Microbiology Sample Collection PDF

Sample Collection & transport  Objectives General consideration for sample collection Sample safety considerations Rejection criteria Collection of different samples from different sites Transportation Reference  General consideration for proper sample co...

Sample Collection & transport  Objectives General consideration for sample collection Sample safety considerations Rejection criteria Collection of different samples from different sites Transportation Reference  General consideration for proper sample collection -Every laboratory should provide proper guidelines for collection of samples -All diagnostic information depends on quality of sample recieved -If sample collection, transport, media are not proper, it will give false results  Collect sample before administering antimicrobial agents when possible. Collect sample with as little contamination from indigenous microbiota as possible to ensure that the sample will be representative of the infected site.  Utilize appropriate collection devices. Use sterile equipment and aseptic technique to collect specimens to prevent introduction of microorganisms during invasive procedures. Clearly label the specimen container with the patient’s name and identification number. Always include date and time of collection and your initials.  Collect an adequate amount of specimen. Inadequate amounts of specimen may yield false-negative results. Identify the specimen source and/or specific site correctly so that proper culture media will be selected during processing the laboratory.  Collect specimens in sturdy, sterile, screw-cap, leak proof containers with lids that do not create an aerosol when opened. Collect sample after proper preparation of area by spirit and povidone iodine  Sample Safety considerations Follow universal precaution guidelines. Treat all specimens as potentially biohazardous. Laboratory workers should use appropriate barrier protection (such as gloves and laboratory coat or gown) when collecting or handling specimens. If splashing may occur, protective eyewear, face masks, and aprons may be necessary.  Do not contaminate the external surface of the collection container and/or its accompanying paperwork. Minimize direct handling of specimens in transit from the patient to the laboratory. Use plastic sealable bags with a separate pouch for the laboratory requisition orders or transport carriers (for example, small buckets with rigid handles).  Label High risk Specimens Sputum with suspected Tuberculosis Fecal samples suspected with Cholera, Typhoid, Serum when suspected with HIV/ HBV/HCV, infections  REJECTION CRITERIA Leaking/broken container Insufficient amount Improper labelling More time lag between collection and transport Improper transport media Improper transport temperature Hemolysed sample  Important questions before collecting a specimen Are you suspecting an Infection ? If so what is the Nature of infection, eg Bacterial, Viral, Mycological or Parasitological Which tests are your priority ? When to collect the specimen ? How to collect the specimen ? Am I choosing the correct container ? Why to send the specimens promptly, if not what I should do ?  A Request form Should include: -Name ,Age ,Sex,Address -IPD/ OPD No ,ward, -Time and Date, -Urgent / Routine, -Type of specimen -Investigation needed -History of patient -Provisional diagnosis -Doctor’s name and sign  When to Request Transport Medium When facilities are not available to perform the desired tests at the place of collection or laboratory located far away, request the Diagnostic laboratories to advice on transportation of specimens, and consider how to preserve and transport in ideal medium before it is processed Popularly used transport medium are -Amie 's transport Medium: Gonococcal infection -Carry blair medium: stool -V.R Medium: Stool  Collection of different samples Blood Urine Stool Rectal swab Sputum Csf Mycology samples Wound swabs Water sample  Blood Take proper precaution (gloves) Avoid contamination Palpate vein Apply disinfectant Use sterile needle and syringe Collect 5-10 ml blood for two sets of culture each In children collect 2-5 ml Infuse it into BHI after cleaning with spirit  Blood for serology Same precautions and method Collect blood into plain vacutte It will coagulate Centrifuge it at 1500-2000 rpm for 5 mins Thus serum will be separated  Urine For females Rinse area with soap and water Clean it with sterile gauze piece With both labia apart allow first few ml of urine to drain Take mid stream clean catch urine This will prevent contamination Collect it into wide,sterile,leak proof container  Transport it directly to