References

Barth, Patricia Orlandi, Eliane Wurdig Roesch, Larissa Lutz, Ândrea Celestino de Souza, Luciano Zubaran Goldani, and Dariane Castro Pereira. 2023. “Rapid Bacterial Identification by MALDI-TOF MS Directly from Blood Cultures and Rapid Susceptibility Testing: A Simple Approach to Reduce the Turnaround Time of Blood Cultures.” Braz. J. Infect. Dis. 27 (1): 102721.

Bosilkovski, Mile, Fariba Keramat, and Jurica Arapović. 2021. “The Current Therapeutical Strategies in Human Brucellosis.” Infection 49 (5): 823–32.

Edgar, Robert. 2018. “Taxonomy Annotation and Guide Tree Errors in 16S rRNA Databases.” PeerJ 6 (e5030): e5030.

Edgar, Robert C. 2018a. “Accuracy of Taxonomy Prediction for 16S rRNA and Fungal ITS Sequences.” PeerJ 6 (e4652): e4652.

———. 2018b. “Updating the 97% Identity Threshold for 16S Ribosomal RNA OTUs.” Bioinformatics 34 (14): 2371–75.

Franco, Marı́a Pı́a, Maximilian Mulder, Robert H Gilman, and Henk L Smits. 2007. “Human Brucellosis.” Lancet Infect. Dis. 7 (12): 775–86.

Hagiya, Hideharu, Kouhei Ohnishi, Miyako Maki, Naoto Watanabe, and Tomoko Murase. 2013. “Clinical Characteristics of Ochrobactrum Anthropi Bacteremia.” J. Clin. Microbiol. 51 (4): 1330–33.

Henz, Stefan R, Daniel H Huson, Alexander F Auch, Kay Nieselt-Struwe, and Stephan C Schuster. 2005. “Whole-Genome Prokaryotic Phylogeny.” Bioinformatics 21 (10): 2329–35.

Hofer, Ursula. 2018. “The Majority Is Uncultured.” Nature Reviews Microbiology 16 (12): 716–17. https://doi.org/10.1038/s41579-018-0097-x.

Hördt, Anton, Marina Garcı́a López, Jan P Meier-Kolthoff, Marcel Schleuning, Lisa-Maria Weinhold, Brian J Tindall, Sabine Gronow, Nikos C Kyrpides, Tanja Woyke, and Markus Göker. 2020. “Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.” Front. Microbiol. 11 (April): 468.

Johnson, Jethro S, Daniel J Spakowicz, Bo-Young Hong, Lauren M Petersen, Patrick Demkowicz, Lei Chen, Shana R Leopold, et al. 2019. “Evaluation of 16S rRNA Gene Sequencing for Species and Strain-Level Microbiome Analysis.” Nat. Commun. 10 (1): 5029.

Laine, Christopher G, Valen E Johnson, H Morgan Scott, and Angela M Arenas-Gamboa. 2023. “Global Estimate of Human Brucellosis Incidence.” Emerg. Infect. Dis. 29 (9): 1789–97.

Maiden, Martin C J, Melissa J Jansen van Rensburg, James E Bray, Sarah G Earle, Suzanne A Ford, Keith A Jolley, and Noel D McCarthy. 2013. “MLST Revisited: The Gene-by-Gene Approach to Bacterial Genomics.” Nat. Rev. Microbiol. 11 (10): 728–36.

Mazloom, Reza, Leighton Pritchard, C Titus Brown, Boris A Vinatzer, and Lenwood S Heath. 2022. “LINgroups as a Principled Approach to Compare and Integrate Multiple Bacterial Taxonomies.” In Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. New York, NY, USA: ACM.

Meier-Kolthoff, Jan P, Alexander F Auch, Hans-Peter Klenk, and Markus Göker. 2013. “Genome Sequence-Based Species Delimitation with Confidence Intervals and Improved Distance Functions.” BMC Bioinformatics 14 (1): 60.

Moreno, Edgardo, José Marı́a Blasco, Jean Jacques Letesson, Jean Pierre Gorvel, and Ignacio Moriyón. 2022. “Pathogenicity and Its Implications in Taxonomy: The Brucella and Ochrobactrum Case.” Pathogens 11 (3).

Moreno, Edgardo, Earl A Middlebrook, Pamela Altamirano-Silva, Sascha Al Dahouk, George F Araj, Vilma Arce-Gorvel, Ángela Arenas-Gamboa, et al. 2023. “If You’re Not Confused, You’re Not Paying Attention: Ochrobactrum Is Not Brucella.” J. Clin. Microbiol. 61 (8): e0043823.

Ondov, Brian D., Todd J. Treangen, Páll Melsted, Adam B. Mallonee, Nicholas H. Bergman, Sergey Koren, and Adam M. Phillippy. 2016. “Mash: Fast Genome and Metagenome Distance Estimation Using MinHash.” Genome Biology 17 (1). https://doi.org/10.1186/s13059-016-0997-x.

Pritchard, Leighton, C Titus Brown, Bailey Harrington, Lenwood S Heath, N Tessa Pierce-Ward, and Boris A Vinatzer. 2022. “Could a Focus on the ‘Why’ of Taxonomy Help Taxonomy Better Respond to the Needs of Science and Society?” Front. Microbiol. 13 (May): 887310.

Tian, Long, Reza Mazloom, Lenwood S Heath, and Boris A Vinatzer. 2021. “LINflow: A Computational Pipeline That Combines an Alignment-Free with an Alignment-Based Method to Accelerate Generation of Similarity Matrices for Prokaryotic Genomes.” PeerJ 9 (e10906): e10906.

Tindall, B J. 1999. “Misunderstanding the Bacteriological Code.” Int. J. Syst. Bacteriol. 49 Pt 3 (3): 1313–16.

Woese, C R, O Kandler, and M L Wheelis. 1990. “Towards a Natural System of Organisms: Proposal for the Domains Archaea, Bacteria, and Eucarya.” Proc. Natl. Acad. Sci. U. S. A. 87 (12): 4576–79.