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2. Sample collection ,transport and acceptance and rejection.pptx

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MohanSinghDhakad1

This document provides guidelines for collecting, transporting, and testing various clinical specimens for microbiological analysis. It discusses sample types including body fluids, cerebrospinal fluid, blood, urine, respiratory samples, gastrointestinal samples, ear swabs, eye swabs, and abscess or wound samples. For each sample type, it provides information on containers, transport times and temperatures, and appropriate microbiological tests. The document aims to ensure proper specimen collection and handling to optimize pathogen recovery and identification.

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Sample collection, transport and acceptance and rejection criteria DR MOHAN SINGH DHAKAD PG 1ST YR RESIDENT( MD MICROBIOLOGY )
1) Body fluid 2)CSF 3) Blood 4) Urine 5) Respiratory system 6) GIT 7)Ear 8) Eye 9)Pus 10) Others B. Sample Transport C. Acceptance and Rejection Criteria Type of sample collection
2. Sample collection ,transport and acceptance and rejection.pptx
1.BODY FLUID FROM STERILE SITES • Percutaneous aspiration of  Pleural fluid:  Peritoneal fluid  Pericardial fluid  Synovial fluid  Hydrocele fluid
2. Sample collection ,transport and acceptance and rejection.pptx
1.Body Fluids Specimen Ascites (peritoneal), bile, joint (synovial), pericardial, pleural Container Sterile, screw cap tube or anaerobic transporter or direct inoculation into blood culture bottles, or capped syringe Patient Preparation Disinfect skin with iodine preparation before aspirating specimen Special Instruction Needle aspiration Transport to lab Within 15 min do not refrigerate Primary plating media May use an aerobic and anaerobic culture bottle set for body fluids, Blood Agar,Chocolate A , Thio, mac Anaerobic media Brucella Blood A , Bacteroid Bile Esculin agar, Laked blood agar with Kanamycin and Vancomycin Direct examination Gram Staining
COLLECTION • Body fluids specimen are collected by percutaneous aspiration from respective sites, usually as a blind procedure( pleural fluid, peritoneal fluid, synovial fluid), or sometimes under radiological guidance(pericardial fluid and amniotic fluid).  Skin preparation:- Site of collection needs to be disinfected with alcohol-iodine. Followed by percutaneous aspiration using sterile syringe and needle under strict aseptic precautions The collected specimen is transferred on to a sterile universal container.  Enriching in blood Culture bottle:-Depending upon the volume of fluid collected, a portion of specimen collected can be inoculated on blood culture bottle at the site of collection (Pediatric bottle <5ml, adult bottle 5-10 ml)  Advantage:- isolation of the pathogen by this method is found better especially important for synovial fluid and peritoneal fluid collected from patient with continuous ambulatory peritoneal dialysis(CAP).  Transport:- immediately to the laboratory , if any delay is expected, the sample should be store at 37°C or RT, but never refrigerate.
Specimen 2.Cerebrospinal Fluid (CSF) Container Sterile, screw cap tube Patient Preparation Disinfect skin with iodine or chlorhexidine before aspirating specimen. Special Instruction Consider rapid testing(Gram stain , cryptococcal antigen) Transport to lab ≤15 min RT Never refrigerate for bacteriology.
3.Blood Specimen Blood Container Blood culture media set (aerobic and anaerobic bottle) Patient Preparation Disinfect venipuncture site with chlorhexidine /alcohol. Special Instruction Draw blood at time of febrile episode; draw two sets from right and left arms; do not draw more than four sets in a 24-h period; draw ≥20 mL/set (adults) or 1–20 mL/set (pediatric) depending on patient’s weight; or per manufacturer’s instructions Transport to lab Within 2 h/RT Primary plating media Blood culture bottles, aerobic; consider isolator tubes fungi and other intracellular agents. Anaerobic media Blood culture bottles, anaerobic. Direct examination direct Gram stain from positive blood culture bottles.
2. Sample collection ,transport and acceptance and rejection.pptx
4.Urine Specimen A. Clean catch midstream (CMS) Container Sterile, screw cap container Containers that include a variety of chemical urinalysis preservatives may also be used. Patient Preparation Females: clean area with soap and water, then rinse with water; hold labia apart and begin voiding in commode; after several mL have passed, collect midstream. Males: clean glans with soap and water, then rinse with water; retract foreskin; begin voiding in commode; after several mL have passed, collect midstream Special Instruction - Transport to lab Preserved ≤24 h/RT Unpreserved ≤1/2 h/RT Primary plating media BA, Mac ,CLED Optional: chromogenic agar, Anaerobic media Direct examination Check for pyuria, Gram stain not recommended.
4.Urine Specimen B. Straight catheter (in and out) Container Sterile, screw-cap container or urine transport tube with boric acid preservative Patient Preparation Clean urethral area (soap and water) and rinse (water) Special Instruction Insert catheter into bladder; allow first 15 mL to pass; then collect remainde Transport to lab Unpreserved ≤1/2 h/RT Preserved ≤ 24 h/RT Primary plating media BA, Mac Optional: chromogenic agar Anaerobic media Direct examination Gram or check for pyuria
4.Urine Specimen C. Suprapubic aspirate Container Sterile, screw cap container or anaerobic transporter Patient Preparation Disinfect skin. Special Instruction Needle aspiration above the symphysis pubis through the abdominal wall into the full bladder Transport to lab Immediately/RT Primary plating media BA, Mac, CNA Thio Anaerobic media BBA, LKV, BBE Direct examination check for pyuria
Respiratory tract sample A. Upper - • Oral swab • Nasal swab: • Nasopharyngeal swab • Nasopharyngeal aspirate • nasopharyngeal wash • Sinus aspirate B. Lower • Sputum • Endotracheal aspirate (ETA) • Bronchoalveolar lavage (BAL) • Broncheal brush
5.Respiratory Tract Specimen A.UPPER a.Nasal Container Swab transport Patient Preparation - Special Instruction Premoisten swab with sterile saline; insert approximately 1–2 cm into nares; rotate against nasal mucosa. Transport to lab ≤2 h/RT Primary plating media BA, chromogenic agar for MRSA screening Anaerobic media - Direct examination -
5.Respiratory Tract Specimen A.Upper b.Nasopharynx Container Swab moistened with Stuart’s or Amie’s medium Patient Preparation - Special Instruction Insert flexible swab through nose into posterior nasopharynx and rotate for 5 s; specimen of choice for Bordetella pertussis Transport to lab ≤15 min,/ RT without transport media, ≤2 h/RT using transport media Primary plating media BA, CA Anaerobic media - Direct examination -
. Upper RT: Container: • Swab moistened with Stuart’s or Amie’s medium Collection: 1.Oral swab: • Remove the oral secretions or debris from the surface of lesion with swab and discard • Using 2nd swab ,vigorously specimen the lesion avoiding any areas of normal tissue 2. nasal swab: • Use swab moistened with sterile saline. • Insert approx. 2cm into nares • Rotate swab against nasal mucosa
3. Nasopharyngeal • A. Swabs: • To collect nasopharyngeal cells, all mucus is removed • Small flexible nasopharyngeal swab is inserted along the nasal septum to the posterior pharynx • Rotate slowly for 5 sec. against the mucosa several times • B. Aspirate : • Is collected with a plastic tube attached to 10 ml syringe or suction catheter • C. Washings: • Is obtained with a rubber suction bulb by instilling and withdrawing 3-7 ml of sterile buffer saline
5.Respiratory Tract Specimen C. Pharynx (throat) Container Swab moistened with Stuart’s or Amie’s medium Swab dry with or without silica gel for S. pyogenes and C. diphtheriae Patient Preparation - Special Instruction Swab posterior pharynx and tonsils Transport to lab ≤2 h/RT Primary plating media BA Anaerobic media - Direct examination -
5.Respiratory Tract Specimen Lower b.Sputum Container Sterile, screw top container Patient Preparation Have patient brush teeth and then rinse or gargle with water before collection. Special Instruction Have patient collect from deep cough; specimen should be examined for suitability for culture by Gram stain; induced sputa on pediatric or uncooperative patients may be watery because of saline nebulization. Transport to lab ≤2 h/RT Primary plating media BA, CA, Mac, Cystic fibrosis patients, add BCSA/, OFPBL, Mannitol salt and IMA Anaerobic media - Direct examination Gram and other special stains as requested (e.g., Legionella DFA, acid-fast stain)