the laboratory after proper labelling If delay in transport, preserve it at 4-6 degree centigrade 10000-100000 cfu/ml will show contamination mostly For males Wash hands and retract prepuce before collecting sample  If it is not possible to obtain urine, suprapubic aspiration or catheterization may be used Catheterised urine should not be used ideally bcz of presence of bacteria in urethra For that first apply disinfectant over infusion port and then collect urine  Stool Collect it into wide mouth,clean, sterile,leak proof container Label properly Min 5 gms is needed if solid stool And 2 ml if liquid stool It should not be contaminated with urine If not possible to collect it as in children, elderly, debilitated patients– collect rectal swab  Do not referigerate stool If delay in transport preserve it into 10% formalin, buffered glycerol saline  Rectal swab Take sterile swab Apply it in anal canal Rotate it for 10 seconds Avoid contact with skin Seal it directly into swab container to prevent contamination Transport immediately to lab , if not possible,preserve at 4-6 degree centigrade  Sputum Wide container of 50-100 ml capacity For M.TB two samples are collected 1st at on the spot and 2nd at next day morning Morning sample is more reliable bcz of colonization of bacteria in LRT at night Before this ask patient to gargle with normal saline and take deep breath and then take sample in one bout  This will prevent contamination There should not be saliva or liquid If there are >25 epithelial cell per LPF, sample is rejected as it shows contamination It should be collected before antibiotic treatment has started  Procedure to collect CSF Collect only 3-5 ml into a labeled sterile container Removal of large volume of CSF lead to headache, The fluid to be collected at the rate of 4-5 drops per second.  If sudden removal of fluid is allowed may draw down cerebellum into the Foramen magnum and compress the Medulla of the Brain  Preservation of CSF It is important when there is delay in transportation of specimens to Laboratory do not keep in Refrigerator, which tends to kill H. Influenza If delay is anticipated leave at Room Temperature.  MYCOLOGY SAMPLES Clean site with 70% ethanol to help eliminate surface contaminants. Using a scalpel, skin scrapings should be made from the active periphery of the lesion. For nails Scrapings should be deep enough to assure acquiring recently invaded tissue Submit scrapings in a sterile Petri dish or container. Hair - Use forceps to pluck involved hairs from the edges of the patches. Submit hair, including shaft, in a sterile Petri dish or container.  Other - Collect and submit specimens as described for specific type. Specimens associated with the systemic and deep seated mycoses are obtained from a wide variety of sources. They should be obtained, whenever possible, under aseptic conditions and in sufficient quantity for both microscopic and cultural examinations.  Samples from wounds The ideal sample is pus or exudates should be submitted in a small screw- capped bottle in firmly stoppered tube or syringe or a sealed capillary tube. Fragments of excised tissue removed at wound toilet or curettings from infected sinuses and other tissues should be sent in a sterile container.  The swabs are inefficient sampling device and tends to desiccate the specimen and trap the bacteria which are then not released on to culture plate  Water for bacteriology Water course or reservoir - collect from a depth of at least 20 cm Dug well - do not allow the bottle to touch the sides of the well  Collection At least 200 ml of water sample from the source In sterile glass bottles OR autoclavable plastic bottles tight screw capped lid securely fitting stoppers/caps an overhanging rim  Handling and transportation Test the water sample within 3 hours of collection keep at ambient temperature If delayed: pack sample on ice test refrigerated sample within 24 hours  Transportation of samples Stool, csf and sputum should be transported at room temperature, not in refrigerator Urine , swabs, skin samples,water & food samples are transported asap at room temp,but if it is not possible, preserve them in refrigerator  References Koneman’s color atlas and Textbook of diagnostic microbiology,sixth addition,chapter 2-guidelines for collection,page-74,76,81,83,93,100 Mackie & McCartney:Practical Medical Microbiology,14th edition,chapter:5,Sample collection:page-95-96 IDSP guidelines- www.idsp.nic.in/idsp/IDSP_2WeekCourse.../ WorkLaboIDSP.ppt  NACO guidelines- naco.gov.in/upload/Blood%20Saftey/Sample%20 Trtansport.pdf Role of specimen collection in infectious disease by Dr. T. V. Rao MD WHO guidelines 2011 Thank You