Medical Microbiology – Specimen Collection

If you are a patient and have been asked to collect a specimen of urine or faeces by a health professional, please use the following links for guidance:(1) Urine (MSU) specimen collection.
(2) Faeces (stool) specimen collection
Use the links below to find information on the recommended way to collect specimens for sending to the microbiology laboratory at the North Devon District Hospital.

Blood Cultures
Blood for Antimicrobial assay
Chlamydia Examination
CSF and operative specimens
Eye Swabs
High Vaginal, Cervical and Urethral Swabs
HSV Investigation (Viral Swab)
Intravascular line tips
MRSA screen
Nose Swabs
Pernasal swabs for pertussis
Respiratory Samples for Flu A/B and RSV
Seminal analysis
Skin scrapings, hair and nail clippings
Throat Swabs
Wound swabs and Pus swabs

Syndromic Requesting

Appropriate Swabs/Containers/Transport media and Their use(s)


For routine culture and sensitivity testing, use the white top sterile universal bottle – this should be sent to the laboratory as soon as possible. The minimum volume required is 1ml.

For CMV test use a plain sterile universal container and send or take to the laboratory immediately accompanied by a completed blue and white Microbiology request form.

Use a plain universal for Legionella and pneumococcal antigen.

Contaminating bacteria from the external genitalia may give rise to misleading results. Therefore we can only accept the following specimens for routine culture:

  • Catheter or cystoscopy specimens
  • Mid-stream urine specimens
  • Supra-pubic aspirates

Please note that urinary catheter tips will not be processed as they do not provide helpful microbiological information.

Mid-stream specimens are collected as follows:


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

  • Separate the labia and with cotton wool or a sponge moistened with water, wipe the vulva from the front to the back. Disinfectant MUST NOT be used.
  • With the labia still separated allow some urine to pass into the toilet, then, without stopping, allow urine to pass into a sterile borate container and fill to the line.
  • Pass the remaining urine into the toilet.


Clean the glans penis with soap and water. Commence micturition, and when a few millilitres of urine have been passed introduce a sterile borate container into the stream and fill the container to the line.

In elderly or very ill patients nursing assistance may be required.

Send to the laboratory. The specimen can be preserved in a refrigerator at 4°C prior to transport.

Specimens showing signs of contamination, e.g. with faecal material, are of no value and will not be cultured.

Investigation for Chlamydia from male urine specimens (see under examination for chlamydia).

The majority of urine results will be available the following day.

Collection of Catheter Specimens of Urines (CSUs)

The specimen should not be collected from the drainage bag, only from the sampling port. Clean the sampling port with an alcoholic 2% chlorhexidine swab. Insert the syringe into the sampling port and aspirate urine. Transfer 15ml urine to a red topped sterile boric acid bottle.

Urine for culture for Mycobacterium tuberculosis (TB)

Culture for Mycobacterium tuberculosis is only performed when white cells are present in the urine. Submit a MSU specimen in a red-topped boric acid container (GPs) or plain, white topped container (hospital users), indicating that Mycobacterium tuberculosis culture is required. This will be examined as a normal MSU. If white cells are present, 3 x 250ml urine containers should be ordered (using the Pathology Supplies order Form) so that three consecutive early morning specimens can be collected for examination for TB. If there are no white cells present in the MSU, Mycobacterium tuberculosis culture is not indicated.

Urine for microscopy for Schistosomiasis

Collect a urine specimen in a plain (non-boric acid) container. This should be collected between 10:00 and 14:00 hrs, as this is when the highest concentration of eggs is found.

In patients with haematuria, eggs may be found trapped in the blood and mucus in the terminal portion of the urine specimen. It is therefore preferable to obtain a complete urine sample collected between 10am – 2pm. Alternatively, submit terminal stream urines collected over a whole 24 hour period. (24hr urine containers (brown container/yellow top) are available from Pathology stores.

If the urine cannot be examined within an hour of collection, it is advisable to add 1ml of undiluted formalin to preserve any eggs that may be present.

Collection of High Vaginal, Cervical and Urethral Swabs

Very little information can be expected from swabs which are contaminated with material from the lower vagina. Swabs should be taken using a speculum under direct vision where possible. Transport medium must always be used.

Examination for Gonococci
High vaginal swabs are not useful; an endocervical swab MUST be sent if GC is to be excluded.

Chlamydia Examination

Click here for specimen collection guides


NB. Take specimens for bacteriology first.

