Department of Clinical Microbiology
	Guidelines for Specimen Collection Contact Details Turnaround Times Reports Rejecting Specimens Collection of Specimens MRSA Screening Protocol Antibotic Monitoring Diagnosis of Infectious Diseases Virology Viral Illnesses Virology Tests

Guidelines for proper specimen collection and transport

• Collect specimen before administering antimicrobial agents when possible.
• Use sterile containers and aseptic technique to collect specimens to prevent introduction of microorganisms during invasive procedures.
• Collect an adequate amount of specimen. Inadequate amounts of specimen may yield false negative results.
• Specimens obtained using needle aspiration should be transferred to a sterile container and transported to the laboratory as soon as possible. If there is only a small volume of material in syringe add some sterile saline, mix and transfer to a sterile container.

1. All specimens with no significant growth will be issued within 48 hours. Results on possible pathogens will be issued as soon as possible. All significant results will be telephoned to the clinician to initiate optimal antibiotic therapy or to implement infection control measures, if considered appropriate.
   
2. On blood cultures preliminary results will be issued at 48 hours. Final result will be issued at the end of 7 days incubation except for patients with suspected endocarditis or brucellosis, which will be after 14 days incubation.
   
3. Serology tests are usually batched once or twice a week and therefore turnaround time will depend on the arrival of the sample on the appropriate day. However single urgent serology tests can be requested if considered appropriate.
   
4. Direct examination for AAFB is available on the same day. Cultures of positive mycobacteria are usually available between 3 - 6 weeks; confirmation of positive mycobacterium tuberculosis within 48 hours; sensitivity and confirmation of other mycobacterium species 6 weeks.

Tests referred to reference laboratories have a normal turnaround time from a few days to a few weeks depending on the type of investigation. If the results are required urgently please ring the laboratory.


Back to Top

Reports
These will be delivered at the earliest possible moment. Results of routine investigations will not normally be given over the telephone. Telephone requests must be kept to an essential minimum in the interest of safety, as verbal reports may lead to transcription errors. Urgent reports will be telephoned by the medical or laboratory staff.

Reasons for rejecting specimens for bacteriological examination

1. Specimens submitted in an unsterile container.
2. Tissue/specimen received in formalin or other fixative.
3. Improperly labelled samples and samples from patients whose details do not correspond with the request form are not meeting miminum data set.
4. Specimens received on a dry swab.
5. Specimens which have leaked or where the container has been damaged during transport to the laboratory.
6. Blood cultures that have been refrigerated.
7. Swabs received from upper respiratory tract infection for Respiratory Syncytial Virus.
8. Faeces samples wrapped in toilet paper.

Blood cultures: These should be part of the routine investigation of every pyrexial illness. Ideally, 3 sets of blood cultures should be collected per febrile episode; each set should be separated by at least 1 hour from the previous specimen. This provides maximum recovery of organisms in patients with intermittent bacteremia. They should be drawn prior to the initiation of antibiotic therapy. In cases of endocarditis 3 sets of blood cultures should be taken within 2-4 hours before starting antibiotic therapy.

Back to Top

Back to Top


When taking blood cultures the following procedure should be followed:

1. Carefully clean the venepuncture site with two swabs soaked in 70% isopropyl alcohol.
2. Allow the skin to dry before taking the blood. (Note: Do not palpate the vein after disinfecting the skin prior to inserting the needle).
3. Draw blood through a syringe needle and deliver 10 ml blood into blood culture bottles. (Note: A new needle should be used for each venepuncture).

Note: False positive blood cultures have occurred when blood has been transferred from other sample tubes to the blood culture medium. It is essential therefore that blood is transferred direct from the syringe used for venepuncture to the blood culture bottle. If the blood has been taken for other investigations it is essential to inoculate the blood culture bottle first to minimise the risk of contamination.

Back to Top

Breast milk: Decontaminate the skin and send approximately 2 ml of sample in a sterile container.

Chlamydia : Roche PCR - Chlamydia Swab Collection Kit

USE MICROBIOLOGY REQUEST FORM - Disregard request form in Chlamydia collection kit.

UNISEX COLLECTION KIT - 12578 - Remel M4RT

Consisting of: One red capped tube of M4RT medium
One small stainless steel shafted Dacron tipped swab
One large plastic shafted Dacron tipped swab

INTENDED USE

Remel’s M4RT is a tubed medium validated for the transport of clinical specimens to the laboratory for testing with the Roche PCR Chlamydia tranchomatis assay.

