Updating taxonomy is critical for clinical labs.
Controversy surrounding microbial nomenclature has existed for decades, perhaps even centuries. Initial attempts in the 1700s to ascribe taxonomic designations to discoveries within the emerging field of prokaryotic science implemented rules that were used for botanical species. Should one delve into this topic with some degree of detail, the taxon Staphylococcus aureus, originally published by Rosenbach in 1884 (1), may be encountered. Effective (in other words, properly described) synonyms of this taxon also described in 1884 included “Staphylococcus pyogenes
aureus” (ascribed also by Rosenbach) and “Micrococcus aureus.” Just 1 year later, the designation “Staphylococcus pyogenes citreus” was used by Passet. In 1896, Lehmann and Neumann reported findings relative to “Micrococcus pyogenes,” which was later determined to be an additional synonym of S. aureus. For those of you scoring at home, that would be 12 years and five effectively published names—only one of which (obviously, the first one) is valid.
Now imagine a similar scenario potentially occurring with hundreds of newly discovered microbes (some of which are relevant to medical microbiology). It has been estimated that toward the latter stages of the 20th century, upwards of 30,000 taxa were available to describe various prokaryotes (2). A great proportion of these designations were likely redundant and/or the results of duplicated efforts. In 1973, the Plenary Session of the First Congress for Bacteriology convened to establish a contemporary approach for systemic nomenclature of bacteria. This resulted in the initial rendition of the International Code of Nomenclature of Bacteria (known to many as “the Code”), published in 1975 (3). The Code promulgated multiple reforms in prokaryotic taxonomy, one of which was the creation of the Approved Lists of Bacterial Names, which took effect in January 1980 (4). This standardization distilled the number of valid prokaryotic taxa to approximately 2,300, with all other names rejected from further use.
A second important reform emanating from the Code entailed the publication of (valid) novel or revised prokaryotic taxa in what is now entitled the International Journal of Systematic and Evolutionary Microbiology (IJSEM), either by primary publication or acceptance on an IJSEM validation list for taxa previously and effectively published in a non-IJSEM journal. In essence and in tandem with the Code, IJSEM is the clearinghouse or voice of the International Committee on Systematics of Prokaryotes (ICSP)—the ultimate authority on bacterial taxonomy. While the proverbial taxonomic buck stops with the ICSP, this group defines its role through the Code as “an instrument of scientific communication … [providing] the critical links between nomenclature, classification, and characterization; past, present and future” (5). That said, the responsibility of taxon discovery and revision remains in the hands of the microbiologist; perhaps more importantly, the responsibility for application and implementation of novel and revised taxonomy also resides with the (clinical) microbiologist.
Benefits of accurate nomenclature and taxonomic revisions.
Newer molecular methods, such as whole-genome sequencing, provide greater clarity of taxonomic status and have both added to our understanding of prokaryotic taxonomic classifications and clarified prior ambiguous relationships within families and genera. For clinical microbiologists, these contributions support the cornerstone of our discipline, which is communication of accurate information to the users of our laboratories. As researchers, how we identify an organism has immense consequences for our understanding of pathogenesis, epidemiology, and the microbiome in health and disease. Researchers need to speak the same “language”; otherwise, development of novel diagnostics, such as metagenomic next-generation sequencing (mNGS), that depend upon curated and accurate databases may be negatively impacted (6).
In addition to creating an explosion of novel species with standing in nomenclature (now numbering 17,642) (7), modern molecular tools have enabled better understanding of disease pathogenesis. For example, in a study by Potter et al., the authors used several modalities of in silico analysis of 103 whole genomes of Gardnerella spp. to elucidate and better define species within this genus (8). Using tetranucleotide frequency analysis, the authors clarified that there are 9 genomospecies among the 103 Gardnerella vaginalis and Gardnerella sp. genomic deposits in the National Center for Biotechnology Information database. All of these genomospecies were isolated from patients with clinical bacterial vaginosis (BV), indicating that multiple Gardnerella species beyond G. vaginalis can contribute to this clinical entity (8). The authors verified the taxonomic status of Gardnerella piotti sp. nov. and proposed potential conflicts in the taxonomic status of Gardnerella leopoldii sp. nov. and Gardnerella swidsinskii sp. nov.; they appeared to be the same species (8). This work also explored, to a limited extent, putative virulence genes that are important in understanding the biology of BV and genetic differences between commensal and pathogenic species (8). The authors discussed how phylogenetic methods and the reassignment of species into new genera have delineated the biology of other organism groups, such as the cutaneous propionibacteria (now Cutibacterium spp. and other genera), which possess genes encoding various systems that allow adaptation to different skin niches (8, 9).