A clinician collected or self-taken vaginal swab is the specimen of choice for diagnosing Chlamydia trachomatis. (Vaginal swab specimens are as sensitive and specific as cervical swabs). Cervical samples are acceptable when pelvic examinations are done, but vaginal swab specimens are an appropriate sample type even when a full pelvic examination is being performed.

A vaginal swab specimen has a higher sensitivity than a urine sample.

White cells and blood can produce either an invalid or false negative result therefore:

  • Do NOT collect specimens from patients that are menstruating.
  • If taking an endocervical swab, first remove any excess mucus/pus from the endocervix with a separate swab prior to taking the sample. (Discard the cleaning swab).


Urine is the preferred sample type for for diagnosing Chlamydia trachomatis in men.

The patient should not have urinated for at least one hour. Collect approximately 10-20ml of first voided urine into a sterile white capped universal container.

NB. Male urethral swabs are no longer available.

Lymphogranuloma venereum (LGV): In order to diagnose LGV, different samples from those listed may be indicated; please discuss with Consultant Medical Microbiologist.

Eye swabs

NB. Do not use fluorescein as this can interfere with the test.

  1. Apply a local anaesthetic.
  2. Prior to collecting the specimen, remove any excess exudate using suitable material such as a swab. (Discard the swab/cleaning material).
  3. Using a swab from a female PCR sample kit, firmly swab the inner surface of the upper and lower eyelids to collect epithelial cells. Do NOT pre-moisten the swab in the transport medium.
  4. Place swab in sample tube, snap off at the score line and replace cap.

HSV Speicmen Collection (Viral Swab)

  • Proper specimen collection from the patient is extremely critical for optimal results.
  • Specimens for HSV 1 and 2 testing should be collected in the acute stage of the disease whenever possible, preferably within 3 days and less than 7 days after onset of illness (eruption of lesions).

Specimens should be collected as follows:

A) Vesicles present (clear fluid-filled blister)

  1. Wash/wipe the surface of the lesion with sterile saline.
  2. Carefully uncap (disrupt) the vesicle with a Flock swab (preferred), needle or scalpel and collect the fluid with the FLOQSwab.
  3. With the same FLOQSwab, vigorously rub the base of the vesicle to collect cells at the base of the lesion.
  4. Transfer the swab to its MSwab transport tube. Leverage the swab shaft against the edge of the tube to break at pre-scored point.
  5. Close the cap firmly while ensuring that the upper end of the swab shaft is in the centre of the cap.

B) Vesicles absent (ruptured, weeping vesicle or crusted ulcer)

  1. If crust absent (ruptured and/or weeping vesicle):-
    1. Using a dry FLOQSwab or one pre-moistened with two drops of sterile physiological saline, collect cells by vigorously rubbing the base of the lesion.
    2. Transfer swab to the MSwab transport tube. Leverage the swab shaft against the edge of the tube to break at pre-scored point.
    3. Close the cap firmly while ensuring that the upper end of the swab shaft is in the centre of the cap.
  1. If there is crust on the lesion (crusted ulcer):-
    1. Gently remove crust using a FLOQSwab pre-moistened with sterile saline.
    2. Collect specimen by vigorously rubbing the base of the lesion.
    3. Alternatively, gently abrade the lesion with a sterile scalpel or needle until serous fluid emerges (avoid bleeding) and collect the sample with a pre-moistened FLOQSwab by vigorously rubbing the base of the vesicle.
    4. Transfer swab sample to MSwab transport tube. Leverage the swab shaft against the edge of the tube to break at pre-scored point.
  • Ensure the sample is correctly labeled and that the specimen form is completed fully.
  • Send to the laboratory in a plastic specimen bag as soon as possible.

Collection of Faeces

Faeces are essential for all enteric examinations. Specimens in toilet paper, nappies, margarine tubs, etc., or rectal swabs are not acceptable. Please state if the patient has been abroad, or is on antimicrobial therapy as the range of tests set up will be determined by the clinical information provided. Also state if the patient is a food handler.

  • Do not mix urine with the stool sample; patient should be encouraged to urinate first.
  • Place a wide mouth container (potty, empty plastic food container (e.g 1 litre ice cream carton) in the bowl, or put clean newspaper or plastic wrap over the toilet seat bowl (to prevent the specimen from falling into the toilet bowl).
  • Pass the stool onto the potty, plastic container, newspaper or plastic wrap.
  • Using a spatula, half-fill a faeces container. Do not fill more than a third full if the specimen is liquid. (Minimum sample volume is approx. 2ml).
  • Flush the remainder of the stool sample down the toilet.

