1. Clinical Microbiology Laboratory: the place and the contribution to clinical field

2. Analytical curriculum
1. The logic of the Clinical Microbiology. Blood culture in the diagnosis of infections.
2. CSF examination in CNS infectious diagnosis.
3. Laboratory diagnosis of the respiratory tract infectious.
4. Laboratory diagnosis of urinary tract infectious.
5. Laboratory diagnosis of genital tract infectious.
6. Laboratory diagnosis of diarrheic syndrome. Burned wounds infcetions.

3. Clinical Microbiology:
Offers important laboratories data for the etiological diagnosis of the infectious diseases;
Aims antimicrobial therapy when it is possible and necessary;
Oversee antimicrobial therapy efficiency
Is a “work instrument” of the clinician.

4. The patient ask:
I will be O.K.? / I will die? / I will have side effects ?
My family members are safe because of this disease?
How much it will cost me?

5. The hospital managers are asking us: how much it cost ?
Direct: diagnosis, therapy, prophylaxis;
Indirect: lose of work days.

6. Start: the patient with clinical - epidemiologic circumstances
Physician:
judgement
Clinical
ipothesis
Physician:
judgement
Clinical decision
Analysis paper
Request of analysis
Antibiogram
Complete identification
Adequate Sample prelevation:
Labeling,
Conservation
transport
to laboratories
Subcultivation
Pre – result,
if it is possible
Identification of
clinical semnificative
samples
Recording
Cultivation for isolation: adequate culture media, atmosphere, temperature
Direct exam:
Macroscopic/
naked eye;
Microscopic;
Other methods

7. Microbiology make observations and measure exposure to the variations and the errors
Biological
Pre-analytical
Analytical
Post-analytical

8. Errors in clinical microbiology
Biological errors:
vaginal microbial flora at different ages;
colonization of old age person’s oropharynx with gram negative bacilli;
microbial colonization of the patients with lung diseasses;
Preanalytic errors:
Physiological:
Urine quantity / day;
Antimicrobial therapy;
Sampling of pathologic products (choosing the right product, moment of sampling, type of sampling), labeling, preservation, transport to the lab, anlysis paper request;

9. Errors in clinical microbiology
Analytical variations:
diagnostic kit used (culture media, reagents, instruments, automatic equipments);
knowledge and experience of each person from laboratory;
Post-analytical variations:
between the result obtaining in the lab until it will be received from the clinician;
errors regarding miss-copying the results of analysis.

10. Microbiology make observations and measure exposure to variations and errors
Biological errors: pregnancy, children, elderly, associated diseases (diabetus, etc.)
Pre-analytical errors: samples’ s sampling (time, quantity, sterile procedures, etc)
Analytical: sensitivity, specificity, reproductibility, etc
Post-analytical: results communication (electronic, writing, data transfer, etc)

11. What and how much must the student and the clinician should know about this?

12. There is difference between the methods of diagnosis diseases due by pathogenic microorganisms ( classic / emergent);
Conditioned pathogenic microorganisms / opportunistics - anti infectious defense deficiency;
Poly etiological syndromes;
In conditions of the rise of microorganism’s resistance to antibiotics.

13. Pathogenic microorganisms
Qualitative results:
acid fast bacilli = Mycobacterium tuberculosis – lung tuberculosis (the absence from normal flora from respiratory tract);
difficult to analyze for urine: acid fast bacilli can be M. smegmatis (saprophytic bacteria – no pathogen); the need for final identification
Salmonella Typhi – enteric fever
Interpretation for “healthy carriers” ?

14. Opportunistic bacteria
Simple presence = normal
High amount (significant amount)+ inflammatory cells = disease
e.g. presence of Streptococcus pneumoniae in sputum (106 CFU)
e.g. presence of Escherichia coli in urine (105 CFU – colony forming units)

15. Acute lobar pneumonia – sample prelevation

17. Examination (macroscopically – naked eye)

19. Sputum sample (tuberculosis)

20. Saliva elimination

21. S. pneumoniae – sputum smear 1000X

22. S. pneumoniae – sputum smear 1000X (QS > +1)

23. 100x – CES – NO EXAMINATION whith 1000X

24. Acid fast bacilli

25. Sputum cultivation

27. Streptococcus pneumoniae – sensitivity to optochin α haemolytic colonies

28. Identification (Ag – Ab reaction)

30. Treatment

31. Charles Nicolle’ s foreseeing – 1932
“ there is will be new diseases, one of them will slow disappear, and other will manifest in forms which today we don’t know…”

32. Clinical microbiology’s exigency:
Performance methods: efficiency versus effectivenes, accuracy;
Performance of the methods:
Informational tide controlled between clinics and laboratories;
Norms and standardize.

33. Test efficiency Sensitivity Specificity Predictive positive
Predictive negative
TEST’S EFFICIENCY

34. Pathologic circumstance
Test’s
results
Pathologic circumstance
Present
Absent
Totals
Positive a c
a + c
Negative b d
b + d
a + b
c + d N

35. Specificity is the percentage of person who do
not have a disease who yield a negative test result d / c +d;
Sensitivity is the percentage of a individuals with a specific disease who yield a positive result a / a + b;
Predictive value for a positive test is a proportion of those who have a disease among those who gave positive results: a / a + c;
Predictive negative value of the test is a proportion of those who do not have disease among those who gave negative test results : d / b +d.
Efficiency measure the proportion of the correct diagnosis classification: a +d / N.

36. Precision
The similitude between the results of the same repeated test on similar samples from the same patients

40. Standardize norms: Norms of sampling; Transport;
Preservation for quality.

41. The quality manual of laboratories:
Methodologies and technical – all the time at disposition. “Now phone without wire”
The guarantee for the reactive’ s quality: certificate of quality;
Precision of equipments;
Quality control.

42. Laboratory accreditation
Internal versus external quality control
Procedures (for all operations: sampling, smear examination, cultivation and culture media, sterilization, etc)
Accreditation for each tests (ELISA, isolation and identification of Streptoccous pneumoniae in sputum, etc)