Microbiological processing from a clinical perspective

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. IeFlucloxacillin 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 15-20 years away)