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Corynebacterium fournierii sp. nov., isolated from the female genital tract of a patient with bacterial vaginosis

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Abstract

Strain Marseille-P2948T, a novel Gram-positive, catalase-positive bacterium was isolated from a vaginal sample of a patient with bacterial vaginosis. It was characterised using the taxonogenomic approach. Phylogenetic analysis revealed that the 16S rRNA and the rpoB genes exhibit 98.7 and 93.4% similarity, respectively, with those of Corynebacterium ureicelerivorans strain IMMIB RIV-301T. Biochemical tests of strain Marseille-P2948T gave results that were similar to those of other validly named Corynebacterium species, whereas chemotaxonomic tests showed the presence of C16:0, C18:1n9, C18:0, and C18:2n6 in the fatty acid profile. The draft genome of strain Marseille-P2948T is 2,383,644 bp long in size with a G+C content of 65.03%. Of the 2210 predicted genes, 2147 are protein-coding genes and 63 are RNAs. Based on phenotypic, phylogenic and genomic results, it was concluded that the isolate represents a new species within the genus Corynebacterium. The name Corynebacterium fournierii sp. nov. is proposed and the type strain is Marseille-P2948T (= CSUR P2948 = DSM 103271).

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Abbreviations

CSUR:

Collection de souches de l’Unité des Rickettsies

DSM:

Deutsche Sammlung von Mikroorganismen

MALDI-TOF:

Matrix-assisted laser-desorption/ionization time-of-flight

TE buffer:

Tris-EDTA buffer

URMITE:

Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes

References

  • Belay N, Mukhopadhyay B, De Macario EC, Galask R, Daniels L (1990) Methanogenic bacteria in human vaginal samples. J Clin Microbiol 28:1666–1668

    PubMed  PubMed Central  CAS  Google Scholar 

  • Bernard KA, Funke G (2015) Corynebacterium. In: Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J, DeVos P et al (eds) Bergey’s manual of systematics of archaea and bacteria. Wiley, Chichester, pp 1–70

    Google Scholar 

  • Braun MS, Zimmermann S, Danner M, Rashid HO, Wink M (2016) Corynebacterium uropygiale sp. nov., isolated from the preen gland of Turkeys (Meleagris gallopavo). Syst Appl Microbiol 39:88–92

    Article  PubMed  CAS  Google Scholar 

  • Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J (2009) DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25:119–120

    Article  PubMed  CAS  Google Scholar 

  • Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA (2012) Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28:464–469

    Article  PubMed  CAS  Google Scholar 

  • Chen HH, Li WJ, Tang SK, Kroppenstedt RM, Stackebrandt E, Xu LH et al (2004) Corynebacterium halotolerans sp. nov., isolated from saline soil in the west of China. Int J Syst Evol Microbiol 54:779–782

    Article  PubMed  CAS  Google Scholar 

  • Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2016) GenBank. Nucleic Acids Res 44:D67–D72

    Article  PubMed  CAS  Google Scholar 

  • Devriese LA, Riegel P, Hommez J, Vaneechoutte M, De Baere T, Haesebrouck F (2000) Identification of Corynebacterium glucuronolyticum strains from the urogenital tract of humans and pigs. J Clin Microbiol 38:4657–4659

    PubMed  PubMed Central  CAS  Google Scholar 

  • Dione N, Sankar SA, Lagier JC, Khelaifia S, Michele C, Armstrong N et al (2016) Genome sequence and description of Anaerosalibacter massiliensis sp. nov. New Microbes New Infect 10:66–76

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP, Raoult D (2000) 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 38:3623–3630

    PubMed  PubMed Central  CAS  Google Scholar 

  • Dubourg G, Lagier JC, Armougom F, Robert C, Hamad I, Brouqui P et al (2013) The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics. Eur J Clin Microbiol Infect Dis 32:637–645

    Article  PubMed  CAS  Google Scholar 

  • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fettweis JM, Brooks JP, Serrano MG, Sheth NU, Girerd PH, Edwards DJ et al (2014) Differences in vaginal microbiome in African American women versus women of European ancestry. Microbiology 160:2272–2282

