INTRODUCTION — The goal of microbiologic evaluation is to provide accurate, clinically pertinent results in a timely manner. The quality of the specimens submitted to the microbiology laboratory is critical for optimal specimen evaluation.
The general techniques of specimen collection and handling that have been established both to maximize the yield of organisms and isolate relevant pathogens from specimens obtained from different body sites will be reviewed here (table 1A-D). The techniques of collecting specific specimens such as blood, sputum, and urine are discussed in more detail separately. (See "Detection of bacteremia: Blood cultures and other diagnostic tests" and "Sputum cultures for the evaluation of bacterial pneumonia" and "Sampling and evaluation of voided urine in the diagnosis of urinary tract infection in adults".)
SPECIMEN COLLECTION — Valid interpretation of the results of culture can be achieved only if the specimen obtained is appropriate for processing. As a result, care must be taken to collect only those specimens that may yield pathogens, rather than colonizing flora or contaminants. Specific rules for the collection of material vary, depending upon the source of the specimen, but several general principles apply [1-3]:
●Make every effort to obtain specimens prior to the initiation of antimicrobial therapy.
●Use strict aseptic technique when cultures are obtained in the operating room, during a lumbar puncture, in the bronchoscopy suite, or in radiology. Simple clean technique is usually appropriate in office settings or when outing sputum, urine, and wound cultures are obtained.
●When obtaining specimens from normally sterile sites such as pleural or joint spaces, cerebrospinal fluid, or the peritoneum, take care to minimize contamination by the normal colonizing flora of the skin or mucous membranes.
●Collect an adequate volume of specimen; send tissue or fluid whenever possible rather than submitting a specimen collected on a swab.
●If the specimen is collected in a syringe, follow hospital protocol for safely transporting the sample to the lab. This may include removing the cap using techniques that prevent needlestick injuries from the contaminated needle (eg, scoop technique, mechanical needle-removal devices). Remove the needle and replace it with a cap prior to transport.
●Label all specimen containers with identifying information about the patient (name and hospital number or birth date) and the specimen source, date, and time of collection.
●Complete all paper or electronic requisitions completely and precisely, including requested details on patient history, antimicrobial therapy, and specimen source, so that the laboratory can best determine the appropriate method for processing the specimen.
●Notify the laboratory in advance if special tests are requested or if unusual pathogens, including potential agents of bioterrorism, are suspected.
●Place warning labels on specimens from patients suspected of having highly contagious diseases and notify the laboratory supervisor.
●Coordinate the processing of specimens that are being submitted for both microbiologic and pathologic evaluations. It is often better to send a single specimen to the laboratory and to have it divided there by an experienced pathologist rather than submitting separate specimens. If a single sample is submitted, it must not be placed in the preservatives routinely used for pathology specimens (eg, formalin) until a portion is separated for culture.
●If there is any question about the optimal sample to collect, call the microbiology laboratory before obtaining specimens.
SPECIMEN TRANSPORT — In general, specimens may be sent to the microbiology laboratory in sterile, leak-proof containers enclosed within leak-proof, sealed plastic bags. In the case of fluids obtained in syringes (eg, paracentesis, joint aspirate, needle drainage of abscess), most organisms remain viable for significant periods of time in the syringe used for collection. It has long been advocated that these specimens be sent in the original syringe. However, in the era of universal precautions, some laboratories encourage transfer of the material to another container prior to transport, while others recommend transport in the original syringe after the needle is removed and replaced with a cap. In our institution, the microbiology laboratory prefers to receive specimens in the original syringe as long as the needle has been replaced with a cap but will also accept specimens in other containers.
Prompt transport of specimens to the microbiology laboratory is essential in order to optimize the yield of cultures and the interpretation of results. Delays in processing may result in the overgrowth of some microorganisms or the death of more fastidious ones. Desiccation of the sample must also be avoided.
Samples for bacterial culture should ideally arrive in the microbiology laboratory within one to two hours of collection. If a delay is unavoidable, most specimens (with the exception of blood, cerebrospinal fluid, joint fluid, and cultures for Neisseria gonorrhoeae) should be refrigerated until transported. It is important to add that refrigeration should occur in a refrigerator approved for specimen storage.
Specimen rejection by the laboratory — Common reasons for rejection of specimens by microbiology laboratories include:
●Inconsistent information on the requisition and the specimen label (eg, different patient names)
●Specimen received in a leaking or broken container
●Specimens received in syringes with the needle in place. Such specimens pose a needlestick danger to the microbiology lab staff. In the extremely rare circumstance that such a specimen is received by our lab, our policy is for the tech to contact the sending physician. If another specimen could not reasonably be obtained (for example vitreous fluid), we require the sending physician to come to the laboratory and remove the needle under a biohazard hood, after which we will process the specimen.
●Specimen obviously contaminated
●Inappropriate test request based upon the source of the specimen (table 1A-D) or clinical situation (eg, request for a stool culture for enteric pathogens in a patient hospitalized for more than three days)
●Inappropriate transport medium for the requested test (eg, anaerobic cultures requested for specimen submitted in aerobic transport media)
●Insufficient quantity of specimen
●Specimen transported at an inappropriate temperature
●Prolonged specimen transport time
It is important that the microbiology laboratory notify the responsible physician promptly when a specimen is rejected so that appropriate measures can be taken to obtain more material. If there is a labeling problem, the person responsible for collecting the specimen may be able to rectify the paperwork error. In situations in which obtaining another specimen is not feasible (eg, surgical or other invasive procedure required to obtain the original specimen), the laboratory may have to proceed with specimen processing, even though the validity of the results may be compromised. Such decisions typically are made in collaboration with the patient's physician, and laboratory reports usually are accompanied by a disclaimer.
Examples of specimens that are unsuitable for culture include :
●Swabs of pressure-induced skin and soft tissue injury, perirectal abscess, periodontal lesion, burn wound, gangrenous ulcer; if possible, aspirates or tissue samples should be submitted instead. The limited role of swabs for pressure-induced injuries is discussed in detail separately. (See "Infectious complications of pressure-induced skin and soft tissue injury", section on 'Microbiologic evaluation'.)
●Foley catheter tip
In addition, some laboratories, including our own, no longer perform cultures of intravenous catheter tips, based on lack of utility . We will culture peritoneal dialysis catheter tips.
SUMMARY AND RECOMMENDATIONS
●Importance of proper collection of samples – The goal of microbiologic evaluation is to provide accurate, clinically pertinent results in a timely manner. The quality of the specimens submitted to the microbiology laboratory is critical for optimal specimen evaluation. (See 'Introduction' above.)
●Collection technique – Valid interpretation of the results of culture can be achieved only if the specimen obtained is appropriate for processing. As a result, care must be taken to collect only those specimens that may yield pathogens, rather than colonizing flora or contaminants. (See 'Specimen collection' above.)
●Processing the sample – The requesting clinician can help to ensure that the specimens are processed appropriately by completing requisitions accurately and by providing the laboratory with as much relevant information as possible. (See 'Specimen collection' above.)
●Transporting the sample – In general, specimens may be sent to the microbiology laboratory in sterile, leak-proof containers enclosed within leak-proof, sealed plastic bags. Prompt transport of specimens to the microbiology laboratory is essential in order to optimize the yield of cultures and the interpretation of results. Delays in processing may result in the overgrowth of some microorganisms or the death of more fastidious ones. Desiccation of the sample must also be avoided. (See 'Specimen transport' above.)
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