Pocket Guide to Clinical Microbiology, Third Edition
Authors: Partrick R. Murray1, Yvonne R. Shea2Category: Clinical Microbiology
This publication will do for the field of clinical laboratory immunology what the Pocket Guide to Clinical Microbiology has done for clinical microbiology. Intended as a convenient guide to the use and interpretation of immunologic tests, it covers immunologic diseases and other diseases in which immunologic tests are useful for diagnosis and focuses on the appropriate use of such tests.
Providing a ready reference to the most common immunological tests in use today, it allows the reader to judge the suitability and appropriateness of tests ordered and aids in their interpretation. Suggestions for auxiliary tests are also offered.
A Quick Reference is provided at the beginning of each topic, leading to a more detailed description of each point. A list of common abbreviations used in clinical immunology and a thorough glossary are also included.
Electronic Only, 274 pages, index.
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Section 1 : Taxonomic Classification of Medically Important Microorganisms
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Abstract:
This section talks about taxonomic classification of medically important microorganisms, which are bacteria, human viruses, fungi and parasites. In bacteria, Eubacteria have been subdivided into at least 11 divisions, including 5 with medically important organisms that include roteobacteria, "gram-positive" bacteria, spirochaetes, aerobic and anaerobic bacilli in RNA superfamily V and chlamydiae. Taxonomic classification of human viruses includes single-stranded, nonenveloped DNA viruses, double-stranded, nonenveloped DNA viruses and double-stranded, enveloped DNA viruses. The taxonomic classification of fungal organisms is complex because fungi can be classified by different methods. The correct phylogenic taxonomy for fungi is represented in the section. Fungi, or the kingdom Eumycota, are divided into four divisions: chytridomycota, zygomycota, ascomycota, and basidiomycota. Taxonomic classification of parasites talks about various kingdoms, including protozoa and chromista.
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Section 2 : Indigenous and Pathogenic Microbes of Humans
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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.
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Section 3 : Specimen Collection and Transport
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This section presents tables that summarize and document the salient features of the specimen collection and transport. The most important aspects of microbiological testing are collection of the right specimen and transport of the specimen to the testing site in a manner that ensures the reliability of the diagnostic procedure (e.g., culture, microscopy, and antigen or antibody tests). Table 3.1 provides a list of bacteriology along with collection and transport guidelines. Specimen type includes abscess, blood, bone marrow aspirate and burn. Table 3.2 includes specimen collection and transport guidelines for infrequently encountered bacteria. Table 3.3 presents guidelines for collection of specimens for anaerobic culture. The section also talks about virology and general specimen guidelines. Table 3.4 focuses on mycology and collection and transport guidelines. Table 3.5 is on parasitology. Table 3.6 provides guidelines for processing stool specimens for parasites. Table 3.7 provides a list of agents of bioterrorism along with specimen guidelines.
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Section 4 : Bacterial Diagnosis
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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.
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Section 5 : Viral Diagnosis
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This section talks about viral diagnosis. Viral infections have historically been diagnosed by culture in primary or continuous cell lines and by detection of antibody responses to infection. This has changed in recent years. Traditional cell cultures in glass test tubes or plastic petri dishes have been replaced in many laboratories by the shell vial culture method. Antigen capture immunoassays, which allow for the direct detection of viruses in clinical specimens, have also been developed. The section summarizes the tests currently available for the laboratory diagnosis of the most common viral infections. Table 5.1 lists the detection methods for viruses. Table 5.2 presents cells used for viral isolation. Specific diagnostic tests were performed for RNA viruses which include alphavirus, arenavirus, astrovirus, calicivirus, and rotavirus and DNA viruses that include adenovirus, cytomegalovirus (CMV) and Epstein-Barr virus (EBV). Table 5.3 includes EBV serologic profiles under different conditions. Table 5.4 offers Hepatitis B virus markers in different stages of infection and convalescence. Transmissible spongiform encephalopathies diagnosis is based on clinical history, and histopathologic examination of brain tissues diagnosis has also been made on the basis of examination of tonsillar and appendix biopsy specimens.
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Section 6 : Fungal Diagnosis
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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.
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Section 7 : Parasitic Diagnosis
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Diagnosis of most parasitic infections has traditionally been made by the microscopic examination of clinical material. This requires that highly trained technologists spend a significant amount of time examining individual specimens. In recent years, immunoassays have been developed to detect the more common parasites (e.g., Entamoeba histolytica, Giardia lamblia, and Cryptosporidium parvum). This section summarizes the tests currently available for the laboratory diagnosis of the most common parasitic infections. Table 7.1 lists detection methods for parasites. Microscopy contains different Stains which includes acid-fast trichrome chromotrope stain, calcofluor white stain and delafield's hematoxylin stain. Specific diagnostic tests were performed for free-living amebae, intestinal and urogenital protozoa, blood and tissue protozoa. Table 7.2 includes trophozoites of common intestinal amebae. Table 7.3 presents cysts of common mtestinal amebae. Table 7.4 is on trophozoites of flagellates. Table 7.5 is about cysts of flagellates. Table 7.6 offers morphological characteristics of ciliates, coccidia, microsporidia, and tissue protozoa. Table 7.7 lists morphological characteristics of protozoa found in blood. Table 7.8 provides morphological characteristics of blood and tissue nematodes. Table 7.9 is on morphological characteristics of helminths. Table 7.10 is key to identification of common arthropods.
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Section 8 : Vaccines, Susceptibility Testing Methods, and Susceptibility Patterns
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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.
There are no separately available contributors for this publication.