STORAGE

This product is ready for use and no further preparation is necessary. The product should be stored in its original container at room temperature (range 2-30oC) until used. Do not incubate prior to use.

PRODUCT DETERIORATION

This product should not be used (1) there is evidence of contamination (2) there is evidence of leakage (3) the colour has changed from light pink (4) the expiration date has passed, or (5) there are other signs of deterioration.

SPECIMEN COLLECTION

Specimens should be collected and handled following the recommended guidelines below.

Female Endo-Cervical Samples

1. Remove mucus from exocervix with large swab and discard.
2. Insert the small swab into the endocervical canal until tip is no longer visible.
3. Rotate 3-5 seconds. Withdraw, avoid contact with vaginal surfaces.

Male Urethral Samples

1. If possible avoid urination for 1 hour prior to sampling.
2. Insert small swab 2-4 cm into the urethra.
3. Rotate 3-5 seconds. Withdraw

A. Aseptically remove cap from vial.
B. Insert swab into medium.
C. Break swab shaft evenly at the scored line (approx 5 cm from the non-swab end of the shaft).
D. Replace cap to vial and close tightly.
E. Label with appropriate patient information.
F. Send to the laboratory for processing.

SPECIMEN TRANSPORT AND STORAGE

Following collection, the specimen should be promptly sent to the laboratory. If possible, specimens should be refrigerated before transit. Once delivered to the laboratory specimens be refrigerated at 2-80 until tested.

Note: Urine specimen are stable for 24 hours at 18-20°C.
Urine specimens that will not be transported within 24 hours of collection must be stored at 2-8°C and transported within 5 days.

Back to Top

C.S.F.: Specimens should be taken into three plastic universal containers, stating the order in which they are collected, and the doctor responsible must ensure that these are always examined without delay by contacting the Laboratory on-call BMS. Blood should be taken for blood glucose level and sent to the Clinical Chemistry laboratory.

Ear swab: Aspirate ( tympanocentesis) for otitis media; moist swab for otitis externa. In cases of otitis externa in which the ear drum is ruptured, collect exudate by inserting a sterile swab through an auditory speculum to collect the exudate.

Enterobius vermicularis: See under "Worm".

Epididymis: Use a needle and syringe to aspirate material from the epididymis and transfer it into a sterile container.

Eye swab: Collect the specimen by swabbing ; pass moistened swab two times over lower inferior tarsal conjunctival fornix. Avoid eye lid and lashes. If purulent material is seen this should be collected on a sterile cotton swab and delivered to the laboratory.

Back to Top

Faeces: Patient can be instructed to pass stool directly into a sterile, wide-mouthed, leak proof container with a tight fitting lid.

Fluid from sterile site: Disinfect the skin and collect the specimen under sterile aseptic conditions. The sample should be put into a sterile container provided by the laboratory and should be sent as soon as possible.

Gastric lavage: This should be sent on patients who are unable to produce quality sputum. It should be performed when the patient wakes up in the morning so that sputum swallowed during sleep is still in the stomach. Three samples are required on separate morning.

Gastric biopsies for H. pylori: Gastric antral mucosal biopsies for culture of H. pylori should be sent in transport medium containing 0.5 ml of normal sterile saline provided by the laboratory. The biopsy must be sent to the laboratory within 2 hours of collection.

Gonococci: High vaginal swabs are not useful for examination of gonococci. Specimens should be taken from the cervix and urethra. Urethral swabs should be taken from the male. Swabs should be inoculated at the bedside or be sent in transport medium within 30 minutes. The laboratory should be informed of the specimen. Dry swabs are of no value for gonococcal culture.

Back to Top

High vaginal swab: Swabs should be taken using a speculum for direct vision where possible. Transport medium must always be used.

IV catheter tip: Clean the insertion site with iodophor or alcohol and aseptically remove the cannula after the alcohol has dried. If purulent material presents at the exit site it should be swabbed and sent for culture. The tip of the cannula (approximately 2 inches or 5 cm) should be sent to microbiology in a sterile container. If central line infection is suspected take 2 sets of blood culture, one from peripheral vein and one from a central line. The site of blood culture collection must be mentioned on the request form.

Mouth swab: (for yeast or fusospirochetal disease) Rinse the mouth with sterile saline and wipe the lesion with dry sterile gauze. Swab or scrap an area of exudate or ulceration.

