Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus (Zhang 2008) and description of Phytobacter ursingii sp. nov.

Marcelo Pillonetto; Lavinia N. Arend; Helisson Faoro; Helena R. S. D’Espindula; Jochen Blom; Theo H. M. Smits; Marcelo T. Mira; Fabio Rezzonico

doi:10.1099/ijsem.0.002477

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f Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus (Zhang 2008) and description of Phytobacter ursingii sp. nov.

Authors: Marcelo Pillonetto^1,2 , Lavinia N. Arend² , Helisson Faoro³ , Helena R. S. D’Espindula¹ , Jochen Blom⁴ , Theo H. M. Smits⁵ , Marcelo T. Mira^1,† , Fabio Rezzonico^5,†
- VIEW AFFILIATIONS
- ¹ 1Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba-PR, Brazil ² 2Molecular Bacteriology Division, Central Public Health Laboratory, State of Paraná, São José dos Pinhais-PR, Brazil ³ 3Carlos Chagas Institute, FIOCRUZ, Curitiba-PR, Brazil ⁴ 4Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany ⁵ 5Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
*Correspondence: Fabio Rezzonico [email protected]
First Published Online: 10 November 2017, International Journal of Systematic and Evolutionary Microbiology 68: 176-184, doi: 10.1099/ijsem.0.002477
Subject: New Taxa - Proteobacteria

Received: 19/04/2017
Accepted: 31/10/2017
Cover date: 01/01/2018

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Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus (Zhang 2008) and description of Phytobacter ursingii sp. nov., Page 1 of 1

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The species Phytobacter diazotrophicus and the associated genus Phytobacter were originally described by Zhanget al. [Arch Microbiol 189 (2008), 431–439] on the basis of few endophytic nitrogen-fixing bacteria isolated from wild rice (Oryza rufipogon) in China. In this study, we demonstrate that a number of clinical isolates that were either described in the literature, preserved in culture collections, or obtained during a 2013 multi-state sepsis outbreak in Brazil also belong to the same genus. 16S rRNA gene sequencing, multilocus sequence analysis based on gyrB, rpoB, atpD and infB genes, as well as digital DNA–DNA hybridization support the existence of a second species within the genus Phytobacter . All isolates from the recent Brazilian outbreak, along with some older American clinical strains, were found to belong to the already described species Phytobacter diazotrophicus , whereas three clinical strains retrieved in the USA over a time span of almost four decades, could be assigned to a new Phytobacter species. Implementation of an extended set of biochemical tests showed that the two Phytobacter species could phenotypically be discriminated from each other by the ability to utilize l-sorbose and d-serine. This feature was limited to the strains of the novel species described herein, for which the name Phytobacter ursingii sp. nov. is proposed, with ATCC 27989T (=CNCTC 5729T) as the designated type strain. An emended description of the species Phytobacter diazotrophicus and of the genus Phytobacter is also provided.

†
These authors contributed equally to this work.
Four supplementary tables and one supplementary figure are available with the online version of this article.

Keyword(s): Erwinia herbicola, sepsis, misidentification, outbreak, total parenteral nutrition, Pantoea agglomerans

