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Objections to the Transfer of Francisella Novicida to the Subspecies Rank of Francisella Tularensis

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Objections to the Transfer of Francisella Novicida to the Subspecies Rank of Francisella Tularensis Objections to the transfer of Francisella novicida to the subspecies rank of Francisella tularensis We disagree with a recent proposal by Perhaps most importantly, recent findings Institute of Allergy and Infectious Huber et al. to transfer Francisella novicida from the analysis of multiple genome Diseases, National Institutes of Health, to the subspecies rank of Francisella sequences of F. tularensis versus F. novicida Hamilton, MT 59840, USA tularensis (Huber et al., 2010). We believe have indicated that the increased host- 3National Research Council Canada, that the proposal is not appropriate in association of F. tularensis is tied to Institute for Biological Sciences, Ottawa, light of all currently available knowledge. evolution as a population lineage ON K1C 2M7, Canada disconnected from F. novicida, even In 1989, Hollis et al. (1989) argued that 4Laboratory of Mycobacterial Diseases though genome-wide average nucleotide F. novicida and F. tularensis could be and Cellular Immunology, Center for identities exceeded 97 % (Larsson et al., considered to be one species as judged Biologics Evaluation and Research, US 2009). We propose that different from DNA–DNA hybridization Food and Drug Administration, Rockville, population structures and otherwise experiments (Hollis et al., 1989). Their MD 20852, USA disparate evolutionary patterns in publication was not valid according to the 5Division of CBRN Defense and Security, F. tularensis and F. novicida should be requirements outlined in the Bacteri- Swedish Defense Research Agency, SE- considered as arguments for retaining ological Code (Lapage et al., 1992; Tindall 901 82 Umea˚, Sweden separate species names. A comparison of et al., 2006). As a result, the proposed 6 17 genomes of members of the genus Department of Biological Sciences, elimination of the species F. novicida and Francisella has shown that the emergence Northern Arizona University, Flagstaff, its demotion to a biogroup of F. tularensis of F. tularensis, in an evolutionary and AZ 86011-5640, USA was not included among prokaryotic population genetic framework, was a 7Genome Sciences, University of names with standing in nomenclature. speciation event with no signs of reversals. Washington, Seattle, WA 98195-5065, Notably, earlier publications considered F. For example, there were no traces of USA novicida and F. tularensis to be separate genetic exchange between F. tularensis and 8 species based on differences in phenotype Department of Biochemistry and F. novicida. The analysis provided genetic including chemotaxonomic markers, Microbiology, University of Victoria, information that was more precise than distinct ecological roles, different clinical Victoria, BC V8W 3P6, Canada crude DNA–DNA hybridization values for and epidemiological characteristics, and 9 defining the genetic relationships between Centers for Disease Control and differing abilities and modes of invasion Prevention, Division of Vector-Borne F. tularensis and F. novicida. Recent intense and mechanisms of tissue damage in Infectious Diseases, Bacterial Diseases efforts, including evolutionary and mammals (Larson et al., 1955; Olsufiev Branch, 1300 Rampart Road, CSU population criteria, have provided a useful et al., 1959; Skerman et al., 1980). Foothills Campus, Fort Collins, CO theoretical framework for defining 80521, USA From a practical standpoint, separate prokaryotic species (Achtman & Wagner, species names are useful in a 2008; Gevers et al., 2005; Koeppel et al., Correspondence: Anders Johansson microbiological laboratory or a clinical 2008). We believe that such a framework ([email protected]) setting and also as a basis for regulations should be taken into consideration in the governing the handling of medically taxonomy of the genus Francisella. important organisms. For example, Achtman, M. & Wagner, M. (2008). Microbial diversity and the genetic nature of microbial laboratory handling of F. tularensis, but 1 2 Anders Johansson, Jean Celli, species. Nat Rev Microbiol 6, 431–440. not F. novicida, is associated with a high 3 4 Wayne Conlan, Karen L. Elkins, Gevers, D., Cohan, F. M., Lawrence, J. G., 5 6 risk of airborne laboratory-acquired Mats Forsman, Paul S. Keim, Spratt, B. G., Coenye, T., Feil, E. J., 5 7 infection. Importantly, it is fairly easy to Pa¨ r Larsson, Colin Manoil, Francis Stackebrandt, E., Van de Peer, Y., distinguish F. novicida and F. tularensis on E. Nano,8 Jeannine M. Petersen9 Vandamme, P. & other authors (2005). the basis of their different growth and and Anders Sjo¨ stedt1 Opinion: re-evaluating prokaryotic species. Nat metabolic requirements on artificial media. Rev Microbiol 3, 733–739. 