“Enteric flora happens…”

The Art of Microbiology,

Enteric flora (a mixture of bacteria of enteric origin) causes problems for clinicians and microbiologists alike.

The reporting of enteric flora from superficial swabs often triggers a prompt switch to a broad spectrum antibiotic by the clinicians, in order to cover all the possible bacterial species that one might find in enteric flora. I have seen this happen a few times over the past week, to the extent that I sometimes wonder whether this is the best way of reporting such a result…

The bacteria that are found in enteric flora hardly ever cause superficial wound infections (particularly in immunocompetent patients), and even when they do, the laboratory cannot possibly be of any help here because we don’t know which one in the cocktail is the culprit.

In addition one may see a laboratory report with a heavy growth of enteric flora along with a light growth of either Pseudomonas aeruginosa, Bacteroides fragilis, Candida albicans or Streptococcus agalactiae. However, enteric flora naturally contains these micro-organisms anyway, so no surprise there.

Just more unnecessary antibiotics for the patient…

A good proportion of swabs from the peri-anal area will grow enteric flora. This goes without saying, and only demonstrates the relative futility of such swabs…

What about sterile site cultures? When we see ‘enteric flora’ in such areas as peritoneal fluid or pleural fluid, we need to strongly suspect that faecal material has managed to get in there. For example a patient with a perforated appendix will have enteric flora cultured from their peritoneal fluid, the patient with an esophago-pleural fistula will have enteric flora in their pleural fluid.

This does not mean however that we have to start working up every different organism in the mixture (it is faeces after all!). Only if there is clearly a dominant organism, which can certainly happen after a period of time has elapsed under antibiotic pressure, should one consider ID and susceptibilities.

In summary we need to see enteric flora for what it is, and be brave enough to call it as such…

Michael

 

“Mixed Cultures”

The Art of Microbiology,

I am an avid proponent of multi-culturalism. However I am not such a big fan of mixed cultures when it comes to agar plates in the laboratory. Here are a few Q&As offering my personal views on the topic.

 

Do mixed cultures always represent contamination?

Not necessarily. The organisms within a mixed culture may or may not be contaminants. A mixed culture does not imply that no infection is present, nor that all the bacteria present are harmless. It just means that with the cocktail of organisms we have on the plate in front of us there may not be a lot that we can do to help the clinician by working up individual organisms.

 

What defines a mixed culture?

I generally regard a mixed culture as one containing three or more organisms. However if one micro-organism is particularly predominant (or clearly a recognised pathogen over and above the others present) then I may make an exception depending on the clinical scenario.

 

Do we still over-work mixed cultures in the laboratory?

Undoubtedly. Sometimes we just try too hard. Sometimes we just need to take a step back and have the courage to say “This is mixed, lets report it as such”. Some people have much lower thresholds than others for working up mixed cultures, so there is definite heterogeneity in how these culture plates are dealt with. I also anecdotally get the impression that if staff are quiet, the threshold for working up mixed cultures is lower. If staff are very busy, then there is more of a tendency to “cut to the chase” and just report it out as mixed. I believe that some staff feel they are not doing their job properly if they don’t work up individual colonies in a mixed culture.

 

Should mixed cultures from sterile sites be worked up?

Because they are sterile sites and thus more critical samples, the threshold for working mixed cultures up should naturally be a bit lower. However the same fundamental principles still apply; “ Can I help the clinician by working these colonies up?” Mixed enteric organisms from peritoneal fluid post perforated appendix, mixed Coagulase Negative Staphylococci from blood cultures, and mixed respiratory organisms from BAL fluid generally should be all reported as and for what they are. An example of where I would have a lower threshold for working up individual colonies in a mixed culture is in something like a liver abscess.

 

Sometimes I feel a tinge of guilt about changing a report to mixed flora where someone has spent time and effort over the previous few days diligently working up individual organisms. However it is only by doing this that behaviour and philosophies change…..

Michael