Formed stool samples and repeat samples from inpatients are not routinely examined.

Fluid and / unformed stool samples are routinely examined for the following:

  • Salmonella spp.
  • Shigella spp.
  • Campylobacter spp.
  • E. Coli 0157 – cause of haemorrhagic colitis/Haemolytic Uraemic Syndrome ( HUS )
  • Norovirus

The above list is not exclusive: other pathogens such as Yersinia and Cryptosporidium oocysts may be looked for depending on clinical details.

Foreign Travel

If there is an appropriate history of foreign travel, culture for Vibrio (including V. cholerae and V. parahaemolyticus) will be performed.

A concentrate for ova, cysts and parasites will also be performed where there is history of foreign travel to Central or South America, Africa or Asia.

Clostridium difficile

Testing for C. difficile toxin is performed daily; on weekdays on specimens received before 15:00hrs, on weekends and Bank Holidays – on specimens received before 10:00hrs. Specimens received after these times will be tested the following day.

C. difficile testing: samples should be refrigerated unless they are tested within 2 hours of collection.

C. difficile will be tested on fluid/mucoid/ bloodstained stools from inpatients and community patients >2 yrs old.

C. difficile will not be tested:

  • On non- fluid stools
  • On patients <2 years old
  • If two samples have been sent in the previous 10 days
  • If positive within the last 28 days; if still symptomatic, discuss with the Consultant Medical Microbiologist

Samples tested early in a C difficile infection may test as toxin negative. If symptoms continue, and C. difficile remains a clinical possibility, please repeat after 48 hours.

Rotavirus & Adenovirus

Rotavirus and Adenovirus testing is routinely performed on all stools from Caroline Thorpe, and fluid stools from in patients, those in nursing homes, and food handlers.

Investigations for Ova, Cysts & Parasites

A concentrate for ova, cysts and parasites is performed routinely on the following stool samples:

  • Patients with persistent / intermittent GI symptoms for > 2 weeks.
  • Patients with eosinophilia
  • Patients who have returned from Central / South America, Africa or Asia.
  • Query worms seen in sample.

In other circumstances, please request on form and provide appropriate clinical details.

Helicobacter pylori Testing

This is a stool antigen test which is currently performed daily and confirmation tests are done weekly. It is a non-invasive enzyme immunoassay (EIA) test that has shown high sensitivity and specificity and the ability to confirm eradication. It detects the presence of H pylori and cannot be performed within 2 weeks of taking a PPI (Protein Pump Inhibitor) or within 4 weeks of antibiotics as both these suppress bacteria and can cause false negatives. A pea sized stool is required in a universal container.

Details of when to test and how to treat H pylori infection are provided by Public Health England in the link below:

·     PHE H. pylori in dyspepsia: test and treat

Sellotape slides

“Sellotape” slides are used in the diagnosis of threadworm and the procedure should be carried out first thing in the morning. The laboratory provides a glass slide and transport container. Cut a 4″ strip of sellotape, press the sticky middle 1-2″ firmly against the perianal skin. Stick the sellotape on to the microscope slide lengthways, tucking the ends over. The slide should then be labelled and placed in the plastic slide container and sent to the laboratory with a completed microbiology form in a plastic transport bag.

Collection of Sputum Samples

Send the specimen in a wide-mouthed container. The best specimens are those produced early in the morning from a deep cough, before the patient drinks, eats or cleans their teeth. Specimens which are more than 48 hrs old will not be processed. (Minimum sample volume is approx 1ml).

If sputum is to be examined for M tuberculosis, three separate specimens should be sent on consecutive days – ideally the first specimen of the day. For the diagnosis of Pneumocystis carinii pneumonia (PCP), induced sputum or bronchoalveolar lavage is more reliable. Please discuss with Consultant Medical Microbiologist. Sputum specimens must be sent in separate bags.

If Legionella or Pneumococcal antigen is to be excluded, please send a urine sample in either a plain universal or boric acid container.

Collection of Throat Swabs

Take these with the aid of a good light and tongue depressor. Use transport medium and send as soon as possible. Appropriate clinical details will allow the laboratory to apply culture for the relevant organism(s) (e.g Neisseria meningitidis)

Collection of Nose Swabs

Swabs for the isolation of Staphylococcus aureus and other pathogens should be taken from both anterior nares and nasal septum with a swab which has been premoistened with the transport medium.

