Assays
Gentamicin (q.v.), Vancomycin (q.v.) & Teicoplanin levels are assayed in biochemistry. All other assay samples are sent to microbiology, from where they are sent to a reference laboratory. These can take up to 14 days for a final report (especially for unusual assays). For Gentamicin, Vancomycin & Teicoplanin dosing go to anti-microbial guidelines on the trust intranet. A 5ml clotted sample is required for all assays.
Bacteriological Swabs
Specimen: The Bacteriology department uses liquid culture medium for all swabs, using COPAN E-swabs: pink tops for general/MRSA culture, flexible shaft for pernasal specimens (blue top) and orange swabs for ENT/urethral use. The swab comes in a sterile pack; after sampling place the swab in the tube that contains transport medium. See also Chlamydia swabs.
Specimens should reach the laboratory without delay. If there is a delay in the specimen reaching the laboratory, please ensure the specimens are refrigerated. Some bacteria (e.g. Neisseria gonorrhoeae) will become non-viable. For diagnosis of gonorrhoea or PID, cervical swabs are essential and should be transported to the laboratory without delay.
Comments: Be sure to obtain a representative sample. Label the specimen carefully. On the request form, please give all relevant history, especially of current or recent antimicrobial treatment. High vaginal swabs are unsuitable for the diagnosis of gonorrhoea or pelvic inflammatory disease.
Blood Culture (available from pathology specimen reception)
Specimen: One aerobic and one anaerobic bottle should be used (green and orange tops). There is also a paediatric bottle (yellow top) available for children/small volumes. Volumes of blood added should be 10ml per bottle, or 5ml per paediatric bottle. Specimens should reach the laboratory without delay.
Comments: If taking several blood samples for other investigations please make sure the blood cultures are taken first. Blood cultures are part of the investigation of serious bacterial infections, and are best taken before treatment begins. The specimens should not delay antibiotic therapy in septic patients. Ensure the correct labelling of the bottles. Please give all relevant clinical details, especially current or recent antimicrobial treatment. In the investigation of suspected subacute bacterial endocarditis, we recommend that several blood cultures be taken (please follow microbiology guidelines) and that this is mentioned in the clinical details.
Cerebrospinal Fluid
Specimen: Put 1-2ml into a sterile labelled universal container. In cases of suspected subarachnoid haemorrhage collection of CSF should be placed in three containers to compare the degree of bloodstaining. Only one specimen is required if the cell count is the only test required (e.g. neurology patients). Biochemistry will require separate specimens and forms for xanthachromia, protein and glucose. Please contact biochemistry for special requirements. Specimens should reach the laboratory without delay. A telephone call to the lab will alert us to it’s arrival.
Comments: Be sure to label the specimen containers. Please give all relevant clinical details on the request form, especially current or recent antimicrobial treatment. Samples must not be refrigerated.
Chlamydia Swabs
Specimen: The specimen may be taken from the eye, urethra or cervix. Specimens should reach the laboratory without delay.
Comments: There are instructions on each pack. Observe the expiry date. Before taking a urethral swab, ensure that the patient has not passed urine for one hour. Detailed information on chlamydia results can be found here.
Faeces
Specimen: Place the specimen in a sterile container – do not over-fill the container. The specimen should reach the Laboratory without delay. If examination for clostridium difficile is required, this investigation must be approved by the relevant clinician.
Comments: Be sure to label the specimen container. Give all relevant history especially date of onset, food history, foreign travel, abdominal pain, contacts, and antimicrobial treatment.
Fungal Specimens
Specimen: Skin scrapings, nail parings and hair should be collected into a “dermapak” (available on request from bacteriology) or collected into black paper and placed in a dry sterile universal container. Do not use glass slides. Any other specimens for mycology should be sent in the container appropriate for that specimen type e.g. sputums and corneal scrapes.
Nasopharyngeal Aspirates (do not send the ‘y’ tube)
Specimen: Send the aspirate in a sterile universal container. Specimens should reach the Laboratory within 24 hours. Specimens must not be received in latex gloves or in plastic bags as these samples will be rejected.
