Specimen Collection In Infectious Diseases

1. Specimen CollectionIn Infectious Diseases Dr.T.V.Rao MD Professor Of Microbiology

2. Specimen collection in Microbiology to isolate and identify the causative agents forms back bone of the investigative procedures. In developing world, lack of awareness and casual attitude among junior staff hampers the definitive diagnosis. Specific procedures in collecting specimens will certainly improve the quality of services of Microbiology Departments Why specimen collection is Important in Microbiology

3. 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 ?

4. Fishing for Diagnosis in Laboratories, Is it worth? • The physicians and Microbiologists should be aware of the clinical manifestations, before undertaking the test. • Microbiological tests are expensive and technically demanding • Causal testing of Microbiological tests are counterproductive.

5. Every laboratory should formulate guidelines on procedures for each major category of specimens and requests. Every laboratory should assist extra examinations,outwith the standard procedures may be required if specifically requested by the Physician or if the clinical information provided on the request form suggests that an unusual infection may be present. Policies on Specimen Collection.

6. Why Proper written Request • Your request is a legal document. • Identifies all the outcome of test. • No interchange of results. • Short forms are dangerous • Signature of the Doctor / Nurse is essential in legible form, can help to contact in case of results which can save a patient. • When the patient is serious, write a Tele contact number which can help in prompt delivery of results

7. An Ideal Request form • Name xxxx Age Sex • IP/ OP No xyz Time Date • Ward xx123 Urgent / Routine • Nature of specimen • Investigation needed Doctor/Staff Contact No 1234567

8. On sending the sample the Physician will be anticipating the early reports, the Microbiologists should promptly dispatch results in all life saving investigations. However the Doctors must be made aware limitation of the investigations and discuss the pros and cons of the Laboratory reports When one Expects the Results

9. On many occasions less than ideal sample is received in laboratory. The rejection of clinical samples should be done with great care and wisdom of only senior staff who should take the responsibility. In the welfare of the patient samples can be repeatedly collected for better diagnosis, as we need repeated isolation to confirm uncommon pathogens. When to Repeat Diagnostic Tests

10. When to Collect the Earliest Specimen • Start collection of specimens for all cultures before starting an Antibiotic. • The advice is ideal but may not be possible, as many prescribe Antibiotics before considers the Microbiological diagnostic options.

11. 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 Stuart's Transport Medium V.R Medium

12. What containers to use • Containers must be leak proof, • Unbreakable • For cultures sterile containers a Must

13. Label High risk Specimens • Sputum with suspected Tuberculosis • Fecal samples suspected with Cholera, Typhoid, • Anthrax ? • Serum when suspected with HIV/ HBV/HCV, infections

14. Blood for Culturing

15. Blood Collection for Culturing • Most important investigation • An appropriate procedures in collection and processing, identifying and timely reporting can be Life saving

16. Collection of Blood • A scientific approaches and dedicated staff participating in blood collection will eliminate the basic failure as Contamination • Improper handling of syringes increases chances of contamination • Contamination hampers the ideal reporting, • A valuable time is lost • The goal in blood collection is avoiding the contamination

17. Collecting the Blood for Culturing • Teach the staff how to collect the Blood. • The nurse are advised on principles of aseptic precautions by self as washing hands and wearing gloves • Proper areas of disinfection with good antiseptic solutions.

18. Hygienic precautions will decrease contamination • The staff should be advised how to disinfect the skin over vein, to use a fresh sterile syringe for the venepuncture with fresh sterile needle before inoculating culture bottle • The staff should disinfect their hands before doing the procedure.

19. Proper handling of Syringe is essential to obtain a blood specimen • The staff should hold the needle by its butt, not shaft. Either with sterile forceps or with fingers covered with a dry sterile rubber glove, and protect self with potentially infective pathogens

20. The staff are warned that contamination is very likely if the specimen is collected from an indwelling peripheral venous catheter instead of from a fresh venpuncture. Do not collect from existing or indwelling catheters

21. Always collect the Blood specimens in Hygienic areas • All procedures in relation to processing of the samples should be done in a sterile environment, or bacteria free areas. • Despite insistence on aseptic precautions, most laboratories report finding contamination in 1-5% of the blood cultures.

22. Cerebrospinal fluid examination

23. Specimen collection for CSF Examination • Lumbar puncture to collect the CSF for examination to be collected by Physician trained in procedure with aseptic precautions to prevent introduction of Infection.

24. Procedure to collect CSF • The trained physician will 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

25. CSF needs a New and Sterile container • Fresh sterile screw capped container to be used. • Reused containers, not to be used, contamination from the previous specimens misrepresent the present specimen.

26. Lumbar puncture for CSF collection • The best site for puncture is inter space between 3 and 4 lumbar vertebrae ( Corresponds to highest point of iliac crest )‏ The Physician should wear sterile gloves and conduct the procedure with sterile precautions, The site of procedure should be disinfected and sterile occlusive dressing applied to the puncture site after the procedure.

