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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

Commonly encountered clinical conditions and the most frequent etiological agents

Surgical specimens

Surgical specimens may be obtained by aspiration of a localized abscess or other surgical procedures. The surgeon should be advised to obtain several small representative tissue samples and any purulent exudate. If possible, cotton swabs should be avoided. The exudate should be collected using a needle and syringe. If cotton swabs must be used, as much exudate as possible should be collected and dispensed into appropriate containers for dispatch to the laboratory. Upon receipt, the laboratory should review the information provided and then plan cultures for the organisms likely to be found in the particular specimen.

A few examples of conditions and organisms found in different types of surgical specimen are given below:


The peritoneal cavity is likely to contain Gram-negative enteric bacteria, Gram-negative anaerobic rods (Bacteroides fragilis), and clostridia.

• A walled-off abscess may contain any type of organism, either single or multiple species: Gram-positive cocci and Gram-negative bacilli are most frequently isolated. Anaerobic bacteria and amoebae may also need to be considered, depending on the abscess site.

Lymph nodes are frequently involved in systemic infections. They become swollen and often quite tender, and purulent exudate frequently accumulates. If the node is fluctuant, the liquid contents can be aspirated by a physician. Lymph node biopsies or aspirates from children should be cultured for Mycobacterium tuberculosis and other mycobacteria. In addition to being cultured for staphylococci, streptococci, and Gram-negative enterics, lymph nodes may be good specimens for the diagnosis of systemic and subcutaneous mycoses (histoplasmosis, sporotrichosis).

Skin and subcutaneous tissue are prime targets for both abscesses and wound infections. As a general rule, subcutaneous abscesses are caused by staphylococci. Open, weeping skin lesions often involve β-haemolytic streptococci and/or staphylococci, as in impetigo. Another variety of skin lesion requiring some surgical intervention, and often seen as a hospital-acquired infection, is decubitus ulcer or bed sore. The bacteria are frequently skin commensals or intestinal flora that have proliferated in the most external part of the ulcer and create an unpleasant odour and appearance. The organisms most commonly isolated from biopsy tissue are enteric bacilli; the same organisms may be found in cultures of the superficial exudate. It is not always possible to evaluate the role of these organisms in decubitus ulcers, but healing requires that the ulcer be kept clean, dry, and free of bacteria. Occasionally organisms in a decubitus ulcer may find their way into the blood stream, producing serious complications.

Burns, especially second- and third-degree burns, are prone to infection with a variety of bacterial species. It is very important that careful surgical débridement be carried out prior to obtaining material for culture. Staphylococci and Pseudomonas aeruginosa are most commonly encountered.

Exudates. Sometimes a serous or purulent fluid will collect in a cavity that normally possesses a very small amount of sterile fluid, e.g., the pericardial sac, pleural cavity, bursa, or joint. Needle aspiration under aseptic conditions will yield a laboratory specimen from which the infecting organism may be isolated and identified. Bacteria are usually the cause, but fungi or viruses may also be responsible. The infections are usually monospecific, but mixed aerobic and anaerobic infections do occur. Aspirates from the pleural cavity may yield pneumococci, streptococci, H. influenzae, anaerobic streptococci, or Bacteroides spp.

Penetrating wounds

Any lesion caused by a penetrating object that breaks the skin is likely to contain a mixture of microorganisms; these organisms are generally part of the skin flora or of the normal microbial flora of soil and water. A penetrating wound involving damage to the intestines will lead to an even greater threat because the intestinal flora may contribute to infection of the wound. In the case of an animal bite, the flora of the oral cavity of the biting animal will also be present. Rabies is one of the most important infections due to animal bite in most parts of the world and prompt laboratory testing and prophylactic immunization are essential in known or suspected cases of rabies. However, rabies will not be dealt with in detail in this manual.

Penetrating or cutting wounds may be caused by sharp or blunt objects. Metal, glass, wood, etc. are frequently responsible for penetrating wounds, whether caused by accident or deliberately (e.g., stab or gun shot). Tetanus resulting from a penetrating wound is a life-threatening disease in a nonimmunized individual. Similarly, wound botulism may go undiagnosed, if the physician and the microbiologist are not aware of this possibility. The diagnoses of tetanus and botulism are best made clinically, and laboratory support should be provided by a central reference laboratory. People working with animals or their products are at risk of infection with spores of Bacillus anthracis, which may gain access through small wounds or skin abrasions and produce the typical black eschar of anthrax. Other soil organisms, such as Clostridium perfringens, may be involved in deep penetrating wounds and give rise to gas gangrene.

Animal bites or scratches occur frequently in both urban and rural areas. The bite may be from a domestic pet, a farm animal, or a wild animal. Rabies must be the prime and immediate concern. Once the possibility of rabies has been eliminated, the other possible etiological agents are many and varied. The mouths of all animals contain a heterogeneous flora consisting of aerobic and anaerobic bacteria, yeasts, protozoa, and viruses. Infections resulting from bites or scratches are predominantly caused by bacteria. A prime example is infection by Pasteurella multocida, which often follows a dog or cat bite if the bite has not been properly cleansed and treated. Human bites may sometimes result in a serious mixed infection of aerobic and anaerobic bacteria.

Nosocomial wound infections

One of the main concerns in the care and treatment of hospitalized patients is that they should not be harmed in the course of the diagnosis and treatment of their illness. Unfortunately, 5 - 10% of hospitalized patients do acquire an infection while in hospital. Nosocomial infections are costly and can usually be avoided or greatly reduced. Many hospital-acquired infections are known to occur in surgical departments. The rate of postoperative wound infection varies from hospital to hospital, and within a given hospital is likely to be highest in patients who have undergone abdominal, thoracic, or orthopaedic surgery. Surgical wound infections may occur shortly after surgery or several days postoperatively. The site of infection may be limited to the suture line or may become extensive in the operative site. Staphylococcus aureus (usually penicillin-resistant, and now often meticillin-resistant) is the biggest offender, followed closely by E. coli and other enteric bacteria. Anaerobic bacteria from the patient’s large bowel may gain access to the operative site, making a mixed infection a serious and fairly frequent occurrence in hospitals in which the postoperative wound care and infection prevention programmes are weak. Bacteroides fragilis and, occasionally, Clostridium perfringens may invade the blood stream, resulting in a systemic and frequently fatal postoperative infection.

An infrequent but challenging infection may follow dental or oral surgery, when a sinus tract from the inside works its way to the skin surface on the face or neck and the discharge contains the “sulfur” granules of actinomycosis.

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