Specimen collection and transport • Sputum • Spontaneous: Early morning specimen generated after a bout of cough. • Having the patient brush his or her teeth and gargle with water immediately before obtaining the sputum specimen reduces the number of contaminating oropharyngeal bacteria
Grading for Sputum sample
5.Respiratory Tract Specimen B.Lower a. BAL, Broncheal brush, endotracheal aspirate Container Sterile, screw top container Patient Preparation - Special Instruction Anaerobic culture appropriate only if sheathed (protected) catheter used. Transport to lab ≤2 h/RT Primary plating media BA, CA, Mac, Columbia agar with colistin and Nalidixic acid Anaerobic media BBA, LKV (only acceptable for protected bronchoscopic brushing in anaerobic transport) Direct Gram and other special stains as requested (e.g., Legionella DFA, acid-
Type of container • Collect in a sterile leak proof screw-cap container. • Rejection criteria. • For sputum and endotracheal aspirate specimens • Reject duplicate specimens received on the same day unless the initial sample was inappropriate for culture according to microscopic evaluation. Do not accept repeat cultures at intervals of less than every 48 hours. • Reject the following specimens for diagnosis of lower respiratory tract disease: ♦ 24 hours sputum collection ♦ Contaminated sputum and endotracheal specimens as per Gram stain rejection criteria (see below ) ♦ Specimens that are visually saliva only ♦ Specimens that are visibly contaminated with toothpaste or other substances ♦ Nasal washes or swabs of nares to diagnose sinusitis • Sputum samples are highly contaminated with normal anaerobic flora of the upper respiratory tract. Therefore, anaerobic culture should not be done.
Endotracheal aspirate (ETA) • Endotracheal aspiration should be done with a sterile technique using a 22 inch, 12F suction catheter. The catheter should be introduced through the endotracheal tube for at least 30 cm. Gentle aspiration is then performed without instilling saline solution. The first aspirate is discarded. • The second aspirate should be collected after tracheal instillation of 5 ml saline in a mucus collection tube. [If very little secretion is produced by the patient, chest vibration or percussion for 10 minutes should be used to increase the retrieved volume (> 1 ml)]. • The specimens should be sent to laboratory and cultured within 1 hour of collection
Bronchoalveolar lavage (BAL) In this procedure 120 ml of saline should be infused into a lung segment through the bronchoscope to obtain cells and protein of the pulmonary interstitium and alveolar spaces. Send a portion of it to the laboratory. Sinus aspirate Collection of specimens from patients with sinusitis should be performed by otolaryngologists who perform nasal endoscopy or sinus puncture and aspiration.
2. Sample collection ,transport and acceptance and rejection.pptx
6.GI Tract Specimen A. Gastric wash or lavage Container Sterile, screw cap tube Patient Preparation Collect in early AM before patient eats or gets out of bed. Special Instruction Most gastric aspirates are on infants for AFB. Transport to lab ≤15 min/RT Primary plating media BA, CA, Mac, CNA(Columbia agar), EB (enrichmenr broth) Anaerobic media - Direct examination Gram/AO( acridin orange ) stain
6.GI Tract Specimen D. Stool (feces) routine culture Container Clean, leak proof container; transfer feces to enteric transport medium (Cary-Blair medium) Patient Preparation - Special Instruction Routine culture should include Salmonella, Shigella, and Campylobacter; specify Vibrio, Aeromonas, Plesiomonas, Yersinia, Escherichia coli O157:H7, if needed. Transport to lab Within 24 h/ RT in holding media Unpreserved ≤1 h/RT Primary plating media BA, Mac, Campy, EB; Anaerobic media - Direct examination Methylene blue for fecal leukocytes; optional: Shiga toxin testing.
6.GI Tract Specimen E. Clostridiodes difficile Container Sterile, leakproof container Patient Preparation - Special Instruction - Transport to lab ≤1 h, RT 1–24 h, 4°C Primary plating media CCFA Anaerobic media - Direct examination -
6.GI Tract Specimen F.Escherichia coli O157-H7 or other Shigatoxin producing serotypes Container Sterile leak proof container, or Cary Blair holding medium Patient Preparation - Special Instruction - Transport to lab ≤1 h, RT unpreserved ≤24 h, RT or 4°C in swab transport system Primary plating media Mac-sorbitol Anaerobic media - Direct examination -
7. Ear Specimen inner Container sterile, screw- cap tube or anaerobic transporter Patient Preparation clean ear canal with mild soap solution Special Instruction aspirate material behind drum with syringe if eardrum intact; use flexible shaft swab to collect material from ruptured eardrum Transport to lab ≤2 h Primary plating media BA, CA (add thio if prior antimicrobial therapy) Anaerobic media BBA Direct examination Gram
7. Ear Specimen External Container swab moistened with Stuart’s or Amie’s Patient Preparation Wipe away crust with sterile saline. Special Instruction firmly rotate swab in outer canal. Transport to lab ≤2 h/RT Primary plating media BA CA Mac Anaerobic media Direct examination Gram
8.Eye Specimen Conjunctiva Container Direct culture inoculation to BA and Choc; or swab transport system Patient Preparation - Special Instruction Sample both eyes; use separate swabs premoistened with sterile saline Transport to lab ≤15 min/RT Primary plating media BA, CA Anaerobic media - Direct examination Gram, Acridin Orange stain, histologic stains (e.g., Giemsa)
8.Eye Specimen Aqueous/ vitreous fluid Container Sterile, screw cap tube Patient Preparation Prepare eye for needle aspiration Special Instruction - Transport to lab ≤15 min/RT Primary plating media BA, CA Anaerobic media Direct examination Gram-
8.Eye Specimen C.Corneal scrapings Container Bedside inoculation of BHI 10% Patient Preparation Clinician should instill local anesthetic before collection. Special Instruction Used kimura spatula Transport to lab ≤15 min/RT Primary plating media BHI , SDA with antibiotics Anaerobic media Direct examination Gram stain-
Corneal scrapping collected by
9.Abscess (Also Lesion, Wound, Pustule, Ulcer) Specimen Deep Container Anaerobic transporter Patient Preparation Wipe area with sterile saline or 70% alcohol Special Instruction Aspirate material from wall or excise tissue. Transport to lab ≤2 h Primary plating media BA, CA, Mac, CNA Anaerobic media BBA, LKV, BBE Direct examination Gram
9.Abscess (Also Lesion, Wound, Pustule, Ulcer) Specimen Superficial Container Recommend -swab transport system or aerobic swab moistened with Stuart’s or Amie’s medium Patient Preparation Wipe area with sterile saline or 70% alcohol. Special Instruction Aspirate or tissue are preferred if possible, pass swab deeply into the lesion along leading edge of wound. Transport to lab ≤2 h Primary plating media BA, CA, Mac, CNA optional Anaerobic media BBA, LKV, BBE Direct examination Gram
Hair, Nails, or Skin Scrapings (for Fungal Culture) Specimen Container Clean, screw- top tube Patient Preparation Nails or skin: wipe with 70% alcohol Special Instruction Hair: collect hairs with intact shaft. Nails: send clippings of affected area. Skin: scrape skin at leading edge of lesion Transport to lab Within 72 h/RT Primary plating media SDA, Anaerobic media Direct examination KOH mount
2. Sample collection ,transport and acceptance and rejection.pptx
2. Sample collection ,transport and acceptance and rejection.pptx
2. Sample collection ,transport and acceptance and rejection.pptx
2. Sample collection ,transport and acceptance and rejection.pptx
2. Sample collection ,transport and acceptance and rejection.pptx
• The specimen was received in a fixative (formalin), which, in essence, kills any microorganism present. • The specimen has been received for anaerobic culture from a site known to have anaerobes as part of the normal microbiota (vagina, mouth). • The specimen is dried. • Processing the specimen would produce information of questionable medical value (e.g., Foley catheter tip)
Container • Sterile screw-cap tube or anaerobic transporte Specimen transport • Submit to laboratory as soon as possible • Do not refrigerate. • Label specimens with patient demographics and date, time, and site of collection,e.g. left knee joint fluid.