1. Kwon SW, Go SJ, Kang HW, Ryu JC, Jo JK. Phylogenetic analysis of Erwinia species based on 16S rRNA gene sequences. Int J Syst Bacteriol 1997; 47: 1061– 1067 [CrossRef] [PubMed]
[Google Scholar]
2. Cruz AT, Cazacu AC, Allen CH. Pantoea agglomerans, a plant pathogen causing human disease. J Clin Microbiol 2007; 45: 1989– 1992 [CrossRef] [PubMed]
[Google Scholar]
3. Rezzonico F, Smits THM, Montesinos E, Frey JE, Duffy B. Genotypic comparison of Pantoea agglomerans plant and clinical strains. BMC Microbiol 2009; 9: 204 [CrossRef]
[Google Scholar]
4. Rezzonico F, Stockwell VO, Tonolla M, Duffy B, Smits TH. Pantoea clinical isolates cannot be accurately assigned to species based on metabolic profiling. Transpl Infect Dis 2012; 14: 220– 221 [CrossRef] [PubMed]
[Google Scholar]
5. Rezzonico F, Smits THM, Duffy B. Misidentification slanders Pantoea agglomerans as a serial killer. J Hosp Infect 2012; 81: 137– 139 [CrossRef]
[Google Scholar]
6. Brenner DJ, Fanning GR, Leete Knutson JK, Steigerwalt AG, Krichevsky MI. Attempts to classify Herbicola group-Enterobacter agglomerans strains by deoxyribonucleic acid hybridization and phenotypic tests. Int J Syst Bacteriol 1984; 34: 45– 55 [CrossRef]
[Google Scholar]
7. Bergman KA, Arends JP, Schölvinck EH. Pantoea agglomerans septicemia in three newborn infants. Pediatr Infect Dis J 2007; 26: 453– 454 [CrossRef] [PubMed]
[Google Scholar]
8. Bicudo EL, Macedo VO, Carrara MA, Castro FF, Rage RI. Nosocomial outbreak of Pantoea agglomerans in a pediatric urgent care center. Braz J Infect Dis 2007; 11: 281– 284 [CrossRef] [PubMed]
[Google Scholar]
9. Boszczowski I, Nóbrega de Almeida Júnior J, Peixoto de Miranda EJ, Pinheiro Freire M, Guimarães T et al. Nosocomial outbreak of Pantoea agglomerans bacteraemia associated with contaminated anticoagulant citrate dextrose solution: new name, old bug?. J Hosp Infect 2012; 80: 255– 258 [CrossRef] [PubMed]
[Google Scholar]
10. Gonçalves CR, Vaz TM, Leite D, Pisani B, Simoes M et al. Molecular epidemiology of a nosocomial outbreak due to Enterobacter cloacae and Enterobacter agglomerans in Campinas, São Paulo, Brazil. Rev Inst Med Trop Sao Paulo 2000; 42: 1– 7 [CrossRef] [PubMed]
[Google Scholar]
11. Habsah H, Zeehaida M, van Rostenberghe H, Noraida R, Wan Pauzi WI et al. An outbreak of Pantoea spp. in a neonatal intensive care unit secondary to contaminated parenteral nutrition. J Hosp Infect 2005; 61: 213– 218 [CrossRef]
[Google Scholar]
12. van Rostenberghe H, Noraida R, Wan Pauzi WI, Habsah H, Zeehaida M et al. The clinical picture of neonatal infection with Pantoea species. Jpn J Infect Dis 2006; 59: 120– 121
[Google Scholar]
13. Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral J-P et al. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 2000; 38: 3623– 3630
[Google Scholar]
14. Hauben L, Moore ER, Vauterin L, Steenackers M, Mergaert J et al. Phylogenetic position of phytopathogens within the Enterobacteriaceae. Syst Appl Microbiol 1998; 21: 384– 397 [CrossRef] [PubMed]
[Google Scholar]
15. Pavan ME, Franco RJ, Rodriguez JM, Gadaleta P, Abbott SL et al. Phylogenetic relationships of the genus Kluyvera: transfer of Enterobacter intermedius Izard et al. 1980 to the genus Kluyvera as Kluyvera intermedia comb. nov. and reclassification of Kluyvera cochleae as a later synonym of K. intermedia. Int J Syst Evol Microbiol 2005; 55: 437– 442 [CrossRef] [PubMed]
[Google Scholar]
16. Dauga C. Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies. Int J Syst Evol Microbiol 2002; 52: 531– 547 [CrossRef] [PubMed]
[Google Scholar]
17. Delmas J, Breysse F, Devulder G, Flandrois J-P, Chomarat M. Rapid identification of Enterobacteriaceae by sequencing DNA gyrase subunit B encoding gene. Diagn Microbiol Infect Dis 2006; 55: 263– 268 [CrossRef]
[Google Scholar]
18. Brady C, Cleenwerck I, Venter S, Vancanneyt M, Swings J et al. Phylogeny and identification of Pantoea species associated with plants, humans and the natural environment based on multilocus sequence analysis (MLSA). Syst Appl Microbiol 2008; 31: 447– 460 [CrossRef] [PubMed]
[Google Scholar]
19. Glaeser SP, Kämpfer P. Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol 2015; 38: 237– 245 [CrossRef]
[Google Scholar]
20. Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015; 38: 209– 216 [CrossRef] [PubMed]
[Google Scholar]
21. Dunne WM, Westblade LF, Ford B. Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis 2012; 31: 1719– 1726 [CrossRef] [PubMed]
[Google Scholar]
22. Tamura K, Sakazaki R, Kosako Y, Yoshizaki E. Leclercia adecarboxylata gen. nov., comb. nov., formerly known as Escherichia adecarboxylata. Curr Microbiol 1986; 13: 179– 184 [CrossRef]
[Google Scholar]
23. Gavini F, Mergaert J, Beji A, Mielcarek C, Izard D et al. Transfer of Enterobacter agglomerans (Beijerinck 1888) Ewing and Fife 1972 to Pantoea gen. nov. as Pantoea agglomerans comb. nov. and Description of Pantoea dispersa sp. nov. Int J Syst Bacteriol 1989; 39: 337– 345 [CrossRef]
[Google Scholar]
