A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiologya
Open accessAbstract
The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician/advanced practice provider and the microbiologists who provide enormous value to the healthcare team. This document, developed by experts in laboratory and adult and pediatric 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. This document presents a system-based approach rather than specimen-based approach, and includes bloodstream and cardiovascular system infections, central nervous system infections, ocular infections, soft tissue infections of the head and neck, upper and lower respiratory infections, infections of the gastrointestinal tract, intra-abdominal infections, bone and joint infections, urinary tract infections, genital infections, and other skin and soft tissue infections; or into etiologic agent groups, including arthropod-borne 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 emphasized. There is intentional redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a guidance for physicians in choosing tests that will aid them to quickly and accurately diagnose infectious diseases in their patients.
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Current guidelines recommend targeted PCRs in specific situations rather than routine syndromic testing.
“Current guidelines therefore recommend targeted PCRs in specific situations rather than routine syndromic testing (10–14).”
From Optimized use of the FilmArray Meningitis/Encephalitis panel for early discontinuation of antibiotic therapy (2026) · cites this paper as [11]
In XIV. VIRAL SYNDROMES (page unavailable), the guide recommends testing for the most likely agents and says broad initial testing for numerous viruses is typically not cost-effective. The Stool Culture section also calls for selective use of multiplex tests. These passages support selective testing, but the guide does not make the claimed general recommendation to use targeted PCRs instead of routine syndromic testing across conditions; its Bronchitis and Bronchiolitis section notes that broad respiratory NAAT panels have largely replaced older tests in many institutions. (LLM, conf=0.83)
Experimental — accuracy not yet measuredIn our cohort, a targeted PCR approach would have missed 10 (18%) bacterial meningitis cases caused by H. influenzae, S. agalactiae, and E. coli K1.
“In our cohort, such an approach would have missed 10 (18%) bacterial meningitis cases caused by H. influenzae, S. agalactiae, and E. coli K1 (10–14).”
From Optimized use of the FilmArray Meningitis/Encephalitis panel for early discontinuation of antibiotic therapy (2026) · cites this paper as [11]
Table 6 (Etiologic Agents; page unavailable) lists H. influenzae, S. agalactiae, and E. coli as bacterial meningitis agents. The guide does not evaluate the targeted PCR approach or establish which organisms it would miss. The 10 cases (18%) are presented as the citing authors’ own cohort result, not as a finding from this guide. (LLM, conf=0.79)
Experimental — accuracy not yet measured
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Flagged first, then by citations
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Cited by
Sorted by citations
Nicolau-Guillaumet, N., Moutel, M., Plouzeau-Jayle, C., Pean de Ponfilly, G., Courbin, V., Ranc, A.-G., Revillet, H., Mourvillier, B., Hentzien, M., Muggeo, A., et al. (2026) · Microbiology Spectrum · doi:10.1128/spectrum.00566-26 · Cited by 1 · see citing works
- Authors
- Miller, J. M., Binnicker, M. J., Campbell, S., Carroll, K. C., Chapin, K. C., Gilligan, P. H., Gonzalez, M. D., Jerris, R. C., Kehl, S. C., Patel, R., Pritt, B. S., Richter, S. S., Robinson-Dunn, B., Schwartzman, J. D., Snyder, J. W., Telford, S., Theel, E. S., Thomson, R. B., Weinstein, M. P., & Yao, J. D.
- Affiliations
- Microbiology Technical Services, LLC, Dunwoody, Georgia
- Mayo Clinic (US)
- Yale University (US)
- Johns Hopkins Medicine (US)
- Rhode Island Hospital (US)
- University of North Carolina at Chapel Hill (US)
- Children's Healthcare of Atlanta (US)
- Medical College of Wisconsin (US)
- Cleveland Clinic (US)
- Beaumont Health (US)
- Dartmouth–Hitchcock Medical Center (US)
- University of Louisville (US)
- Tufts University (US)
- Endeavor Health (US)
- Rutgers, The State University of New Jersey (US)
- Corresponding author
- Miller, J Michael
- ORCID
- Venue
- Clinical Infectious Diseases
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-06-28
- Volume
- 67
- Issue
- 6
- Pages
- e1-e94
- ISSN
- 1058-4838 (ISSN-L)
- 1537-6591
- PMC
- PMC7108105
- OpenAlex
- W4211113261
- Cited by
- 641
- References
- 277
- Citations by year
- 2026: 74 · 2025: 104 · 2024: 94 · 2023: 108 · 2022: 87 · 2021: 76 · 2020: 57 · 2019: 34 · 2018: 7
- FWCI
- 33.75
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Clinical Infectious Diseases (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Pfizer
- Infectious Diseases Society of America
- Cleveland Clinic
- Beaumont Health System
- Dartmouth College
- BioFire Diagnostics
- Astellas Pharma
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
- Health Sciences › Medicine › Physiology › Clinical Laboratory Practices and Quality Control
- Health Sciences › Medicine › Epidemiology › Sepsis Diagnosis and Treatment
- Keywords
- infectious disease diagnosis, diagnostic test selection, sample collection, sample transport, bloodstream infection, central nervous system infection, respiratory infections, urinary tract infection, bone and joint infections, skin and soft tissue infections, arthropod-borne diseases, viral syndrome, parasitic infection, turnaround time
- MeSH terms
- Communicable Disease Control, Communicable Diseases, Humans, Respiratory Tract Infections, Societies, Scientific, Specimen Handling, United States, Soft Tissue Infections, Clinical Laboratory Techniques
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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