Back to Top

Nasal swabs: (for detection of staphylococcal carrier) Insert a sterile swab into the nose until resistance is met at the level of the turbinates (approximately 1 inch into the nose). Rotate the swab against the nasal mucosa and repeat the process on the other side.

Nasopharyngeal swabs: See "Pernasal/nasopharyngeal swab".

Nasopharyngeal aspirate for RSV: In infants and small children the secretion is obtained by a No. 8 French soft plastic feeding tube attached through a valve containing sputum trap to a suction apparatus. The sterile catheter tip is introduced through each nostril to the nasopharynx and suction is intermittently applied while the catheter is slowly withdrawn. This process may be repeated once so that 0.2-0.8 ml of secretion is obtained in the trap container. However, if this procedure yields no secretion 0.5-1 ml of sterile saline can be injected into the posterior nares via the catheter and resuctioned into the trap. Transport medium or neutral broth must not be added to the secretions. Nasal, pernasal or throat swabs are not suitable for detection of RSV, therefore these samples will not be processed by the laboratory.

Neonatal screening swabs: The following bacteriological investigations are recommended:

Early-onset sepsis (< 48 hours after birth)

The above "surface" cultures also apply to babies with maternal risk factors eg prolonged rupture of membranes in the delivery suite. It is useful to request obstetricians for maternal cultures ie high vaginal swabs, blood culture and placental culture, if possible.

Late-onset sepsis (> 48 hours after birth)

Endotracheal tube aspirates: Babies receiving artificial ventilation should have endotracheal cultures sent routinely once a week. Suspected pneumonia in a baby on artificial ventilation is an indication for culture of endotracheal secretions.

Pernasal/nasopharyngeal swab (for detection of N. meningitidis and B. pertussis): Use special nasopharyneal swab available from the microbiology on request. Gently insert flexible-wire calcium alginate-tipped swabs through the posterior nasopharynx (taking care not to touch the skin); close to the septum and floor of the nose.
Rotate the swab and allow to remain for few seconds and gently remove the wire. Place swab in the transport medium for N. meningitidis and transport the swab to the laboratory as soon as possible. For B. pertussis hand the swab to the BMS for direct plating on to appropriate media at the bedside.

Prostatic massage: This is used to diagnose chronic prostatitis and performed by a digital massage through the rectum. Collect the specimen in a sterile tube or on a sterile swab.

Rectal swabs (for N. gonorrhoea and Herpes Simplex virus): Pass the tip of a sterile swab approximately 1 inch beyond the anal sphincter. Carefully rotate the swab to sample the anal crypts (leave swab for 15-30 seconds), and withdraw the swab. Send swab in appropriate transport medium.

Back to Top

Sinus aspirate: This must be performed by a specially trained physician or ENT surgeon who will obtain the material from maxillary, frontal, or other sinuses, using a syringe aspiration technique. The content of the syringe should be put into a sterile container and transported to the laboratory as soon as possible.

Sputum: The patient should be instructed to remove dentures, rinse the mouth and gargle with tap water and not with antiseptic mouthwash. Instruct the patient not to expectorate saliva or postnasal discharge into the container. Specimens must be submitted in a wide-mouthed container and sent to the laboratory without delay. Specimen containers with obvious external contamination will be discarded due to the infection risk to all staff handling the specimen. Early morning specimens are preferred; in hospital physiotherapy assisted sample are useful. (A minimum of 3 early morning sputum samples are required for the investigation of suspected pulmonary tuberculosis.)

Stool culture: see "Faeces".

Back to Top

Throat swab: Take a cotton wool swab and, depressing the tongue with a spatula, direct the swab to the back of the throat with the other hand and swab the tonsillar pillars and the oropharynx, rotating the swab as this is done. If a pseudo membrane is present , the swab should be taken from beneath the membrane or part of the membrane should be cultured if possible. Place the swab in appropriate transport medium. The swab must be sent immediately for culture, since many pathogenic bacteria survive only for a short time on a dry swab. Transport medium should be used.

Note: Do not take throat samples if epiglottis is inflamed as sampling may cause serious respiratory obstruction.

Urethral swab: (for N. gonorrhoea and C. trachomatis) The specimen should be collected at least 2 hours after the patient has urinated. Insert a thin urogenital swab 2-4 cm into the endourethra and gently rotate. Leave in place for a few seconds before withdrawing.

