Bacteriology/CL3

Please click on the hyperlink to be taken to the relevant test entry in the Test Database

Genital swabs for bacterial culture / URETHRAL SWAB MICROSCOPY CULTURE AND SENSITIVITIES
GENITAL SWABS (HVS) MICROSCOPY, CULTURE & SUSCEPTIBILITY / For general aspects of taking genital swab samples we recommend that users follow either their local protocols or “The Royal Marsden Manual of Clinical Nursing Procedures”.
Link to generic advice sheet on using e-swabs: How to use liquid e-swabs
Low vaginal swabs (LVS)
  • Use pink top e-swab
  • Insert the swab into the lower part of the vagina and rotate gently but firmly.
High vaginal swabs (HVS)
  • Use speculum to separate the vaginal walls.
  • Wipe away any excess cervical mucus with a cotton swab.
  • Use pink top e-swab to sample as high as possible in the vaginal vault.
Penile (urethral) swabs
  • Use orange top urethral e-swab
  • The patient should not have passed urine for at least one hour.
  • Retract prepuce. Pass the swab gently through the urethral meatus and rotate gently.

Selotape slide / FAECES PARASITOLOGY / Sampling instructions for the investigation of threadworm (Enterobius vermicularis):
  • Apply clear sellotape to the perianal region, pressing the adhesive side firmly against the left and right perianal folds several times. Fold the tape in half, adhesive side inwards and place in sterile universal. Label sample, complete microbiology request form and clearly label as selotape for Enterobius vermicularis.
  • Alternatively, a moistened cotton swab can be used to swab the perianal area. Place the swab in a sterile universal container. Label sample, complete microbiology request form and clearly label as perianal swab for Enterobius vermicularis.

Upper respiratory swabs for bacterial culture / THROAT, EYES, EARS, NOSE AND MOUTH SWAB MICROSCOPY CULTURE & SUSCEPTIBILITY
PERNASAL SWAB CULTURE & SUSCEPTIBILITY / For general aspects of taking upper respiratory swab samples we recommend that users follow either their local protocols or “The Royal Marsden Manual of Clinical Nursing Procedures”.
NB: Sending actual pus is preferable to swabs if present.
Link to generic advice sheet on using e-swabs: How to use liquid e-swabs
Throat swab for M,C&S
  • Ask patient to sit upright facing a strong light, tilt headbackwards, open mouth and stick out tongue.
  • Depress tongue with a spatula.
  • Ask patient to say ‘Ah’.
  • Quickly but gently roll the swab over any area of exudate or inflammation or over the tonsils and posterior pharynx.
  • Carefully withdraw the swab, avoiding touching any otherarea of the mouth or tongue.
Eye swab for M,C&S
  • Ask patient to look upwards.
  • Using aseptic technique, hold the swab parallel to the cornea and gently rub the conjunctiva in the lower eyelids from nasal side outwards.
  • Swab any pus or exudates as well as any lesion of interest.
  • If both eyes are to be swabbed, label swabs ‘right’ and ‘left’ accordingly.
  • NB: Separate samples must be collected into appropriate transport media for detection of viruses, chlamydia or Neisseria gonorrhoeae.
Ear Swab for M,C&S
  • Ensure no antibiotics or other therapeutic drops have been used in the aural region three hours before taking the swab.
  • Using aseptic technique, rotate swab gently once at the entrance of the auditory meatus to collect any pus or exudates.
Nose swab for M,C&S
  • Ask patient to tilt head backwards.
  • Moisten swab with sterile saline.
  • Insert swab inside the anterior nares with the tip directed upwards and gently rotate. Swab any pus or exudates.
  • Repeat the procedure with the same swab in the other nostril.
Mouth swab for M,C&S
  • Sample pus if present, otherwise sample 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.
Pernasal swab for M,C&S
  • Pernasal swabs can be ordered from Pathology Stores in the usual way.
  • Remove cap from media tube by twisting.
  • Gently insert the fine, flexible pernasal (turquoise top) swab along the floor of the nasal cavity until it touches the posterior naso-pharynx & rotate 2-3 times before withdrawing. If obstruction is encountered, withdraw and re-insert through other nostril.
  • Insert the swab into the charcoal media tube.
  • Ensure the swab is labelled accurately along with the completed request form.

