1887

Abstract

Four bacterial strains were isolated from two different colony sources of the wax moth . They were characterized by a polyphasic approach including 16S rRNA gene sequence analysis, core-genome analysis, average nucleotide identity (ANI) analysis, digital DNA–DNA hybridization (dDDH), determination of G+C content, screening of antibiotic resistance genes, and various phenotypic analyses. Initial analysis of 16S rRNA gene sequence identities indicated that strain GAL7 was potentially very closely related to and , having 99.5–99.9 % sequence similarity. However, further analysis of whole genome sequences revealed a genome size of 3.69 Mb, DNA G+C content of 42.35 mol%, and low dDDH and ANI values between the genomes of strain GAL7 and closest phylogenetic relative NBRC 100478 of 59.0 and 94.5 %, respectively, indicating identification of a putative new species. In addition, all novel strains encoded the atypical vancomycin-resistance gene . Results of phylogenomic, physiological and phenotypic characterization confirmed that strain GAL7 represented a novel species within the genus , for which the name sp. nov. is proposed. The type strain is GAL7 (=DSM 112306=NCTC 14608).

Funding
This study was supported by the:
  • Wellcome Trust (Award 220876/Z/20/Z)
    • Principle Award Recipient: LindsayJ Hall
  • Wellcome Trust (Award 100974/C/13/Z)
    • Principle Award Recipient: LindsayJ Hall
  • Biotechnology and Biological Sciences Research Council (Award BB/R012490/1)
    • Principle Award Recipient: LindsayJ Hall
  • Wellcome Trust (Award 110072/Z/15/Z)
    • Principle Award Recipient: AnthonyMaxwell
  • Biotechnology and Biological Sciences Research Council (Award BB/P012523/1)
    • Principle Award Recipient: AnthonyMaxwell
  • National Centre for the Replacement, Refinement and Reduction of Animals in Research (Award NC/R001782/1)
    • Principle Award Recipient: HarrietCC Gooch
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2021-12-17
2022-05-29
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References

  1. Teixeira LM, Merquior VLC. Enterococcus. In Filippis de, McKee M. eds Molecular Typing in Bacterial Infections (Infectious Disease) Totawa, NJ: Humana Press; 2013
    [Google Scholar]
  2. Jett BD, Huycke MM, Gilmore MS. Virulence of enterococci. Clin Microbiol Rev 1994; 7:462–478 [View Article] [PubMed]
    [Google Scholar]
  3. Gilmore MS, Clewell DB, Courvalin P, Dunny GM, Murray BE et al. The Enterococci. In The Enterococci: Pathogenesis, Molecular Biology, and Antibiotic Resistance Washington: ASM Press; 2002 [View Article]
    [Google Scholar]
  4. Ceci M, Delpech G, Sparo M, Mezzina V, Sánchez Bruni S et al. Clinical and microbiological features of bacteremia caused by Enterococcus faecalis. J Infect Dev Ctries 2015; 9:1195–1203 [View Article] [PubMed]
    [Google Scholar]
  5. Nigo M, Munita JM, Arias CA, Murray BE. What’s new in the treatment of enterococcal endocarditis?. Curr Infect Dis Rep 2014; 16:431 [View Article] [PubMed]
    [Google Scholar]
  6. Flores-Mireles AL, Walker JN, Caparon M, Hultgren SJ. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat Rev Microbiol 2015; 13:269–284 [View Article] [PubMed]
    [Google Scholar]
  7. Miller WR, Munita JM, Arias CA. Mechanisms of antibiotic resistance in enterococci. Expert Rev Anti Infect Ther 2014; 12:1221–1236 [View Article] [PubMed]
    [Google Scholar]
  8. Sifaoui F, Arthur M, Rice L, Gutmann L. Role of penicillin-binding protein 5 in expression of ampicillin resistance and peptidoglycan structure in Enterococcus faecium. Antimicrob Agents Chemother 2001; 45:2594–2597 [View Article] [PubMed]
    [Google Scholar]