Urine: The first sample of the day is best because bacteria will have had an opportunity to grow in the bladder overnight and it is much more likely that significant numbers will be detected in this sample than one collected later in the day. Suprapubic aspirates (SPA) are the best samples from babies and young children. Mid-stream urine (MSU) specimens are collected as follows:

Male: The glans penis is cleaned with soap and water. Micturition is commenced and when a few ml of urine have been passed, a sterile wide-mouthed urine container is introduced into the stream and the container is filled.

Females: If the patient is able to collect urine without assistance from the nursing staff, they should be instructed as follows:

1. Separate the labia and with cotton wool or a sponge moistened with water, wipe the vulva from the front to the back. Disinfectants must not be used.
   
2. With the labia still separated allow some urine to pass into the toilet, and then, without stopping, allow some to pass into a sterile container.
   
3. Pass the remaining urine into the toilet.

In elderly or very ill patients nursing assistance is required.

The urine must be collected in a sterile plastic urine container and delivered to the laboratory within one hour of collection. Where this is not possible the specimen can be preserved in a refrigerator at 4°C (never frozen).

Urine specimens from catheterized (CSU) patients should be obtained from a sampling port or sleeve. This must first be disinfected by wiping with a 70% isopropyl alcohol impregnated swab. The sample may then be aspirated using a sterile needle and syringe and transferred into a sterile container. Do not disconnect the bag to obtain urine sample. Do not take urine sample from the drainage bag as these samples reflect the bacterial count in the bag and not the patient's urinary tract.

Collection of patients with neuropathic or ileal bladders presents difficulty in interruption and should be performed only if there is an indication for treatment, such as pyrexia or constitutional upset. In the cases of ileal bladders collection of urine should be collected by careful catheterization of the stoma. (Three early morning samples are required for investigation if renal tuberculosis is suspected.)

Back to Top

Worm: Stool should be sent for ova, cyst and parasites. For Enterobius vermicularis ova (Pinworm infection) a perianal swab should be sent to the laboratory. The specimen is best obtained between 22.00hr and midnight or early in the morning, before defecation or bathing. A cotton-wool swab in a dry container is required. Wear gloves during the procedure and wash hands and nails thoroughly. Spread buttocks apart, and rub the moistened cotton wool swab over the area around the anus, but do not insert into the anus. Place the cotton wool swab back into its container (no transport medium required). Occasionally, an adult worm may be collected from a patient and sent in saline or water for identification. It is recommended that samples should be taken for at least 4 to 6 consecutive days. If the results of all these are negative the patient can be considered free of infection. Specimens should be transported and processed as soon as possible.

Wound and pus swabs: If there is any volume of pus present it should be collected with a syringe into a sterile container rather than onto a swab. The site of origin of the material must be stated. Anaerobes and fastidious organisms die if subjected to delay or dehydration. Transport medium should be used for swabs.

Back to Top

Antibiotic Monitoring

• All aminoglycosides (gentamicin, netilmicin, amikacin, tobramycin and streptomycin), chloramphenicol, and vancomycin must be monitored by taking peak and trough samples and dose adjusted according to renal function and serum level of antibiotic. Consult medical microbiologist for monitoring of other antibiotics i.e. streptomycin, teicoplanin, flucytosine, cycloserine and co-trimoxazole.
  
• Paired samples are required i.e. pre (trough) and post (peak) dose samples. So called 'random levels' are difficult, and may be impossible to interpret unless they are overtly above the normal peak concentration.
  
• 5-10 ml clotted blood sample should be taken from the peripheral vein and not from IV cannula or central line.
  
• Sample must arrive in laboratory by 1.30pm at Craigavon Area Hospital. Specimens received after this time will not be assayed the same day unless special arrangements are made. On weekends and public holidays, the sample must arrive at Craigavon Area Laboratory by 10.30 am. Aminoglycosides are assayed at 10 am, 2 pm, 5 pm and 10 pm.
  
• If the antibiotic assays are required at Daisy Hill or South Tyrone Hospitals then the requesting doctor must make prior arrangements to the BMS at the Craigavon Area Hospital Laboratory. It is the responsibility of the requesting doctor to arrange the transport to the CAH laboratory.
  
• Patients on antifungal therapy need monitoring of antifungal drugs and monitoring of renal, hepatic and haematological functions. Advice on monitoring of antibiotics is available from consultant medical microbiologist Craigavon Area Hospital 01762 334444 ext 2654.
  
