Sample Collection Procedure PDF

# Procedure: Clinical Sample Collection ## Urine - Urine has a long history of specimen analysis in clinical laboratories. - After blood, urine is the most widely used specimen for diagnostic testing, monitoring of disease status, and detection of drugs. - Urine testing can be done by both automat...

# Procedure: Clinical Sample Collection ## Urine - Urine has a long history of specimen analysis in clinical laboratories. - After blood, urine is the most widely used specimen for diagnostic testing, monitoring of disease status, and detection of drugs. - Urine testing can be done by both automated methods and traditional manual methods. - Pre-analytical error in urine specimens is often difficult to detect. - It is important for laboratories to have processes in place to ensure compliance with best practice in specimen collection, handling, and transport. - The use of preservatives wherever appropriate is critical. - Various diseases that can be detected from urine samples include urinary tract infections, vaginitis, sexually transmitted diseases (STDs) like Chlamydial infections. - Infectious pathogens found in urine samples include *Escherichia coli, Proteus mirabilis, Klebsiella pneumoniae, Enterococcus fecalis, Staphylococcus aureus, Candida albicans*. ### Various methods of urine collection for microbial analysis include: - **Random specimen collection:** - This is the specimen most commonly sent to the laboratory for analysis, primarily because it is the earliest to obtain and readily available. - This specimen is usually submitted for urinalysis and microscopic analysis, although it is not the specimen of choice for either test. - A random sample can sometimes give an inaccurate view of a patient's health if the specimen is too diluted, and the values are artificially lowered. - **First morning specimen:** - This is the specimen of choice for urinalysis and microscopic analysis, since the urine is generally more concentrated. - **Midstream clean catch method:** - This is the preferred type of specimen for culture and sensitivity testing because of the reduced incidence of cellular and microbial contamination. - Patients are required to first cleanse the urethral area with castile soap towel. - They should then void the first portion of the urine stream into the toilet. - These steps significantly reduce the opportunities to enter urine stream. - Then urine midstream is collected into a clean container (any excess urine should be voided into the toilet). - This method of collection can be conducted at any time of day or night. - **Catheter collection specimen:** - This assisted procedure is conducted when the patient is bedridden or cannot urinate independently. - The healthcare provider inserts a catheter into the bladder through the urethra to collect the urine specimen. - **Suprapubic aspiration specimen:** - This method is used when a bedridden patient cannot be catheterized or a non-sterile specimen is required. - **Pediatric specimen:** - For infants and small children, a special urine collection bag is adhered to the skin surrounding the urethral area. - Once the collection is completed, the urine is poured into a collection cup or transferred directly into an evacuated tube with a transfer straw. ## Faeces - A stool analysis is a series of tests done on a stool (feces) sample to help diagnose certain conditions affecting the digestive tract. - These conditions can include infection (such as from parasites, viruses, or bacteria), poor nutrient absorption, or cancer. - The pH of the stool also may be measured. - Infectious bacterial pathogens found in stool samples include *Staphylococcus aureus, Klebsiella pneumoniae, Salmonella cholerasuis, Escherichia coli, Candida albicans*. - Viruses such as rotavirus can also be found in stools. - Parasitic diseases such as strongyloidiasis and whipworm can be diagnosed by examining stools under a microscope for the presence of worm larvae or eggs. ### Method of stool collection - A fresh stool sample is collected in a clean container. - The stool sample should not be contaminated with urine or water. - Once it has been collected, the stool sample should be taken to the laboratory within 2 hours after collection or should be transferred into a vial containing a preservative and taken to the lab as soon as possible. - The container must be labeled with the name, date of birth, and the date of collection. - Something must be placed in the toilet to catch the stool, such as an empty plastic food container, or