24. Mergaert J, Verdonck L, Kersters K. Transfer of Erwinia ananas (synonym, Erwinia uredovora) and Erwinia stewartii to the genus Pantoea emend. as Pantoea ananas (Serrano 1928) comb. nov. and Pantoea stewartii (Smith 1898) comb. nov., respectively, and description of Pantoea stewartii subsp. indologenes subsp. nov. Int J Syst Bacteriol 1993; 43: 162– 173 [CrossRef]
[Google Scholar]
25. Harada H, Oyaizu H, Kosako Y, Ishikawa H. Erwinia aphidicola, a new species isolated from pea aphid, Acyrthosiphon pisum. J Gen Appl Microbiol 1997; 43: 349– 354 [CrossRef] [PubMed]
[Google Scholar]
26. Brady CL, Cleenwerck I, Venter SN, Engelbeen K, de Vos P et al. Emended description of the genus Pantoea, description of four species from human clinical samples, Pantoea septica sp. nov., Pantoea eucrina sp. nov., Pantoea brenneri sp. nov. and Pantoea conspicua sp. nov., and transfer of Pectobacterium cypripedii (Hori 1911) Brenner et al. 1973 emend. Hauben et al. 1998 to the genus as Pantoea cypripedii comb. nov. Int J Syst Evol Microbiol 2010; 60: 2430– 2440 [CrossRef] [PubMed]
[Google Scholar]
27. Brady C, Cleenwerck I, Venter S, Coutinho T, de Vos P. Taxonomic evaluation of the genus Enterobacter based on multilocus sequence analysis (MLSA): proposal to reclassify E. nimipressuralis and E. amnigenus into Lelliottia gen. nov. as Lelliottia nimipressuralis comb. nov. and Lelliottia amnigena comb. nov., respectively, E. gergoviae and E. pyrinus into Pluralibacter gen. nov. as Pluralibacter gergoviae comb. nov. and Pluralibacter pyrinus comb. nov., respectively, E. cowanii, E. radicincitans, E. oryzae and E. arachidis into Kosakonia gen. nov. as Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov. and Kosakonia arachidis comb. nov., respectively, and E. turicensis, E. helveticus and E. pulveris into Cronobacter as Cronobacter zurichensis nom. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov., respectively, and emended description of the genera Enterobacter and Cronobacter. Syst Appl Microbiol 2013; 36: 309– 319 [CrossRef] [PubMed]
[Google Scholar]
28. Minogue TD, Daligault HE, Davenport KW, Bishop-Lilly KA, Bruce DC et al. Draft genome assemblies of Enterobacter aerogenes CDC 6003-71, Enterobacter cloacae CDC 442-68, and Pantoea agglomerans UA 0804-01. Genome Announc 2014; 2: e01073-14 [CrossRef] [PubMed]
[Google Scholar]
29. Maki DG, Rhame FS, Mackel DC, Bennett JV. Nationwide epidemic of septicemia caused by contaminated intravenous products. Am J Med 1976; 60: 471– 485 [CrossRef]
[Google Scholar]
30. Ewing WH, Fife MA. Enterobacter agglomerans (Beijerinck) comb. nov. (the Herbicola-Lathyri bacteria). Int J Syst Bacteriol 1972; 22: 4– 11 [CrossRef]
[Google Scholar]
31. Felts SK, Schaffner W, Melly MA, Koenig MG. Epidemiologic, clinical, and laboratory investigation of an outbreak in one hospital. Ann Intern Med 1972; 77: 881– 890 [Crossref]
[Google Scholar]
32. Zhang GX, Peng GX, Wang ET, Yan H, Yuan QH et al. Diverse endophytic nitrogen-fixing bacteria isolated from wild rice Oryza rufipogon and description of Phytobacter diazotrophicus gen. nov. sp. nov. Arch Microbiol 2008; 189: 431– 439 [CrossRef] [PubMed]
[Google Scholar]
33. Rezzonico F, Vogel G, Duffy B, Tonolla M. Application of whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry for rapid identification and clustering analysis of Pantoea species. Appl Environ Microbiol 2010; 76: 4497– 4509 [CrossRef] [PubMed]
[Google Scholar]
34. Benslama O, Boulahrouf A. High-quality draft genome sequence of Enterobacter sp. Bisph2, a glyphosate-degrading bacterium isolated from a sandy soil of Biskra, Algeria. Genom Data 2016; 8: 61– 66 [CrossRef] [PubMed]
[Google Scholar]
35. Sheppard AE, Stoesser N, Wilson DJ, Sebra R, Kasarskis A et al. Nested Russian doll-like genetic mobility drives rapid dissemination of thecarbapenem resistance gene bla _KPC. Antimicrob Agents Chemother 2016; 60: 3767– 3778 [CrossRef] [PubMed]
[Google Scholar]
36. Rezzonico F, Smits TH, Born Y, Blom J, Frey JE et al. Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees. Int J Syst Evol Microbiol 2016; 66: 1583– 1592 [CrossRef] [PubMed]
[Google Scholar]
37. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33: 1870– 1874 [CrossRef] [PubMed]
[Google Scholar]
38. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T et al. GenDB–an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 2003; 31: 2187– 2195 [CrossRef] [PubMed]
[Google Scholar]
39. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C et al. EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic Acids Res 2016; 44: W22– W28 [CrossRef] [PubMed]
[Google Scholar]
40. Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC. Whole-genome prokaryotic phylogeny. Bioinformatics 2005; 21: 2329– 2335 [CrossRef] [PubMed]
[Google Scholar]
41. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57: 81– 91 [CrossRef] [PubMed]
[Google Scholar]
42. de Maayer P, Cowan DA. Flashy flagella: flagellin modification is relatively common and highly versatile among the Enterobacteriaceae. BMC Genomics 2016; 17: 377 [CrossRef] [PubMed]
[Google Scholar]

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