  Suggested Serum Levels for Antimicrobial Agents

	Antimicrobial	Patient Group	Serum Levels		Comments
			Trough (μ/ml) (just before next dose)	Peak (μg/ml) (after 60 min unless statedotherwise)
	Aminoglycosides Gentamicin, Netilmicin and Tobramycin	Most infections and Staph. aureus endocarditis. Gram -ve pneumonia. Infective Endocarditis.	<2 <2 <1	>5 >7 2-3	In normal renal function: assay at dose 2-4.1 Assay earlier if there is renal impairment or other factors associated with increased toxicity. Assay 2-3 times per week.
	Amikacin	All patients receiving drug.	<10	20	Assay 2-3 times per week.
	Streptomycin	All patients receiving drug.	<5	15-40	After 5 In dose and then every 2-4 weeks or if there is a change in renal function.
	Glycopeptides Vancoymcin	All patients receiving drug.	5-10	18-26 (2hr post infusion)	Monitor level on 3rd dose; earlier if change in renal function or other risk factor.
	Teicopianin	Severe non-Staphylococcal infection, intravenous drug abuser and renal impairment. Severe Staph. aureus infection. Staph. aureus endocarditis.	10-20 10-20 >20	40-<60 40-<60 40-<60	Assay 1-2 times per week.
	Other Antimicrobial Agents Chloramphenicol	All patients, especially neonates.	5-10	15-25	Seek advice from microbiologist.
	Flucytosine	All patients, especially in changing renal function, bone marrow suppression, those receiving amphotericin B, or suspected non-compliance.	30-40	70-80	Check serum level 30 minutes after IV, 2 hours after oral dose.
	Amphotericin B	Assay seldom indicated.

