Clinical Microbiology Laboratory:

the place and the contribution to

clinical field

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.

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.

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?

The hospital managers are asking us: how much it cost ?

Direct: diagnosis, therapy, prophylaxis;Indirect: lose of work days.

Physician:judgement

Clinicalipothesis

Request of analysis

Adequate Sample

prelevation:Labeling,

Conservationtransport

to laboratories

Recording

Direct exam:Macroscopic/naked eye;Microscopic;Other methods

Start: the patient with clinical - epidemiologic circumstances

Physician:judgement

Clinical decision

Analysis paper

Antibiogram

Complete identification

Subcultivation

Identification of clinical

semnificative samples

Cultivation for isolation: adequate culture media, atmosphere, temperature

Pre – result, if it is possible

Microbiology make observations and measure exposure to the variations and

the errors

BiologicalPre-analytical

AnalyticalPost-analytical

Errors in clinical microbiologyBiological 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;

Errors in clinical microbiologyAnalytical 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.

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)

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.

Pathogenic microorganismsQualitative 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” ?

Opportunistic bacteriaSimple presence = normalHigh amount (significant amount)+

inflammatory cells = diseasee.g. presence of Streptococcus pneumoniae

in sputum (106 CFU)e.g. presence of Escherichia coli in urine (105

CFU – colony forming units)

Acute lobar pneumonia – sample prelevation

Examination (macroscopically – naked eye)

Sputum sample (tuberculosis)

Saliva elimination

S. pneumoniae – sputum smear 1000X

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

100x – CES – NO EXAMINATION whith 1000X

Acid fast bacilli

Sputum cultivation

Streptococcus pneumoniae – sensitivity to optochin α haemolytic colonies

Identification (Ag – Ab reaction)

Treatment

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…”

Clinical microbiology’s exigency:

Performance methods: efficiency versus effectivenes, accuracy;

Performance of the methods:

Informational tide controlled between clinics and laboratories;

Norms and standardize.

Test efficiency

SensitivitySpecificity

Predictive positivePredictive negative

TEST’S EFFICIENCY

Test’sresults

Pathologic circumstance

Present Absent Totals

Positive a c a + c

Negative b d b + d

Totals a + b c + d N

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.

Precision

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

Standardize norms:

Norms of sampling;Transport;Preservation for quality.

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.

Laboratory accreditationInternal versus external quality controlProcedures (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)