spread clean newspaper or plastic wrap over the rim of the toilet. - The sample should not touch the inside of the toilet. - The spoon or spatula that comes with the container must be used to place the sample in a clean screw-top container, and the lid should be screwed shut. - Around a third of the container must be filled. - Anything used to collect the sample must be put in a plastic bag, tied up, and discarded in the bin. - After collection, hands must be washed thoroughly with soap and warm running water. #### For Infants - Another way to collect a stool sample is to loosely place plastic wrap across the rim of the toilet, under the seat. - Then place the stool sample in a clean, sealable container before taking to the laboratory. - Plastic wrap can also be used to line the diaper of an infant or toddler who is not yet using the toilet. - For infants, a stool sample is usually collected with a swab of the rectum. ## Blood - Blood is the most widely tested clinical sample around the globe. - Multiple tests for specific blood components (such as a glucose test or a cholesterol test) are often grouped together into one test panel called a blood panel or blood work. - Blood tests are often used in healthcare to determine physiological parameters. - Laboratory analysis is performed on a blood sample that is usually extracted from a vein. - Blood work is performed to measure mineral content, pharmaceutical drug effectiveness, and organ function. ### Various methods of Blood sample collection: - **Finger-prick method:** - The best locations for finger prick are the 3rd (middle) and 4th (ring) fingers of the nondominant hand. - Do not use the tip of the finger or the center of the finger. - Avoid the side of the finger where there is less soft tissue, where vessels and nerves are located, and where the bone is closer to the surface. - The 2nd (index) finger tends to have thicker, callused skin. - The fifth finger tends to have less soft tissue overlying the bone. - Avoid puncturing a finger that is cold or cyanotic, swollen, scarred, or covered with a rash. - When a site is selected, put on gloves, and cleanse the selected puncture area. - Massage the finger toward the selected site prior to the puncture. - Using a sterile safety lancet, make a skin puncture just off the center of the finger pad. - The puncture should be made perpendicular to the ridges of the fingerprint so that the drop of blood does not run down the ridges. - Wipe away the first drop of blood, which tends to contain excess tissue fluid. -Collect drops of blood into the collection tube/device by gentle pressure on the finger. - Avoid excessive pressure or "milking" that may squeeze tissue fluid into the drop of blood. - Cap, rotate, and invert the collection device to mix the blood collected. - Have the patient hold a small gauze pad over the puncture site for a few minutes to stop the bleeding. - Dispose of contaminated materials/supplies in designated containers. - **Venous blood Collection (Venipuncture Method)** - Venipuncture or venepuncture is the process of obtaining intravenous access for the purpose of intravenous therapy or for blood sampling of venous blood. - In healthcare, this procedure is performed by medical laboratory scientists, and other nursing staff. - Venipuncture is one of the most routinely performed invasive procedures and is carried out for any of five reasons: - To obtain blood for diagnostic purposes - To monitor levels of blood components - To administer therapeutic treatments including medications, nutrition, or chemotherapy - To remove blood due to excess levels of iron or erythrocytes (red blood cells) - To collect blood for later uses, mainly transfusion either in the donor or in another person - Blood is most commonly obtained from the superficial veins of the upper limb. - The median cubital vein, which lies within the cubital fossa anterior to the elbow, is close to the surface of the skin without many large nerves positioned nearby. - **Why is venous blood advantageous over arterial blood?