Rejection criteria- • when fluid specimens are received on a swab. Specimens received by the laboratory in a syringe with the needle still attached should be rejected because of the risk of a needless sharp exposure by laboratory staf. • . The laboratory may reject specimens that have clotted in a capped syringe because they cannot be processed for culture without inadvertently contaminating the specimen
5. Throat swab: • Depress the tongue with a tongue depressor • Introduce the swab between the tonsillar pillars and behind the uvula without touching the lateral walls of the buccal cavity • Swab back and forth across • The posterior pharynx • Any exudates or membrane should be taken for specimen :
• Lower respiratory tract • 1)Sputum • Container :sterile screw-cap cup or other suitable sterile collection assembly of about 100 ml capacity. • Early morning specimen generated after bout of cough • Transport the specimen to laboratory as soon as possible
2)Endotracheal aspirate (ETA) • should be done with a sterile technique using a 22 inch, 12F suction catheter • The catheter should be introduced through the endotracheal tube for at least 30 cm. The first aspirate is discarded. • The second aspirate should be collected after tracheal instillation of 5 ml saline in a mucus collection tube. Transport The specimens to laboratory and cultured within 1 hour of collection.
3.Bronchoalveolar lavage (BAL) • to obtain cells and protein of the pulmonary interstitium and alveolar spaces. • In this procedure 120 ml of saline should be infused into a lung segment through the bronchoscope • Type of container of respiratory specimen : collect in sterile leak proof screw cap container
Rejection criteria For sputum and endotracheal aspirate specimen • Duplicate specimen received on same day • 24 hours sputum collection • Specimen that are visually saliva only • Visibly contaminated with tooth paste or other substances • Nasal wash or nasal swabs of nare to diagnose sinusitis
For BAL, and lung aspirate specimen • BAL & lung aspirate specimens should never be rejected • For specimens delayed in transit more than 2 hours without refrigeration, indicate on the report that the delay in transit may compromise the culture results
Pus • Specimen collection :Preferably collect specimen prior to initiation of therapy and only from wounds that are clinically infected or deteriorating or that fail to heal over a long period • Wound or abscess aspirates • Samples collected by using a syringe and needle should be placed in a sterile container or blood collection tube without anticoagulant (e.g., Vacutainer® or similar type) for submission to the laboratory • also be placed in a sterile tube containing anaerobic medium like RCM if an anaerobic culture is required
Open Wound • Remove all superficial exudates. • Remove overlying debris with scalpel and swabs or sponges. • Collect biopsy or curette sample from base or advancing margin of lesion PUS :Aspirate the deepest portion of the lesion or exudate with a syringe and needle Tissue biopsy sample:tissue biopsy samples should be collected from areas within and adjacent to the area of infection. . Anerobic medium like RCM if required Transport within 30 minutes. Do not refrigerate or incubate before or during transport
*Transport within 30 minutes & Do not refrigerate or incubate before or during transport • Rejection criteria • For anaerobic culture, avoid swab collection if aspirates or biopsy samples can be obtained. • Do not accept specimens for microbiological analysis in container with formalin
urine Container :sterile, wide mouth, screw capped • 1 Midstream clean catch urine • 2 Indwelling catheter. • 3 Suprapubic collection • 4 Percutaneous nephrostomy (PCN) aspirate • 5 Cystoscopy specimens
1)Midstream clean catch urine • most common type of urine specimen • after very thorough preliminary cleaning of external genitalia with soap and water. Antiseptics should not be used for this purpose. • 2) indwelling catheter • specimen should be collected by disinfecting a portion of the catheter tubing with alcohol & puncturing the tubing directly with a sterile syringe with needle and aspirating the urine • Rejection of sample: collected from the drainage bag
3)Suprapubic collection • It avoids urethral contamination but is invasive • reserved for infants and adults, • Disinfect the skin above the bladder and plunge a sterile needle with syringe into the bladder; aspirate the urine and transfer to a sterile container.
Fecal Specimens • Specimen collection and transport • container. • sterile screw-capped disposable 40 ml container. • A small quantity of solid/semisolid stool or one third of the container in case of watery stool
• The sample should be immediately transported to the laboratory on collection. • If there is a delay in transporting faecal specimens or if samples need to be sent by post, one of the following transport media may be employed: ♦ Phosphate buffered glycerol saline solution ♦ Stuart’s transport medium ♦ Cary and Blair transport medium
Pus • Specimen collection- • Wound or abscess aspirates. • Open wounds.
. Body Fluids From Sterile Site Specimen collection • Body fluids from sterile sites should be collected by percutaneous aspiration for pleural, pericardial, peritoneal, amniotic, and synovial fluids. • Use care to avoid contamination with commensal microbiota. • Clean the needle puncture site with alcohol, and disinfect it with an iodine solution [1- 2% tincture of iodine or a 10% solution of povidone iodine (1% free iodine)] to prevent specimen contamination or infection of patient (if tincture of iodine is used, remove with 70% ethanol after the procedure to avoid burn). • Aseptically perform percutaneous aspiration with syringe and needle to obtain pleural, pericardial, peritoneal, or synovial fluid.
