Tag Archives: enteric flora

“Too much information”

The Art of Microbiology, ,

Can the microbiology lab give too much information to the clinicians?

Take the following hypothetical example regarding reporting of enteric type organisms:

Patient X presents with acute appendicitis with perforation. They are taken to theatre for appendicectomy and peritoneal washout, and started on IV cefuroxime and metronidazole. The sample of peritoneal fluid is returned from the microbiology lab as being “mixed enteric flora”. the patient recovers well, and they are discharged after 3 days on oral co-amoxiclav to complete a 1 week course of antibiotics.

Patient Y presents with acute appendicitis with perforation. They are taken to theatre for appendicectomy and peritoneal washout, and started on IV cefuroxime and metronidazole. However, in this patient, the microbiology lab decides to work up the individual organisms in the peritoneal fluid sample. The report states that the patient has grown an ESBL E.coli, an Enterococcus faecium, a Pseudomonas aeruginosa and a Candida albicans. Even though the patient is recovering well, the clinician feels obliged to cover the organisms that the micro lab has grown and reported, and changes the antibiotic therapy to meropenem, vancomycin and fluconazole. The patient unfortunately develops a bout of Clostridium difficile diarrhoea (!), extending their hospital stay by a week.

Microbiology labs can get very nervous about reporting “mixed enteric flora” from sterile site samples. They really shouldn’t be.

Here are a few pointers as to when it may be reasonable for the microbiology laboratory to report “mixed enteric flora”

  • Non-sterile site samples:- almost always
  • When several organism types are present- the number of different microorganism types present in a sample is inversely proportional to the value the lab can provide to the clinician
  • When no specific organism is dominant over the others
  • When source control has been achieved-this is important as in the hypothetical example above.
  • Drain samples- generally of low value unless the drain has just been inserted
  • When the clinical microbiologist has liaised with clinical team and clear that patient is doing well on current therapy- Treat the patient, not the result.

Such an approach saves the lab time and money, and may also be beneficial to the patient, as demonstrated above. Sometimes in our efforts to do the right thing, we end up trying just a bit too hard…

Michael

 

 

 

“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