Ophthalmology
In addition to routine swabs (Bacteriological swabs, Viral swabs) we also provide slides and slide boxes for corneal scrapes, plus a selection of agar plates for direct culture via prior discussion with the Laboratory staff. If acanthamoeba is suspected please contact the laboratory for advice. Please do not send the scalpel used to take the scrape.
Peritoneal Dialysis Fluid
Specimen: Send approximately 20ml in a sterile container. Inject 5ml of fluid into each of two blood culture bottles. Send the specimens to the Laboratory without delay.
Comments: Be sure to label the specimen containers. Please give all the relevant clinical details on the request form, especially current or recent antimicrobial treatment.
Pleural Fluid
Treat as Synovial (joint) fluid
Polymerase Chain Reaction (PCR)
Suitable samples for testing are: EDTA blood (purple top), green virocult tubes and CSF. On occasion, urine or vesicle fluid may be tested. Vesicle fluid for PCR should be drawn into a syringe (all sharps must be removed from the syringe before transfer to the laboratory) or onto a glass slide; please contact the laboratory for advice. Tissue and corneal scrape material can also be sent and must be send in a sterile container.
Serology
Specimen: In most cases 5ml of clotted blood is required. We also examine cerebrospinal fluid when appropriate.
Comments: For screening purposes (i.e. evidence of past infection or immunisation), one sample is sufficient. For diagnostic purposes paired sera may be necessary; a report will be issued on receipt of the first specimen requesting a second specimen and clinical details (especially date of onset). Please provide a full history and date of onset of symptoms. The request should be made on ICE or in some cases a manual microbiology request form.
Tests for microbiology should not be combined with other departments.
Sputum
Specimen: A sputum specimen (for non-mycobacterial culture) should be the result of one single expectoration. Use a sterile universal container. It should reach the Laboratory without delay, specimens older than 24 hours are of limited value. If a delay is anticipated the specimen should be refrigerated until transport to the lab can be arranged.
Comments: If the sample is greater than 48 hours, it will not be processed. Be sure to label the specimen container. Give details of current or recent antimicrobial treatment. Sputums for legionella culture must be sent with appropriate request form.
Synovial (joint) Fluid
Specimen: Place up to 20ml of fluid into a sterile universal container. Specimens should reach the Laboratory without delay. Biochemistry, cytology and TB culture (if requested) will each require separate specimens and forms.
Comments: Be sure to label the specimen containers. Please give all relevant clinical details on the request form, especially of current or recent antimicrobial treatment. Crystal investigations are performed in Cytology.
Tissue
Specimen: Place the specimen in a sterile universal container. Note that samples in formalin are not suitable for microbiology. The specimen should reach the Laboratory without delay.
Comments: Be sure to label the specimen container. Please give all relevant clinical details on the request form, especially current or recent antimicrobial treatment. when multiple samples are sent, a separate form for each sample is requested.
Tuberculosis (and other mycobacterial) Specimens
Specimen: Collect the sample required for testing in a sterile universal container or sputum sample container. If urine and/or sputum need to be investigated, send three consecutive early-morning specimens in sterile containers.
Urine
Specimen: Use red topped universal containers that contain boric acid. For chlamydia use a white topped sterile universal bottle (no boric acid) and fill to the line, not the brim. Specimens should reach the Laboratory within 48 hours.
Paediatric/small volume urines (less than 10ml) should be sent in 7ml red topped universals with boric acid. If unable to obtain 5ml or more contact the laboratory for advice.
For paediatric samples the lab can examine urines sent in white topped universals, but this will only be done with the prior consent of the on-call duty microbiologist, and the specimen should arrive within four hours of collection. The lab should be informed it is coming.
Comments: Be sure to label the specimen container. Give details of recent and current antimicrobial treatment.
Viral Swabs
Use Virocult swabs (green capped), the instructions are similar to those for Bacteriological swabs.
Virology
Many tests are done on blood samples in serum separator container tubes. We also examine cerebrospinal fluid, faeces, urine, and vesicle fluid.