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close this bookBasic Laboratory Procedures in Clinical Bacteriology (WHO; 1991; 128 pages)
View the documentPreface
View the documentIntroduction
open this folder and view contentsQuality assurance in microbiology
close this folderPart I. Bacteriological investigations
open this folder and view contentsBlood
open this folder and view contentsCerebrospinal fluid
open this folder and view contentsUrine
open this folder and view contentsStool
open this folder and view contentsLower respiratory tract infections
open this folder and view contentsUpper respiratory tract infections
open this folder and view contentsSexually transmitted diseases
close this folderPurulent exudates, wounds, and abscesses
View the documentIntroduction
View the documentCommonly encountered clinical conditions and the most frequent etiological agents
View the documentCollection and transportation of specimens
View the documentMacroscopic evaluation
View the documentMicroscopic examination
View the documentCulture
View the documentIdentification
View the documentSusceptibility testing
open this folder and view contentsAnaerobic bacteriology
open this folder and view contentsAntimicrobial susceptibility testing
open this folder and view contentsPart II. Essential media and reagents for isolation and identification of clinical pathogens
View the documentSelected further reading
View the documentSelected WHO publications of related interest
View the documentBack Cover

Collection and transportation of specimens

It is not possible, here, to describe in detail the procedures for specimen collection from each type of wound, abscess, etc. It should be obvious that this is a task that requires close cooperation between the laboratory and the physician. In many instances, there is only one opportunity to obtain a specimen - second specimens are non-existent in many cases. Therefore, proper collection, transport, and storage of these specimens are of the greatest importance, and compromises should be avoided. Once a specimen has been obtained, packaged, and dispatched to the laboratory, it should be processed as soon as possible. After the preliminary examinations have been completed and the cultures made, the rest of the specimen should be properly labelled, stoppered, and refrigerated, until it is certain that no additional laboratory tests are needed.


Once an abscess, or multiple abscesses, have been found, the physician or surgeon and the microbiologist should consult on what is to be done. The technique for collecting pus and pieces of the abscess wall is a surgical procedure. A syringe and needle are used to aspirate as much as possible of the purulent material, which is then aseptically transferred to sterile specimen containers. If such containers are not available, the specimen should be kept in the syringe with the needle capped, and the syringe itself should be transported to the laboratory. This material should be processed immediately by the laboratory; both aerobic and anaerobic cultures can be made from a single specimen.

A similar situation exists when the surgeon encounters one or more walled-off abscesses in an organ, or in the thorax, abdomen, or pelvis, during the course of a surgical procedure for another purpose. In anticipation of this, the laboratory should arrange to have stored, in the sterile surgical supplies, a kit for obtaining the contents of such abscesses so that specimens can be delivered promptly to the laboratory for processing. Every effort should be made to avoid the use of swabs for collecting a small amount of specimen, when a large amount is actually present. A swab can justifiably be used to collect very small amounts of pus, or pus from sites that require care, e.g., from the eye. When pieces of tissue are obtained from the abscess wall, the laboratory technician should either grind the tissue, using a small amount of sterile broth as a diluent, or mince the tissue into very small pieces using sterile scissors. Aerobic and anaerobic cultures should be prepared as indicated on “Culture”.

Infected lacerations, penetrating wounds, postoperative wounds, burns, and decubitus ulcers

No single standard procedure for specimen collection can be formulated. However, certain fundamental guidelines should be followed to obtain the best possible specimen for laboratory analysis. After carefully cleaning the site, the surgeon should look beneath the surface for collections of pus, devitalized tissue, the oozing of gas (crepitation), or any other abnormal sign. Segments of the tissue involved that are to be used for cultures should be removed and placed on sterile gauze for processing as described above. Pus or other exudate should be carefully collected and placed in a sterile tube. Swabs may be used if necessary.

Sinus tract or lymph node drainage

When a sinus tract or lymph node shows evidence of spontaneous drainage, the drainage material should be collected carefully, using a sterile Pasteur pipette fitted with a rubber bulb, and placed in a sterile tube. If discharge is not evident, the surgeon should obtain the purulent material using a sterile syringe and needle or probe. Again the use of swabs should be avoided if at all possible.


The abnormal accumulation of fluid within a body cavity such as the pleural space, a knee joint, or the peritoneal space, requires a surgical procedure to aspirate the accumulated material into a sterile container for subsequent delivery to the laboratory for microbiology and cytology. In those cases where the accumulation persists and an open drain is put in place, it is necessary to collect the drainage fluid in an aseptic manner for subsequent culture and other tests.

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