  9. Fisher K, Phillips C. The ecology, epidemiology and virulence of Enterococcus. Microbiology 2009; 155:1749–1757 [View Article] [PubMed]
    [Google Scholar]
  10. Arias CA, Murray BE. The rise of the Enterococcus: beyond vancomycin resistance. Nat Rev Microbiol 2012; 10:266–278 [View Article] [PubMed]
    [Google Scholar]
  11. Jarosz J. Gut flora of Galleria mellonella suppressing ingested bacteria. J Invertebr Pathol 1979; 34:192–198 [View Article] [PubMed]
    [Google Scholar]
  12. Allonsius CN, Van Beeck W, De Boeck I, Wittouck S, Lebeer S. The microbiome of the invertebrate model host Galleria mellonella is dominated by Enterococcus. Anim Microbiome 2019; 1:7 [View Article] [PubMed]
    [Google Scholar]
  13. Duplouy A, Hornett EA. Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts. PeerJ 2018; 6:e4629 [View Article] [PubMed]
    [Google Scholar]
  14. Kwadha CA, Ong’amo GO, Ndegwa PN, Raina SK, Fombong AT. The biology and control of the greater wax moth, Galleria mellonella. Insects 2017; 8:E61 [View Article] [PubMed]
    [Google Scholar]
  15. Tsai CJ-Y, Loh JMS, Proft T. Galleria mellonella infection models for the study of bacterial diseases and for antimicrobial drug testing. Virulence 2016; 7:214–229 [View Article] [PubMed]
    [Google Scholar]
  16. Lange A, Schäfer A, Bender A, Steimle A, Beier S et al. Galleria mellonella: a novel invertebrate model to distinguish intestinal symbionts from pathobionts. Front Immunol 2018; 9:2114 [View Article] [PubMed]
    [Google Scholar]
  17. Pereira MF, Rossi CC, da Silva GC, Rosa JN, Bazzolli DMS. Galleria mellonella as an infection model: an in-depth look at why it works and practical considerations for successful application. Pathog Dis 2020; 78:ftaa056. [View Article] [PubMed]
    [Google Scholar]
  18. LeMoine CM, Grove HC, Smith CM, Cassone BJ. A very hungry caterpillar: polyethylene metabolism and lipid homeostasis in larvae of the greater wax moth (Galleria mellonella). Environ Sci Technol 2020; 54:14706–14715 [View Article] [PubMed]
    [Google Scholar]
  19. Johnston PR, Rolff J. Host and symbiont jointly control gut microbiota during complete metamorphosisSymbiont Jointly Control Gut Microbiota during Complete Metamorphosis. PLoS Pathog 2015; 11:e1005246 [View Article] [PubMed]
    [Google Scholar]
  20. Alcon-Giner C, Dalby MJ, Caim S, Ketskemety J, Shaw A et al. Microbiota supplementation with bifidobacterium and Lactobacillus modifies the preterm infant gut microbiota and metabolome: an observational study. Cell Rep Med 2020; 1:100077 [View Article] [PubMed]
    [Google Scholar]
  21. Baker DJ, Aydin A, Le-Viet T, Kay GL, Rudder S et al. CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes. Genome Med 2021; 13:21. [View Article] [PubMed]
    [Google Scholar]
  22. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
  23. Parte AC. LPSN--list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–6 [View Article] [PubMed]
    [Google Scholar]
  24. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  25. Kiu R. BACTspeciesID: identify microbial species and genome contamination using 16S rRNA gene approach; 2020 https://github.com/raymondkiu/bactspeciesID
  26. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  27. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 2019; 47:W256–W259 [View Article] [PubMed]
    [Google Scholar]
  28. 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]
  29. Naser SM, Vancanneyt M, Hoste B, Snauwaert C, Vandemeulebroecke K et al. Reclassification of Enterococcus flavescens Pompei et al. 1992 as a later synonym of Enterococcus casseliflavus (ex Vaughan et al. 1979) Collins et al. 1984 and Enterococcus saccharominimus Vancanneyt et al. 2004 as a later synonym of Enterococcus italicus Fortina et al. 2004. Int J Syst Evol Microbiol 2006; 56:413–416 [View Article] [PubMed]
