Summary
Rapid advances in genomic sequencing are reshaping microbial classification and nomenclature, creating challenges for clinical microbiology laboratories. While some updates improve patient care, others disrupt established workflows. Laboratories must carefully evaluate the clinical relevance of proposed name changes to ensure accurate and consistent reporting.
Isabella W. Martin, MD
March 2026—Rapid advances in genomic sequencing are reshaping how microorganisms are classified and named. While these changes improve scientific accuracy and deepen understanding of infectious diseases, they also create practical challenges for clinical microbiology laboratories and the patient-facing health care providers who rely on clear and consistent laboratory reports to diagnose and treat patients. A group of members of the CAP Microbiology Committee recently published an opinion paper to spread awareness among nonlaboratory health care providers about the complexities of this situation and to urge collaboration around adoption of new nomenclature in the clinical laboratory (Dien Bard J, et al. Clin Infect Dis. Published online Sept. 23, 2025. doi:10.1093/cid/ciaf474).
Taxonomy is the science of grouping organisms based on shared traits and genetic relationships, while nomenclature refers to the official names assigned to those organisms. Each major group of microbes follows its own international naming rules. As genetic technologies such as whole genome sequencing become more common, basic scientists are discovering that many organisms are more—or less—closely related than previously thought. This has led to frequent updates in microbial names.
For clinical laboratories, these changes have direct downstream effects. Updated nomenclature may appear in organism identification systems before clinicians are familiar with the new names, creating potential for confusion in result interpretation, antimicrobial decision-making, and recognition of recurrent infections. Inconsistent adoption of nomenclature changes across diagnostic platforms and electronic health records further compounds this challenge.
In some cases, nomenclature updates clearly benefit patient care. Recognition of newly defined species has improved the understanding of antimicrobial resistance patterns and supported the development of species-specific susceptibility testing criteria. For example, description of Staphylococcus pseudintermedius as an important and often multidrug-resistant veterinary pathogen enabled not only its recognition as a cause of opportunistic infections in immunocompromised patients but also the development of species-specific antimicrobial susceptibility testing breakpoints to optimize treatment. In other cases, however, name changes driven primarily by phylogenetic data may offer limited clinical value while disrupting established diagnostic and treatment workflows. An example of this can be found in the proposed change of the genus name Candida into multiple different teleomorph names such as Pichia, Debaryomyces, Torulopsis, and Kluyveromyces.
Complicating the nomenclature landscape is that the “rules” for nomenclature vary by organism group. Bacterial nomenclature is governed by the International Code of Nomenclature of Prokaryotes, which regulates naming but does not designate an “official” taxonomy. As a result, both older and newer names may remain valid, requiring laboratories to make deliberate choices about which names to report. Fungal nomenclature, governed by the International Association for Plant Taxonomy, has undergone particularly extensive changes following the adoption of DNA-based classification and the “One Fungus, One Name” principle, sometimes outpacing clinical guidance and patient-facing provider familiarity. Parasite nomenclature, governed by the International Commission on Zoological Nomenclature, has been less disruptive to routine laboratory practice, while viral taxonomy, overseen by the International Committee on Taxonomy of Viruses, is structured in a way that largely preserves clinically familiar virus and disease names despite taxonomic reclassification.
New expert groups, including international committees focused on prokaryotic and fungal nomenclature, are working to provide clearer guidance for clinically relevant name changes. For example, an ad hoc committee focused on the nomenclature of clinical fungi was formed in 2023 under the auspices of the International Society for Human and Animal Mycology, European Confederation of Medical Mycology, and Fungal Diagnostics Laboratory Consortium, with the goal of creating a consensus guideline for fungal name changes for clinical use. These efforts aim to balance scientific accuracy with the need for stability, clarity, and effective communication in laboratory reporting.
Members of the CAP’s Microbiology Committee and Checklists Committee have recognized the challenges associated with changes in nomenclature in the clinical laboratory as well as the varied potential impacts to clinical care. The CAP checklist requirement pertaining to taxonomy and nomenclature (MIC.11375), first implemented in 2014, has evolved over the past decade in response to these challenges. In its current form it emphasizes consistency and thoughtfulness in nomenclature adoption, rather than mandatory adoption of every taxonomic update. Laboratories are encouraged to evaluate whether a proposed name change is scientifically valid, clinically meaningful, and operationally feasible before implementation. Additionally, the CAP’s microbial proficiency testing challenges and their associated educational material foster accurate and adequate organism identification, reinforcing best practices in patient care.
As microbial taxonomy continues to evolve, clinical laboratories play a critical role in translating scientific advances into actionable clinical information. Careful, coordinated adoption of nomenclature changes—aligned with laboratory capabilities and clinical impact—will remain essential to maintaining high-quality diagnostic services and supporting safe, effective patient care.
Dr. Martin was vice chair of the CAP Microbiology Committee through 2025. She is medical director of the clinical microbiology laboratory at Dartmouth-Hitchcock Medical Center, Lebanon, NH, and associate professor of pathology and laboratory medicine, Dartmouth Geisel School of Medicine, Hanover, NH.