Collections of Pernasal swabs for pertussis

Ordinary swabs in transport medium are not suitable. Special fine flexible wire-mounted post nasal swabs are available from the laboratory together with the necessary special transport medium. The yield of B. pertussis is increased by taking a postnasal swab.

Wound swabs and Pus swabs

If there is any volume of pus present it should be collected with a syringe into a sterile universal container rather than on to 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 must always be used for swabs. Pus is always preferable to a wound swab, and essential if M. tuberculosis is to be identified. There is a better yield from wound swabs if the swab is premoistened with transport medium before it is taken.

Eye Swabs

All conjunctival swabs should be sent in transport medium. Apply a local anaesthetic.
In neonates a sample should also be taken for examination for Chlamydia. (See separate section on examination for Chlamydia).

All conjunctival swabs should be sent in transport medium. Apply a local anaesthetic.

MRSA screening (Methicillin Resistant Staphylococcus Aureus)

A screen comprises a series of swabs (pre-moistened in sterile saline) from:

  • Axilla
  • Nose
  • Throat
  • Groin / Perineum
  • Any wounds / i.v. sites
  • Any skin lesions / eczema etc / leg ulcer swab

A catheter specimen of urine should also be sent if appropriate.

Screening swabs from inpatients are generally inoculated at ward level into salt broths using wooden shafted cotton tipped swabs. The salt broth must be clearly labelled with the patients details. Click here for instructions for wards on “MRSA Screening Using Salt Broths.”

MRSA screening swabs may also be sent in routine transwabs (black) media.

Only one request form needs to be sent per patient.


Collection of skin scrapings, hair and nail clippings for the diagnosis of superficial fungal infections

Material should be sent in a DERMAPAK kit available from the laboratory, in which full instructions are given. The pack is not sterile, so bacterial culture is not appropriate from the same specimen.

Material from skin lesions is collected by gently scraping off material from the outer edges of the lesion, usually with the edge of a glass microscope slide or a scalpel blade. The edge is most likely to contain viable fungus.

Scalp scrapings are obtained as above but should include hair stubs. Hairs may be plucked from the scalp with forceps, but cut hairs are unsatisfactory as infection is usually below the surface near the scalp. The material should be transported to the laboratory as for skin scrapings.

Clippings should be taken from the discoloured or brittle parts of the nail and cut back as far as possible from the free edge as some fungi are restricted to the lower parts. Scrapings can also be taken from under the nail to supplement the clippings. Nail clippings often fail to grow fungi even if present. Whole nails can be sent to the Laboratory in a sterile Universal container.

Collection of Blood Cultures

Click here for Blood Culture Collection poster.

The Bactec system used at North Devon District Hospital allows automatic monitoring of the blood cultures. All blood culture bottles are continuously monitored over a 5 day period (7 days for those with clinical details of infective endocarditis) and positive results are relayed to the appropriate requester as soon as identified. An interim negative report is sent after 32 hours incubation, but bottles will continue to be monitored until 5 days have passed.

Number and Timing of Samples

Only take blood for culture when there is a clinical need to do so and not as routine

  • Generally, two sets of blood cultures are preferred. This increases detection of pathogens and helps distinguish contaminants.
  • If infective endocarditis is considered, please send a TOTAL of 3 sets of blood cultures initially and discuss with a Consultant Medical Microbiologist. These should be taken via different venepuncture sites.
  • The timing of blood cultures does not need to coincide with spikes in temperature as the likelihood of a positive blood culture is not related to peaks of fever.

Previous antimicrobial therapy

  • Ideally, blood cultures should be taken prior to antimicrobial treatment. When a patient is already receiving antimicrobials, blood cultures should be taken immediately before the next dose, with the exception of paediatric patients.

Blood volume

  • Blood culture volume is the most significant factor affecting the detection of organisms in bloodstream infection.  False negatives may occur if inadequate blood culture volumes are submitted.
  • The adult blood culture set consists of two bottles, one with a grey flip-off cap and label and the other with a purple flip-off cap and label. Optimum blood draw is 8-10ml in each bottle.
  • A paediatric bottle with pink flip-off cap and label is available with an optimum blood draw of 1-3 ml. If only a small amount of blood can be obtained, such as in those with difficult venous access, it would be appropriate to use a paediatric bottle.