** - Veins are superficial while arteries are deep-seated, hence it is easy to collect samples from veins. - Because veins have thinner walls. - The size of a vein is larger than a corresponding artery hence more volume of blood can be collected. - Less force and pressure has to be applied to extract blood from veins due to low venous pressure. - Note: Established criteria for the proper collection of venous blood specimens are necessary to maintain the biological integrity of patient samples for laboratory analyses. - Blood samples should always be handled with care and treated as potentially infectious material. ### Heelstick procedure for infants - The recommended location for blood collection on a new-born baby or infant is the heel. - Pre-warming the infant's heel (42° C for 3 to 5 minutes) is important to increase the flow of blood for collection. - Wash your hands, and put on gloves. ­Clean the site to be punctured with an alcohol sponge. - Dry the cleaned area with a dry gauze pad. - Hold the baby's foot firmly to avoid sudden movement. - Using a sterile blood safety lancet, puncture the side of the heel in the appropriate regions shown above. - Make the cut across the heel print lines so that a drop of blood can well up and not run down along the lines. - Wipe away the first drop of blood with a piece of clean, dry cotton gauze. - Since newborns do not often bleed immediately, use gentle pressure to produce a rounded drop of blood. - Do not use excessive pressure because the blood may become diluted with tissue fluid. - Fill the required microtainer as needed. - When finished, elevate the heel, place a piece of clean, dry cotton on the puncture site, and hold it in place until the bleeding has stopped. - Apply tape or Band-Aid to the area if needed. - Be sure to dispose of the lancet in the appropriate sharps container. - Dispose of contaminated materials in appropriate waste receptacles. - Remove your gloves and wash your hands. ## Cerebrospinal Fluid - Cerebrospinal fluid (CSF) is a clear, colorless body fluid found in the brain and spine. - It is produced in the choroid plexuses of the ventricles of the brain. - It acts as a cushion or buffer for the brain's cortex, providing basic mechanical and immunological protection to the brain inside the skull. - Diseases diagnosed using CSF are Meningitis, Encephalitis, Tuberculosis, Alzheimer's disease. ### Methods for CSF Collection - **Lumbar Puncture Method** - Under local anesthesia, a hollow needle is inserted into the base of the spine and into the spinal canal, which contains the spinal cord and the nerves coming from it. - The pressure within the spinal canal is usually measured, and some CSF sample is collected for testing. - For getting the sample, the patient is asked to lie on his side with knees pulled up towards his chest and the chin tucked downwards. - The back of the patient is cleaned with a disinfectant, and the personnel collecting the sample will inject local anesthesia to create numbness. - A spiral needle is then injected. - Once the needle is in position, the CSF pressure is measured, and a sample between 1-10 ml is withdrawn/collected. - The needle is cleaned, and a bandage is placed on the needle side. - After collection of CSF part of the specimen is centrifuged for about 5 minutes at 3000rpm while the remaining portion is left uncentrifuged. - The uncentrifuged portion is used to determine the total WBC count to help in preliminary diagnosis of acute pyogenic bacterial infections or tuberculosis meningitis. - The centrifuged portion of CSF is taken, and the sediment is carefully separated from the supernatant fluid. - The supernatant is used for diagnostic purpose, and the sediment for culture purpose. - **Other methods of CSF collection** - Sometimes a patient cannot have a lumbar puncture because of a back deformity, possible infection or brain herniation. - Then the following methods are used for extraction of CSF. - **Cisternae puncture** uses a needle placed below the occipital bone (back of the skull). - This can be dangerous because it is so close to the brain stem. - It is usually done with fluoroscopy. - **Ventricular puncture** is usually done in patients with possible brain herniation. - It is rarely used method and often done in the operating room. - A hole is drilled in the skull, and a needle is inserted directly into the brain's ventricles. - CSF collection is often combined with other procedures. - For example dye may be inserted into your CSF for a myelogram. - This is an X-ray or CT-scan of your brain and spine. ## Throat - The purpose of a throat swab culture is to detect the presence of organisms in the throat that could cause infection. - For example, the presence of group A streptococcus bacteria (*Streptococcus pyogenes*) in your throat is a key sign that you may have strep throat. - A throat swab culture, or throat culture, is a test commonly used to diagnose bacterial infections in the throat. - These infections can include strep throat, pneumonia, tonsillitis, whooping cough, and