Guide To Diagnosis Of Infectious Diseases

	Infectious Condition	Type of Specimen	Comments
	Actinomycosis	Pus with "sulphur granules" if present.	Actinomyces-Like Organisms (ALO's) are occasionally seen from cervical smears examinations. These may be ignored in a woman who is well and has no symptoms of pelvic actinomyces.
	AIDS	Clotted blood.Treat specimen as High Risk.	For details refer to HIV Testing
	Amoebiasis	Warm specimen of faeces (<1 hour) for microscopy.Clotted blood for serology.
	Anthrax	Direct sample of cutaneous lesions; use swab to obtain vesicular fluid. Treat specimen as High Risk.	Consult medical microbiologist and inform microbiology laboratory before sending specimen.
	Antibiotic Assays	Refer to Antibiotic Assays.
	Anti Streptolysin (ASOT) & Anti-DNAse B Titre	Clotted blood.
	Anti-Streptococcal Antibody	Clotted blood.	The tests performed are anti-streptolysin O, anti-DNAse B and anti-hyaluronidase titre.
	Anti-Staphylococcal Antibody	Clotted blood.	Useful for diagnosis of deep-seated infection in joints & bone eg osteomyelitis caused by Staph. aureus.
	Aspergillosis	Clotted blood for precipitin test against A. fumigatus.
	Allergic alveolitis	Clotted blood.
	Bornholm Disease	See under Coxsackie.
	Bordetella pertussis	See under Whooping Cough.
	Borrelia burgdorferi	See under Lyme disease.
	Breast Milk	Refer to Breast Milk.
	Bronchiolitis	See under RSV.
	Brucella Infections	Blood culture. Clotted blood for serology.Treat specimen as High Risk.
	Candida Infections	Blood culture. Swab from suspected lesion. Clotted blood for precipitins in suspected systemic disease.
	Clostridium difficile Toxin	Faecal sample.	Please give history of exposure to antibiotic(s).
	Cryptosporidium	Faecal sample.
	Chickenpox	Swab from vesicle or scraping from lesion in viral transport medium. Clotted blood.
	Chlamydia	Refer to Chlamydia.
	Conjunctivitis (bacterial)	Eye swab for bacterial culture.
	Conjunctivitis (viral)	Eye swab in viral transport medium.
	Coxsackie Virus Infections	Throat swab in viral transport medium, faeces and CSF where relevant for virus isolation. Serology is of limited value.
	Croup	See under Whooping Cough.
	Cysticercosis (Taenia solium)	Faeces for proglottids or eggs.Clotted blood for IFAT.	Intestinal infection with T. saginata gives negative IFAT results.
	Cytomegalovirus infection	Clotted blood. Fresh urine.
	Diarrhoea	Faecal sample for Salmonella, Shigella, Campylobacter & E. coli:0157 are performed routinely on all specimens. Additional examination will be performed on request or patient's history.	Please provide information on age, history of foreign travel and clinical symptoms.
	Diphtheria	Nose, throat and skin swab if appropriate. Treat specimen as High Risk.	Consult medical microbiologist and inform laboratory staff before sending specimen.Blood can be checked for antibody.
	Dysentery (bacillary)	Faecal sample.
	Dysentery (protozoal)	See under Amoebiasis.
	Echovirus Infections	Throat swab in viral transport medium, faeces and CSF where indicated for virus culture.
	Encephalitis	Refer to Virology Tests.
	Endocarditis	Take 3 sets of blood cultures within 2-4 hour period before starting antibiotic therapy.	Refer to Blood Cultures.
	Enteric Fever (typhoid & paratyphoid)	Blood, faeces and urine for culture.Blood culture.Treat specimen as High Risk.	Widal tests are no longer routinely recommended for diagnosing typhoid fever because the results may be influenced by immunization, endemic antibody levels and non-specific reactions.
	Enterobius vermicularis	Refer to Worm.
	Epstein-Barr Virus	Clotted blood.
	Farmers' Lung	Clotted blood.
	Fascioliasis (Fasciola hepatica)	Clotted blood for IFAT.
	Filariasis (Tissue Nematodes)	Clotted blood for ELISA.Thick blood films.
	Fungus infections of Skin, Hair & Nails	Skin scraping in Dermapack Portion of nail and hair stump for fungal examination.
	Giardiasis	Faeces examination for cysts or duodenal aspirate for trophozoites. Clotted blood for IFAT.
	Glandular Fever	See under Infectious mononucleosis.
	Gonorrhoea	Pus swab from cervix, urethra and rectum in transport medium.
	H. pylori	Gastric biopsy for culture and sensitivity sent to laboratory in transport medium (0.5ml saline). Clotted blood for antibody. Refer to page 18 under Gastric biopsies for H.pylori.
	Hepatitis A, B & C	Clotted blood.
	Herpes simplex	Vesicle fluid in viral transport medium. Clotted blood.	Serology tests are useful if the rise in antibody titre is found in primary infection but have no value in recurrences.
	Herpes zoster	See under Chickenpox.
	HIV Infection	Clotted blood. Treat specimen as High Risk.	Refer to HIV Testing.
	Hydatid Disease (Echinococcus granulosus)	Clotted blood for serology.
	Influenza	Refer to Viral Illnesses.
	Infectious mononucleosis	Clotted blood for Paul Bunnell and Monospot Test.
	Legionnaire's Disease	Sputum for culture.Paired sera (5- 21 days apart). Urine for antigen.	Please discuss with medical microbiologist before sending cultures.
	Leishmaniasis	Impression smear of lesion Biopsy for histopathology. Clotted blood for IFAT. Spleen, lymph node and bone marrow aspirate.	Please discuss with medical microbiologist.
	Leptospiral Infections	Clotted blood. Urine.
	Lyme Disease	Clotted blood for ELISA.
	Malaria	Thick and thin films sent yo Haematology Department. Clotted blood.	Serology is useful for retrospective diagnosis, or for investigation of splenomegaly or nephrotic syndrome in those who might have been exposed to malaria.
	Measles	Refer to Viral Illnesses
	Meningitis (bacterial)	CSF for culture & PCR for N.meningitidis. Blood culture.Throat or nasopharyngeal swab.Tissue fluid aspirate from skin for culture of N.meningitidis.	ETDA sample for PCR and acute & convalescent serum (2-6 weeks apart) sample for antibody against N.meningitidis.
	Meningitis (viral)	CSF and faeces for virology.Clotted blood. Refer to Tests Profiles for Virology.
	Mumps	Throat swab in viral transport medium.Clotted blood. Refer to Test Profiles for Virology.
	Myalgic Encephalomyelitis (Chronic Fatigue Syndrome)	Serology is of little value.
	Mycoplasma infections	Paired sera for atypical screen.
	Mycobacteria	See under Tuberculosis.
	Neonatal Screening Swab	Refer to Neonatal Screening Swabs
	Orf (contagious pustular dermatitis)	Fluid from lesion for virology.
	Ornithosis	See under Psittacosis.
	Parvovirus	Refer to Viral Illnesses
	Pertussis	See under Whooping Cough.
	Pneumocystis carinii	Sputum sample to Histopathology.	Currently serology test is not available for diagnosis of P. carinii.
	Pneumonia (atypical)	Sputum, Bronchoalveolar Lavage, Throat/Nasal/Pernasal/nasopharyngeal swab Tracheal secretions.
	Poliomyelitis	Faecal sample for virology.
	Psittacosis	Paired sera.
	Q (Query) fever (Coxiella burneti)	Paired sera.	Consider in culture negative endocarditis and atypical chest infection.
	Rheumatoid Serology	Clotted blood.
	Respiratory Syncytial Virus (RSV)	Nasopharyngeal aspirate. Refer to Nasopharyngeal aspirate.
	Rotavirus	Faeces for virology.
	Rubella Infection	Throat swab in viral transport medium.Paired sera.
	Rubella Immunity	Clotted blood.
	Schistosomiasis	Urine and rectal biopsy for schistosomiasis.Clotted blood.	Consult medical microbiologist for advice.
	Strongyloides	Clotted blood. Faeces for worms.
	Syphilis	Clotted blood.	Total Antibody (ELISA). TPPA + NDCL on positive ELISA tests.
	Tetanus	Clotted blood.	Tetanus is a clinical diagnosis.
	Toxocara	Clotted blood.
	Toxoplasmosis	Clotted blood.
	Trypanosomiasis	Clotted blood for IFAT.Thick and thin blood films. Haematology.
	Tuberculosis (pulmonary)	3 (minimum) early morning sputum samples.Pleural fluid (if present) for AAFB and culture. Treat specimen as High Risk.	Sample should be taken before starting anti-tuberculosis therapy.
	Tuberculosis (non-pulmonary)	Lymph node and other biopsy for culture in a sterile container with no fixative.	Sample for histology should be sent separately.
	Tuberculosis (urinary)	3 ( minimum) early morning urine samples for AAFB and culture.
	Typhoid	See under Enteric Fever.
	Vincent's Angina	Throat swab or swab from inflamed gum margins.
	Visceral Larva Migrans	Clotted blood.	Requests should be made for tests for filariasis, strongyloidiasis and toxocariasis.
	Whooping Cough	Pernasal swab plated at bedside.Refer to Pernasal/ Nasopharyngeal Swab.	Please inform the laboratory to have BMS attend ward. Cough plates have no value in diagnosing whooping cough.
	Worms	Faeces for ova, cysts & parasites. Whole worm or segment of tapeworm can be sent to laboratory for identification. Refer to Worm.
	Yersinia enterocolitica	Faecal sample. Clotted blood for serology.
IFAT Immunofluorescent Antibody Technique, CSF Cerebrospinal Fluid, RSV Respiratory Syncytial Virus, ELISA Enzyme-Linked Immunosorbent Assay.

