Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021

Multi-year comparison of VITEK MS performance for identification of rarely encountered pathogenic gram-positive organisms (GPOs) in a large integrated Canadian healthcare region

This multi-year study (2014-2019) compared identification of rare and unusual gram-positive organisms (GPOs) by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (VITEK MS; bioMérieux, Laval, Quebec) to 16S rRNA gene sequencing (16S) according to our laboratory routine workflow. 16S is done if initial MALDI-TOF MS results are discordant or wrong, or there are no results. GPO isolates were first analyzed by standard phenotypic methods and MALDI-TOF MS using direct deposit with full formic acid extraction; MALDI-TOF was repeated if no result occurred. Medically approved 16S analyses were done using fast protocols. Isolate sequences were analyzed using the Integrated Database Network System bacterial database (SmartGene, Lausanne, Switzerland). 655 GPO isolates were recovered from 648 specimens; >1 isolate was recovered from 7 (1%). A total of 451 (68.9%) aerobic gram-positive bacilli (GPBs) and 204 (31.1%) aerobic gram-positive cocci (GPCs) were mainly recovered from bloodstream infections (35%), sterile fluids and deep tissues (35%), and abscesses/deep wounds (17%). Accurate genus vs species identities were obtained for 59% and 49.4% GPB, and 81% and 53.9% GPC, respectively. Wrong or no results were obtained for 9% and 31% of GPB and 7% and 12% of GPC; 15% of GPBs and 5.3% of GPC identification errors occurred due to absence from the instrument's database. VITEK MS performance remained stable for GPB and GPC isolates due to few species additions to the database. VITEK MS databases need to be continually updated to include an increasing number of rare and unusual GPOs causing invasive human infections. 16S remains important for identification of GPOs where MALDI-TOF fails.IMPORTANCEMALDI-TOF MS has transformed the identification of commonly encountered GPOs in the clinical laboratory, but rare and unusual bacteria continue to challenge the technology. This study verified the performance of VITEK MS for identification of a broad range of rare and unusual clinical GPO isolates by our large reference laboratory workflow over a multi-year period. Although most GPOs were accurately identified by MALDI-TOF MS, a small number of common GPC isolates (6.3%) (i.e., Enterococcus/Staphylococcus/Streptococcus) requiring sequencing for identification were studied. Approximately 13% of aerobic GPBs and 5.3% of GPCs could not be accurately identified by MALDI-TOF due to lack of an organism in the instrument's database. MALDI-TOF MS databases should be continuously updated and validated, and laboratories should have a workflow for the identification of unusual or rarely encountered GPOs that includes 16S rRNA gene sequencing whenever MALDI-TOF cannot give a definitive identification.

An update on novel taxa and revised taxonomic status of bacteria isolated from domestic companion and agricultural animals described in 2023

With the proliferation of abundant bacterial genomic data comes the recognition of new organisms as well as a better understanding of the relatedness of known bacteria. Recognizing the associated taxonomic changes enhances communication and understanding about the significance of novel organisms and deeper understanding of known pathogens. This review addresses the addition of multiple gastrointestinal bacteria that form the normal microbiota in a variety of animals including honeybees as well as novel bacteria from domestic animals including an alpha-hemolytic Streptococcus species from guinea pigs, two Moraxella spp. from cows and goats, a new Capnocytophaga species from cats, a thermophilic Campylobacter species from pigs, and the new Exercitatus genus in Family Pasteurellaceae. Several revisions to the nomenclature also appeared in 2023 including the change of Clostridium spiroforme, which causes anorexia and diarrhea in domestic rabbits, to Thomasclavelia spiroformis comb. nov. and Mannheimia ovis to Mannheimia pernigra.

Update on novel validly published and included bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2023

Taxonomy is a systematic practice in which microorganisms are granted names to facilitate and standardize multi-disciplinary communication. We summarize novel bacterial taxa derived from human clinical material that were published in peer-reviewed literature and/or included by the International Journal of Systematic and Evolutionary Microbiology during calendar year 2023, as well as taxonomic revisions that have been published/included by the same entity. While the majority of newly discovered facultative and anaerobic organisms were derived from microbiome surveillance, noteworthy novel taxa in the realm of pathogenicity potential include those related to Aerococcus spp., several Corynebacterium spp., Exercitatus varius gen. nov., sp. nov., and Mycoplasma phocimorsus sp. nov. With respect to nomenclature revision, the Bacillus and Clostridium genera continue to be visited annually. Creation of novel anaerobic Gram-negative bacillus genera Hallella, Hoylesella, Leyella, Segatella, and Xylanibacter impacted several Bacteroides spp. and Prevotella spp. Additional studies are necessary to ascertain the clinical significance of several of these microbes.