• Immediately place a portion of the joint fluid or peritoneal fluid collected from patients with CAPD or SBP into aerobic and anaerobic blood culture bottles, retaining some (0.5 ml) in syringe for Gram stain and direct plating. • Use the minimum and maximum volumes recommended by the bottle manufacturer (generally up to 10 ml is the maximum for each bottle). • Alternatively, inoculate the blood culture bottles after receipt in the laboratory. • Submit other fluids and the remainder of specimens after inoculation of blood culture bottles in one of the following: a sterile, gassed-out tube or a sterile blood collection tube without preservative; however, fluids in such tubes may clot during transport.
Specimen transport • Submit to laboratory as soon as possible • Do not refrigerate. • Label specimens with patient demographics and date, time, and site of collection,e.g. left knee joint fluid. • Record the patient diagnosis for improved processing of specimen
Note: • If specimens inoculated into blood culture bottles are received, Gram stain cannot be performed. • Collect specimen prior to antimicrobial therapy for greatest diagnostic sensitivity. • Do not submit specimens from drains after they have been infused with antimicrobial agents. • Call physician when fluid specimens are received on a swab. • Contact physician if specimen is insufficient for the number of tests requested . • Swabs constitute the least desirable sample for culture of body fluids and should be discouraged, since the quantity of sample may not be sufficient to ensure recovery of a small number of organisms. • Routine bacterial culture is sufficient for culture for Candida species, if blood culture bottles are used or specimen is centrifuged.
Important considerations • Specimens received by the laboratory in a syringe with the needle still attached should be rejected because of the risk of a needless sharp exposure by laboratory staff. The physician should be immediately contacted to recollect the sample and send it in proper container. Note: Establish a policy for the proper collection and transport of clinical specimens not collected on swabs. Educate the physicians that needles must be removed from the syringe and the syringe cap secured prior to transport to avoid leakage. • Syringes that have been capped (with needle removed) prior to transport may be accepted for culture provided the specimen has not clotted inside the syringe and there is no leakage during transport which could result in contamination of the culture. The laboratory may reject specimens that have clotted in a capped syringe because they cannot be processed for culture without inadvertently contaminating the specimen
Ocular Specimens Specimen collection and transport Note: Most eye specimens should be collected by an ophthalmologist. These specimens should be inoculated onto culture media at the bedside, in the clinic or the physician’s office. Considerations • Provide fresh media to the clinical areas routinely collecting ocular cultures, and instruct physicians to immediately transport inoculated media and slides to the laboratory. • Obtain viral and chlamydial samples before topical anesthetics are instilled. • Obtain samples for chlamydial cultures with calcium alginate swabs. Note: Calcium alginate swabs may be toxic for Neisseria gonorrhoeae (for which rayon or cotton swabs could be used) . • For viral cultures, use Dacron or cotton swabs with non-wood shafts
RESPIRATORY SPECIMENS • Purpose :To isolate and identify the potentially pathogenic organisms from upper and lower respiratory tracts (URT and LRT) aiding in the diagnosis of infections. • Type of specimen: • A sputum • B Endotracheal aspirate(ETA) • C Bronchoalveolar lavage • D Sinus aspirate • Type of container •
Specimen collection and transport • Collect specimen resulting from deep cough in a sterile screw-cap cup or other suitable sterile collection assembly of about 100 ml capacity. • To prevent contamination of the outside of the container, the patient should be instructed to press the rim of the container under the lower lip to catch the entire expectorated cough sample.
• Tightly screw on the cap of the container. Wipe off any spilled material on its outside with a tissue moistened with disinfectant, but take care not to let any disinfectant enter the container. Such communication with patients can be rewarding. In addition, patients should remove dentures during the specimen collection. • Early-morning sputum samples should be obtained because they contain pooled overnight secretions in which pathogenic bacteria are more likely to be concentrated. Twenty four hour collections should be discouraged. • Deliver the specimen to the laboratory as quickly as possible, preferably within 2 hours, for delicate bacterial, viral and mycoplasma pathogens may die out during longer delay.
For BAL, lung aspirates and OLB specimens • BAL specimens, lung aspirates, and OLB specimens should never be rejected by the laboratory, since the patient has undergone an invasive procedure for their collection. • • For specimens delayed in transit more than 2 hours without refrigeration, indicate on the report that the delay in transit may compromise the culture results. • • Anaerobic culture should be performed on lung aspirates, pleural fluid, and OLB specimens by request or when the original specimen Gram stain demonstrates morphotypes suggestive of anaerobic infection
Pus • Purpose: To isolate and identify bacterial etiological agent(s) in deep-seated pus/wound specimens • Specimen collection • • Preferably collect specimen prior to initiation of therapy and only from wounds that are clinically infected or deteriorating or that fail to heal over a long period. • • Cleanse surrounding skin or mucosal surfaces. • • For closed wounds and aspirates, disinfect with 2% chlorhexidine or 70% alcohol followed by an iodine solution [1 to 2% tincture of iodine or a 10% solution of povidone-iodine (1% free iodine)]. Remove iodine with alcohol prior to specimen collection. • • For open wounds, debride, if appropriate, and thoroughly rinse with sterile saline prior to collection. Sample viable infected tissue, rather than superficial debris.
• Wound or abscess aspirates • • Samples collected by using a syringe and needle should be placed in a sterile container or blood collection tube without anticoagulant (e.g., Vacutainer® or similar type) for submission to the laboratory. • • A portion of the sample should also be placed in a sterile tube containing anaerobic medium like RCM if an anaerobic culture is required.
Pus • Aspirate the deepest portion of the lesion or exudate with a syringe and needle. • Collect a biopsy sample of the advancing margin or base of the infected lesion after excision and drainage. • For bite wounds, aspirate pus from the wound, or obtain it at the time of incision, drainage, or debridement of infected wound
Pus • Aspirate the deepest portion of the lesion or exudate with a syringe and needle. • Collect a biopsy sample of the advancing margin or base of the infected lesion after excision and drainage. • For bite wounds, aspirate pus from the wound, or obtain it at the time of incision, drainage, or debridement of infected wound
Tissues and biopsy samples • • Tissue biopsy samples should be collected from areas within and adjacent to the area of infection. Large enough tissue samples should be collected to perform all of the tests required (i.e., 3 to 4 mm biopsy samples). • • If anaerobic culture is required, a separate piece of tissue should be submitted in a sterile tube containing anaerobic medium like RCM. • • Collect swabs only when tissue or aspirate cannot be obtained. • • Limit swab sampling to wounds that are clinically infected or those that are chronic and non-healing. • • Remove superficial debris by thorough irrigation and cleansing with non-bacteriostatic sterile saline. If wound is relatively dry, collect with two cotton-tipped swabs moistened with sterile saline.
• Gently roll swab over the surface of the wound approximately five times, focusing on area where there is evidence of pus or inflamed tissue. • Note: Organisms may not be distributed evenly in a burn wound, so sampling different areas of the burn is recommended. Blood cultures should be used to monitor patient status.
Standard precautions to be followed while handling the specimen • Note: Syringes with the needle attached should not be accepted due to the sharps and biohazard risk to staff. • Grossly contaminated specimen or leaky containers and collection containers of doubtful sterility must be noted and mentioned. • • Deliver aspirates and tissues to the laboratory within 30 minutes for best recovery. • • Keep tissues moist to preserve organism viability. • • Do not refrigerate or incubate before or during transport. If there is a delay, keep sample at room temperature, because at lower temperature there is likely to be more dissolved oxygen, which could be detrimental to anaerobes.