MRSA screening / MRSA SCREEN / Link to trust guidance:
AND poster:
Pernasal swab for PCR (non-culture) detection of Bordetella pertussis / REAL-TIME PCR DETECTION OF BORDETELLA PERTUSSIS / Pernasal swab for PCR
  • Pernasal swabs can be ordered from Pathology Stores in the usual way.
  • Remove cap from media tube by twisting.
  • Gently insert the fine, flexible pernasal (turquoise top) swab along the floor of the nasal cavity until it touches the posterior naso-pharynx & rotate 2-3 times before withdrawing. If obstruction is encountered, withdraw and re-insert through other nostril.
  • Insert the swab back into the empty tube DO NOT use the charcoal tube for PCR tests.
  • Ensure the swab is labelled accurately along with the completed request form.

Wound / ulcer and skin swabs for bacterial culture / WOUND, ULCER, SKIN SWAB CULTURE & SUSCEPTIBILITY. / Skin swabs
  • For cutaneous sampling, moisten swab with sterile saline and roll e-swab along the area of skin to be sampled.
Wound swabs
  • Rotate the e-swab swab tip over a 1 cm square area of viable tissue, at or near the centre of the wound for 5 seconds, applying enough pressure to express tissue fluid from the wound bed.
  • If the wound is dry, the tip of the swab should be moistened with sterile saline.
  • NB: If pus is present, it should be aspirated using a sterile syringe and decanted into a sterile specimen pot.
Ulcer swabs
  • Cleanse the wound with tap water or saline to remove surface contaminants.
  • Slough and necrotic tissue should also be removed.
  • Swab viable tissue displaying signs of infection whilst rotating the e-swab.

Blood Cultures / Normal BLOOD CULTURE
For Mycobacteria MYCOBACTERIAL PRIMARY CULTURE AND MICROSCOPY / Already linked to from heftpathogy sample page:
See also HEFT guideline “Blood Culture Sampling in Patients Receiving Haemodialysis”:

Info on page for mycobacteria:
If blood cultures for M.tuberculosis / MAI are required, please telephone the TB laboratory to request TB blood culture bottle(s). TB blood cultures received in routine MC&S blood culture bottles cannot be tested.
See also HEFT “Guideline for the Diagnosis of Tuberculosis in Adults”:

Red top blood (Serum) for antibiotic assays / GENTAMICIN ANTIBIOTIC ASSAY
GENTAMICIN, TOBRAMYCIN ONCE DAILY REGIME
TEICOPLANIN ANTIBIOTIC ASSAY
TOBRAMYCIN ANTIBIOTIC ASSAY
VANCOMYCIN ANTIBIOTIC ASSAY / For taking blood samples we recommend that users follow either their local protocols or “The Royal Marsden Manual of
Clinical Nursing Procedures”.
Please see HEFT guidelines for specific antibiotics requiring therapeutic drug monitoring (TDM):
Samples for antibiotic level assays:
  • For trough levels: following venepuncture, withdraw the volume of blood appropriate to the blood sample bottle (red top) using the vacuum-assisted collection system.
  • Clearly label blood sample bottle and appropriate form with ‘pre-drug administration blood’.
  • Administer intravenous antibiotics as prescribed via the patient’s established vascular access device.
  • If peak level required: within an allotted time after administration, withdraw the volume of blood appropriate to the blood sample bottle (red top) using the vacuum-assisted collection system.
  • Clearly label blood sample bottle and appropriate form with ‘post-drug administration blood’.
  • If CVAD used: the device must be flushed thoroughly before taking the blood sample. Take and discard enough blood to clear the device of any residual flushes solution or medications (usually 5–10 mL is sufficient), then attach vacuum-assisted collection system to take drug level sample. Indicate on blood sample bottle and appropriate form that sample is from a CVAD.
  • Ensure microbiology request forms are completed correctly, including date, exact time and dosage of previously administered dose.
  • Arrange prompt delivery to the microbiology laboratory.

