BHR HOSPITALS – MICROBIOLOGY
GUIDANCE ON THE TAKING OF MICROBIOLOGICAL SAMPLES
Since the Bacteriology department is concerned with isolation of significant
organisms from the site of an infection, it is important that the following principles
are followed: The sample site is clean and free from antiseptic cream or lotions
 The correct specimens are taken and, where applicable, transferred into the
correct transport media (Refer to: Microbiology-the service and table of
bacterial and serology/virology investigations, specimen collection and
turnaround time (TAT) (5622)).
 Dispose of all consumables used in the taking of the specimen in the
appropriate way.
Preparation of the Patient
Ensure that the patient is fully informed as to the nature of the investigation to be
performed and that their consent is obtained. They must understand what the
procedure involves, why they need it and what the consequences may be if the
investigation is not performed.
Where a patient has to go away and obtain a sample themselves they must be fully
instructed in the procedure for obtaining that specimen.
The following links provide instructions for patients:
1. How should I collect and store a stool sample?
How should I collect and store a stool (faeces) sample? - Health questions - NHS
Choices
2. How should I collect and store a urine sample?
How should I collect and store a urine sample? - Health questions - NHS Choices
3. Urine collection for Chlamydia NAAT
http://catalog.bd.com/ecat/help/f88/urine-collection-chart.pdf
4. Instructions for self collection of vaginal swabs for NAAT
http://www.bd.com/ds/technicalCenter/technicalBulletins/tb_0_222801.pdf
Q Pulse record: Pathology 5620
Approved / Authorised by: R. Davis
Revision: 2
Last updated: March 2017
Page 1 of 10
BHR HOSPITALS – MICROBIOLOGY
GUIDANCE ON THE TAKING OF MICROBIOLOGICAL SAMPLES
Action
Explain and discuss procedure with the person
Rationale
To ensure the person understands the
procedure and gives consent
To prevent contamination
To prevent contamination
To prevent cross infection
Collect equipment and check all expiry dates
Wash hands
Wear gloves
Take the swab using the correct technique
Place the specimen/swab in the correct labelled To ensure the organisms for investigation
container
are preserved
Send the specimen/swab to the laboratory with To ensure optimum conditions for
completed documentation
laboratory examination
Dispose of equipment as per trust policy
Antimicrobial assays
Antral washings
Aspirates and fluids from normally sterile sites
Blood cultures
Collection of central nervous system specimens (CNS)
Ear swab
Eye swab
Faeces
Genital tract swabs
Helicobacter pylori
Intrauterine contraceptive devices
Intravascular devices
Mouth swabs
MRSA Screens
Nasal and pernasal swabs
Procedure for the collection of pus or exudate
Peritoneal dialysis fluid
Schistosomiasis
Serology/Virology requests
Skin, nail and hair for mycology
Sputum
Throat Swabs
Tissues and biopsies
Urine
Wounds and ulcers
Q Pulse record: Pathology 5620
Approved / Authorised by: R. Davis
Revision: 2
Last updated: March 2017
Page 2 of 10
BHR HOSPITALS – MICROBIOLOGY
GUIDANCE ON THE TAKING OF MICROBIOLOGICAL SAMPLES
Antimicrobial assays – Please refer to the Antibiotic Assays section.
Antral washings
Ideally an ENT surgeon should collect the specimen. Transfer to a sterile universal
container. Ensure the cap is tightly screwed on.
Aspirates and fluids from normally sterile sites
Collect the specimen with a sterile syringe. Transfer a maximum of 20ml into a sterile
universal container. Ensure the cap is tightly screwed on. Ascitic fluids may also be
inoculated in to a blood culture set.
Blood cultures- Please refer to the infection control section on the intranet.
Collection of central nervous system specimens (CNS)
CNS specimens for culture include cerebrospinal fluid (CSF-obtained either by
subdural tap, ventricular aspiration or lumber puncture), brain abscess aspirate and
brain biopsy. These samples are obtained by the clinician under sterile operative
conditions.
If more than one sample of CSF is taken, then these must be labelled sequentially. If
there is a clinical suspicion of subarachnoid haemorrhage (SAH) send the 1st and 3rd
samples with a request for differential cell count.
NB – we do not offer a spectrophotometric assay for xanthochromia. This test is
performed in the Biochemistry department.
Requests for PCR will be vetted by the Microbiology consultants before they can be
referred.
Ear swab
No drops should have been used 3 hours prior to taking the swab. Place the swab in
the ear canal. Rotate gently. Place the swab in the plastic transport sheath.
Eye swab
Microbiology (bacteriology): Gently evert the lower eyelid to expose the conjunctival
membrane. Rub the swab gently over the conjuntival membrane avoiding the cornea.