2. Sample collection ,transport and acceptance and rejection.pptx
2. Sample collection ,transport and acceptance and rejection.pptx
2. Sample collection ,transport and acceptance and rejection.pptx
2. Sample collection ,transport and acceptance and rejection.pptx

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2. Sample collection ,transport and acceptance and rejection.pptx

  • 1. Sample collection, transport and acceptance and rejection criteria DR MOHAN SINGH DHAKAD PG 1ST YR RESIDENT( MD MICROBIOLOGY )
  • 2. 1) Body fluid 2)CSF 3) Blood 4) Urine 5) Respiratory system 6) GIT 7)Ear 8) Eye 9)Pus 10) Others B. Sample Transport C. Acceptance and Rejection Criteria Type of sample collection
  • 4. 1.BODY FLUID FROM STERILE SITES • Percutaneous aspiration of  Pleural fluid:  Peritoneal fluid  Pericardial fluid  Synovial fluid  Hydrocele fluid
  • 6. 1.Body Fluids Specimen Ascites (peritoneal), bile, joint (synovial), pericardial, pleural Container Sterile, screw cap tube or anaerobic transporter or direct inoculation into blood culture bottles, or capped syringe Patient Preparation Disinfect skin with iodine preparation before aspirating specimen Special Instruction Needle aspiration Transport to lab Within 15 min do not refrigerate Primary plating media May use an aerobic and anaerobic culture bottle set for body fluids, Blood Agar,Chocolate A , Thio, mac Anaerobic media Brucella Blood A , Bacteroid Bile Esculin agar, Laked blood agar with Kanamycin and Vancomycin Direct examination Gram Staining
  • 7. COLLECTION • Body fluids specimen are collected by percutaneous aspiration from respective sites, usually as a blind procedure( pleural fluid, peritoneal fluid, synovial fluid), or sometimes under radiological guidance(pericardial fluid and amniotic fluid).  Skin preparation:- Site of collection needs to be disinfected with alcohol-iodine. Followed by percutaneous aspiration using sterile syringe and needle under strict aseptic precautions The collected specimen is transferred on to a sterile universal container.  Enriching in blood Culture bottle:-Depending upon the volume of fluid collected, a portion of specimen collected can be inoculated on blood culture bottle at the site of collection (Pediatric bottle <5ml, adult bottle 5-10 ml)  Advantage:- isolation of the pathogen by this method is found better especially important for synovial fluid and peritoneal fluid collected from patient with continuous ambulatory peritoneal dialysis(CAP).  Transport:- immediately to the laboratory , if any delay is expected, the sample should be store at 37°C or RT, but never refrigerate.
  • 8. Specimen 2.Cerebrospinal Fluid (CSF) Container Sterile, screw cap tube Patient Preparation Disinfect skin with iodine or chlorhexidine before aspirating specimen. Special Instruction Consider rapid testing(Gram stain , cryptococcal antigen) Transport to lab ≤15 min RT Never refrigerate for bacteriology.
  • 9. 3.Blood Specimen Blood Container Blood culture media set (aerobic and anaerobic bottle) Patient Preparation Disinfect venipuncture site with chlorhexidine /alcohol. Special Instruction Draw blood at time of febrile episode; draw two sets from right and left arms; do not draw more than four sets in a 24-h period; draw ≥20 mL/set (adults) or 1–20 mL/set (pediatric) depending on patient’s weight; or per manufacturer’s instructions Transport to lab Within 2 h/RT Primary plating media Blood culture bottles, aerobic; consider isolator tubes fungi and other intracellular agents. Anaerobic media Blood culture bottles, anaerobic. Direct examination direct Gram stain from positive blood culture bottles.
  • 11. 4.Urine Specimen A. Clean catch midstream (CMS) Container Sterile, screw cap container Containers that include a variety of chemical urinalysis preservatives may also be used. Patient Preparation Females: clean area with soap and water, then rinse with water; hold labia apart and begin voiding in commode; after several mL have passed, collect midstream. Males: clean glans with soap and water, then rinse with water; retract foreskin; begin voiding in commode; after several mL have passed, collect midstream Special Instruction - Transport to lab Preserved ≤24 h/RT Unpreserved ≤1/2 h/RT Primary plating media BA, Mac ,CLED Optional: chromogenic agar, Anaerobic media Direct examination Check for pyuria, Gram stain not recommended.
  • 12. 4.Urine Specimen B. Straight catheter (in and out) Container Sterile, screw-cap container or urine transport tube with boric acid preservative Patient Preparation Clean urethral area (soap and water) and rinse (water) Special Instruction Insert catheter into bladder; allow first 15 mL to pass; then collect remainde Transport to lab Unpreserved ≤1/2 h/RT Preserved ≤ 24 h/RT Primary plating media BA, Mac Optional: chromogenic agar Anaerobic media Direct examination Gram or check for pyuria
  • 13. 4.Urine Specimen C. Suprapubic aspirate Container Sterile, screw cap container or anaerobic transporter Patient Preparation Disinfect skin. Special Instruction Needle aspiration above the symphysis pubis through the abdominal wall into the full bladder Transport to lab Immediately/RT Primary plating media BA, Mac, CNA Thio Anaerobic media BBA, LKV, BBE Direct examination check for pyuria
  • 14. Respiratory tract sample A. Upper - • Oral swab • Nasal swab: • Nasopharyngeal swab • Nasopharyngeal aspirate • nasopharyngeal wash • Sinus aspirate B. Lower • Sputum • Endotracheal aspirate (ETA) • Bronchoalveolar lavage (BAL) • Broncheal brush
  • 15. 5.Respiratory Tract Specimen A.UPPER a.Nasal Container Swab transport Patient Preparation - Special Instruction Premoisten swab with sterile saline; insert approximately 1–2 cm into nares; rotate against nasal mucosa. Transport to lab ≤2 h/RT Primary plating media BA, chromogenic agar for MRSA screening Anaerobic media - Direct examination -
  • 16. 5.Respiratory Tract Specimen A.Upper b.Nasopharynx Container Swab moistened with Stuart’s or Amie’s medium Patient Preparation - Special Instruction Insert flexible swab through nose into posterior nasopharynx and rotate for 5 s; specimen of choice for Bordetella pertussis Transport to lab ≤15 min,/ RT without transport media, ≤2 h/RT using transport media Primary plating media BA, CA Anaerobic media - Direct examination -
  • 17. . Upper RT: Container: • Swab moistened with Stuart’s or Amie’s medium Collection: 1.Oral swab: • Remove the oral secretions or debris from the surface of lesion with swab and discard • Using 2nd swab ,vigorously specimen the lesion avoiding any areas of normal tissue 2. nasal swab: • Use swab moistened with sterile saline. • Insert approx. 2cm into nares • Rotate swab against nasal mucosa
  • 18. 3. Nasopharyngeal • A. Swabs: • To collect nasopharyngeal cells, all mucus is removed • Small flexible nasopharyngeal swab is inserted along the nasal septum to the posterior pharynx • Rotate slowly for 5 sec. against the mucosa several times • B. Aspirate : • Is collected with a plastic tube attached to 10 ml syringe or suction catheter • C. Washings: • Is obtained with a rubber suction bulb by instilling and withdrawing 3-7 ml of sterile buffer saline
  • 19. 5.Respiratory Tract Specimen C. Pharynx (throat) Container Swab moistened with Stuart’s or Amie’s medium Swab dry with or without silica gel for S. pyogenes and C. diphtheriae Patient Preparation - Special Instruction Swab posterior pharynx and tonsils Transport to lab ≤2 h/RT Primary plating media BA Anaerobic media - Direct examination -
  • 20. 5.Respiratory Tract Specimen Lower b.Sputum Container Sterile, screw top container Patient Preparation Have patient brush teeth and then rinse or gargle with water before collection. Special Instruction Have patient collect from deep cough; specimen should be examined for suitability for culture by Gram stain; induced sputa on pediatric or uncooperative patients may be watery because of saline nebulization. Transport to lab ≤2 h/RT Primary plating media BA, CA, Mac, Cystic fibrosis patients, add BCSA/, OFPBL, Mannitol salt and IMA Anaerobic media - Direct examination Gram and other special stains as requested (e.g., Legionella DFA, acid-fast stain)
