Clinical Bacteriology Past Paper PDF S/Y 2022-2023

CLINICAL BACTERIOLOGY 1ST SEM - MIDTERMS Microbiology and Parasitology (20%) Hannah Fierela B. Limpiado S/Y 2022-2023...

CLINICAL BACTERIOLOGY 1ST SEM - MIDTERMS Microbiology and Parasitology (20%) Hannah Fierela B. Limpiado S/Y 2022-2023 BSMT-L3 LESSON 5: SPECIMEN COLLECTION, HANDLING, TRANSPORT AND SPECIMEN PRESERVATION PRESERVATION 1. BORIC ACID A. Time of Collection - Urine B. Specimen Transport - Maintains the appropriate C. Specimen Storage Conditions colony counts D. Specimen Preservation E. Specimen Labeling 2. POLYVINYL ALCOHOL (PVA) OR BUFFERED FORMALIN F. Specimen Requisition - Stool G. Rejection of Unacceptable Specimen - Maintains the integrity of trophozoites and cysts of ova H. Appropriate Collection Techniques and parasite (O&P) Validity of any test result is primarily dependent on the quality of 3. STUART’S MEDIUM, AMIES MEDIUM, CARY AND BLAIR specimens received MEDIUM - Transport media / holding media TIME OF COLLECTION - Maintain the viability of microorganism without If possible, specimens should be collected during the acute supporting the growth of microorganism phase (early phase of illness) of infection and before the - No death and no overgrowth application of antimicrobial therapy 4. ANTICOAGULANTS SPECIMEN TRANSPORT - Prevents clotting of specimens (blood, bone marrow, ✓ Ideally, specimens should be sent to the laboratory as soon synovial fluid) as possible. In some cases, within 1-2 hours of collection, samples - Concentration and type of anticoagulant is important must be transported - Many organisms are inhibited ✓ Specimens must be placed in a leak-proof container ✓ If delay is anticipated, observe temperature requirements SODIUM POLYANETHOL SULFONATE (SPS) of suspected organism/s when transporting samples - 0.025% - 0.03% (others up to 0.05%) - Best anticoagulant for blood cultures SPECIMEN STORAGE CONDITIONS - Anti complementary, antiphagocytic ✓ Room (ambient) Temperature – 22°C - Interferes with actions of antimicrobials ✓ Refrigerator temperature – 4°C - Inhibits growth of some strains of Neisseria ✓ Body temperature (incubator) – 37°c - addition of 1.2% gelatin counteract SPS Inhibitory ✓ Freezer temperature – -20°C; -70°C if effect to some bacteria processing will be delayed more than 4 days HEPARIN - Viral cultures Room Temperature - Inhibits growth of gram (+) bacteria and yeasts Abscess Inner ear sample Bone Lesion Genital sample Tissue PRECAUTION: Wound Throat sample Preserved urine Use of the following anticoagulants are yet to be established in Body fluid Nasal sample microbiology therefore, must not be used: citrate - blue top SPECIMEN STORAGE CONDITIONS Ethylenediaminetetraacetic acid INCUBATOR - EDTA Cerebrospinal fluid for bacteria - lavender top Yellow top REFRIGERATOR a popular brand uses yellow top in two ways ▪ Catheter (IV) tips 1. SPS (Sodium Polyanethol Sulfonate) ▪ CSF for viruses 2. ACD (Trisodium Citrate Citric Acid Dextrose) ▪ Outer ear samples - not appropriate for microbiology ▪ Feces (unpreserved) ▪ Sputum Therefore, as a general rule… ▪ Urine(unpreserved) Do not refer to the use of tubes by color as different ▪ Feces for (C. Difficile toxin up to 3 days; >3 days store at -70°C) manufacturers have different combination of tube color and anticoagulant present Always refer to a tube with respect to the anticoagulant it carries CLINICAL BACTERIOLOGY 1ST SEM - MIDTERMS Microbiology and Parasitology (20%) Hannah Fierela B. Limpiado S/Y 2022-2023 BSMT-L3 SPECIMEN LABELING 1. Patient’s name 2. Hospital number 3. Birthdate 4. Date and time of collection 5. Specimen source/type SPECIMEN REQUISITION 1. Patient’sname 2. Hospital number 3. Birth date/age 4. Specimen source/type 5. Date and time collected 6. Date and time received 7. Examination Requested 8. Address/telephone number 9. Diagnosis 10. Date of Admission 11. Current antimicrobial therapy 12. Ordering physician 13. Medico-legal cases: nature of incident, date