Improvements in taxonomic methods have clarified unusual phenotypes in clinical microbiology. Corynebacterium diphtheriae, an important human pathogen, was historically classified into four biovars based upon a variety of phenotypic characteristics (Gravis, Mitis, Intermedius, and Belfanti). Biovar Belfanti was unique among the biovars in that it lacked the tox gene, was nitrate negative, and was associated with chronic nonspecific rhinitis and not the disease diphtheria (10, 11). C. diphtheriae biovar Belfanti was subsequently designated a new species, Corynebacterium belfanti sp. nov., and the biovar designations are no longer used (11). Subsequent genomic studies by Tagini and colleagues have clarified two clades of C. diphtheriae as subspecies diphtheriae and lausannense (12). Laboratories are unlikely to identify C. diphtheriae to the subspecies level; however, any identification of an isolate as C. diphtheriae should prompt confirmation by local public health laboratories.
Appropriate and accurate nomenclature can assist with enhancing epidemiological investigations. Several recent examples are highlighted here. In 2002, an outbreak of necrotizing enterocolitis in a hospital in Canada identified organisms recovered from the blood and stool of six ill neonates as Clostridium clostridioforme (13, 14). However, since this organism historically was not common among such cases in the institution, as well as uncommonly associated in the literature with enterocolitis, the isolate was sent to a reference laboratory for additional characterization (13, 14). After extensive evaluation and characterization by the reference laboratory, it was concluded that this organism was a novel species, subsequently named Clostridium neonatale sp. nov. (14). Enterobacter bugandensis originally came to attention as an unusual cause of neonatal sepsis among 17 infants in Tanzania (15). It was noteworthy for its multidrug resistance phenotype as a consequence of harboring the CTX-M-15 resistance determinant (15). Once characterized, this paved the way for additional detection among patients from other geographic locations and further ascertainment of this organism’s enhanced virulence potential (10, 15–17). A final similar example of the impact of understanding disease associations and the epidemiology of infections lies within the genus Elizabethkingia. Prior to the discovery of Elizabethkingia anophelis, E. meningoseptica was believed to be the cause of a vast array of hospital-acquired infections, ranging from pneumonia and bacteremia in adults to meningitis in neonates. High morbidity and mortality were reported with these infections (18, 19). However, subsequent studies have determined that E. anophelis is the major cause of bacteremia and other infections and is likely the most virulent of the six known species of Elizabethkingia (18, 19).
The Clinical and Laboratory Standards Institute’s guidance for appropriate antimicrobial susceptibility testing (AST) is increasingly based on accurate species detection. The various methods of testing for oxacillin resistance among species of coagulase-negative staphylococci provide one example of this point (20). In addition, if a laboratory has failed to embrace the revisions in taxonomic assignment of Actinobacillus spp. (specifically, A. actinomycetemcomitans) to the Aggregatibacter genus, then an incorrect method of susceptibility testing may be applied (21, 22). As more novel species are added to the order Enterobacterales, correct nomenclature assignments have implications for predicting antimicrobial resistance and possible expansion of testing for carbapenemase producers. For example, the newly recognized Providencia huaxiensis sp. nov. was discovered during routine surveillance for carbapenem-resistant Enterobacterales at a hospital in China (10, 23).
Many microbiologists and clinicians view nomenclature changes as a pain point for AST interpretation and subsequent clinical efficacy. The revision of Enterobacter aerogenes to Klebsiella aerogenes is often cited as an example of the potential dangers of embracing taxonomic changes. However, in our laboratory practice, we report both names and add an isolate comment just below the organism identification, as follows: “Klebsiella aerogenes, formerly Enterobacter aerogenes, may quickly develop resistance during therapy with third-generation cephalosporins (e.g., ceftriaxone, ceftazidime) due to production of AmpC beta-lactamases. This does not apply to cefepime.” We have not received feedback from our stewardship team nor from our clinicians of potential harm related to this nomenclature change (K. C. Carroll, personal communication). Collaboration with antimicrobial stewardship and infectious disease services facilitated implementation and correct interpretation of this change.
With really no choice but to accommodate these revisions and additions to microbial taxonomy, it is fortunate that clinical microbiologists have access to resources that can assist with implementation of nomenclature changes into daily practice. As stated above, IJSEM represents the primary vehicle for communication from the ICSP. The microbiologist has the opportunity to assimilate this primary literature monthly or to peruse online resources, such as the List of Prokaryotic Names with Standing in Nomenclature (LPSN; www.bacterio.net), a website that is updated concomitant to valid IJSEM publication. Within the past 5 to 10 years, Diagnostic Microbiology and Infectious Diseases (24) and Journal of Clinical Microbiology (10) have committed to the publication of annual/biennial compendia that attempt to summarize medically relevant novel/revised taxonomy, largely on the basis of IJSEM primary literature or validation lists. In addition, a Clinical and Laboratory Standards Institute document is in progress to provide guidance to clinical and veterinary diagnostic laboratories relative to the implementation of novel/revised bacterial and fungal nomenclature into routine laboratory operations and the potential timing of these actions.
Progress in microbial taxonomy will continue. The clinical microbiologist must engage proactively in the assimilation of this progress, incorporate important tenets into laboratory practice, and succinctly (yet accurately) communicate changes to clinical partners and key stakeholders. Outcome studies may be warranted to provide tangible evidence of the impact of taxonomic revisions on clinical practice. The clinical microbiologist should eagerly participate in such endeavors.
Karen C. Carroll and Erik Munson