Place the blue top swab in the plastic transport sheath.
Chlamydia: Take this after the Microbiology specimen. The aim is to collect epithelial
Q Pulse record: Pathology 5620
Approved / Authorised by: R. Davis
Revision: 2
Last updated: March 2017
Page 3 of 10
BHR HOSPITALS – MICROBIOLOGY
GUIDANCE ON THE TAKING OF MICROBIOLOGICAL SAMPLES
cells. Gently rub the special Chlamydia swab over the conjunctival membrane
avoiding the cornea. Place the swab in Chlamydia transport medium, snip off the
shaft and screw the cap on.
Virology: Moisten the swab in sterile saline before taking the specimen (never
moisten the swab in viral transport medium). Follow procedures as for the
Microbiology swab. Snap off the swab tip into viral transport medium.
Faeces
Send a two spatula full portions or 5-10ml if liquid. Ask the patient to defecate into a
clean bedpan or other convenient container if at home. Use the plastic spoon to
transfer a portion of faeces into the blue top container. For liquid faeces use a plastic
medicine spoon. Take care not to contaminate the outside of the faeces pot. N.B.
Rectal swabs are not suitable for the detection of enteric pathogens.
Routine screens are for Salmonella, Shigella, Campylobacter and E.coli 0157.Vibrio
and Yersinia screens depend on clinical information.
Cl.diificile (GDH/Toxin) screened on liquid stools from patients >2yrs old.
Rotavirus/adenovirus screens are done on neonates <5yrs old.
Cryptosporidium screened for on liquid stools from children <14yrs old, HIV positive
patients and on specific requests.
Outbreaks:
Most hospital outbreaks of diarrhoea and/or vomiting are caused by either
Clostridium difficile or Norovirus. Please contact the Infection Control Consultant for
advice.
Amoebic dysentery – for examination of amoebic trophozoites the specimen must
reach the laboratory in advance. For all investigations, if more than one specimen is
to be submitted, ensure that these are obtained on successive days (see section on
faecal parasites). N.B. Specimen must be fresh and warm.
Sellotape slide: These are not processed see section on faecal parasites. If Segments
of tapeworm or worms are seen then please send these in a blue top container or
plain universal.
Genital tract swabs:
Microbiology: Cervical and high vaginal swabs must be taken with the aid of a
speculum. It is important to avoid vulval contamination of the swab. For Trichomonas,
Q Pulse record: Pathology 5620
Approved / Authorised by: R. Davis
Revision: 2
Last updated: March 2017
Page 4 of 10
BHR HOSPITALS – MICROBIOLOGY
GUIDANCE ON THE TAKING OF MICROBIOLOGICAL SAMPLES
swab the posterior fornix. If there is obvious candida plaques swab the lesions. If
pelvic infection, including gonorrhoea, is suspected, swab the cervical os.
Introduce the speculum: roll the swab in the endocervis. Place the swab in the plastic
transport sheath containing the black charcoal-containing Amies medium.
For Chlamydia trachomatis investigations send a cervical swab in Chlamydia transport
medium. Place the swab in Chlamydia transport medium, snip off the shaft and screw
the cap on.
Use the CT/GC collection kit or the self take vaginal NAAt pack.
If herpes simplex is suspected send an additional swab in viral transport medium.
Moisten the swab in sterile saline before taking the specimen. Never moisten swab in
viral transport media. Follow procedures as for the Microbiology swab. Snap off the
swab tip into viral transport medium.
Urethral swabs: Avoid contamination with micro-organisms from the vulva or the
foreskin. Use the ENT (orange top) swabs for this purpose. The patient should not
have passed urine for at least 1 hour. For males, if discharge is not apparent attempt
to ‘milk’ it out of the penis. Pass the swab gently through the urethral meatus and roll
around. Place the swab in the plastic transport sheath.
Chlamydia: Take this specimen after the Microbiology swab. Pass the swab through
the urethral meatus and gently but firmly roll it over all the surfaces of the urethral
epithelium for 1-2 seconds then withdraw. Place the swab in chlamydia transport
medium, snip off the shaft and screw the cap on. Or use the urine collection kit.
Helicobacter pylori
Helicobacter antigen test- please see section under investigations.
Helicobacter biopsy:
Gastric biopsy specimens are usually taken from the gastric antrum at endoscopy.
Specimens should be transported as soon as possible (preferably within 6 hours). The
biopsy should be placed in a sterile universal container, containing a small amount (12ml) of sterile isotonic saline to preserve moisture.
Intrauterine contraceptive devices (IUCDs)
These are NOT processed by the laboratory.
