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Isolation and characterization of a novel lytic bacteriophage vB_Efm_LG62 infecting Enterococcus faecium

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Abstract

Enterococcus faecium has been classified as a “high priority” pathogen by the World Health Organization. Enterococcus faecium has rapidly evolved as a global nosocomial pathogen with adaptation to the nosocomial environment and the accumulation of resistance to multiple antibiotics. Phage therapy is considered a promising strategy against difficult-to-treat infections and antimicrobial resistance. In this study, we isolated and characterized a novel virulent bacteriophage, vB_Efm_LG62, that specifically infects multidrug-resistant E. faecium. Morphological observations suggested that the phage has siphovirus morphology, with an optimal multiplicity of infection of 0.001. One-step growth tests revealed that its latent growth was at 20 min, with a burst size of 101 PFU/cell. Phage vB_Efm_LG62 was verified to have a double-stranded genome of 42,236 bp (35.21% GC content), containing 66 predicted coding sequences as determined by whole genomic sequencing. No genes were predicted to have functions associated with virulence factors or antibiotic resistance, indicating that the phage vB_Efm_LG62 has good therapeutic potential. Our isolation and characterization of this highly efficient phage aids in expanding our knowledge of E. faecium-targeting phages, and provides additional options for phage cocktail therapy.

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Data availability

The genomic information of phage vB_Efm_LG62 is available in the NCBI GenBank (Accession number OP018674). Further inquiries can be directed to the corresponding author/s.

References

  1. Schleifer KH, Kilpper-Balz R (1984) Transfer of Streptococcus faecalis and Streptococcus faecium to the Genus Enterococcus nom. rev. as Enterococcus faecalis comb. nov. and Enterococcus faecium comb. nov. Int J Syst Bacteriol 34:31–34. https://doi.org/10.1099/00207713-34-1-31

    Article  Google Scholar 

  2. Vu J, Carvalho J (2011) Enterococcus: review of its physiology, pathogenesis, diseases and the challenges it poses for clinical microbiology. Front Biol 6:357–366. https://doi.org/10.1007/s11515-011-1167-x

    Article  CAS  Google Scholar 

  3. Agudelo Higuita NI, Huycke MM (2014) Enterococcal disease, epidemiology, and implications for treatment. In: Gilmore MS, Clewell DB, Ike Y, Shankar N (eds) Enterococci: from commensals to leading causes of drug resistant infection. Massachusetts Eye and Ear Infirmary, Boston

    Google Scholar 

  4. Jabbari Shiadeh SM, Pormohammad A, Hashemi A, Lak P (2019) Global prevalence of antibiotic resistance in blood-isolated Enterococcus faecalis and Enterococcus faecium: a systematic review and meta-analysis. Infect Drug Resist 12:2713–2725. https://doi.org/10.2147/IDR.S206084

    Article  PubMed  PubMed Central  Google Scholar 

  5. Zhou X, Willems RJL, Friedrich AW, Rossen JWA, Bathoorn E (2020) Enterococcus faecium: from microbiological insights to practical recommendations for infection control and diagnostics. Antimicrob Resist Infect Control 9:130. https://doi.org/10.1186/s13756-020-00770-1

    Article  PubMed  PubMed Central  Google Scholar 

  6. Domingo-Calap P, Georgel P, Bahram S (2016) Back to the future: bacteriophages as promising therapeutic tools. Hla 87:133–140. https://doi.org/10.1111/tan.12742

    Article  CAS  PubMed  Google Scholar 

  7. Lebeaux D, Merabishvili M, Caudron E, Lannoy D, Van Simaey L, Duyvejonck H et al (2021) A case of phage therapy against pandrug-resistant Achromobacter xylosoxidans in a 12-year-old lung-transplanted cystic fibrosis patient. Viruses. https://doi.org/10.3390/v13010060

    Article  PubMed  PubMed Central  Google Scholar 

  8. Kuipers S, Ruth MM, Mientjes M, de Sevaux RGL, van Ingen J (2019) A dutch case report of successful treatment of chronic relapsing urinary tract infection with bacteriophages in a renal transplant patient. Antimicrob Agents Chemother. https://doi.org/10.1128/AAC.01281-19

    Article  PubMed  PubMed Central  Google Scholar 

  9. Zhvania P, Hoyle NS, Nadareishvili L, Nizharadze D, Kutateladze M (2017) Phage therapy in a 16-year-old boy with netherton syndrome. Front Med (Lausanne) 4:94. https://doi.org/10.3389/fmed.2017.00094

    Article  PubMed  Google Scholar 

  10. Chan BK, Turner PE, Kim S, Mojibian HR, Elefteriades JA, Narayan D (2018) Phage treatment of an aortic graft infected with Pseudomonas aeruginosa. Evol Med Public Health 2018:60–66. https://doi.org/10.1093/emph/eoy005