1 Indeed, in Table 2 of Huber et al. (2010) Department of Clinical Microbiology, Hollis, D. G., Weaver, R. E., Steigerwalt, A. G., data are provided that contradict their own Umea˚ University, SE-901 85 Umea˚, Wenger, J. D., Moss, C. W. & Brenner, D. J. (1989). proposal by presenting 11 metabolic Sweden Francisella philomiragia comb. nov. (formerly Yersinia philomiragia) and Francisella 2 reactions that are distinct between Tularemia Pathogenesis Section, tularensis biogroup novicida (formerly F. novicida and F. tularensis (Huber et al., Laboratory of Intracellular Parasites, Francisella novicida) associated with human 2010). Rocky Mountain Laboratories, National disease. J Clin Microbiol 27, 1601–1608. Downloaded from www.microbiologyresearch.org by DOI 10.1099/ijs.0.022830-0 Printed in Great Britain 1717 IP: 54.70.40.11 On: Thu, 25 Oct 2018 13:10:51 Letters to the Editor Huber, B. E., Escudero, R., Busse, H. J., systematics. Proc Natl Acad Sci U S A 105, tularensis, a facultative intracellular pathogen. Seibold, E., Scholz, H. C., Anda, P., Ka¨ mpfer, P. 2504–2509. PLoS Pathog 5, e1000472. & Splettstoesser, W. D. (2010). Description of Lapage, S. P., Sneath, P. H. A., Lessel, E. F., Olsufiev, N. G., Emelyanova, O. S. & Dunayeva, Francisella hispaniensis sp. nov., isolated from Skerman, V. B. D., Seeliger, H. P. R. & Clark, T. N. (1959). Comparative study of strains of B. human blood, reclassification of Francisella W. A. (editors) (1992). International Code of tularense in the old and new world and their novicida (Larson et al. 1955) Olsufiev et al. 1959 Nomenclature of Bacteria (1990 Revision). taxonomy. J Hyg Epidemiol Microbiol Immunol as Francisella tularensis subsp. novicida comb. Bacteriological Code. Washington, DC: American 3, 138–149. nov., and emended description of the genus Society for Microbiology. Francisella. Int J Syst Evol Microbiol 60, 1887– Skerman, V. B. D., McGowan, V. & Sneath, 1896. Larson, C. L., Wicht, W. & Jellison, W. L. (1955). P. H. A. (editors) (1980). Approved lists of A new organism resembling P. tularensis isolated bacterial names. Int J Syst Bacteriol 30, 225–420. Koeppel, A., Perry, E. B., Sikorski, J., Krizanc, D., Warner, A., Ward, D. M., Rooney, from water. Public Health Rep 70, 253–258. Tindall, B. J., Ka¨ mpfer, P., Euze´ by, J. P. & A. P., Brambilla, E., Connor, N. & other authors Larsson, P., Elfsmark, D., Svensson, K., Oren, A. (2006). Valid publication of names of (2008). Identifying the fundamental units of Wikstro¨ m, P., Forsman, M., Brettin, T., Keim, P. prokaryotes according to the rules of bacterial diversity: a paradigm shift to & Johansson, A. (2009). Molecular evolutionary nomenclature: past history and current practice. incorporate ecology into bacterial consequences of niche restriction in Francisella Int J Syst Evol Microbiol 56, 2715–2720. Objections to the transfer of Francisella novicida to the subspecies rank of Francisella tularensis – response to Johansson et al. The description of novel species requires experiments, F. novicida is genetically close the results from the literature and the the careful selection and use of a wide to F. tularensis (Hollis et al., 1989) and the results from our investigations, but also for variety of methodologies. As pointed out phenotypic differences observed (Huber et sake of consistency, it is obvious that our by Tindall et al. (2010), experience gained al., 2010) are in agreement with the proposal to assign F. novicida to F. over the past six decades has continued to subspecies concept. Another important tularensis as a novel subspecies is well demonstrate the value of comparing point supporting this taxonomic supported. different datasets and also of basing the rearrangement is the acceptance of the new Below are some additional replies to description and delineation of taxa on as combination within the scientific certain arguments proposed by Johansson wide a dataset as possible. A combination community. The use of this not yet validly et al. (2010) to support their stance against of data acquired from DNA-based published new combination may be related the reclassification of F. novicida. methods (DNA–DNA hybridization, gene to the fact that in Bergey’s Manual of sequences, genomic fingerprints) and Systematic Bacteriology (often erroneously It is argued, that: phenotyping (chemotaxonomic, considered as the ‘bible’ of bacterial ‘From a practical standpoint, sep- physiological and morphological traits) systematics by those interested in bacterial arate species names are useful in a provides a sound basis for the taxonomy of taxonomy), the transfer of F. novicida to microbiological laboratory or a the prokaryotes (Tindall et al., 2010). The Francisella tularensis subsp. novicida was clinical setting and also as a basis decision as to whether two bacteria are recommended in the chapter dealing with for regulations
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