Ellen Jo Baron, J. Michael Miller, Melvin P. Weinstein, Sandra S. Richter, Peter H. Gilligan, Richard B. Thomson Jr., Paul Bourbeau, Karen C. Carroll, Sue C. Kehl, W. Michael Dunne, Barbara Robinson-Dunn, Joseph D. Schwartzman, Kimberle C. Chapin, James W. Snyder, Betty A. Forbes, Robin Patel, Jon E. Rosenblatt, and Bobbi S. Pritt

Clin Infect Dis. (2013) doi: 10.1093/cid/cit278

The critical role of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by both laboratory and clinical experts, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. Sections are divided into anatomic systems, including Bloodstream Infections and Infections of the Cardiovascular System, Central Nervous System Infections, Ocular Infections, Soft Tissue Infections of the Head and Neck, Upper Respiratory Infections, Lower Respiratory Tract infections, Infections of the Gastrointestinal Tract, Intraabdominal Infections, Bone and Joint Infections, Urinary Tract Infections, Genital Infections, and Skin and Soft Tissue Infections; or into etiologic agent groups, including Tickborne Infections, Viral Syndromes, and Blood and Tissue Parasite Infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. There is redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a reference to guide physicians in choosing tests that will aid them to diagnose infectious diseases in their patients.

Fulltext

Part I: Clinical Conditions, Diseases and Syndromes
Chapter 1. Infections of the Respiratory Tract and Associated Structures
Chapter 2. Infections of the Gastrointestinal Tract and Associated Structures
Chapter 3. Infections of the Urinary Tract
Chapter 4. Infections of the Genital System
Chapter 5. Prenatal, Perinatal and Puerperal Infections
Chapter 6. Infections of the Central Nervous System
Chapter 7. Skin Infections
Chapter 8. Wound and Soft Tissue Infections, Local and Generalised Sepsis
Chapter 9. Infections of the Cardiovascular System
Chapter 10. Infections of the Reticuloendothelial System
Chapter 11. Infections of the Skeletal System
Chapter 12. Eye Infections
Chapter 13. Thryoditis
Chapter 14. Multi-system, Generalised and Disseminated Infections
Chapter 15. Fever of Undetermined Origin (Pyrexia of Unknown Origin)
Part II: Organisms
Chapter 16. Viruses
Chapter 17. Bacteria
Chapter 18. Fungi
Chapter 19. Animal Parasites
Part III: Treatments
Chapter 20. Antivirals
Chapter 21. Antibacterials
Chapter 22. Antifungals
Chapter 23. Antiparasitic Agents
Part IV: Laboratory Procedures
Chapter 24. Collection, Handling and Processing of Specimens
Chapter 25. Microscopy
Chapter 26. Culture
Chapter 27. Identification of Isolates
Chapter 28. Antimicrobial Susceptibility Testing
Chapter 29. Non-cultural Methods
Chapter 30. Reporting Results

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Introduction to Infectious Diseases
Robert B. Couch

Infections of the Respiratory System
Purushothama V. Dasaraju and Chien Liu

Microbiology of the Circulatory System
Lawrence L. Pelletier, Jr.

Microbiology of the Gastrointestinal Tract
Sherwood L. Gorbach

Microbiology of the Nervous System
Richard T. Johnson

Microbiology of the Genitourinary System
Allan R. Ronald and Michelle J. Alfa

Microbial Infections of Skin and Nails
Raza Aly

Microbiology of Dental Decay and Periodontal Disease
Walter J. Loesche

Bone, Joint, and Necrotizing Soft Tissue Infections
Jon T. Mader and Jason Calhoun