Kit preparation

  • Prior to use, each vial should be checked for damage and evidence of contamination such as cloudiness, leakage, bulging or indented septum. DO NOT USE any vial showing signs of damage or contamination.
  • Label bottles with surname, forename, date of birth and NHS or hospital number in space on bottles provided.
  • If using printed labels, ensure they do not cover the removable bottle barcodes; please do not remove bottle barcode labels.
  • For ease of volume control, mark the fill level on the side of the bottle prior to blood collection.
  • Remove flip-off caps from bottles and swab the tops with a 2% chlorhexidine in 70% isopropyl alcohol swab (if not available, use alcohol swab – iodine is not recommended) and allow to dry.

Skin preparation

  • Wash your hands with soap & water or use alcohol hand rub.
  • Clean any visibly soiled skin on the patient with soap & water and then dry.
  • Apply a tourniquet and palpate to identify vein.
  • Clean skin with a 2% chlorhexidine in 70% isopropyl alcohol impregnated swab (if not available, use an alcohol swab) and allow to dry.

If a culture is being collected from a central venous catheter, disinfect the access port with a 2% chlorhexidine in 70% isopropyl alcohol impregnated swab and allow to dry (if not available, use alcohol swab).

Sample collection – winged blood collection (preferred method)

It is IMPORTANT to use the correct kit if this method is used  i.e. a BD Vacutainer® Push Button Blood Collection Set with Pre-Attached Holder.

It is IMPORTANT that the bottle being inoculated is held at a position below the patient’s arm with the bottle in an upright position (stopper uppermost). This will prevent any potential back flow of media from the blood culture bottle. Monitor the draw process closely at all times during collection to assure proper flow is obtained and to avoid flow of the bottle contents into the adapter tubing.

Due to the presence of chemical additives in the culture bottle, it is important to prevent possible back flow and subsequent adverse reactions.

1. Wash and dry your hands again or use alcohol hand rub and apply clean examination gloves (sterile gloves are not necessary).

2. Attach winged blood collection set to blood collection adapter cap.

3. Insert needle into prepared site. Do not palpate again after cleaning.

4. If blood is being collected for other tests, always collect the blood culture first.

5. Place adapter cap over the vial and pierce the septum. Hold the bottle upright and use the 5 ml graduation marks on the side of the vial to monitor the volume collected.

Adult Set: Starting with the blue capped (aerobic) bottle, inoculate  8-10 ml of blood into each bottle. It is essential that bottles are not overfilled; use the 5 ml graduation marks on the side of the vial to monitor the volume collected.

Paediatric Bottle: Inoculate 1-3 ml of blood into the bottle.

6. When the desired volume has been drawn, other blood samples can then be collected as required.

7. Remove the tubing set from the vial.

8. After collection and while the needle is still in the vein, place gauze pad or cotton ball on the venepuncture site allowing it to cover the front barrel of the winged push-button device. Grasp the body of the device with the thumb and middle finger and activate the push button with the tip of the index finger to withdraw the needle from the patient.

9. To ensure complete and immediate retraction of device, make sure to keep fingers and hands away from the end of the blood collection set during retraction. Do not impede retraction. Make sure that the needle is fully retracted and is in the shielded position.

10. Apply pressure to the venepuncture site.

11. Cover the puncture site with an appropriate dressing.

12. Discard winged blood collection set in a sharps container.

13. Wash hands after removing gloves.

Sample collection – Needle and syringe method

1. Wash & dry your hands again or use alcohol hand rub and apply clean examination gloves (sterile gloves are not necessary).

2. Insert needle. Do not palpate again after cleaning.

3. Collect 16 – 20 ml of blood (1-3 ml for paediatric bottle) and release tourniquet.

4. Cover the puncture site with an appropriate dressing.

5. If blood is being collected for other tests, always inoculate the blood cultures first.

Adult Set: Inoculate 8-10 ml of blood into each bottle starting with the purple capped bottle (anaerobic): do not change the needle between sample collection & inoculation. It is essential that bottles are not overfilled; use the 5 ml graduation marks on the side of the vial to monitor the volume collected.

Paediatric Bottle: Inoculate 1-3 ml of blood into the bottle.