Back to Top

Virology

The Regional Virus Reference Laboratory is based at the Royal Hospitals Trust in Belfast. Out of hours service is available for agreed emergency testing in Virology. Contact the switchboard at the Royal Hospitals Trust telephone 02890-240503 who will make contact with the virology BMS on call.

Request forms

The following data must be legibly recorded on a microbiology (serology) request form; specimens should be clearly labelled and dated.

1. Date of onset of illness.

2. Provisional clinical diagnosis or any relevant information.

3. Examination requested.

It is a waste of time to send specimens from a patient with an obscure illness weeks or months after the onset, in the expectation that the Regional Virus Laboratory will examine them for all known viruses. Requests such as "viral screening", "routine virology" or "viral studies" without accompanying clinical information should be avoided.

The following test profiles (screen) may be requested i.e. Arthralgia screen, Atypical pneumonia screen, CNS screen, Gastroenteritis screen (faeces), Hepatitis screen, Intra-uterine infection screen, Mononucleosis screen and Exanthem screen.

Back to Top

Procedures used for diagnosing viral illnesses

Serological tests

Serological tests are routinely available for diagnosing the following viral infections:

and the following agents: Q fever (Coxiella burnetii), Mycoplasma pneumoniae, Chlamydia group (Chlamydia pneumoniae, Chlamydia psittacci and Chlamydia trachomatis).

† † IgM Assay. IgM normally will become positive 5 days into the clinical illness, with IgG changes some days later.

