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A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2013 Recommendations by the Infectio

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A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2013 Recommendations by the Infectio Clinical Infectious Diseases Advance Access published July 10, 2013 IDSA GUIDELINES A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2013 Recommendations by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM)a Ellen Jo Baron,1,2 J. Michael Miller,3 Melvin P. Weinstein,4 Sandra S. Richter,5 Peter H. Gilligan,6 Richard B. Thomson Jr.,7 Paul Bourbeau,8 Karen C. Carroll,9 Sue C. Kehl,10 W. Michael Dunne,11 Barbara Robinson-Dunn,12 Joseph D. Schwartzman,13 14 15 16 17 17 17 Kimberle C. Chapin, James W. Snyder, Betty A. Forbes, Robin Patel, Jon E. Rosenblatt, and Bobbi S. Pritt Downloaded from 1Department of Pathology, Stanford University School of Medicine, Stanford, California; 2Cepheid, R&D, Sunnyvale, California; 3Microbiology Technical Services, LLC, Dunwoody, Georgia; 4Department of Medicine and Pathology, Robert Wood Johnson Medical School, New Brunswick, New Jersey; 5Department of Clinical Pathology, Cleveland Clinic, Cleveland, Ohio; 6Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina; 7Department of Pathology, NorthShore University HealthSystem, Evanston, Illinois; 8Scientific Affairs, BD Diagnostics, Sparks, Maryland; 9Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; 10Department of 11 Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin; bioMerieux, Inc., Durham, North Carolina, and Department of Pathology and http://cid.oxfordjournals.org/ Immunology, Washington University School of Medicine, St. Louis, Missouri; 12Department of Pathology, William Beaumont Hospital to Beaumont Health System, Royal Oak, Michigan; 13Department of Pathology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire; 14Department of Pathology, Brown Alpert Medical School, Providence, Rhode Island; 15Department of Laboratory Medicine, University of Louisville, Louisville, Kentucky; 16Department of Pathology, Virginia Commonwealth University Medical Center, Richmond, Virginia; and 17Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 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 by guest on July 11, 2013 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 Re- spiratory Infections, Lower Respiratory Tract infections, Infections of the Gastrointestinal Tract, Intraabdomi- nal 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 de- tailed 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. Keywords. laboratory diagnosis; microbiology testing; specimen processing; physician-laboratory communica- tion; medical laboratories. Received 19 April 2013; accepted 22 April 2013. aAlthough accurate and authoritative, IDSA considers adherence to the recom- mendations in this guide to be voluntary, with the ultimate determination regarding Clinical Infectious Diseases their application to be made by the physician in the light of each patient's individual © The Author 2013. Published by Oxford University Press on behalf of the Infectious circumstances. Diseases Society of America. All rights reserved. For Permissions, please e-mail: Correspondence: Ellen Jo Baron, PhD, Cepheid, R&D, 1315 Chesapeake Terrace, [email protected]. Sunnyvale, CA 94089, USA ([email protected]). DOI: 10.1093/cid/cit278 Guide to Utilization of the Microbiology Lab • CID • 1 EXECUTIVE SUMMARY Table Introduction-1. Transport Issues (General Guide)a Introduction Collection Device, Unlike other areas of the diagnostic laboratory, clinical microbi- Specimen Specimen Temperature, and ology is a science of interpretive judgment that is becoming Type Required Ideal Transport Time more complex, not less. Even with the advent of laboratory auto- Aerobic bacterial Tissue, fluid, aspirate Sterile container, RT, culture biopsy, etc immediately mation and the integration of genomics and proteomics in mi- Swab (2nd choice) – Swab transport crobiology, interpretation of results still depends on the quality flocked swabs are device, RT, 2 h of the specimens received for analysis. Prokaryotic microorgan- recommended isms, while genetically less complex than multicellular eukary- Aerobic and Tissue, fluid, aspirate, Sterile anaerobic anaerobic biopsy, etc container, RT, otes, are uniquely suited to adapt to environments where bacterial culture immediately antibiotics and host responses apply pressures that encourage Swab (2nd choice) – Anaerobic swab their survival. A laboratory instrument may or may not detect flocked swabs are transport device, effective RT, 2 h those mutations, so a specialist in microbiology is needed to facil- Fungus culture; Tissue, fluid, aspirate, Sterile container, RT, itate microbiology laboratory result interpretation. Clearly, all AFB culture biopsy, etc 2h microbes grow, multiply, and die very quickly. If any of those Swab (2nd choice) (for Swab transport events occur during specimen collection, transport, or storage, yeast and device, RT, 2 h superficial the results of analysis will be compromised and interpretation mycobacterial could be misleading. Therefore, attention to preanalytical speci- infections only) Downloaded from men management in microbiology is critical to accuracy. Virus culture Tissue, fluid, aspirate, Viral transport media, biopsy, etc on ice, immediately fi Physicians need con dence that the results provided by the Swab – flocked swabs Virus swab transport microbiology laboratory are accurate, significant, and clinically are recommended device, RT, 2 h relevant. Anything less is below the community standard of care. Suspected agent Refer to Centers for Disease Control and of bioterrorism Prevention website: http://emergency.cdc. http://cid.oxfordjournals.org/ In order to provide that level of quality, however, the laboratory gov/documents/PPTResponse/ requires that all microbiology specimens be properly selected, col- table2specimenselection.pdf lected, and transported to optimize analysis and interpretation. Serology 5 mL serum Clot tube, RT, 2 h Because result interpretation in microbiology depends entirely on Antigen test As described in the Closed container, laboratory RT, 2 h the quality of the specimen submitted for analysis, specimen specimen collection management cannot be left to chance, and those that collect spec- manual imens for microbiologic analysis must be aware of what the phy- NAAT 5 mL plasma EDTA tube, RT, 2 h sician needs as well as what the laboratory needs, including Other specimen Closed container, by guest on July 11, 2013 RT, 2 h ensuring that specimens arrive at the laboratory for analysis as quickly as possible after collection (Introduction-Table 1). Abbreviations: NAAT, nucleic acid amplification test; RT, Room Temperature. a Contact the microbiology laboratory regarding appropriate collection and At an elementary level, the physician needs answers to 3 very transport devices and procedures since transport media such as Cary-Blair or basic questions from the laboratory: Is my patient’s illness parasite preservative transport for stool specimens, boric acid for urines, caused by a microbe? If so, what is it? What is the susceptibility specialized containers for Mycobacterium tuberculosis are often critical for successful examination. The time from collection to transport listed will profile of the organism so therapy can be targeted? To meet optimize results; longer times may compromise results. those needs, the laboratory requires very different information. The microbiology laboratory needs a specimen that has been appropriately selected, collected, and transported to the labora- tory for analysis. Caught in the middle, between the physician interactions. Clearly, the best outcomes for patients are the and laboratory, are those who select and collect the specimen result of strong partnerships between the clinician and the lab- and who may not know or understand what the physician or oratorian specialist. This document illustrates this partnership the laboratory needs to do their work. Enhancing the quality of and emphasizes the importance of appropriate specimen man- the specimen is everyone’s job,
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