Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases

Authoring Organization

Publication Month/Year

March 5, 2024

Last Updated Month/Year

March 12, 2024

Supplemental Implementation Tools

Document Type


External Publication Status


Country of Publication


Document Objectives

The critical nature 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 experts in both adult and pediatric laboratory and clinical medicine, 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 arboviral 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. In addition, the pediatric needs of specimen management are also addressed. 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.

Inclusion Criteria

Male, Female, Adolescent, Adult, Child, Infant, Older adult

Health Care Settings

Laboratory services

Intended Users

Epidemiology infection prevention, nurse, nurse practitioner, physician, physician assistant



Diseases/Conditions (MeSH)

D007753 - Laboratories, D007755 - Laboratories, Hospital, D059232 - Laboratory Personnel, D013677 - Medical Laboratory Science, D064790 - Clinical Laboratory Services, D019411 - Clinical Laboratory Techniques


specimen management, microbiology specimens, Microbiology Laboratory, specimen handling

Source Citation

J Michael Miller, Matthew J Binnicker, Sheldon Campbell, Karen C Carroll, Kimberle C Chapin, Mark D Gonzalez, Amanda Harrington, Robert C Jerris, Sue C Kehl, Sixto M Leal, Robin Patel, Bobbi S Pritt, Sandra S Richter, Barbara Robinson-Dunn, James W Snyder, Sam Telford, Elitza S Theel, Richard B Thomson, Melvin P Weinstein, Joseph D Yao, Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2024 Update by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM), Clinical Infectious Diseases, 2024;, ciae104, https://doi.org/10.1093/cid/ciae104