6. Discard needle and syringe in a sharps container.

7. Wash hands after removing gloves.

Record procedure and send samples to laboratory

  • Record the procedure with indication for culture, time, site of venepuncture and any complications in the patient’s record.
  • Ensure the bottles are correctly labelled and that the specimen form is completed fully, including the name and designation of the person who took the sample printed on the form.
  • Send to the laboratory in a plastic specimen bag as soon as possible. (Samples received out of hours are loaded onto a satellite blood culture analyser within Pathology Specimen Reception by Laboratory on-call staff).
  • Please note – Samples must not be refrigerated.


Collection of Intravascular line tips

The skin in the region of the intravascular catheter should be cleaned with alcohol and the catheter withdrawn with sterile forceps. The terminal 5 cm of the catheter tip should be cut off with sterile scissors and placed in a dry sterile container to transport to the laboratory in a labelled container. If the line has been used in total parenteral nutrition please indicate on request form.

Collection of blood for Antimicrobial assay

Gentamicin and Vancomycin assays:
These are now performed by the Biochemistry department.

Other assays:
Other assays such as Tobramycin and Amikacin levels are sent to a reference laboratory for testing. Please contact a Consultant Medical Microbiologist for advice. 3.5ml of clotted blood – gold top – is required (minimum 1ml).

Collection of Cerebrospinal fluid (CSF) and operative specimens

Some specimens are collected by invasive procedures, e.g. lumbar puncture, bone marrow aspiration, bronchoscopy, or at operation under general anaesthetic. Such specimens tend to be non-repeatable and from normally sterile sites, hence results of culture or microscopy are of special importance. Please ensure all specimens are labelled appropriately and accompanied with an appropriately completed request form with full clinical details. Notify the laboratory of their impending arrival.

With the exception of the following, samples should be sent to the laboratory in a sterile 30ml universal container:

Cerebrospinal fluid samples
Three samples clearly numbered 1, 2 and 3 should be sent to the Microbiology laboratory in sterile 30ml universal containers.
Click here for specimen collection requirements for biochemical analysis (total protein/glucose/sub-visible xanthochomia)

Tissue samples
Individually wrapped sterile 30ml or 60ml containers are available on request from the Pathology stores.
Alternatively, tissue samples taken in theatre can be directly inoculated into cooked meat broths available on request from the Microbiology laboratory.

Ascitic fluid samples
Samples should be sent to the laboratory in a set of blood culture bottles and a sterile 30ml universal container for a Gram film and cell count.

Corneal scrape
Contact the Microbiology laboratory who will then arrange for a member of staff to attend the clinic with the appropriate culture media and slides for direct inoculation of the sample.

Collection of Respiratory Samples for Flu A/B and RSV for Testing Using PCR

Nasal Swab

  • 1 dry sterile swab plus viral transport medium (Copan MSwab blue-top tube and swab)

1. Tilt patient’s head back 70 degrees.

2. While gently rotating the swab, insert swab less than one inch into nostril (until resistance is met at turbinates).

3. Rotate the swab several times against nasal wall and repeat in other nostril using the same swab.

4. Place tip of the swab into sterile viral transport media tube and cut off the applicator stick.


It is very important to give full clinical details, including any recent exposure, travel history and onset date so that the correct tests are selected. It is not helpful to request simply “Serology” or “Virology”. The more information that is provided, the more useful the results will be.

Failure to provide relevant clinical information may introduce an unnecessary delay since such samples will be stored pending relevant clinical information.

Where there is difficulty in selecting the appropriate investigations, it is always best to discuss with a Consultant Medical Microbiologist.


  • In general, 3.5ml of clotted blood (gold top) is required (minimum 1ml per test). Paediatric samples can be sent in a brown-capped 1.1ml microtube. Ideally a baseline specimen is collected at the start of illness for comparison with a convalescent specimen collected 10 days later to demonstrate a rising titre. Date of onset is vitally important since a “convalescent” specimen alone may provide a spurious “significant” / “diagnostic” titre.
  • Most PCR tests (e.g. to diagnose meningococcal infections, CMV, or HIV viral load etc.) require a 3.5ml EDTA (purple top) specimen instead. Paediatric samples can be sent in a purple-capped 1.1ml microtube. If in doubt, contact the Microbiology department.

Antenatal bloods for screening of infectious diseases in pregnancy are tested in house for HIV, Hepatitis B and Syphilis serology. All other serology specimens are referred to reference laboratories for testing.