Urines for M,C&S / URINE MICROSCOPY, CULTURE AND SUSCEPTIBILITY / Instructions for patient self-collection of urine (MSU) sample:
Add links to patient leaflets
Instructions for urine sample collection in hospital:
Add link to hospital flow chart poster
Urines for non-culture tests / STREPTOCOCCUS PNEUMONIAE URINE ANTIGEN
VIRAL URINE SCREEN
LEGIONELLA URINE ANTIGEN
CONGENITAL CYTOMEGALOVIRUS (CMV) PCR / Urine samples for non-culture tests
  • Collect urine in a clean container and transfer to a 20ml white top sterile sample container.

Urines for mycobacterial (TB) culture / MYCOBACTERIAL PRIMARY CULTURE AND MICROSCOPY / Urine samples for mycobacterial culture
  • Collect three early morning urine specimens (i.e. from the first urination after waking).
  • Each specimen is to be collected on a different day.
  • Use a clean container to collect sufficient urine to fill a 20ml white top sterile sample container.
  • Ensure the bottles are labelled with the day of collection i.e. 1, 2 or 3.
See also HEFT “Guideline for the Diagnosis of Tuberculosis in Adults”:

Joint aspirates / JOINT ASPIRATE MICROSCOPY, CULTURE & SUSCEPTIBILITY
16S PCR AND SEQUENCING
MYCOBACTERIAL PRIMARY CULTURE AND MICROSCOPY / For general aspects of taking joint aspirates we recommend that users follow either their local protocols or “The Royal Marsden Manual of Clinical Nursing Procedures”.
Joint aspirates
  • All aspirate samples should be collected aseptically and transferred directly to sterile sample containers with no additives of any kind.
See also HEFT “Guidelines for the Investigation and Treatment of Prosthetic Joint Infections”:

See also HEFT “Guideline for the Diagnosis of Tuberculosis in Adults”:

Pus and Fluids (including pleural, ascitic and vitreous fluid) / PUS/FLUIDS MICROSCOPY, CULTURE & SUSCEPTIBILITY
PLEURAL FLUIDS,INTERCOSTAL FLUID MICROSCOPY,CULTURE & SUSCEPTIBILITY
ASCITIC FLUID MICROSCOPY, CULTURE & SUSCEPTIBILITY
VITREOUS FLUID VIRAL SCREENING
16S PCR AND SEQUENCING
MYCOBACTERIAL PRIMARY CULTURE AND MICROSCOPY / For general aspects of taking pus and fluid samples we recommend that users follow either their local protocols or “The Royal Marsden Manual of Clinical Nursing Procedures”.
Fluid and Pus Samples
  • All fluid and pus samples should be collected aseptically and transferred directly to sterile sample containers with no additives of any kind.
For TB culture
See also HEFT “Guideline for the Diagnosis of Tuberculosis in Adults”:

For pleural fluids
See also HEFT Guideline “Investigation of a Pleural Effusion”:

Continuous ambulatory peritoneal dialysis (CAPD) fluid / CAPD FLUIDS MICROSCOPY, CULTURE & SUSCEPTIBILITY / For general aspects of CAPD fluid samples we recommend that users follow either their local protocols or “The Royal Marsden Manual of Clinical Nursing Procedures”.
CAPD Samples
  • CAPD fluid should be aseptically transferred from the bag directly to sterile sample containers with no additives of any kind.

Bacterial isolates / VTEC O157
16S PCR AND SEQUENCING
CARBAPENEMASE-PRODUCING ENTEROBACTERIACEAE RT-PCR
COLISTIN RESISTANT GRAM NEGATIVE ORGANISMS FROM CYSTIC FIBROSIS PATIENTS / Bacterial isolates
  • Please refer bacterial isolates for testing as slope cultures

Mycobacterial culture / MYCOBACTERIAL IDENTIFICATION
MYCOBACTERIUM TUBERCULOSIS SUSCEPTIBILITY TESTING
MYCOBACTERIAL EPIDEMIOLOGICAL TYPING / Mycobacterial isolates
  • Please refer mycobacterial isolates for testing as LJ slope cultures or as liquid culture
  • Link to sending MGIT poster