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fichorova R, Fraga J, Rappelli P, Fiori PL (2017) Trichomonas vaginalis infection in symbiosis with Trichomonasvirus and Mycoplasma. Res Microbiol. https://doi.org/10.1016/j.resmic.2017.03.005

    Article  PubMed  Google Scholar 

  • Fournier PE, Lagier JC, Dubourg G, Raoult D (2015) From culturomics to taxonomogenomics: a need to change the taxonomy of prokaryotes in clinical microbiology. Anaerobe 36:73–78

    Article  PubMed  Google Scholar 

  • Fudou R, Jojima Y, Seto A, Yamada K, Kimura E, Nakamatsu T et al (2002) Corynebacterium efficiens sp. nov., a glutamic-acid-producing species from soil and vegetables. Int J Syst Evol Microbiol 52:1127–1131

    PubMed  CAS  Google Scholar 

  • Funke G, Efstratiou A, Kuklinska D, Hutson RA, Zoysa AD, Engler KH et al (1997) Corynebacterium imitans sp. nov. isolated from patients with suspected diphtheria. J Clin Microbiol 35:1978–1983

    PubMed  PubMed Central  CAS  Google Scholar 

  • Gouret P, Vitiello V, Balandraud N, Gilles A, Pontarotti P, Danchin EG (2005) FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform. BMC Bioinform 6:1

    Article  CAS  Google Scholar 

  • Gouret P, Thompson JD, Pontarotti P (2009) PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees. BMC Bioinform 10:298

    Article  Google Scholar 

  • Gouret P, Paganini J, Dainat J, Louati D, Darbo E, Pontarotti P et al (2011) Integration of evolutionary biology concepts for functional annotation and automation of complex research in evolution: the multi-agent software system DAGOBAH. In: Pontarotti P (ed) Evolutionary biology—concepts, biodiversity, macroevolution and genome evolution. Springer, Berlin, pp 71–87

    Chapter  Google Scholar 

  • Herbst-Kralovetz MM, Pyles RB, Ratner AJ, Sycuro LK, Mitchell C (2016) New systems for studying intercellular interactions in bacterial vaginosis. J Infect Dis 214:S6–S13

    Article  PubMed  PubMed Central  Google Scholar 

  • Hoyles L, Ortman K, Cardew S, Foster G, Rogerson F, Falsen E (2013) Corynebacterium uterequi sp. nov., a non-lipophilic bacterium isolated from urogenital samples from horses. Vet Microbiol 165:469–474

    Article  PubMed  CAS  Google Scholar 

  • Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:1

    Article  CAS  Google Scholar 

  • Khamis A, Raoult D, La Scola B (2004) rpoB gene sequencing for identification of corynebacterium species. J Clin Microbiol 42:3925–3931

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    Article  PubMed  Google Scholar 

  • Klenk HP, Meier-Kolthoff JP, Göker M (2014) Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64:352–356

    Article  PubMed  CAS  Google Scholar 

  • Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C et al (2012) Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 18:1185–1193

    Article  PubMed  CAS  Google Scholar 

  • Lagier JC, Hugon P, Khelaifia S, Fournier PE, La Scola B, Raoult D (2015) The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 28:237–264

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lagier JC, Khelaifia S, Alou MT, Ndongo S, Dione N, Hugon P et al (2016) Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol 1:16203

    Article  PubMed  CAS  Google Scholar 

  • Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, Prohaska SJ (2011) Proteinortho: detection of (Co-) orthologs in large-scale analysis. BMC Bioinform 12:1

    Article  Google Scholar 

  • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Matuschek E, Brown DFJ, Kahlmeter G (2014) Development of the EUCAST disk diffusion antimicrobial susceptibility testing method and its implementation in routine microbiology laboratories. Clin Microbiol Infect 20:O255–O266

    Article  PubMed  CAS  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:1

    Article  Google Scholar 

  • Menard JP, Fenollar F, Henry M, Bretelle F, Raoult D (2008) Molecular Quantification of Gardnerella vaginalis and Atopobium vaginae loads to predict bacterial vaginosis. Clin Infect Dis 47:33–43

