1887

Abstract

Members of the genus are fastidious bacteria that predominantly colonise the female genital tract and are significantly associated with reproductive disorders and genital and neonatal disease. From a taxonomical perspective, the genus only comprises the species . Numerous reports on a second species, ‘’, have been published, but the name has never been validated. The same is the case for ‘’, which was previously shown to belong to the same species as ‘’. We studied strains DSM 16631 and DSM 16630, which have been identified and deposited as ‘’ previously. At the time of isolation, these strains were found to be most closely related to, but clearly different from, based on 16S rRNA gene sequence similarities. Both strains proved to be almost indistinguishable from ‘’ based on molecular, morphological and physiological traits. The 16S rRNA gene sequence analysis revealed that strain DSM 16631 was assigned to the genus with a sequence similarity of 95.47 % to CCUG 41628, followed by type strains of (93.03 %), (92.68 %) and (91.97 %) as the next closely related members of the . The novel species was also clearly differentiated from other related taxa by core genome phylogeny, average nucleotide and amino acid identities, DNA–DNA hybridization and MALDI-TOF MS. With respect to chemotaxonomic and physiological patterns, strains DSM 16631 and DSM 16630 were again highly similar to . On the basis of these data, we propose the novel species sp. nov. with the type strain DSM 16631 (=CCUG 52977=CCUG 52889A) and a second strain DSM 16630 (=CCUG 52976=CCUG 52888) that were both isolated from bloodstream infections in women with puerperal fever in France. The G+C content of the DNA of the type strain is 28.4 mol% and the genome size is 1.28 Mbp. Based on the observed extremely high similarities of genotypic and phenotypic traits of the novel proposed species to those reported for ‘’, we recommend using this new name in all further publications on this taxon.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004663
2021-02-22
2021-10-27
Loading full text...

Full text loading...

