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Abstract

Strain 155047 was recovered from human sputum in China in 2021. Preliminary species identification based on limited phenotypic tests assigned the strain to the genus of the family . The genome sequence of the strain was obtained and had ≤84.43 % average nucleotide identity (ANI) and ≤26.3 % DNA–DNA hybridization (isDDH) values with the genomes of type strains of known species. The highest ANI and isDDH matches were with and , respectively. The ANI and isDDH values support that the strain belongs to a novel species of the family . Phylogenomic analysis based on core genes revealed that strain 155047 was located in the lineage. The highest ANI and average amino acid identity values between 155047 and any species of the lineage were 84.43 % and 90.21 %, respectively, lower than the maximum inter-genus pairwise values. This indicates that 155047 belongs to a novel species of a novel genus in the lineage. Strain 155047 could be differentiated from , , and species by a negative reaction for β-galactosidase and the ability to produce acid from -fucose but not from sucrose. The names gen. nov. and sp. nov. are proposed for the novel genus and species, respectively. The type strain is 155047 (= GDMCC 1.2980=JCM 35262).

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2022-08-17
2025-04-19
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References

  1. Alnajar S, Gupta RS. Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family. Infect Genet Evol 2017; 54:108–127 [View Article]
    [Google Scholar]
  2. Wu W, Feng Y, Zong Z. Precise species identification for Enterobacter: a genome sequence-based study with reporting of two novel species, Enterobacter quasiroggenkampii sp. nov. and Enterobacter quasimori sp. nov. mSystems 2020; 5:00527–00520
    [Google Scholar]
  3. Wu W, Zong Z. Genome analysis-based reclassification of Enterobacter tabaci Duan et al. 2016 as a later heterotypic synonym of Enterobacter mori Zhu et al. 2011. Int J Syst Evol Microbiol 2020; 70:1055–1058 [View Article] [PubMed]
    [Google Scholar]
  4. Mezzatesta ML, Gona F, Stefani S. Enterobacter cloacae complex: clinical impact and emerging antibiotic resistance. Future Microbiol 2012; 7:887–902 [View Article]
    [Google Scholar]
  5. CLSI Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Seventh Informational Supplement. M100-S27 Wayne, PA, USA: Clinical and Laboratory Standards Institute; 2017
    [Google Scholar]
  6. Lane D. 16S/23S rRNA sequencing. In Goodfellow M, Stackebrandt E. eds Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–175
    [Google Scholar]
  7. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  8. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002; 30:3059–3066 [View Article] [PubMed]
    [Google Scholar]
  9. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article] [PubMed]
    [Google Scholar]
  10. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article]
    [Google Scholar]
  11. Doijad S, Imirzalioglu C, Yao Y, Pati NB, Falgenhauer L et al. Enterobacter bugandensis sp. nov., isolated from neonatal blood. Int J Syst Evol Microbiol 2016; 66:968–974 [View Article] [PubMed]
    [Google Scholar]
  12. Naum M, Brown EW, Mason-Gamer RJ. Is 16S rDNA a reliable phylogenetic marker to characterize relationships below the family level in the Enterobacteriaceae?. J Mol Evol 2008; 66:630–642 [View Article] [PubMed]
    [Google Scholar]
  13. 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
    [Google Scholar]
  14. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article]
    [Google Scholar]
  15. 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]
  16. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
    [Google Scholar]
  17. 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] [PubMed]
    [Google Scholar]
  18. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  19. Bayliss SC, Thorpe HA, Coyle NM, Sheppard SK, Feil EJ. PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria. Gigascience 2019; 8:giz119 [View Article] [PubMed]
    [Google Scholar]
  20. Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb Genom 2016; 2:e000056 [View Article] [PubMed]
    [Google Scholar]
  21. Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods 2014; 12:59–60 [View Article] [PubMed]
    [Google Scholar]
  22. Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1996
    [Google Scholar]
  23. Wu W, Feng Y, Zong Z. Enterobacter sichuanensis sp. nov., recovered from human urine. Int J Syst Evol Microbiol 2018; 68:3922–3927 [View Article]
    [Google Scholar]
  24. Wu W, Feng Y, Zong Z. Characterization of a strain representing a new Enterobacter species, Enterobacter chengduensis sp. nov. Antonie van Leeuwenhoek 2018; 112:491–500 [View Article]
    [Google Scholar]
  25. Akita H, Matsushika A, Kimura ZI. Enterobacter oligotrophica sp. nov., a novel oligotroph isolated from leaf soil. MicrobiologyOpen 2019; 8: [View Article] [PubMed]
    [Google Scholar]
  26. Wang C, Wu W, Wei L, Feng Y, Kang M et al. Enterobacter wuhouensis sp. nov. and Enterobacter quasihormaechei sp. nov. recovered from human sputum. Int J Syst Evol Microbiol 2020; 70:874–881 [View Article] [PubMed]
    [Google Scholar]
  27. Hoffmann H, Stindl S, Stumpf A, Mehlen A, Monget D et al. Description of Enterobacter ludwigii sp. nov., a novel Enterobacter species of clinical relevance. Syst Appl Microbiol 2005; 28:206–212 [View Article] [PubMed]
    [Google Scholar]
  28. Cho GS, Stein M, Fiedler G, Igbinosa EO, Koll LP et al. Polyphasic study of antibiotic-resistant enterobacteria isolated from fresh produce in Germany and description of Enterobacter vonholyi sp. nov. isolated from marjoram and Enterobacter dykesii sp. nov. isolated from mung bean sprout. Syst Appl Microbiol 2021; 44:126174
    [Google Scholar]
  29. Izard D, Gavini F, Trinel PA, Leclerc H. Deoxyribonucleic acid relatedness between Enterobacter cloacae and Enterobacter amnigenus sp. nov. Int J Syst Bacteriol 1981; 31:35–42 [View Article]
    [Google Scholar]
  30. Yuk KJ, Kim YT, Huh CS, Lee JH. Lelliottia jeotgali sp. nov., isolated from a traditional Korean fermented clam. Int J Syst Evol Microbiol 2018; 68:1725–1731 [View Article] [PubMed]
    [Google Scholar]
  31. Brenner DJ, McWhorter AC, Kai A, Steigerwalt AG, Farmer JJ. Enterobacter asburiae sp. nov., a new species found in clinical specimens, and reassignment of Erwinia dissolvens and Erwinia nimipressuralis to the genus Enterobacter as Enterobacter dissolvens comb. nov. and Enterobacter nimipressuralis comb. nov. J Clin Microbiol 1986; 23:1114–1120 [View Article] [PubMed]
    [Google Scholar]
  32. Steigerwalt AG, Fanning GR, Fife-Asbury MA, Brenner DJ. DNA relatedness among species of Enterobacter and Serratia. Can J Microbiol 1976; 22:121–137 [View Article] [PubMed]
    [Google Scholar]
  33. 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
    [Google Scholar]
  34. Hu Y, Feng Y, Zhang X, Zong Z. Acinetobacter defluvii sp. nov., recovered from hospital sewage. Int J Syst Evol Microbiol 2017; 67:1709–1713 [View Article] [PubMed]
    [Google Scholar]
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