Collection of Sample

Transport

All blood samples may be sent to the laboratory at ambient temperatures. Blood samples from known or suspected HIV, hepatatis B or hepatitis C should be placed in leak proof approved containers and sealed in a plastic bag with a hazard warning sticker, "Danger of Infection - Take Special Care". The request form should be outside the container in an extra pocket of the plastic bag.

Interpretation of serology results

It is often necessary to show a 4 fold or greater rise in antibody titre or viral specific IgM to make a definite diagnosis of recent infection. Viral specific IgM tests may be done on single acute samples of serum but such tests are not available for all virus infections. In babies during the first year of life it may be necessary to take the convalescent serum 4 weeks or more after the acute phase serum in order to show a rise in antibody.

Isolation or identification of virus

Viruses can be grown or viral antigen detected from many viral infections. In addition
Herpes simplex 1 + 2, Enterovirus, Parvovirus B19, Cytomegalovirus, Varicella zoster virus,Small Round Structured Virus(SRSV), Chlamydia trachomatis, C. pneumoniae and C. psittaci can be demonstrated in clinical material by Polymerase Chain Reaction(PCR). Requests for PCR should be telephoned to the laboratory and discussed as these assays are not presently routinely available.

Transport of virus containing material

All viruses should be regarded as labile and specimens (including post-mortem material) should reach the Virus Laboratory with the least possible delay. If the time elapsing between the collection of the specimens and delivery at the Virus Laboratory is greater than 2 hours then the specimen should be stored at 4°C and transported with ice water in an insulated container such as a wide necked vacuum flask or polystyrene box. In respiratory virus infections and in gastroenteritis it is important that the specimens are not frozen. The optimum time for collecting specimens for virus isolation is as early as possible in the course of the illness.

Collection of specimen for virus

Faeces: Specimens should be collected free from urine and antiseptics. The first sample should be obtained, on the day of admission to hospital if possible and two further specimens collected during the next two days. Each sample should fill about one third of a sterile universal container. Preserving fluids or transport medium must not be added.

CSF: Ideally at least 0.5 ml in a sterile bottle.

Pleural or pericardial fluid: These should be sent in sterile bottles.

Throat swabs or other swabs: Most viruses are inactivated by drying so all swabs require liquid transport medium. The viral transport medium is obtained from the Regional Virus Laboratory (stock is kept in hospital microbiology laboratories) and is stored at 4°C. After swabbing the affected site the swab, on a wooden or plastic stick is placed in a bijou (5 ml) bottle containing viral transport medium and broken off level with the bottle top and the lid replaced.

Vesicle fluid or scabs: Vesicle fluid may be aspirated with a tuberculin syringe. The aspirated fluid may be sent in a sterile bijou (5 ml) bottle in a small quantity of viral transport medium. Scrape the lesion base and send the swabs in a dry sterile bottle.

Post-mortem or biopsy specimens: Each organ specimen should be placed in a separate sterile labelled container. Formalin or other fixative must not be added. Specimens should be taken from the main system affected, as well as faeces and blood clot. Tissue specimens collected at post-mortem should be taken aseptically and in a planned order to avoid contamination by the gastrointestinal tract separate sterile instruments should be used for each organ. Success in virus isolation is most likely in cases in which the illness has been short in duration and the post-mortem has been carried out shortly after death. Relevant clinical information must be included for the laboratory to undertake the appropriate investigations.

Electron microscopy

The group of viruses causing human gastroenteritis identified by electron microscopy of faeces are rotaviruses, adenoviruses, astroviruses, caliciviruses, small round viruses, noroviruses (formerly small round structured viruses (SRSV), reoviruses, parvoviruses, coronaviruses and toroviruses. The other group of human skin viruses which can be identified by electron microscopy are; Vaccinia, cowpox and molluscum contagiosum, orf and paravaccinia, herpes simplex and varicella zoster.

Collection of specimens for electronmicroscopy

Vesicular lesions: The base of the vesicle should be gently scraped with a disposable scalpel blade and the small amount of fluid adhering to the blade is wiped on the centre of a clean glass slide, and air dried. It should not be heat fixed or fixed in any other way. Scabs or biopsy material should be sent unfixed in a sterile dry bottle.

Suspected orf or paravaccinia infection: The granulation tissue underlying the skin should be scraped with a disposable scalpel blade and the material transferred to a clean slide and air dried without fixation. The scab should also be sent.

Post-mortem tissue: Send fresh or rapidly frozen tissue.

Back to Top

Test Profiles For Virology

Gastrointestinal