and time of incident, place of incident 14. Sexually transmitted infections: civil status, occupation APPROPRIATE COLLECTION TECHNIQUES: BLOOD REJECTION OF UNACCEPTABLE SPECIMENS Vein selection (ante cubital fossa) Specimen received for anaerobic culture from sites known to have ▪ IV line: below IV line anaerobes as part of the normal flora ▪ Avoid vascular shunts or catheters ▪ Gastric washings ▪ Prosthetic devices are hard to decontaminate completely ▪ Urine other than suprapubic aspiration ▪ Stool (except for C. Difficile – food poisoning) ▪ Vaginal secretions ▪ Oral/mouth/oropharyngeal specimens (except for deep tissues obtained during surgical procedure) ▪ Swabs of ileostomy or colostomy sites ▪ Superficial skin specimens Antisepsis ▪ 70% alcohol ▪ Iodine (betadine) ▪ Iodine tincture (iodine in alcohol) ▪ Chlorhexidine Blood volume 1-3 ml. - Pediatrics 8-10 ml. - Adults Blood volume (Baron et. Al.) CLINICAL BACTERIOLOGY 1ST SEM - MIDTERMS Microbiology and Parasitology (20%) Hannah Fierela B. Limpiado S/Y 2022-2023 BSMT-L3 The clinical presentation or course is not consistent with sepsis ▪ Physician-based not laboratory based criteria The organism causing the infection at a primary site of infection is not the same as that isolated from the blood culture ▪ Isolated organisms must be the same Growth of the following… ▪ Enterobacteriaceae ▪ Streptococcus pneumoniae ▪ Streptococcus pyogenes Number of Blood Cultures ▪ Haemophilus influenzae ▪ Periodicity of microorganism in bloodstream ▪ Pseudomonas aeruginosa ▪ Random for some, continuous for some ▪ Neisseria meningitidis ▪ Two or three samples is a must ▪ Brucella species ▪ Two or three sets is preferred ▪ Bacteroides species ▪ As number of blood cultures is increased, pathogen recovery is ▪ Listeria monocytogenes increased ▪ Staphylococcus aureus ▪ Streptococci Gram (-) anaerobes Timing of Collection ▪ Candida albicans ▪ Not so important ▪ Clostridium perfringens ▪Organisms are released into blood stream at fairly constant rate ▪ Intermittent bacteria is unpredictable: Isolation of commensal microbial flora obtained from patients ✓ Two or three samples be spaced an hour apart suspected to be bacteremic ▪ Immunocompromised patients Studies showed: ▪ Those having prosthetic devices No significant difference in the yield between multiple simultaneous blood cultures or those obtained at intervals. APPROPRIATE COLLECTION TECHNIQUES:CSF Conclusion: Blood volume collected is more critical than timing CSF FUNCTIONS ▪ cushioning and buoyancy for the bulk of the brain Blood Culture Techniques ▪ carries essential metabolites into the neural tissue and cleanses A. Conventional tissues of wastes as it circulates around the brain, ventricles and B. Instrument – based system spinal cord. It produced by choroid plexus B.1 BACTEC Systems (Becton Dickinson - Maryland) B.2 BACT/ALERT Microbial Detection Systems (Biomerieux-North Carolina) B.3. Versa TREK Systems (Thermo Scientific-Ohio) Blood Culture Media ▪ Trypticase Soy Broth ▪ Brain Heart Infusion Broth ▪ Thioglycolate Broth (Supplemented peptone) Columbia or Brucella Broth Collection Interpretation of Blood Culture Results 1. Skin antisepsis is applied before aspirating CSF Growth of: 2. Lumbar puncture done by physician Bacillus species Corynebacterium species, Propionibacterium 3. Placed in sterile containers, screw-capped tube, without acnes, Coagulase negative staphylococci additives ▪ Isolated in one of several cultures 3 – 4 sterile containers are numbered sequentially according to ▪ Bacillus anthracis must be ruled out before dismissing bacillus the order in which they were collected out before dismissing bacillus species as probable contaminants TUBE 1 - chemistry studies: glucose and protein, and immunology studies Growth of multiple organisms from one of several cultures TUBE 2 - culture ▪ Polymicrobial bacteremia is Uncommon TUBE 3 - cell count and differential count TUBE 4 – additional tests CLINICAL BACTERIOLOGY 1ST