References

  1. Harwich MD, Serrano MG, Alves JM, Alves JMP, Reimers MA et al. Genomic sequence analysis and characterization of Sneathia amnii sp. nov. BMC Genomics 2012; 13:S4 [View Article]
    [Google Scholar]
  2. ICNP International code of nomenclature of prokaryotes. Int J Syst Evol Microbiol 2019; 69:S1–S111 [View Article][PubMed]
    [Google Scholar]
  3. Shukla SK, Meier PR, Mitchell PD, Frank DN, Reed KD. Leptotrichia amnionii sp. nov., a novel bacterium isolated from the amniotic fluid of a woman after intrauterine fetal demise. J Clin Microbiol 2002; 40:3346–3349 [View Article]
    [Google Scholar]
  4. Eribe ERK, Paster BJ, Caugant DA, Dewhirst FE, Stromberg VK et al. Genetic diversity of Leptotrichia and description of Leptotrichia goodfellowii sp. nov., Leptotrichia hofstadii sp. nov., Leptotrichia shahii sp. nov. and Leptotrichia wadei sp. nov. Int J Syst Evol Microbiol 2004; 54:583–592 [View Article]
    [Google Scholar]
  5. Verhelst R, Verstraelen H, Claeys G, Verschraegen G, Delanghe J et al. Cloning of 16S rRNA genes amplified from normal and disturbed vaginal microflora suggests a strong association between Atopobium vaginae, Gardnerella vaginalis and bacterial vaginosis. BMC Microbiol 2004; 4:16 [View Article]
    [Google Scholar]
  6. Fredricks DN, Fiedler TL, Marrazzo JM. Molecular identification of bacteria associated with bacterial vaginosis. N Engl J Med 2005; 353:1899–1911 [View Article]
    [Google Scholar]
  7. Fredricks DN, Fiedler TL, Thomas KK, Oakley BB, Marrazzo JM. Targeted PCR for detection of vaginal bacteria associated with bacterial vaginosis. J Clin Microbiol 2007; 45:3270–3276 [View Article]
    [Google Scholar]
  8. Thilesen CM, Nicolaidis M, Lokebo JE, Falsen E, Jorde AT et al. Leptotrichia amnionii, an emerging pathogen of the female urogenital tract. J Clin Microbiol 2007; 45:2344–2347 [View Article]
    [Google Scholar]
  9. Zhou X, Bent SJ, Schneider MG, Davis CC, Islam MR et al. Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods. Microbiology 2004; 150:2565–2573 [View Article]
    [Google Scholar]
  10. Marrazzo JM, Fiedler TL, Srinivasan S, Thomas KK, Liu C et al. Extravaginal reservoirs of vaginal bacteria as risk factors for incident bacterial vaginosis. J Infect Dis 2012; 205:1580–1588 [View Article]
    [Google Scholar]
  11. Nawrot R, Kamieniarz K, Malinowska M, Jozefiak A, Kedzia W. The prevalence of Leptotrichia amnionii in cervical swabs of HPV positive and negative women. Eur J Gynaecol Oncol 2010; 31:425–428
    [Google Scholar]
  12. Haggerty CL, Totten PA, Tang G, Astete SG, Ferris MJ. Identification of novel microbes associated with pelvic inflammatory disease and infertility. Sex Transm Infect 2016; 92:441–446 [View Article]
    [Google Scholar]
  13. Boennelycke M, Jørgen Christensen J, Arpi M, Krause S. Leptotrichia amnionii found in septic abortion in Denmark. Scand J Infect Dis 2007; 39:382–383 [View Article]
    [Google Scholar]
  14. Kacerovsky M, Vrbacky F, Kutova R, Pliskova L, Andrys C et al. Cervical microbiota in women with preterm prelabor rupture of membranes. PLoS One 2015; 10:e0126884 [View Article]
    [Google Scholar]
  15. De Martino SJ, Mahoudeau I, Brettes JP, Piemont Y, Monteil H et al. Peripartum bacteremias due to Leptotrichia amnionii and Sneathia sanguinegens, rare causes of fever during and after delivery. J Clin Microbiol 2004; 42:5940–5943 [View Article]
    [Google Scholar]
  16. Han YW, Shen T, Chung P, Buhimschi IA, Buhimschi CS. Uncultivated bacteria as etiologic agents of intra-amniotic inflammation leading to preterm birth. J Clin Microbiol 2009; 47:38–47 [View Article]
    [Google Scholar]
  17. Devi U, Bora R, Das JK, Malik V, Mahanta J. Sneathia species in a case of neonatal meningitis from Northeast India. Oxf Med Case Reports 2014; 2014:112–114 [View Article]
    [Google Scholar]
  18. Gundi VAKB, Desbriere R, La Scola B. Leptotrichia amnionii and the female reproductive tract. Emerg Infect Dis 2004; 10:2056–2057 [View Article]
    [Google Scholar]
  19. Duployez C, Le Guern R, Faure E, Wallet F, Loiez C. Sneathia amnii, an unusual pathogen in spondylitis: A case report. Anaerobe 2020; 102277:
    [Google Scholar]
  20. Bachy B, Bémer P, Tortellier L, Giraudeau C, Reynaud A et al. Septic arthritis due to a Sneathia species most closely related to Sneathia sanguinegens. J Med Microbiol 2011; 60:1693–1696 [View Article]
    [Google Scholar]
  21. Goto M, Hitomi S, Ishii T. Bacterial arthritis caused by Leptotrichia amnionii . J Clin Microbiol 2007; 45:2082–2083 [View Article]
    [Google Scholar]
  22. Bacci G, Paganin P, Lopez L, Vanni C, Dalmastri C et al. Pyrosequencing unveils cystic fibrosis lung microbiome differences associated with a severe lung function decline. PLoS One 2016; 11:e0156807 [View Article]
    [Google Scholar]
  23. Drell T, Stsepetova J, Simm J, Rull K, Aleksejeva A et al. The influence of different maternal microbial communities on the development of infant gut and oral microbiota. Sci Rep 2017; 7:9940 [View Article]
    [Google Scholar]
  24. Wang H, Funchain P, Bebek G, Altemus J, Zhang H et al. Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas. Genome Med 2017; 9:14 [View Article]
    [Google Scholar]
  25. Spear GT, Gilbert D, Sikaroodi M, Doyle L, Green L et al. Identification of rhesus macaque genital microbiota by 16S pyrosequencing shows similarities to human bacterial vaginosis: implications for use as an animal model for HIV vaginal infection. AIDS Res Hum Retroviruses 2010; 26:193–200 [View Article]
    [Google Scholar]
  26. Spear GT, Kersh E, Guenthner P, Vishwanathan SA, Gilbert D et al. Longitudinal assessment of pigtailed macaque lower genital tract microbiota by pyrosequencing reveals dissimilarity to the genital microbiota of healthy humans. AIDS Res Hum Retroviruses 2012; 28:1244–1249 [View Article]
    [Google Scholar]
  27. Jeon SJ, Vieira-Neto A, Gobikrushanth M, Daetz R, Mingoti RD et al. Uterine microbiota progression from calving until establishment of metritis in dairy cows. Appl Environ Microbiol 2015; 81:6324–6332 [View Article]
    [Google Scholar]