Basic “Atypical Respiratory” screen

Includes Psittacosis / Q-Fever / Mycoplasma / Influenza A + B and Metapneumovirus.
Note that Legionella serology is no longer available; a urine sample for Legionella antigen is the preferred diagnostic specimen.

Basic “PUO” screen

Best discussed with a Consultant Medical Microbiologist. In cases where bacterial infection is suspected, a CRP level may be helpful, since viral infections have little effect on CRP.

Tropical “PUO” screen

In cases of suspected “tropical” infections, it is always worthwhile discussing the case with a Consultant Medical Microbiologist, who can expedite pertinent serology and other investigations that can be tailored to the organism suspected.


Many other serological tests are available – if in doubt, contact a Consultant Medical Microbiologist for advice.

TB Gamma Interferon Testing (Quantiferon – TB Gold)

Requests for gamma interferon testing for TB immunity will be via a Consultant Medical Microbiologist only unless requested by Rheumatology or Dermatology outpatient departments.

The TB gold blood collection kit is a single patient pack issued only by the Microbiology laboratory and contains four blood collection tubes, a 21G needle, a safety tube holder and an instruction sheet.

Please notify the Microbiology department prior to sending TB-Gold samples to the laboratory as there are strict incubation times that must be adhered to.

Procedure for taking Quantiferon TB Gold specimens

  • Ensure that tubes are at room temperature (17-25oC) before filling.
  • For each patient collect 1ml of blood by venepuncture directly into each of the 3 Quantiferon collection tubes.
    Note 1. As the 1ml tubes draw blood relatively slowly, keep the tube on the needle for 2-3 seconds once the tube appears to have completed filling to ensure the correct volume is drawn.
    Note 2. The black mark on the side of the tubes indicates the 1ml fill volume. This method has been validated for volumes ranging from 0.8 to 1.2ml. If the level of blood in any tube is not close to the indicator line, it is recommended to repeat the test.
  • If a ‘butterfly needle’ is being used to collect blood, a purge tube should be used to ensure that the tubing is filled with blood prior to the Quantiferon TB tubes being used.
  • Immediately after filling tubes, shake them 10 times just firmly enough to ensure the entire inner surface of the tube is coated with blood.   NB. Over-energetic shaking may cause gel disruption and could lead to aberrant results.
  • Label the tubes appropriately and complete a Microbiology request form.
  • The tubes and request form must be sent to the Microbiology laboratory within 16 hours of collection. Do not refrigerate or freeze the blood samples.

Seminal Analysis

Please note:
There are specific times when semen specimens are accepted by the laboratory. For all types of semen sample an appointment is necessary. Please click the link below for full details.

Click here for instructions on when and how to obtain a semen sample and when appointments are necessary.

In cases of persistent non-motile sperm, the referring clinician should advise the individual regarding the cessation of other contraceptive precautions. Further fresh samples should be examined and these must reach the laboratory within one hour.

Vasectomy Reversals
These will be treated as a fertility semen analysis unless otherwise indicated on the request form.
Specimens should be received in the laboratory within 1 hour of the sample being produced for fertility analysis and 4 hours for post vasectomy samples.

Semen Analysis Specimen Collection Kit
Specimen collection kits for semen analysis (post vasectomy and infertility investigations) are available on request from Pathology stores Tel: (01271) 322342.

The sample collection kit includes the following: –
∙ Cytotoxicity tested specimen container (60ml, white top, wide mouth Sterilin container).
∙ Microbiology request form
∙ Instruction sheet
∙ Specimen bag

Reporting Semen Analysis Results

There are new reference ranges for all the fertility parameters which incorporate a pathological, borderline and normal range. These are ESHRE guidelines and replace the ranges outlined by WHO 2010 manual.  These references ranges are physically too large to be incorporated in their entirety as part of our lab reports, so we only report the ‘Normal’ ranges and have included the full reference range table below:

Table of normal range for semen infertility results (ESHRE guidelines)1
Total sperm count<2020-79>=80106/ejaculate
Motility (motile)<4040-59>=60%
Motility (rapid)<3535-49>=50%
Morphology typical forms by Strict criteria<44-13>14%
TZI (Tetrazoospermic index)>1.81.61-1.8<=1.60
  1. Human Reproduction, Vol.26, No.12 pp. 3207–3212, C.L.R. Barratt, Bjorndahl, R. Menkveld, and D. Mortimer 2011 ESHRE Special Interest Group for Andrology Basic semen analysis course:a continued focus on Accuracy, Quality,Efficiency and Clinical relevance

Syndromic Requesting for Infections

Syndromic requesting is available for primary care users. This can be useful when deciding which tests to request for a particular syndrome group, e.g. hepatitis, inoculation injury sexual health and fertility. By selecting a syndrome group you can then select a specific syndrome that best describes your patient, this in turn shows you the correct tests to request in the GP Ordercoms system.