    [Google Scholar]
  30. 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] [PubMed]
    [Google Scholar]
  31. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
    [Google Scholar]
  32. Seemann T, Klotzl F, Page AJ. snp-dists: Pairwise SNP distance matrix from a FASTA sequence alignment; 2018 https://github.com/tseemann/snp-dists
  33. Seemann T. ABRicate: Mass screening of contigs for antimicrobial and virulence genes; 2018 https://github.com/tseemann/abricate
  34. Clark NC, Teixeira LM, Facklam RR, Tenover FC. Detection and differentiation of vanC-1, vanC-2, and vanC-3 glycopeptide resistance genes in enterococci. J Clin Microbiol 1998; 36:2294–2297 [View Article] [PubMed]
    [Google Scholar]
  35. Watanabe S, Kobayashi N, Quiñones D, Hayakawa S, Nagashima S et al. Genetic diversity of the low-level vancomycin resistance gene vanC-2/vanC-3 and identification of a novel vanC subtype (vanC-4) in Enterococcus casseliflavus. Microb Drug Resist 2009; 15:1–9 [View Article] [PubMed]
    [Google Scholar]
  36. Cetinkaya Y, Falk P, Mayhall CG. Vancomycin-resistant enterococci. Clin Microbiol Rev 2000; 13:686–707 [View Article] [PubMed]
    [Google Scholar]
  37. Collins MD, Farrow JAE, Jones D. Enterococcus mundtii sp. nov. Int J Syst Bacteriol 1986; 36:8–12 [View Article]
    [Google Scholar]
  38. Sichtig H, Minogue T, Yan Y, Stefan C, Hall A et al. FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. Nat Commun 2019; 10:3313 [View Article] [PubMed]
    [Google Scholar]
  39. Shao Y, Forster SC, Tsaliki E, Vervier K, Strang A et al. Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature 2019; 574:117–121 [View Article] [PubMed]
    [Google Scholar]
  40. Mattarelli P, Holzapfel W, Franz CMAP, Endo A, Felis GE et al. Recommended minimal standards for description of new taxa of the genera Bifidobacterium, Lactobacillus and related genera. Int J Syst Evol Microbiol 2014; 64:1434–1451 [View Article] [PubMed]
    [Google Scholar]
  41. Andrews JM. Determination of minimum inhibitory concentrations. J Antimicrob Chemother 2001; 48 Suppl 1:5–16 [View Article] [PubMed]
    [Google Scholar]
  42. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
    [Google Scholar]
  43. Li YQ, Gu CT. Enterococcus pingfangensis sp. nov., Enterococcus dongliensis sp. nov., Enterococcus hulanensis sp. nov., Enterococcus nangangensis sp. nov. and Enterococcus songbeiensis sp. nov., isolated from Chinese traditional pickle juice. Int J Syst Evol Microbiol 2019; 69:3191–3201 [View Article] [PubMed]
    [Google Scholar]
  44. Brown DFJ, Wootton M, Howe RA. Antimicrobial susceptibility testing breakpoints and methods from BSAC to EUCAST. J Antimicrob Chemother 2016; 71:3–5 [View Article] [PubMed]
    [Google Scholar]
  45. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182. [View Article] [PubMed]
    [Google Scholar]
  46. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2009; 37:D26–31 [View Article] [PubMed]
    [Google Scholar]
  47. Kiu R. Sequence-stats: generate sequence statistics from FASTA and FASTQ files; 2020 https://github.com/raymondkiu/sequence-stats
  48. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  49. Collins MD, Jones D, Farrow JAE, Kilpperbalz R, Schleifer KH. Enterococcus avium nom. rev., comb. nov.; E. casseliflavus nom. rev., comb. nov.; E. durans nom. rev., comb. nov.; E. gallinarum comb. nov.; and E. malodoratus sp. nov.. Int J Syst Bacteriol 1984; 34:220–223
    [Google Scholar]
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