  • 21. Specimen collection and transport • Sputum • Spontaneous: Early morning specimen generated after a bout of cough. • Having the patient brush his or her teeth and gargle with water immediately before obtaining the sputum specimen reduces the number of contaminating oropharyngeal bacteria
  • 23. 5.Respiratory Tract Specimen B.Lower a. BAL, Broncheal brush, endotracheal aspirate Container Sterile, screw top container Patient Preparation - Special Instruction Anaerobic culture appropriate only if sheathed (protected) catheter used. Transport to lab ≤2 h/RT Primary plating media BA, CA, Mac, Columbia agar with colistin and Nalidixic acid Anaerobic media BBA, LKV (only acceptable for protected bronchoscopic brushing in anaerobic transport) Direct Gram and other special stains as requested (e.g., Legionella DFA, acid-
  • 24. Type of container • Collect in a sterile leak proof screw-cap container. • Rejection criteria. • For sputum and endotracheal aspirate specimens • Reject duplicate specimens received on the same day unless the initial sample was inappropriate for culture according to microscopic evaluation. Do not accept repeat cultures at intervals of less than every 48 hours. • Reject the following specimens for diagnosis of lower respiratory tract disease: ♦ 24 hours sputum collection ♦ Contaminated sputum and endotracheal specimens as per Gram stain rejection criteria (see below ) ♦ Specimens that are visually saliva only ♦ Specimens that are visibly contaminated with toothpaste or other substances ♦ Nasal washes or swabs of nares to diagnose sinusitis • Sputum samples are highly contaminated with normal anaerobic flora of the upper respiratory tract. Therefore, anaerobic culture should not be done.
  • 25. Endotracheal aspirate (ETA) • Endotracheal aspiration should be done with a sterile technique using a 22 inch, 12F suction catheter. The catheter should be introduced through the endotracheal tube for at least 30 cm. Gentle aspiration is then performed without instilling saline solution. The first aspirate is discarded. • The second aspirate should be collected after tracheal instillation of 5 ml saline in a mucus collection tube. [If very little secretion is produced by the patient, chest vibration or percussion for 10 minutes should be used to increase the retrieved volume (> 1 ml)]. • The specimens should be sent to laboratory and cultured within 1 hour of collection
  • 26. Bronchoalveolar lavage (BAL) In this procedure 120 ml of saline should be infused into a lung segment through the bronchoscope to obtain cells and protein of the pulmonary interstitium and alveolar spaces. Send a portion of it to the laboratory. Sinus aspirate Collection of specimens from patients with sinusitis should be performed by otolaryngologists who perform nasal endoscopy or sinus puncture and aspiration.
  • 28. 6.GI Tract Specimen A. Gastric wash or lavage Container Sterile, screw cap tube Patient Preparation Collect in early AM before patient eats or gets out of bed. Special Instruction Most gastric aspirates are on infants for AFB. Transport to lab ≤15 min/RT Primary plating media BA, CA, Mac, CNA(Columbia agar), EB (enrichmenr broth) Anaerobic media - Direct examination Gram/AO( acridin orange ) stain
  • 29. 6.GI Tract Specimen D. Stool (feces) routine culture Container Clean, leak proof container; transfer feces to enteric transport medium (Cary-Blair medium) Patient Preparation - Special Instruction Routine culture should include Salmonella, Shigella, and Campylobacter; specify Vibrio, Aeromonas, Plesiomonas, Yersinia, Escherichia coli O157:H7, if needed. Transport to lab Within 24 h/ RT in holding media Unpreserved ≤1 h/RT Primary plating media BA, Mac, Campy, EB; Anaerobic media - Direct examination Methylene blue for fecal leukocytes; optional: Shiga toxin testing.
  • 30. 6.GI Tract Specimen E. Clostridiodes difficile Container Sterile, leakproof container Patient Preparation - Special Instruction - Transport to lab ≤1 h, RT 1–24 h, 4°C Primary plating media CCFA Anaerobic media - Direct examination -
  • 31. 6.GI Tract Specimen F.Escherichia coli O157-H7 or other Shigatoxin producing serotypes Container Sterile leak proof container, or Cary Blair holding medium Patient Preparation - Special Instruction - Transport to lab ≤1 h, RT unpreserved ≤24 h, RT or 4°C in swab transport system Primary plating media Mac-sorbitol Anaerobic media - Direct examination -
  • 32. 7. Ear Specimen inner Container sterile, screw- cap tube or anaerobic transporter Patient Preparation clean ear canal with mild soap solution Special Instruction aspirate material behind drum with syringe if eardrum intact; use flexible shaft swab to collect material from ruptured eardrum Transport to lab ≤2 h Primary plating media BA, CA (add thio if prior antimicrobial therapy) Anaerobic media BBA Direct examination Gram
  • 33. 7. Ear Specimen External Container swab moistened with Stuart’s or Amie’s Patient Preparation Wipe away crust with sterile saline. Special Instruction firmly rotate swab in outer canal. Transport to lab ≤2 h/RT Primary plating media BA CA Mac Anaerobic media Direct examination Gram
  • 34. 8.Eye Specimen Conjunctiva Container Direct culture inoculation to BA and Choc; or swab transport system Patient Preparation - Special Instruction Sample both eyes; use separate swabs premoistened with sterile saline Transport to lab ≤15 min/RT Primary plating media BA, CA Anaerobic media - Direct examination Gram, Acridin Orange stain, histologic stains (e.g., Giemsa)
  • 35. 8.Eye Specimen Aqueous/ vitreous fluid Container Sterile, screw cap tube Patient Preparation Prepare eye for needle aspiration Special Instruction - Transport to lab ≤15 min/RT Primary plating media BA, CA Anaerobic media Direct examination Gram-
  • 36. 8.Eye Specimen C.Corneal scrapings Container Bedside inoculation of BHI 10% Patient Preparation Clinician should instill local anesthetic before collection. Special Instruction Used kimura spatula Transport to lab ≤15 min/RT Primary plating media BHI , SDA with antibiotics Anaerobic media Direct examination Gram stain-
  • 38. 9.Abscess (Also Lesion, Wound, Pustule, Ulcer) Specimen Deep Container Anaerobic transporter Patient Preparation Wipe area with sterile saline or 70% alcohol Special Instruction Aspirate material from wall or excise tissue. Transport to lab ≤2 h Primary plating media BA, CA, Mac, CNA Anaerobic media BBA, LKV, BBE Direct examination Gram
  • 39. 9.Abscess (Also Lesion, Wound, Pustule, Ulcer) Specimen Superficial Container Recommend -swab transport system or aerobic swab moistened with Stuart’s or Amie’s medium Patient Preparation Wipe area with sterile saline or 70% alcohol. Special Instruction Aspirate or tissue are preferred if possible, pass swab deeply into the lesion along leading edge of wound. Transport to lab ≤2 h Primary plating media BA, CA, Mac, CNA optional Anaerobic media BBA, LKV, BBE Direct examination Gram
  • 40. Hair, Nails, or Skin Scrapings (for Fungal Culture) Specimen Container Clean, screw- top tube Patient Preparation Nails or skin: wipe with 70% alcohol Special Instruction Hair: collect hairs with intact shaft. Nails: send clippings of affected area. Skin: scrape skin at leading edge of lesion Transport to lab Within 72 h/RT Primary plating media SDA, Anaerobic media Direct examination KOH mount
  • 46. • The specimen was received in a fixative (formalin), which, in essence, kills any microorganism present. • The specimen has been received for anaerobic culture from a site known to have anaerobes as part of the normal microbiota (vagina, mouth). • The specimen is dried. • Processing the specimen would produce information of questionable medical value (e.g., Foley catheter tip)
  • 47. Container • Sterile screw-cap tube or anaerobic transporte Specimen transport • Submit to laboratory as soon as possible • Do not refrigerate. • Label specimens with patient demographics and date, time, and site of collection,e.g. left knee joint fluid.