Intravascular devices
Line infection is confirmed by semi-quantitative culture of a removed line. After
Q Pulse record: Pathology 5620
Approved / Authorised by: R. Davis
Revision: 2
Last updated: March 2017
Page 5 of 10
BHR HOSPITALS – MICROBIOLOGY
GUIDANCE ON THE TAKING OF MICROBIOLOGICAL SAMPLES
removing a possibly infected line from a patient, cut off the intravascular portion
using sterile scissors and place it in a sterile universal container. If infection is
suspected in a long line send the intravascular portion immediately adjacent to the
exit site and the tip in separate sterile universal containers.
Urinary catheter tips are NOT processed. Please send a urine sample.
MRSA Screens
These swabs are taken on the advice of the Infection Control team or to comply with
hospital protocols. They are taken to ascertain whether a patient is colonised or has
an MRSA infection.
Using a Transwab (blue top) moisten each swab with sterile water or saline:
 Nasal- Rotate the moistened swab gently but firmly around the anterior nares
of each nostril. One swab can be used for both nostrils.
 Groin- Rotate the moistened swab gently but firmly over each area. One swab
can be used for both groins.
 Throat- Depress the tongue with a spatula. Sample the posterior portion of
the pharynx, tonsillar areas and areas of ulceration exudate or membrane
formation.
Mouth swabs
Sample the mouth including any lesions or inflamed areas. A tongue depressor or
spatula may be helpful to aid vision and avoid contamination from other parts of the
mouth. Place the blue top swab in the plastic transport sheath.
Nasal and pernasal swabs
Nasal swabs are usually taken to detect staphylococcal or meningococcal carriage.
Moisten the swab before swabbing with sterile saline. Swab the anterior nares by
gently rotating the swab in each nostril. Place the swab in the plastic transport
sheath.
Pernasal swabs are used to diagnose whooping cough. Pass the blue top wire swab
gently along the floor of the nose. Place the swab in pertussis transport medium.
Taking these samples in patients with whooping cough may precipitate a paroxysm of
coughing and cause obstruction of the airways. Resuscitation equipment must be
available if whooping cough is suspected. The specimen collector should avoid direct
coughs from the patient.
Q Pulse record: Pathology 5620
Approved / Authorised by: R. Davis
Revision: 2
Last updated: March 2017
Page 6 of 10
BHR HOSPITALS – MICROBIOLOGY
GUIDANCE ON THE TAKING OF MICROBIOLOGICAL SAMPLES
Procedure for the collection of pus or exudate
Where there are clinical signs of infection i.e. inflammation, oedema, pyrexia, pain or
purulent exudate, it is preferable to obtain a specimen of pus rather than to take a
swab.
Pus or exudate can be drawn up in a syringe and transferred into a sterile universal
container.
DO NOT SEND THE SYRINGE WITH THE NEEDLE ATTACHED.
Remove the blue top swab and gently but firmly rotate it on the surface directly
where infection is suspected. Do not take swabs from slough or necrotic tissue. Place
swab into transport medium. Ensure that the specimen containers are labelled
accurately and place, with the completed request form, in the appropriate pockets of
the clear minigrip transport bag for transportation to the microbiology department.
Peritoneal dialysis fluid
Using a fine needle and syringe, aspirate fluid from the peritoneal dialysis bag.
Transfer 20ml into a sterile universal container.
Serology/Virology requests – please refer to the serology /virology section.
Skin, nail and hair for mycology
Skin
Patients’ skin and nails can be cleaned wit 70% alcohol prior to collection of the
specimen. This is especially important if creams, lotions or powders have been
applied.
Skin scrapings should be taken by gently shaving off material from the active edges of
the lesion using a blunt scalpel blade.
Nails
Material should be taken from any discoloured, dystrophic or brittle parts of the nail.
The affected nail should be cut as far back as possible through the entire thickness
and should include any crumbly material. Take nail scrapings if the infection is
superficial.
Hair
Hairs should be plucked from affected areas together with skin scrapings from
associated scalp lesions. Cut hairs are not suitable for direct examination as the
infected area is usually close to the scalp surface.
Q Pulse record: Pathology 5620
Approved / Authorised by: R. Davis
Revision: 2
Last updated: March 2017
Page 7 of 10
BHR HOSPITALS – MICROBIOLOGY
GUIDANCE ON THE TAKING OF MICROBIOLOGICAL SAMPLES
Send material to the laboratory in a Dermapak, if these are unavailable, place sample
into a sterile universal. At least 5mm of skin scrapings are required. Skin scrapings can
also be sent in a plain envelope.
Schistosomiasis
Definitive diagnosis is by demonstration of the characteristic ova in clinical material.
