Bacteriology and Virology
Faeces (all test types)and
Vomit swabs for norovirus / CLOSTRIDIUM DIFFICILE
FAECES CULTURE & SUSCEPTIBILITY
FAECES PARASITOLOGY
VIRAL GASTROENTERITIS SCREEN
NOROVIRUS
CLOSTRIDIUM DIFFICILE RIBOTYPING
MYCOBACTERIAL PRIMARY CULTURE AND MICROSCOPY / Instructions for patient self-collection of faeces sample:
Instructions for faeces sample collection in hospital:
- Ask patient to defaecate into a clinically clean bedpan or receiver.
- If the patient has been incontinent: a sample may be obtained from bedlinen or pads: try to avoid contamination with urine.
- Using the integrated ‘spoon’ in the sample pot lid, scoop enough faecal material to fill a third of the specimen container (or 10–15 mL of liquid stool).
- Apply specimen container lid securely.
- In cases of suspected tapeworms: segments of tapeworm are easily seen in faeces and should be sent to the laboratory for identification.
- Label sample and complete microbiology request form (including relevant information such as onset and duration of diarrhoea, fever or recent foreign travel).
- Dispatch sample to the laboratory as soon as possible or refrigerate at 4–8°C and dispatch within 12 hours.
- Use a red topped virology transport medium kit (labelled as Oxoid IDEIA Chlamydia kit).
- Dip swab into vomit.
- Place the swab in the transport liquid and snap off the swab shaft at the score line so it fits into the sample pot.
- Close the cap tightly and label with patient information.
Trap / INFLUENZA A H7N9 REAL-TIME PCR
RESPIRATORY VIRUSES PCR
REAL-TIME PCR DETECTION OF BORDETELLA PERTUSSIS
MYCOBACTERIAL PRIMARY CULTURE AND MICROSCOPY
MYCOBACTERIAL DETECTION (TB PCR) / For general aspects of taking respiratory samples we recommend that users follow either their local protocols or “The Royal Marsden Manual of Clinical Nursing Procedures”.
Nasopharyngeal wash: vacuum-assisted (trap) aspirate method
- Nasopharyngeal wash should be collected according to local protocols using sterile fluids as the instillate.
- Recovered mucus/fluid should sent in a 20ml white top sterile sample container or other well sealed sterile container.
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.
Tissue (including biopsies, lymph nodes etc.) / TISSUES,BIOPSIES,LYMPH NODES MICROSCOPY, CULTURE & SUSCEPTIBILITY
16S PCR AND SEQUENCING
MYCOBACTERIAL PRIMARY CULTURE AND MICROSCOPY
MTB/RIFAMPICIN RESISTANCE PCR
HHV6 PCR (QUALITATIVE AND QUANTITATIVE) / For general aspects of taking tissue samples we recommend that users follow either their local protocols or “The Royal Marsden Manual of Clinical Nursing Procedures”.
Tissue samples for microbiology
- All tissue samples should be collected aseptically and transferred directly to sterile sample containers with no additives of any kind.
See also HEFT “Guideline for the Diagnosis of Tuberculosis in Adults”:
Cerebrospinal fluid (CSF) / CSF MICROSCOPY, CULTURE & SUSCEPTIBILITY
VIRAL CSF SCREEN
MYCOBACTERIAL PRIMARY CULTURE AND MICROSCOPY
MTB/RIFAMPICIN RESISTANCE PCR
CRYPTOCOCCUS ANTIGEN
HHV6 PCR (QUALITATIVE AND QUANTITATIVE)
16S PCR AND SEQUENCING / For taking CSF samples we recommend that users follow either their local protocols or “The Royal Marsden Manual of Clinical Nursing Procedures”.
CSF samples for microbiology/virology
- Collect specimens preferably before antimicrobial therapy is started, but this must not be delayed unnecessarily pending lumbar puncture and CSF culture.
- CSF is normally collected sequentially into three or more separate containers which should be clearly numbered consecutively on the sample pots (i.e. 1, 2 and 3).
- In adults, we recommend sending samples 1 and 3 for microbiology and sample 2 for biochemistry (protein).
- Ideally a minimum volume of 1mL is needed for each tube but when sample volume is below this it is possible to pool samples.
- For culture for Mycobacterium species (including TB), at least 10mL is preferred where possible as the larger the volume, the greater the culture yield.