    Article  PubMed  CAS  Google Scholar 

  • Mendling W (2016) Vaginal microbiota. In: Schwiertz A (ed) Microbiota of the human body, vol 902. Springer International Publishing, Cham, pp 83–93

    Google Scholar 

  • Mishra AK, Lagier JC, Nguyen TT, Raoult D, Fournier PE (2013) Non contiguous-finished genome sequence and description of Peptoniphilus senegalensis sp. nov. Stand Genomic Sci 7:370–381

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Murray PR, Baron EJ, Jorgensen JH, Landry ML, Pfaller MA (2007) Manual of clinical microbiology, 9th edn. ASM Press, Washington, DC

    Google Scholar 

  • Narayankhedkar A, Hodiwala A, Mane A (2015) Clinicoetiological characterization of infectious vaginitis amongst women of reproductive age group from Navi Mumbai, India. J Sex Transm Dis 2015:1–5

    Article  Google Scholar 

  • Negi V, Singh Y, Schumann P, Lal R (2016) Corynebacterium pollutisoli sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 66:3531–3537

    Article  PubMed  CAS  Google Scholar 

  • Pal K, Roy S, Behera B, Kumar N, Sagiri S, Ray S (2011) Bacterial vaginosis: etiology and modalities of treatment—A brief note. J Pharm Bioallied Sci 3:496

    Article  PubMed  PubMed Central  Google Scholar 

  • Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ramasamy D, Mishra AK, Lagier J-C, Padhmanabhan R, Rossi M, Sentausa E et al (2014) A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 64:384–391

    Article  PubMed  Google Scholar 

  • Romero R, Hassan SS, Gajer P, Tarca AL, Fadrosh DW, Nikita L et al (2014) The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women. Microbiome 2:4

    Article  PubMed  PubMed Central  Google Scholar 

  • Rosselló-Móra R, Trujillo ME, Sutcliffe IC (2017) Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria. Antonie Van Leeuwenhoek 110:455–456

    Article  PubMed  Google Scholar 

  • Sasser M (2006) Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME). MIDI, Technical Note

  • Seng P, Drancourt M, Gouriet F, La Scola B, Fournier P, Rolain JM et al (2009) Ongoing revolution in bacteriology: routine Identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 49:543–551

    Article  PubMed  CAS  Google Scholar 

  • Shukla SK, Bernard KA, Harney M, Frank DN, Reed KD (2003) Corynebacterium nigricans sp. nov.: proposed name for a black-pigmented Corynebacterium species recovered from the human female urogenital tract. J Clin Microbiol 41:4353–4358

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152

    Google Scholar 

  • Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH et al (2014) Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12:635–645

    Article  PubMed  CAS  Google Scholar 

  • Zapata HJ, Quagliarello VJ (2015) The microbiota and microbiome in aging: potential implications in health and age-related diseases. J Am Geriatr Soc 63:776–781

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This study was supported by the Fondation Méditerranée Infection and the French National Research Agency under the “Investissements d’avenir” program, reference ANR-10-IAHU-03. We also thank TradOnline for English reviewing and Frederic Cadoret for administrative assistance.

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Authors and Affiliations

  1. Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France

    Khoudia Diop & Florence Fenollar

  2. Aix-Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France

    Thi Tien Nguyen, Jérémy Delerce, Nicholas Armstrong, Didier Raoult & Florence Bretelle

  3. Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia

    Didier Raoult

  4. Department of Gynecology and Obstetrics, Gynépole, Hôpital Nord, AP-HM, Marseille, France

    Florence Bretelle

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  1. Khoudia Diop
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  2. Thi Tien Nguyen
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Correspondence to Florence Fenollar.

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Diop, K., Nguyen, T.T., Delerce, J. et al. Corynebacterium fournierii sp. nov., isolated from the female genital tract of a patient with bacterial vaginosis. Antonie van Leeuwenhoek 111, 1165–1174 (2018). https://doi.org/10.1007/s10482-018-1022-z

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