27. Transportation to Laboratory • The collected specimen of CSF to be dispatched promptly to Laboratory , delay may cause death of delicate pathogens, eg Meningococci and disintegrate leukocytes

28. 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.

29. Upper Respiratory Infections

30. What are Upper Respiratory Infections • The commonest respiratory infections are localised in Oropharynx, Nasopharynx, and nasal cavity, • Causes Sore thraot,nasal discharge and often fever. Infect larynx,otitis media,sinusitis,conjunctivitis or keratitis. • May present with serious diseases whooping cough, influenza , measles and infectious mononucleosis.

31. Aetiological agents in Upper Respiratory Infections • In most cases the primary infections are caused by virus, difficult to isolate. • But many infections are caused by concomitant carriage or secondary infection with one of the potential pathogens present in the Nasopharynx 1 Pneumococcus .Haemophilus influenza Staphylococcus aureus, and Streptococcus pyogenes. • Drug resistant coli form bacilli or yeasts may dominate the throat flora in patients receiving antibiotics.

32. Specimen collectionin Throat Infections • A plain cotton wool swab should be used to collect as much exudates as possible from tonsils, posterior pharyngeal wall and other area that is inflamed or bears exudates

33. Cooperation of the patient and ideal techniques contributes better results • If cooperated by patient, the swab should be rubbed with rotation over one tonsillar area of the soft palate and uvula, the other tonsillar area and finally the posterior pharynx

34. Collecting the Swab • An adequate view of throat should be ensured by good lighting conditions and the use of a disposable wooden spatula or a tongue depressor to pull outwards and so depress the tongue.

35. Transportation of Throat Swabs • The swab should be replaced in its tube with care not to soil the rim • If it cannot be transported immediately to laboratory it should be placed in a refrigerator at 4ºc until delivery or preferably submitted in a tube of transport medium

36. Nasal specimens • A deep nasal swab generally yields the same information as throat swab. • Nasal swabs are taken to detect healthy carriers than diagnose deep infection • Deep nasal are taken to diagnose S.pyogenes and Diphtheria bacillus.

37. Specimens in sinusitis • Pus collected or aspirated from sinus, or a saline wash out should be examined in a Gram film and by culture on aerobic and anaerobic blood agar plates.

38. Collection of Ear SwabsAcute Otitis Media • Acute Otitis Media – as long as eardrum remains intact, none of the infected exudates can be collected on an ear swab , though culture of the throat swab may give a provisional indication of casual organism

39. Chronic suppurative Otitis media • Swabs of the discharge in the external meatus should be cultured to guide the choice of antibiotics for systemic and topical therapy.

40. Otitis externa • A swab should be taken from the meatus and cultured aerobically on blood agar and MacConkey agar plates for the bacteria. • All specimens should also cultured on Sabouraud’s agar plate with Nystatin 50 units for Candida and Aspergillus.

41. Eye Swabs • Obtaining a adequate specimen is difficult. • It is best to make smears and seed culture plates beside the patient immediately after collecting the material from the eye.

42. Collection of Eye swabs • It is ideal to pick up the material with a loop or on the smoothly rounded tip of a thin glass rod or on the thin serum coated swab • Clinical material from Conjunctiva, i.e. from averted eyelid, • The margin of the eyelid should be avoided.

43. Specimens for Lower Respiratory Infections.

44. Lower Respiratory Infections • Sputum is the material from the lower respiratory infections most commonly submitted for bacteriological examination. The sputum is a mixture of bronchial secretions and inflammatory exudates coughed up into the mouth and expectorated • There are several difficulties both in collecting a suitable sample and interpreting the results of the culture • Busy and uninstructed staff may send collection of saliva to the laboratory. • On several occasions repeat sample may be required to isolate the causative agent.

45. Instruction for collecting sputum • Make the collection in a disposable and wide mouthed screw capped plastic container of 50 – 100 ml capacity. • Collect sputum before antibiotics are given. • Ideal to have when patient wakes up and with first cough.

46. Precautions in handling the specimens • Avoid spilling the material over the rim. • Tightly screw on the cap of the container. • Wipe off any spilled material on its outside with tissue paper • Deliver the specimen quickly to laboratory

47. Sputum Examination for Tuberculosis • Specimen should be collected with biosaftey precautions. • Several specimens should be collected before coming to negative conclusions.

48. Specimens for Urinary Tract Infections

49. Collecting Urine for examination • Collect the Mid stream specimens of Urine • Do not collect spontaneously passed urine without instructions, which can lead to contamination with commensals bacteria Colonized on urethral orifice and perineum

50. Specimen Collection • The urine collected in a wide mouthed container from patients • A mid stream specimen is the most ideal for processing • Female patients passes urine with a labia separated and mid stream sample is collected