1. Microbiological processing from a clinical perspective
Michael Addidle

2. Patients Most samples that are processed come from a patient.
Sometimes the results we put out alters the management of the patient.
Very occasionally, the results we put out may save the life of a patient.

3. Utopian system. Production of microbiological results that are:
Clinically relevant
Timely
Easy to interpret
Accurate
(Cost effective)

4. Turnaround times
The number of days that a sample takes to process is inversely proportional to the effect it will have on the patient’s management.
95% of superficial swabs should be out in 48 hrs. You really need to have a good reason to hold these for longer.

5. Focus on the important samples
Blood cultures, Sterile site samples, cystic fibrosis samples, theatre samples (This is generally where we can make a difference to the patient)
Of lesser importance: Superficial swabs, urines, faeces, sputums
Of lesser importance still: Upper respiratory samples, GU samples, chronic ulcers, pressure sores.

6. Enteric flora is enteric flora
Dont be scared to call mixtures of enteric organisms enteric flora. Particularly low threshold in ulcers, drains, drain sites.
Even in sterile sites, particularly if no dominant organism, enteric flora should be called as such. Classical case is ruptured appendix.
Light growth of Bacteroides when isolated with other enteric organisms=enteric flora

7. Pseudomonas
In chronic wounds causes few problems. Even when it does often better managed by good wound care as opposed to antibiotics.
In sputa: can cause problems in COPD/bronchiectasis patients. However most of the time colonises only.

8. Enterococci
Can cause wound infections, but vast majority of time just colonising.
Would only work up if heavy pure growth in hospital or immunocompromised patient.

9. Reporting of results
Remember that you will know more microbiology than most of the doctors reading your results, including the consultants.
Keep it simple.
Make the antibiotic reporting appropriate.
Don’t be intimidated by silly requests from clinicians. For example : This Staph. aureus is susceptible to flucloxacillin. Could you test against cephazolin please?

10. Pathogen only reporting
Reporting things like enteric flora, skin flora and mixed respiratory flora alongside a pathogenic organism is a waste of time and clouds the report from the relevant bits

11. Minimise the number of organisms you report
The significance of any one organism is inversely proportional to the number of organisms isolated. (exception is cystic fibrosis)
Try as far as possible to avoid reporting more than three organisms on any one sample.

12. Antibiotic Reporting
The antibiotics that we report are generally the antibiotics that will be used.
Doctors are generally not well versed in the subtle differences of one antibiotic over another for treating a particular bacterial infection. Ie Flucloxacillin v Vancomycin for treating Staph aureus.

13. Accurate results Microbiology work-up is an art, not a science.
Good microbiology work-up comes from:
Experience:
Knowledge:
Confidence:

14. Knowledge of particular organisms
If you havent heard of it, don’t waste time learning about it.
Focus learning on the organisms you will come across, but only occasionally. Eg Listeria, HACEK, Pasteurella, Stenotrophomonas, Burkholderia, nutritionally deficient streptococci.

15. Microbiological processing. What does the future hold?
Increase in molecular methods.
PCR for specimens where we are looking for selective organisms. (next 10 years)
Micro-arrays for general specimens. (possibly still years away)