A look at staphylococci from the one health perspective

Staphylococcus aureus and other staphylococcal species are resident and transient multihost colonizers as well as conditional pathogens. Especially S. aureus represents an excellent model bacterium for the "One Health" concept because of its dynamics at the human-animal interface and versatility with respect to host adaptation. The development of antimicrobial resistance plays another integral part. This overview will focus on studies at the human-animal interface with respect to livestock farming and to companion animals, as well as on staphylococci in wildlife. In this context transmissions of staphylococci and of antimicrobial resistance genes between animals and humans are of particular significance.

Update on novel validly published taxa of bacteria isolated from domestic animals described in 2022

Expansion of our knowledge of the microbial world continues to progress at a rapid rate and carries with it an associated need for recognizing and understanding the implications of those changes. Here, we describe additions of novel taxa from domestic animals published in 2022 that are validly published per the International Code of Nomenclature of Prokaryotes. These included new members of Staphylococcaceae, Moraxella nasovis sp. nov. in sheep with respiratory disease, three additions to Campylobacteraceae (including one from chickens with spotty liver disease), and multiple additions of organisms from the microbiota of dogs, pigs, and especially honeybees and other important pollinators. Noteworthy additions were associated with diseases of cattle, including mastitis, endocarditis, orchitis, and endometritis. Also described in 2022 was Pseudochrobactrum algeriense sp. nov., a member of the Brucellaceae family, isolated from the mammary lymph nodes of cows.

An update on novel taxa and revised taxonomic status of bacteria isolated from non-domestic animals described in 2022

Numbers of new and revised microbial taxa are continuously expanding, and the rapid accumulation of novel bacterial species is challenging to keep up with in the best of circumstances. With that in mind, following the template of reports on prokaryotic species isolated from humans, this is now the second publication summarizing new and revised taxa in non-domestic animal species in the Journal of Clinical Microbiology. The majority of new taxa were obtained as part of programs to identify bacteria from mucosal surfaces and the gastrointestinal tract from healthy wildlife. A few notable bacteria included new Erysipelothrix spp. from mammalian and aquatic sources and a novel Bartonella spp. isolated from a rodent, both of which could be considered members of emerging and re-emerging genera with pathogenic potential in humans and animals.

Valid and accepted novel bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2022

Although some nomenclature changes have caused consternation among clinical microbiologists, the discovery of novel taxa and improving classification of existing groups of organisms is exciting and adds to our understanding of microbial pathogenesis. In this mini-review, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2022. Henceforth, these bacteriology taxonomic summaries will appear annually. Several of the novel Gram-positive organisms have been associated with disease, namely, the Corynebacterium kroppenstedtii-like organisms Corynebacterium parakroppenstedtii sp. nov. and Corynebacterium pseudokroppenstedtii sp. nov. A newly described Streptococcus species, Streptococcus toyakuensis sp. nov., is noteworthy for exhibiting multi-drug resistance. Among the novel Gram-negative pathogens, Vibrio paracholerae sp. nov. stands out as an organism associated with diarrhea and sepsis and has probably been co-circulating with pandemic Vibrio cholerae for decades. Many new anaerobic organisms have been described in this past year largely from genetic assessments of gastrointestinal microbiome collections. With respect to revised taxa, as discussed in previous reviews, the genus Bacillus continues to undergo further division into additional genera and reassignment of existing species into them. Reassignment of two subspecies of Fusobacterium nucleatum to species designations (Fusobacterium animalis sp. nov. and Fusobacterium vincentii sp. nov.) is also noteworthy. As was typical of previous reviews, literature updates for selected clinically relevant organisms discovered between 2017 and 2021 have been included.

If You're Not Confused, You're Not Paying Attention: Ochrobactrum Is Not Brucella

Bacteria of the genus Brucella are facultative intracellular parasites that cause brucellosis, a severe animal and human disease. Recently, a group of taxonomists merged the brucellae with the primarily free-living, phylogenetically related Ochrobactrum spp. in the genus Brucella. This change, founded only on global genomic analysis and the fortuitous isolation of some opportunistic Ochrobactrum spp. from medically compromised patients, has been automatically included in culture collections and databases. We argue that clinical and environmental microbiologists should not accept this nomenclature, and we advise against its use because (i) it was presented without in-depth phylogenetic analyses and did not consider alternative taxonomic solutions; (ii) it was launched without the input of experts in brucellosis or Ochrobactrum; (iii) it applies a non-consensus genus concept that disregards taxonomically relevant differences in structure, physiology, population structure, core-pangenome assemblies, genome structure, genomic traits, clinical features, treatment, prevention, diagnosis, genus description rules, and, above all, pathogenicity; and (iv) placing these two bacterial groups in the same genus creates risks for veterinarians, medical doctors, clinical laboratories, health authorities, and legislators who deal with brucellosis, a disease that is particularly relevant in low- and middle-income countries. Based on all this information, we urge microbiologists, bacterial collections, genomic databases, journals, and public health boards to keep the Brucella and Ochrobactrum genera separate to avoid further bewilderment and harm.

An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021

Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.