Pocket Guide to Clinical Microbiology, Third Edition

This section talks about indigenous and pathogenic microbes of humans. Humans are exposed to microbes at birth, which leads to one of three outcomes: transient colonization, persistent colonization, or pathogenic interaction. The majority of organisms is unable to become established on the skin or mucosal surfaces and is considered an insignificant finding when recovered in clinical specimens. The section has a table that lists the organisms most commonly recovered from the body surfaces of healthy individuals, and serves as an interpretive guideline for cultured specimens. Most diseases in humans are caused by infections with endogenous bacteria and yeasts or exposure to opportunistic moulds, parasites, and viruses. However, some interactions between microbes and humans commonly lead to disease. The most common microbes responsible for human disease are summarized in the section. Arthropods, parasites in their own right, can serve as vectors for human disease. A listing of the most common arthropod vectors and their associated diseases is also included. The section includes two other tables which list fungi and parasites isolated from humans and their geographic distribution.

This section provides guidelines for the selection and processing of specimens for the detection of specific bacteria. Testing can be subdivided into microscopy, culture, antigen tests (including immunoassays and molecular diagnostic tests), and antibody tests. Although it is impossible to provide guidelines for all possible infections, the most common bacteria associated with human disease are included. The section has been expanded to include summary tables of identification tests as well as a more detailed discussion of the immunological detection of organisms where appropriate. Tables have been provided that offer recommendations for gram stain and plating media, and list screening specimens for routine bacterial culture and processing specimens for mycobacterial identification. Microscopy includes acridine orange stain, auramine-rhodamine stain, direct fluorescent-antibody stain and gram stain, kinyoun stain. Primary plating media of bacteria includes bacteroides bile-esculin (BBE) agar, blood agar and brilliant green agar. A large number of media have been developed for the selective isolation of Campylobacter spp. from stool specimens. Most contain a brucella basal medium, which preferentially supports the growth of Campylobacter spp. Primary plating media of Mycobacteria includes American thoracic society medium, dubos broth, middlebrook 7H11 agar and petragnani medium. Specific diagnostic tests performed for aerobic gram-positive cocci, aerobic gram-positive rods, acid-fast and partially acid-fast gram-positive rods have been listed in a table. General comments about molecular methods for the identification of bacteria are discussed in the section.

This section talks about fungal diagnosis and mycology specimen collection and transport guidelines. Table 6.1 lists methods for the identification of fungi. Microscopy includes acridine orange stain, Calcofluor white Stain, fluorescent-antibody stain and Kinyoun Stain. Table 6.2 includes characteristic fungal elements seen by direct examination of clinical specimens. Primary plating media includes birdseed agar, brain heart infusion Agar (BHI), dermatophyte test medium (DTM) and mycosel (mycobiotic) agar. Table 6.3 presents mycology plating guide. Specific diagnostic tests were performed for different species which includes Aspergillus Species, Blastomyces dermatitidis and Candida species. Microscopy and culture are sensitive detection methods for Aspergillus species. Molecular methods are being developed for both direct specimen and Aspergillus spp. identification. Table 6.4 provides cultural and biochemical characteristics of yeasts frequently isolated from clinical specimens. Table 6.5 offers characteristics of selected Trichosporon species. Table 6.6 lists characteristics of Aspergillus species. Table 6.7 is on opportunistic moniliaceous fungi.

This section is about vaccines, susceptibility testing methods, and susceptibility patterns. Two important control measures for infectious diseases are vaccination to prevent infection and use of antimicrobial therapy to eradicate infections. The section provides information for both approaches. Tables summarize immunization recommendations for pediatric and adult patients. Information regarding antimicrobial agents is subdivided into three sections: antimicrobial susceptibility testing methods, pharmacokinetic properties of antimicrobial agents, and antimicrobial susceptibility patterns. The susceptibility testing guidelines provided by the National Committee for Clinical Laboratory Standards (NCCLS) are summarized in tables.