  • 48. Rejection criteria- • when fluid specimens are received on a swab. Specimens received by the laboratory in a syringe with the needle still attached should be rejected because of the risk of a needless sharp exposure by laboratory staf. • . The laboratory may reject specimens that have clotted in a capped syringe because they cannot be processed for culture without inadvertently contaminating the specimen
  • 49. 5. Throat swab: • Depress the tongue with a tongue depressor • Introduce the swab between the tonsillar pillars and behind the uvula without touching the lateral walls of the buccal cavity • Swab back and forth across • The posterior pharynx • Any exudates or membrane should be taken for specimen :
  • 50. • Lower respiratory tract • 1)Sputum • Container :sterile screw-cap cup or other suitable sterile collection assembly of about 100 ml capacity. • Early morning specimen generated after bout of cough • Transport the specimen to laboratory as soon as possible
  • 51. 2)Endotracheal aspirate (ETA) • should be done with a sterile technique using a 22 inch, 12F suction catheter • The catheter should be introduced through the endotracheal tube for at least 30 cm. The first aspirate is discarded. • The second aspirate should be collected after tracheal instillation of 5 ml saline in a mucus collection tube. Transport The specimens to laboratory and cultured within 1 hour of collection.
  • 52. 3.Bronchoalveolar lavage (BAL) • to obtain cells and protein of the pulmonary interstitium and alveolar spaces. • In this procedure 120 ml of saline should be infused into a lung segment through the bronchoscope • Type of container of respiratory specimen : collect in sterile leak proof screw cap container
  • 53. Rejection criteria For sputum and endotracheal aspirate specimen • Duplicate specimen received on same day • 24 hours sputum collection • Specimen that are visually saliva only • Visibly contaminated with tooth paste or other substances • Nasal wash or nasal swabs of nare to diagnose sinusitis
  • 54. For BAL, and lung aspirate specimen • BAL & lung aspirate specimens should never be rejected • For specimens delayed in transit more than 2 hours without refrigeration, indicate on the report that the delay in transit may compromise the culture results
  • 55. Pus • Specimen collection :Preferably collect specimen prior to initiation of therapy and only from wounds that are clinically infected or deteriorating or that fail to heal over a long period • Wound or abscess aspirates • Samples collected by using a syringe and needle should be placed in a sterile container or blood collection tube without anticoagulant (e.g., Vacutainer® or similar type) for submission to the laboratory • also be placed in a sterile tube containing anaerobic medium like RCM if an anaerobic culture is required
  • 56. Open Wound • Remove all superficial exudates. • Remove overlying debris with scalpel and swabs or sponges. • Collect biopsy or curette sample from base or advancing margin of lesion PUS :Aspirate the deepest portion of the lesion or exudate with a syringe and needle Tissue biopsy sample:tissue biopsy samples should be collected from areas within and adjacent to the area of infection. . Anerobic medium like RCM if required Transport within 30 minutes. Do not refrigerate or incubate before or during transport
  • 57. *Transport within 30 minutes & Do not refrigerate or incubate before or during transport • Rejection criteria • For anaerobic culture, avoid swab collection if aspirates or biopsy samples can be obtained. • Do not accept specimens for microbiological analysis in container with formalin
  • 58. urine Container :sterile, wide mouth, screw capped • 1 Midstream clean catch urine • 2 Indwelling catheter. • 3 Suprapubic collection • 4 Percutaneous nephrostomy (PCN) aspirate • 5 Cystoscopy specimens
  • 59. 1)Midstream clean catch urine • most common type of urine specimen • after very thorough preliminary cleaning of external genitalia with soap and water. Antiseptics should not be used for this purpose. • 2) indwelling catheter • specimen should be collected by disinfecting a portion of the catheter tubing with alcohol & puncturing the tubing directly with a sterile syringe with needle and aspirating the urine • Rejection of sample: collected from the drainage bag
  • 60. 3)Suprapubic collection • It avoids urethral contamination but is invasive • reserved for infants and adults, • Disinfect the skin above the bladder and plunge a sterile needle with syringe into the bladder; aspirate the urine and transfer to a sterile container.
  • 61. Fecal Specimens • Specimen collection and transport • container. • sterile screw-capped disposable 40 ml container. • A small quantity of solid/semisolid stool or one third of the container in case of watery stool
  • 62. • The sample should be immediately transported to the laboratory on collection. • If there is a delay in transporting faecal specimens or if samples need to be sent by post, one of the following transport media may be employed: ♦ Phosphate buffered glycerol saline solution ♦ Stuart’s transport medium ♦ Cary and Blair transport medium
  • 63. Pus • Specimen collection- • Wound or abscess aspirates. • Open wounds.
  • 64. . Body Fluids From Sterile Site Specimen collection • Body fluids from sterile sites should be collected by percutaneous aspiration for pleural, pericardial, peritoneal, amniotic, and synovial fluids. • Use care to avoid contamination with commensal microbiota. • Clean the needle puncture site with alcohol, and disinfect it with an iodine solution [1- 2% tincture of iodine or a 10% solution of povidone iodine (1% free iodine)] to prevent specimen contamination or infection of patient (if tincture of iodine is used, remove with 70% ethanol after the procedure to avoid burn). • Aseptically perform percutaneous aspiration with syringe and needle to obtain pleural, pericardial, peritoneal, or synovial fluid.
  • 65. • Immediately place a portion of the joint fluid or peritoneal fluid collected from patients with CAPD or SBP into aerobic and anaerobic blood culture bottles, retaining some (0.5 ml) in syringe for Gram stain and direct plating. • Use the minimum and maximum volumes recommended by the bottle manufacturer (generally up to 10 ml is the maximum for each bottle). • Alternatively, inoculate the blood culture bottles after receipt in the laboratory. • Submit other fluids and the remainder of specimens after inoculation of blood culture bottles in one of the following: a sterile, gassed-out tube or a sterile blood collection tube without preservative; however, fluids in such tubes may clot during transport.
