sample collection-Dr Sahar.pdf

By DR / Sahar Ali Mohamed Professor of Medical Microbiology and Immunology  When we talk about specimen: THREE MAIN STEPS ARE PRESENT AND WE MUST TAKE CARE IN EVERY STEP 1. RE-ANALYTICAL STEP: Before go to laborator...

By DR / Sahar Ali Mohamed Professor of Medical Microbiology and Immunology  When we talk about specimen: THREE MAIN STEPS ARE PRESENT AND WE MUST TAKE CARE IN EVERY STEP 1. RE-ANALYTICAL STEP: Before go to laboratory 2. ANALYTIC: at laboratory for microbiologist only 3. POST ANALYTIC: after result come for microbiologist and physician 1. 2. 3. Microbiology Sample (specimen) collection: The process of obtaining tissue or fluids from patients for laboratory analysis and usually to know the pathogenic organism causing disease and to do culture and sensitivity for proper choice of treatment.  Type of samples 1. Blood 2. Serum 3. CSF 4. Urine 5. Stool 6. Sputum 7. Swabs (Eye-Ear-skin-nasopharyngeal-throat- rectal-vaginal-wound-ulcer-Genital region) 8. Aspirate (nasopharyngeal-bronchial) 9. Vomit 10. Tissue sample (Ex. For Mucormucosis) PRE-ANALYTICAL VARIABLES – Proper Instructions to patient – Patient preparation – Sample collection – Sample transportation – Sample storage – Sample preparation COLECCTION  Principles of Successful specimen collection 1. A specimen must be collected at the optimal time(s) in order to recover the pathogen(s) of interest 2. A sufficient quantity of the specimen 3. prober labeling 4. Biosafety and decontamination Infection Control Precautions Hand Hygiene. personal protective equipment (e.g. gloves and aprons) Collect all microbiology test samples prior to antibiotics 5- Minimize contamination as specimen collected close to site of patient infection as possible 6-Correct packaging 7. Rapid transport  Specimen Precaution Equipment and storage 1. Blood 1. Directly inoculated in blood - Venous blood culture bottle Blood culture bottle: Store at 4C - infants: 0.5 – 2. Requires aseptic technique if not reach lab within 24h 2 ml 3. If suspect bacterial endocarditis: - children: 2 – 5 3 sets of blood culture ml - adults: 5 – 10 ml Blood culture bottles  Blood for cultures Catheter drawn blood cultures are equally likely to be truly positive (associated with sepsis), but more likely to be colonized  2-Serum Transport 4-8oC if transport lasts less than 10 days Freeze at -20oC if storage for weeks or months before processing and shipment to reference laboratory Avoid repeated freeze-thaw cycles ◦ destroys IgM To avoid hemolysis: do not freeze unseparated blood  3-Cerebrospinal fluid (CSF) Collection Lumbar puncture Sterile tubes Aseptic conditions Trained person  CSF Handling and transportation Obtained by Lumber puncture Bacteria ◦ pre-warmed to 25-37°C before inoculation OR ◦ transport at ambient temperature (relevant ◦ pathogens do not survive at low temperatures) Viruses ◦ transport at 4-8oC (if up to 48hrs or -70oC for longer duration) Procedure ▪The Physician should wear sterile gloves ▪The site of procedure should be disinfected ▪Sterile occlusive dressing applied to the puncture site after the procedure ▪Usually collect in three labeled containers  For Microbiology, Haematology and biochemistry  If only 1 tube is collected …. First send to Microbiology ▪Transport as soon as possible (ASAP) 4-Urine samples: Collection: Mid-stream clean catch urine to wash away commensals from anterior urethra Early morning concentrated specimen ideal Container:  Sterile  Wide mouthed  Leak proof  Properly labeled Catheterisation: not recommended  2-6% risk of introducing and initiating infection Quantity: > 1ml Should be sent to lab within 30min. If delay up to 24 hrs:  keep in refrigerator  Collected PRIOR to antibiotics. WASH hands properly. Specimen is collected in a screw capped, sterile, wide mouthed plastic container. BEFORE ANTIBIOTICS STERILE CONTAINER  The patient is instructed not to touch the edges and inside of the container FEMALES MALES Clean the area with antiseptic Clean the glans with antiseptic swabs (water and soap),drying, swabs, (water and soap),drying, hold the labia apart and discard discard few ml of urine and the few ml of urine and then collect collect the mid stream sample the midstream sample directly into directly into the sterile container. the sterile container. Discard the rest of the urine. The first portion of urine adequately flushes out the normal anterior urethral flora. Collection from catheterised patients: NEVER COLLECT FROM the urine BAG Collection : ▪ Disinfect the catheter tubing at the junction of the catheter tubing and bag with 70% alcohol ▪ Aspirate fresh urine aseptically using a sterile needle and syringe ▪ Transfer to the sterile container In labeling mention that: ▪ It is catheter sample ▪ Duration of indwelling catheter For post-operative cases: ▪ Mention the antimicrobials being used  Samples from catheterized patients are collected after disinfection of the catheter collection port using 70% ethyl alcohol collecting 5-10ml urine using a sterile syringe. Children and Young infants: Invasive: suprapubic aspiration Noninvasive method: for stimulating urine flow  Tapping just above the pubis with two fingers  1-hr after feed  One tap/sec for 1 min  Resume tapping after 1 hr Specimen collected in infants and Children Supra pubic aspiration Non invasive methods are safe and ideal By tapping just above the pubis with two fingers place on suprapubic region after 1 hour of feed, tapping on at the rate of 1 tap/second for a period of 1 minute, if not successful tapping is repeated once again. The child spontaneously pass the Urine and to be collected after cleansing of genitalia in a sterile container 5- Stool samples Collection: Freshly passed stool samples ◦ avoid specimens from a bed pan Use sterile or clean container Storage ◦ refrigerate at 4oC; do not freeze ◦ store at -15oC - for Ag detection,polymerase chain reaction (PCR) Transport: 4oC (do not freeze)  Rectal swabs Advantage ◦ convenient ◦ adapted to small children, debilitated patients and other situations where voided stool sample not feasible Drawbacks ◦ no macroscopic assessment possible ◦ less material available ◦ not recommended for viruses  6-Sputum Collection Instruct patient to take a deep breath and cough up sputum directly into a wide-mouth sterile container ◦ avoid saliva or postnasal discharge ◦ 2 ml minimum volume  7-Respiratory samples Handling and Transport All respiratory specimens except sputum are transported in appropriate media ◦ bacteria: Amie’s or Stuart’s transport medium ◦ viruses: viral transport medium (VTM) Transport as quickly as possible to the laboratory to reduce overgrowth by oral flora For transit periods up to 24 hours ◦ ambient temperature for bacteria ◦ 4-8°C for viruses Ventilator associated pneumonia (VAP) – appropriate specimen ◦ Blood cultures highly specific but not sensitive (positive in