Workshop 3 Microbiology Laboratory PDF

Workshop-3 Microbiology Laboratory Departments in diagnostic laboratory in hospitals Biochemistry Hematology Virology Immunology Microbiology Histopathology and Cytopathology Role of Microbiology lab ▪ To provide rapid and accurate information about the presence or the absence of microorganisms in a...

Workshop-3 Microbiology Laboratory Departments in diagnostic laboratory in hospitals Biochemistry Hematology Virology Immunology Microbiology Histopathology and Cytopathology Role of Microbiology lab ▪ To provide rapid and accurate information about the presence or the absence of microorganisms in a specimen collected from a patient. ▪ Provide information on the successful treatment by performing antimicrobial susceptibility testing (Resistant, susceptible, intermediate). ▪ Notify infection control or other health authorities of new and emerging infections. ▪ Collect data for research and epidemiology (Reference Lab). Management of clinical specimens 1. 2. 3. 4. Safety in sample handling Specimen selection & collection Transportation/shipment Sample processing 1. Safety (Sample handling) Safety is an important issue to the lab staff and the health care workers since they are unaware of the potential etiologic agent found in the specimen. Therefore, the following safety measurement should be followed: ▪ Personal safety: Gloves, gowns and masks (or/and goggles) when collecting a specimen. ▪ Use leak-proof specimen containers and transport it in a sealable, leak-proof plastic bag with a separate compartment for request form. Leak-proof specimen containers Sealable, Leakproof plastic bag ▪ Never transport syringes with needles to the lab. Instead transfer the contents to a sterile tube or remove the needle with a protective device. syringes with needles 2. Specimen selection & collection Specimens: ▪ Can be solid or fluid (e.g., tissue biopsy, blood, urine, stool, sputum…etc.) ▪ Specimens can be collected from: ▪ Normally sterile site (e.g., blood, CSF) ▪ Non-sterile site (e.g., vagina, throat) ▪ Specimen collection depend on the site of infection 2. Specimen selection & collection General guidelines: 1. Collect the specimen from the actual site of infection, avoiding contamination from adjacent tissues or secretions. 2. Collect the specimen at optimal times (for example, early morning sputum for culture). 3. Whenever possible, collect specimens prior to administration of antimicrobials/antibiotics. 4. Optimize the capture of the anaerobes from specimens by using the proper precautions, procedures, and supplies. Biopsy or needle aspirate are the specimens of choice (swabs are not recommended). 5. Collect adequate volumes. Insufficient materials may yield false-negative results. 6. Place the specimen in a container (e.g. swabs with transport media) designed to promote the survival of suspected agents and to eliminate leakage and potential safety hazards. 3. Transportation/shipment and collection containers Blood culture bottle Collection Swabs with Transport Media sample container (e.g. urine, stool, sputum, etc.) Specimen labeling ❑ Patient information must be provided on the specimen label so that the specimen can be matched up with the order (request) form when it is received in the lab. ❑The request form order by the doctor can be sent to the lab as: Hard (paper) copy or Electronically (computer): laboratory information system (LIS). LIS involves typing or scanning barcodes (if used) and entering the patient information and tests requested. Once the specimens are assigned a laboratory number by the LIS, a sticker is typically printed that can be placed on the tubes or specimen containers. This label has a barcode that can be scanned by automated analyzers and test requests uploaded to the analyzer from the LIS. Specimen labeling The request form should include: ▪ ▪ ▪ ▪ ▪ ▪ ▪ ▪ ▪ Patient name Patient hospital number Age or date of birth of the patient Sex (Female/Male) Collection date and time of the specimen Ordering physician Source of specimen Diagnosis Current antimicrobial therapy Rejection of unacceptable specimens 1. The information on the label does not match the information on the request form. 2. The specimen has been transported at the improper temperature. 3. The specimen has been transported in the improper medium. 4. The quantity of specimen is insufficient for testing. 5. The specimen is leaking. 6. The specimen transport time exceeds 2 hours after collection and the specimen is not preserved. 7. The specimen was received in a fixative (formalin) which kills any microorganism present. 8. The specimen is dried up. 9. Processing the specimen would produce information of questionable medical value (e.g. foley catheter tip). 4. Specimen processing Bacterial Culture Microscope Serological test Analytical profile index (API) Vitek-2 Polymerase Chain Reaction (PCR) Video: Insight in Microbiology Laboratory https://youtu.be/LnOcAgEsySw Optional Videos A tour of the Microbiology Lab -Section one https://www.youtube.com/watch?v=afM7DGjSVn4 A tour of the Microbiology Lab -Section Two https://www.youtube.com/watch?v=_AA_ZM2ryaE A tour of the Microbiology Lab -Section Three https://www.youtube.com/watch?v=gjaQEbqGYnc Media preparation https://youtu.be/cneascR3OEc Binary fission in bacteria-1 http://www.youtube.com/watch?v=3cD3U2pgb5w&feature=related Binary fission in bacteria-2 http://www.youtube.com/watch?v=SLpFJ1JeRYs&feature=related Dividing bacteria (bacilli in one plane) http://www.youtube.com/watch?v=J6akNYlkehY&feature=related Questions All the following principles of specimen collection are necessary to ensure appropriate specimen management EXCEPT: a. Collect the appropriate quantity of specimen. b. Label the specimen accurately with the specific anatomic site and the patient information. c. Select the correct anatomic site to collect the specimen. d. It is acceptable to delay transport of the specimen to the laboratory if in transport media. The requisition form should provide all the following information EXCEPT: a. b. c. d. Patient name or identification number Patient age and gender Patient home address Specific anatomic site A sputum specimen is preferably collected in the: a. b. c. d. Morning. Afternoon. Evening and kept in refrigerator for the next day. No specific time. Obligate aerobes need to grow in the presence of: a. b. c. d. Oxygen Carbon dioxide Nitrogen Hydrogen All of the following specimens are collected from sterile sites EXCEPT: a. b. c. d. Blood culture. CSF. Throat swab. Joint fluid All bacteria that cause human infections grow best at 50°C: a. True b. False Evaluation of Tutors Kindly go to the following website https://portal.ku.edu.kw/sis to Evaluate the teaching Prof. Suhail Ahmed Biology for Health Sciences Spring 2023/2024 University ID ‫الرقم الجامعي‬ ‫الرقم السري‬ ‫للطالب‬ Password