Syndromic requesting will be available for hospital clinicians and their teams as part of the Electronic Healthcare Record system implementation. Until this is completed, if you can’t find the information on which tests to request for suspected infections on this page, please contact the laboratory using the Contact Us page.


Appropriate swabs/containers/transport media and their use(s)




General microbiology
Swab for routine culture

Black capped transwab

Clear plastic packet containing swab on plastic shaft and plastic tube with black transport medium.

Ear swabs & Male urethral swabs for routine culture

Orange capped transwab

Clear plastic packet containing fine swab on wire shaft and plastic tube with black transport medium.

Culture for pertussis

Pale blue capped transwab

Clear plastic packet containing fine swab on wire shaft with plastic tube with black transport medium.



  • Vaginal swab (self taken or clinician collected)
  • Cervical swab

Cobas PCR media uni swab sample packet; clear plastic sleeve containing 1 swab & a yellow capped PCR media tube.

Eye swabs: (Use Cobas PCR female swab)

As above

Men: 10-20ml first voided urine in plain universal container

30ml clear plastic universal container with white cap

CSF, pus , fluids & aspirates

Plain universal container

30ml clear plastic container with white cap

Tissue Samples


Plain universal container

30ml clear plastic container with white cap

For large tissue samples use a 60ml sterile container as for stool / sputum samples.

NB. For tissue samples taken in theatre, individually wrapped 30ml and 60ml containers are available from the Pathology store. Alternatively, directly inoculate the tissue sample into a cooked meat broth (available from the Microbiology department).

Stools / Sputum

60 ml sterile container

Wide necked clear plastic container with yellow cap


Routine culture

Plain universal container

White capped universal container- fill to line (minimum volume is 1 ml)

Culture for TB

(Only undertaken if white cells are seen in a MSU sample)

Boric acid (red top) container (GPs)

Plain (white top) NDHT staff

If TB culture is indicated, (white cells identified in MSU) please order 3 x 250ml metal capped containers using the Pathology Supplies Order Form.

Blood cultures


Standard set 

One BD Bactec Plus Aerobic/F (grey cap) bottle containing 40ml of clear colourless broth and latex beads.
One BD Bactec Lytic/10 Anaerobic/F bottle (purple cap) containing 40ml of clear yellow broth.


Paediatric bottle

Single BD Bactec Peds Plus/F bottle with a pink cap containing 40ml of clear colourless broth and latex beads.

Blood culture for TB

One BD Bactec bottle

White capped bottle with narrow neck containing 40ml of clear broth. Contact laboratory for issue.

Serology tests and antibiotic assays

Clotted blood sample (Min. Volume 3.5ml)

Vacutainer with yellow cap

PCR & viral loads including: –
HIV viral load
HIV genotyping
Hep B viral load
Hep C genotyping
Meningococcal PCR

EDTA blood sample

Vacutainer with purple cap

For other PCR tests contact the laboratory.

Respiratory PCR (Flu A / B / RSV)

Blue capped bottle with dry swab (Copan MSwab)

Clear plastic sleeve containing blue capped bottle and swab

HSV 1 and 2 PCR

(Anogenital, mouth skin and eye swabs)

Blue capped Copan MSwab

Clear plastic sleeve containing blue capped bottle and flock swab.

Norovirus PCR

60ml sterile container

Wide necked clear plastic container with yellow cap

TB gamma interferon testing

 Quantiferon TB-Gold single patient pack

The kit contains four blood collection tubes, a 21G needle, a safety tube holder and an instruction sheet. Contact laboratory for issue.

Skin, nail and hair (for fungal culture)


Small plastic bag containing black cardboard & instructions

Semen samples

60ml non-cytotoxic sterile container

60ml white top, Sterilin non-cytotoxic pot, (available from Pathology Stores as part of the semen analysis specimen collection kit.) Click here for instructions on obtaining a semen sample.
NOTE: If printed, information on this page is only valid on day of printing.

Last updated: January 8, 2020