  • 66. Specimen transport • Submit to laboratory as soon as possible • Do not refrigerate. • Label specimens with patient demographics and date, time, and site of collection,e.g. left knee joint fluid. • Record the patient diagnosis for improved processing of specimen
  • 67. Note: • If specimens inoculated into blood culture bottles are received, Gram stain cannot be performed. • Collect specimen prior to antimicrobial therapy for greatest diagnostic sensitivity. • Do not submit specimens from drains after they have been infused with antimicrobial agents. • Call physician when fluid specimens are received on a swab. • Contact physician if specimen is insufficient for the number of tests requested . • Swabs constitute the least desirable sample for culture of body fluids and should be discouraged, since the quantity of sample may not be sufficient to ensure recovery of a small number of organisms. • Routine bacterial culture is sufficient for culture for Candida species, if blood culture bottles are used or specimen is centrifuged.
  • 68. Important considerations • Specimens received by the laboratory in a syringe with the needle still attached should be rejected because of the risk of a needless sharp exposure by laboratory staff. The physician should be immediately contacted to recollect the sample and send it in proper container. Note: Establish a policy for the proper collection and transport of clinical specimens not collected on swabs. Educate the physicians that needles must be removed from the syringe and the syringe cap secured prior to transport to avoid leakage. • Syringes that have been capped (with needle removed) prior to transport may be accepted for culture provided the specimen has not clotted inside the syringe and there is no leakage during transport which could result in contamination of the culture. The laboratory may reject specimens that have clotted in a capped syringe because they cannot be processed for culture without inadvertently contaminating the specimen
  • 69. Ocular Specimens Specimen collection and transport Note: Most eye specimens should be collected by an ophthalmologist. These specimens should be inoculated onto culture media at the bedside, in the clinic or the physician’s office. Considerations • Provide fresh media to the clinical areas routinely collecting ocular cultures, and instruct physicians to immediately transport inoculated media and slides to the laboratory. • Obtain viral and chlamydial samples before topical anesthetics are instilled. • Obtain samples for chlamydial cultures with calcium alginate swabs. Note: Calcium alginate swabs may be toxic for Neisseria gonorrhoeae (for which rayon or cotton swabs could be used) . • For viral cultures, use Dacron or cotton swabs with non-wood shafts
  • 70. RESPIRATORY SPECIMENS • Purpose :To isolate and identify the potentially pathogenic organisms from upper and lower respiratory tracts (URT and LRT) aiding in the diagnosis of infections. • Type of specimen: • A sputum • B Endotracheal aspirate(ETA) • C Bronchoalveolar lavage • D Sinus aspirate • Type of container •
  • 71. Specimen collection and transport • Collect specimen resulting from deep cough in a sterile screw-cap cup or other suitable sterile collection assembly of about 100 ml capacity. • To prevent contamination of the outside of the container, the patient should be instructed to press the rim of the container under the lower lip to catch the entire expectorated cough sample.
  • 72. • Tightly screw on the cap of the container. Wipe off any spilled material on its outside with a tissue moistened with disinfectant, but take care not to let any disinfectant enter the container. Such communication with patients can be rewarding. In addition, patients should remove dentures during the specimen collection. • Early-morning sputum samples should be obtained because they contain pooled overnight secretions in which pathogenic bacteria are more likely to be concentrated. Twenty four hour collections should be discouraged. • Deliver the specimen to the laboratory as quickly as possible, preferably within 2 hours, for delicate bacterial, viral and mycoplasma pathogens may die out during longer delay.
  • 73. For BAL, lung aspirates and OLB specimens • BAL specimens, lung aspirates, and OLB specimens should never be rejected by the laboratory, since the patient has undergone an invasive procedure for their collection. • • For specimens delayed in transit more than 2 hours without refrigeration, indicate on the report that the delay in transit may compromise the culture results. • • Anaerobic culture should be performed on lung aspirates, pleural fluid, and OLB specimens by request or when the original specimen Gram stain demonstrates morphotypes suggestive of anaerobic infection
  • 74. Pus • Purpose: To isolate and identify bacterial etiological agent(s) in deep-seated pus/wound specimens • Specimen collection • • Preferably collect specimen prior to initiation of therapy and only from wounds that are clinically infected or deteriorating or that fail to heal over a long period. • • Cleanse surrounding skin or mucosal surfaces. • • For closed wounds and aspirates, disinfect with 2% chlorhexidine or 70% alcohol followed by an iodine solution [1 to 2% tincture of iodine or a 10% solution of povidone-iodine (1% free iodine)]. Remove iodine with alcohol prior to specimen collection. • • For open wounds, debride, if appropriate, and thoroughly rinse with sterile saline prior to collection. Sample viable infected tissue, rather than superficial debris.
  • 75. • Wound or abscess aspirates • • Samples collected by using a syringe and needle should be placed in a sterile container or blood collection tube without anticoagulant (e.g., Vacutainer® or similar type) for submission to the laboratory. • • A portion of the sample should also be placed in a sterile tube containing anaerobic medium like RCM if an anaerobic culture is required.
  • 76. Pus • Aspirate the deepest portion of the lesion or exudate with a syringe and needle. • Collect a biopsy sample of the advancing margin or base of the infected lesion after excision and drainage. • For bite wounds, aspirate pus from the wound, or obtain it at the time of incision, drainage, or debridement of infected wound
  • 77. Pus • Aspirate the deepest portion of the lesion or exudate with a syringe and needle. • Collect a biopsy sample of the advancing margin or base of the infected lesion after excision and drainage. • For bite wounds, aspirate pus from the wound, or obtain it at the time of incision, drainage, or debridement of infected wound
  • 78. Tissues and biopsy samples • • Tissue biopsy samples should be collected from areas within and adjacent to the area of infection. Large enough tissue samples should be collected to perform all of the tests required (i.e., 3 to 4 mm biopsy samples). • • If anaerobic culture is required, a separate piece of tissue should be submitted in a sterile tube containing anaerobic medium like RCM. • • Collect swabs only when tissue or aspirate cannot be obtained. • • Limit swab sampling to wounds that are clinically infected or those that are chronic and non-healing. • • Remove superficial debris by thorough irrigation and cleansing with non-bacteriostatic sterile saline. If wound is relatively dry, collect with two cotton-tipped swabs moistened with sterile saline.
  • 79. • Gently roll swab over the surface of the wound approximately five times, focusing on area where there is evidence of pus or inflamed tissue. • Note: Organisms may not be distributed evenly in a burn wound, so sampling different areas of the burn is recommended. Blood cultures should be used to monitor patient status.
  • 80. Standard precautions to be followed while handling the specimen • Note: Syringes with the needle attached should not be accepted due to the sharps and biohazard risk to staff. • Grossly contaminated specimen or leaky containers and collection containers of doubtful sterility must be noted and mentioned. • • Deliver aspirates and tissues to the laboratory within 30 minutes for best recovery. • • Keep tissues moist to preserve organism viability. • • Do not refrigerate or incubate before or during transport. If there is a delay, keep sample at room temperature, because at lower temperature there is likely to be more dissolved oxygen, which could be detrimental to anaerobes.