meningitis. - Most sore throats are caused by a virus. - Many sore throats go away within a few days without any treatment, except for possibly cough drops or a few over-the-counter drugs to help relieve any pain or discomfort. - Your doctor will generally order a throat culture test if you have symptoms that suggest strep throat or another infection. - Redness, swelling, and white streaks or pus on the tonsils, as well as red spots in the roof of the mouth are signs of infections. - These signs don't indicate whether the infection is viral or bacterial, so a throat swab is necessary. - Strep throat is very contagious, so it's important that it is caught early. ### Procedure - Antiseptic mouthwash should be avoided before this test. - Doctor must be told in advance if antibiotics are taken prior to the test as it may affect the result. - The patient is asked to open his/her mouth and tilt his/her head back. - If necessary, the doctor may use a tongue depressor. - This can help the doctor have a better view of the back of your throat. - The patient may alternatively be asked to make a sound of "aahhh". - They will then rub a sterile cotton swab across the back of throat, tonsils, and any other sore areas for a few seconds. - The swab will collect a sample of the secretions being produced in the back of the throat. ## Superficial Sample Collection - Clean lesions with surgical spirit or 70% alcohol before collecting samples. - This minimizes contamination and is an aid to microscopy if greasy ointments or powders have been applied. - Be sure to include as much material as possible so that full laboratory investigations can be carried out. - It is always useful to have enough skin or nail to repeat the culture if necessary. ### For skin: - Collect material by scraping from the edges of the lesions, ideally with a scalpel blade. ### For Nail: - If possible, collect the subungual debris in addition to nail clippings. - Sample the discolored, dystrophic or brittle parts of the nail only, sampling as far back as possible from the distal part of the nail. ### For Hair: - Pluck hairs from the affected area with forceps (infected hairs come out easily) and scrape the scalp with a scalpel. - Preferably, the sample should include hair roots, the contents of plugged follicles, and skin scales. - Hair cut with a scissors is unsatisfactory as the focus of infection is usually below or near the surface of the scalp. - Sterile toothbrushes may be useful but preclude microscopy on the sample. ### Storage of Specimen - Skin and nail specimens should be stored at room temperature, as dermatophyte fungi may be killed at 4-6 C. ### Few diseases and microbes associated with the infections of - **Skin:** - Impetigo: *Staphylococcus aureus* - Cellulitis and Erysipelas: *Streptococcus pyogenes* - Folliculitis: *Propionibacterium acnes* - Trichomycosis: *Corynebacterium tenuis* - **Nails** - Onchomycosis: *Trichophyton rubrum, T mentagrophytes, T megninii* - Candida Onchomycosis: *Candida albicans*. ## Oral Cavity - Within the oral cavity is the tongue, teeth, tissue supporting the teeth (gums and bone), and salivary glands. ### Various Diseases Associated with the Area Are - **Fungal infections** - Candidiasis - Histoplasmomiasis - Periodontitis - Cryptococcosis - **Viral infections** - Herpes Simplex - Herpes Zoster - HPV Infection - CMV Infection - **Bacterial infections** - Linear gingival erythema - Necrotizing Ulcerative - *Mycobacterium avium complex* ### Methods of Sample Collection from Oral Cavity Are - **Swab:** - The sampling approach involves gently rubbing a sterile cotton swab over the lesion tissue and then subsequently inoculating a primary isolation medium such as *Sabouraud's dextrose agar (SDA)*. - **Concentrated Oral Rinse:** - The oral rinse technique involves the patient holding 10 mL of sterile phosphate-buffered saline (0.01 M, pH 7.2) in their mouth for 1 minute. - The solution is then concentrated (10-fold) by centrifugation and a known volume, usually 50 µL inoculated on agar medium using a spiral plating system. - After 24-48 hrs incubation at 37°C, growth is assessed by enumeration of colonies and expressed as colony forming units per mL (efu mL¯¹) of rinse. - **Imprint Culture:** - The imprint method utilizes a sterile foam pad of known size (typically 2.5 cm²), previously dipped in an appropriate liquid medium, such as Sabouraud's broth, immediately before use. - The pad is then placed on the target site (mucosa or intraoral prosthesis) for 30 seconds and then transferred to an agar for culture.