For S.haematobium, a terminal urine sample (the last 10 to 20ml of urine passed on
each occasion) is required. Faecal samples are the best specimens for the detection of
S.mansoni (and S. Japonicum) but as S. mansoni and S. Haematobium overlap in
geographical distribution and can affect both genitourinary and alimentary systems a
terminal urine sample and a minimum of three faecal samples should be sent from all
patients being investigated for schistosomiasis when serology is positive.
Sputum
The aim is to collect deep respiratory secretions without contamination by upper
respiratory tract bacteria. Explain the procedure to the patient and encourage them
to breathe deeply and on exhalation cough to produce sputum directly into a wide
mouth sterile specimen container. Specimens obtained after antibiotic therapy has
been initiated may yield misleading results.
Specimens should be taken properly, ideally with the aid of a physiotherapist, and
should be placed in a universal container. Avoid sending salivary specimens.
If sputum is required for mycobacterial (TB) and fungal investigations, three
specimens should be sent on three different days and sent to the laboratory on the
day of collection ie not batched.
Throat Swabs
Diagnosis of bacterial (eg Streptococus pyogenes) pharyngitis depends on the culture
of a throat swab. Sit the person facing a strong light and depress their tongue with a
spatula. Sample the posterior portion of the pharynx, tonsillar areas of ulceration,
exudation or membrane formation. Try not to touch the lips, tongue, mouth or saliva.
Place the swab in the plastic transport sheath.
Q Pulse record: Pathology 5620
Approved / Authorised by: R. Davis
Revision: 2
Last updated: March 2017
Page 8 of 10
BHR HOSPITALS – MICROBIOLOGY
GUIDANCE ON THE TAKING OF MICROBIOLOGICAL SAMPLES
Tissues and biopsies
Under aseptic conditions transfer material to a sterile container that does not contain
formalin as this inactivates pathogens very rapidly. Send in 0.5ml of sterile saline.
Urine
NB If transport of urine specimens to the laboratory is delayed they should be
refrigerated.
Clean-voided midstream urine if preferred for bacterial and fungal cultures: The
reliability of microscopy and culture results depends on the avoidance of
contamination and prompt treatment.
Detection of red blood cells (haematuria), crystals and casts can help to diagnose
other conditions of the urinary tract not caused by microorganisms.
It is recommended that in females the hands and the perineal area are washed with
soap and water prior to specimen collection. Part the labia and clean the area around
the urethral meatus from front to back. Spread the labia with the fingers of one hand.
In males retract the foreskin, if present, and clean the skin surrounding the urethral
meatus.
To avoid contamination with urethral organisms the patient must be instructed not to
collect the first part of the urine. Start passing urine into the toilet, bedpan or urinal.
When the urine is flowing freely collect urine in a clean sterile container.
Pour urine into a sterile (red top) container containing boric acid as the preservative.
In adults pour up to the 20ml mark on the label.
For neonates pour urine into the small boric acid container up to the line on the side.
First catch urine: For Chlamydia trachomatis, this is needed rather than mid-stream
urine. The first 5-10ml of voided urine is to be sent.
Schistosmiasis: In patients with haematuria, eggs maybe found trapped in the blood
and mucus in the terminal portion of the urine specimen. Peak egg excretion occurs
between noon and 2pm. Therefore collect a terminal specimen or urine at around
midday in a sterile container. Preservatives must not be used. Send sample in a
sterile white top container.
Catheter specimens of urine should be obtained aseptically with a sterile syringe and
needle following disinfection of the catheter specimen port with alcohol. Clamp
Q Pulse record: Pathology 5620
Approved / Authorised by: R. Davis
Revision: 2
Last updated: March 2017
Page 9 of 10
BHR HOSPITALS – MICROBIOLOGY
GUIDANCE ON THE TAKING OF MICROBIOLOGICAL SAMPLES
tubing below the sampling cuff. Clean the sampling cuff with a mediswab. Aspirate
urine using a syringe and transfer to a sterile universal container. Unclamp the tubing.
Patients with long-term catheters are often colonised with one or more
microorganisms. NB: inappropriate attempts to sterilise the urine in asymptomatic
patients with urinary catheters may result in the selection of resistant bacteria.
For investigation of mycobacterial infection send 3 early morning urine specimens
(when the urine is most concentrated) taken on consecutive days.
Wounds and ulcers
Always state the site and nature of the wound. This is essential, as the laboratory may
need to interpret findings against a background of normal flora present in a given part
of the body.
If copious pus or exudate is present, aspirate with a sterile syringe and transfer to a
sterile universal container. If sufficient to aspirate rotate a swab in the centre of the
infected area and place the swab in the blue top plastic transport sheath.
Q Pulse record: Pathology 5620
Approved / Authorised by: R. Davis
Revision: 2
Last updated: March 2017
Page 10 of 10