  28. Machado VS, Oikonomou G, Bicalho ML, Knauer WA, Gilbert R et al. Investigation of postpartum dairy cows’ uterine microbial diversity using metagenomic pyrosequencing of the 16S rRNA gene. Vet Microbiol 2012; 159:460–469 [View Article]
    [Google Scholar]
  29. Swartz JD, Lachman M, Westveer K, O'Neill T, Geary T et al. Characterization of the vaginal microbiota of ewes and cows reveals a unique microbiota with low levels of lactobacilli and near-neutral pH. Front Vet Sci 2014; 1:19 [View Article][PubMed]
    [Google Scholar]
  30. Serrano M, Climent E, Freire F, Martínez-Blanch JF, González C et al. Influence of the ovine genital tract microbiota on the species artificial insemination outcome. A pilot study in commercial sheep farms. High-Throughput 2020; 9:16 [View Article]
    [Google Scholar]
  31. Oultram JWH, Ganda EK, Boulding SC, Bicalho RC, Oikonomou G. A Metataxonomic approach could be considered for cattle clinical mastitis diagnostics. Front Vet Sci 2017; 4:36 [View Article]
    [Google Scholar]
  32. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . Proc Natl Acad Sci U S A 1978; 75:4801–4805 [View Article]
    [Google Scholar]
  33. Yoon SH, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article]
    [Google Scholar]
  34. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. mega X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
    [Google Scholar]
  35. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
    [Google Scholar]
  36. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  37. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article]
    [Google Scholar]
  38. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article]
    [Google Scholar]
  39. Furuno M et al. CDS annotation in full-length cDNA sequence. Genome Res 2003; 13:1478–1487 [View Article]
    [Google Scholar]
  40. Palmer M, Venter SN, McTaggart AR, Coetzee MPA, Van Wyk S et al. The synergistic effect of concatenation in phylogenomics: the case in Pantoea . PeerJ 2019; 7:e6698 [View Article]
    [Google Scholar]
  41. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article]
    [Google Scholar]
  42. Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article]
    [Google Scholar]
  43. Eisenberg T, Nicklas W, Mauder N, Rau J, Contzen M et al. Phenotypic and genotypic characteristics of members of the genus Streptobacillus . PLoS One 2015; 10:e0134312 [View Article]
    [Google Scholar]
  44. 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 [View Article]
    [Google Scholar]
  45. 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 [View Article]
    [Google Scholar]
  46. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  47. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
    [Google Scholar]
  48. Xu L, Dong Z, Fang L, Luo Y, Wei Z et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52–W58 [View Article]
    [Google Scholar]
  49. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–W21 [View Article]
    [Google Scholar]
  50. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2007; 35:W52–W57 [View Article]
    [Google Scholar]
  51. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999; 27:573–580 [View Article]
    [Google Scholar]
  52. Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2017; 45:W30–W35 [View Article]
    [Google Scholar]
  53. Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 2020; 75:3491–3500 [View Article]
    [Google Scholar]
  54. Eisenberg T, Fawzy A, Nicklas W, Semmler T, Ewers C. Phylogenetic and comparative genomics of the family Leptotrichiaceae and introduction of a novel fingerprinting MLVA for Streptobacillus moniliformis. BMC Genomics 2016; 17:864 [View Article]
    [Google Scholar]
  55. Eisenberg T, Glaeser SP, Blom J, Kämpfer P. Genus Sneathia. Bergey’s Manual of Systematics of Archaea and Bacteria 2018
    [Google Scholar]
  56. Blanc-Potard Anne-Béatrice, Solomon F, Kayser J, Groisman EA. The SPI-3 pathogenicity island of Salmonella enterica . J Bacteriol 1999; 181:998–1004 [View Article]
    [Google Scholar]
  57. Gentile GL, Rupert AS, Carrasco LI, Garcia EM, Kumar NG et al. Identification of a cytopathogenic toxin from Sneathia amnii . J Bacteriol 2020; 202: [View Article]
    [Google Scholar]
  58. Eisenberg T, Ewers C, Rau J, Akimkin V, Nicklas W. Approved and novel strategies in diagnostics of rat bite fever and other Streptobacillus infections in humans and animals. Virulence 2016; 7:630–648 [View Article]
    [Google Scholar]
  59. Eisenberg T, Imaoka K, Kimura M, Glaeser SP, Ewers C et al. Streptobacillus ratti sp. nov. isolated from a black rat (Rattus rattus). Int J Syst Evol Microbiol 2016; 66:1620–1626 [View Article][PubMed]
    [Google Scholar]
  60. Rau J, Eisenberg T, Peters M, Berger A, Kutzer P et al. Reliable differentiation of a non-toxigenic tox gene-bearing Corynebacterium ulcerans variant frequently isolated from game animals using MALDI-TOF MS. Vet Microbiol 2019; 237:108399 [View Article]
    [Google Scholar]
  61. Rau J, Eisenberg T, Männig A, Wind C, Lasch P. MALDI-UP – An internet platform for the exchange of MALDI-TOF mass spectra. User guide for http://maldi-up.ua-bw.de/ . Aspects of food control and animal health 2016; 2016:1–17
    [Google Scholar]
  62. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
    [Google Scholar]
  63. Hanff PA, Rosol-Donoghue JA, Spiegel CA, Wilson KH, Moore LH. Leptotrichia sanguinegens sp. nov., a new agent of postpartum and neonatal bacteremia. Clin Infect Dis 1995; 20:S237–S239 [View Article]
    [Google Scholar]
  64. Collins MD, Hoyles L, Törnqvist E, von Essen R, Falsen E. Characterization of some strains from human clinical sources which resemble “Leptotrichia sanguinegens”: description of Sneathia sanguinegens sp. nov., gen. nov. Syst Appl Microbiol 2001; 24:358–361 [View Article]
    [Google Scholar]
  65. Eisenberg T, Glaeser SP, Blom J, Kämpfer P. Family Leptotrichiaceae. Bergey’s Manual of Systematics of Archaea and Bacteria 2018
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004663
Loading
/content/journal/ijsem/10.1099/ijsem.0.004663
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error