SEM - MIDTERMS Microbiology and Parasitology (20%) Hannah Fierela B. Limpiado S/Y 2022-2023 BSMT-L3 VOLUME ▪ Collection is done in an area with open air to avoid spread of 1 ml. – 5 ml infection (up to 10 ml for mycobacteria and fungi) GRAM STAIN: BARTLETT’S SPUTUM SAMPLE CRITERIA TRANSPORT ▪ CSF should be hand-delivered immediately to the laboratory ✓ Streptococcus pneumoniae will not be recovered after an hour or longer ✓ Must be transported in < 15 minutes PRESERVATION ▪ Place in incubator or at room temperature ▪ Never refrigerate if for bacterial culture SPUTUM: INDUCED SAMPLE ▪ Hematology: refrigerate ▪ For patients unable to produce sputum ▪ Chemistry and Serology: -20°C ▪ May be assisted by respiratory therapists who uses postural ▪ Viral studies drainage and thoracic percussion to stimulate acceptable sputum ✓ refrigerate within 23 hours of collection and kept at ▪ Before specimen collection, patient should brush buccal mucosa, 4°C up to 3 days tongue and gums with wet toothbrush ✓ -70°C if longer delay is anticipated High diagnostic yield of Pneumocystis jiroveci pneumonia (PCP) ✓ formerly Pneumocystis carinii, causative agent for the rodent PATHOGENS form of Pneumocystis ▪ Mycobacterium tuberculosis ✓ an opportunistic, atypical fungus infecting ▪ Treponema pallidum immunocompromised hosts ▪ Streptococcus pneumoniae An alternative: AEROSOL-INDUCED specimen for mycobacterial ▪ Haemophilus influenzae and fungal agents ▪ Streptococcus agalactiae ✓ Patient is allowed to breathe aerosolized droplets ▪ Staphylococcus aureus (NEBULIZATION containing 10% 0.85% nacl) until a strong cough ▪ Escherichia coli reflex is initiated ▪ Naegleria or Acanthamoeba spp. ▪ Secretions collected thru induction appear watery resembling ▪ Listeria monocytogenes saliva ▪ Cryptococcus and other fungi ▪ Contain materials directly from alveolar spaces ▪ Staphylococcus spp. ▪ Samples are adequate and acceptable for culture, therefore ▪ Neisseria meningitidis pre-screening is eliminated ▪ Bacteroides spp. ▪ May obviate doing more invasive procedure such as ▪ Enteroviruses bronchoscopy or needle aspiration ▪ Staphylococcus epidermidis ▪ Instruct patient to bring the sample immediately to the ▪ Toxoplasma gondii laboratory APPROPRIATE COLLECTION TECHNIQUES: SPUTUM SPUTUM: ENDOTRACHEAL ASPIRATE ▪ Among the least clinically relevant specimens received for ▪ Patients with tracheostomies are unable to produce sputum in culture though one of the most numerous and time consuming normal fashion specimens ▪ Tracheostomy aspirates or Tracheostomy suction specimens are ▪ Not a sample from the post nasal region and is not a spittle or treated as SPUTUM saliva. Comes from deep within the bronchi ▪ Lower respiratory secretions are easily collected using Lukens Trap SPUTUM: EXPECTORATED SAMPLE ▪ Patients are rapidly colonized by gram (-) bacilli and other ▪ No food intake 1-2 hours before collection nosocomial pathogens ▪ Brush teeth or gargle with water or saline just before ▪ Colonization is not clinically relevant but these organisms may be expectoration aspirated into the lungs and can cause pneumonia ▪ Practice deep breathing, then cough off sputum secretions ▪ Culture results are correlated with clinical signs and symptoms ▪ Deep-coughed sample should be expelled directly in sterile container TRANSPORT AND STORAGE ▪ Emphasize to minimize contamination by saliva (Salivary samples ▪ 5 mm. in diameter ▪ Place in enteric transport media (Cary & Blair) if transport 7. Scales – Dry, horny, platelike lesions exceeds 1 hour 8. Ulcer – Lesion with loss of dermis and epidermis ▪ Can be transported within 24 hours at RT ▪ Can be stored at 4°C for 72 hours SUPERFICIAL WOUND ▪ Routine culture not done for patients >3 days hospital stay and ✓ wipe or irrigate area with sterile saline whose admitting diagnosis was not diarrhea - MUST BE TESTED for ✓ Use aerobic swab moistened with Stuart’s or Amies Medium C. difficile ✓ Swab along leading edge of wound ✓ Transport in