    Article  PubMed  PubMed Central  Google Scholar 

  11. Paul K, Merabishvili M, Hazan R, Christner M, Herden U, Gelman D et al (2021) Bacteriophage rescue therapy of a vancomycin-resistant Enterococcus faecium infection in a one-year-old child following a third liver transplantation. Viruses. https://doi.org/10.3390/v13091785

    Article  PubMed  PubMed Central  Google Scholar 

  12. Uyttebroek S, Chen B, Onsea J, Ruythooren F, Debaveye Y, Devolder D et al (2022) Safety and efficacy of phage therapy in difficult-to-treat infections: a systematic review. Lancet Infect Dis 22:e208–e220. https://doi.org/10.1016/S1473-3099(21)00612-5

    Article  CAS  PubMed  Google Scholar 

  13. Burrowes B, Harper DR, Anderson J, McConville M, Enright MC (2011) Bacteriophage therapy: potential uses in the control of antibiotic-resistant pathogens. Expert Rev Anti Infect Ther 9:775–785. https://doi.org/10.1586/eri.11.90

    Article  PubMed  Google Scholar 

  14. Payaslian F, Gradaschi V, Piuri M (2021) Genetic manipulation of phages for therapy using BRED. Curr Opin Biotech 68:8–14. https://doi.org/10.1016/j.copbio.2020.09.005

    Article  CAS  PubMed  Google Scholar 

  15. Samson JE, Magadan AH, Sabri M, Moineau S (2013) Revenge of the phages: defeating bacterial defences. Nat Rev Microbiol 11:675–687. https://doi.org/10.1038/nrmicro3096

    Article  CAS  PubMed  Google Scholar 

  16. Forde A, Hill C (2018) Phages of life—the path to pharma. Brit J Pharmacol 175:412–418. https://doi.org/10.1111/bph.14106

    Article  CAS  Google Scholar 

  17. Wiegand I, Hilpert K, Hancock RE (2008) Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nat Protoc 3:163–175. https://doi.org/10.1038/nprot.2007.521

    Article  CAS  PubMed  Google Scholar 

  18. CLSI (2020) Performance standards for antimicrobial susceptibility testing, 30th edn. Clinical and Laboratory Standards Institute, Wayen, PA

    Google Scholar 

  19. Song L, Yang X, Huang J, Zhu X, Han G, Wan Y et al (2021) Phage selective pressure reduces virulence of hypervirulent Klebsiella pneumoniae through mutation of the wzc gene. Front Microbiol 12:739319. https://doi.org/10.3389/fmicb.2021.739319

    Article  PubMed  PubMed Central  Google Scholar 

  20. Li E, Wei X, Ma Y, Yin Z, Li H, Lin W et al (2016) Isolation and characterization of a bacteriophage phiEap-2 infecting multidrug resistant Enterobacter aerogenes. Sci Rep 6:28338. https://doi.org/10.1038/srep28338

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Cheng M, Luo M, Xi H, Zhao Y, Le S, Chen LK et al (2020) The characteristics and genome analysis of vB_ApiP_XC38, a novel phage infecting Acinetobacter pittii. Virus Genes 56:498–507. https://doi.org/10.1007/s11262-020-01766-0

    Article  CAS  PubMed  Google Scholar 

  22. Sharma S, Datta S, Chatterjee S, Dutta M, Samanta J, Vairale MG et al (2021) Isolation and characterization of a lytic bacteriophage against Pseudomonas aeruginosa. Sci Rep 11:19393. https://doi.org/10.1038/s41598-021-98457-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Farshadzadeh Z, Taheri B, Rahimi S, Shoja S, Pourhajibagher M, Haghighi MA et al (2018) Growth rate and biofilm formation ability of clinical and laboratory-evolved colistin-resistant strains of Acinetobacter baumannii. Front Microbiol 9:153. https://doi.org/10.3389/fmicb.2018.00153

    Article  PubMed  PubMed Central  Google Scholar 

  24. Liu J, Zhu Y, Li Y, Lu Y, Xiong K, Zhong Q et al (2022) Bacteriophage-resistant mutant of Enterococcus faecalis is impaired in biofilm formation. Front Microbiol 13:913023. https://doi.org/10.3389/fmicb.2022.913023

    Article  PubMed  PubMed Central  Google Scholar 

  25. Antipov D, Raiko M, Lapidus A, Pevzner PA (2020) Metaviral SPAdes: assembly of viruses from metagenomic data. Bioinformatics 36:4126–4129. https://doi.org/10.1093/bioinformatics/btaa490

    Article  CAS  PubMed  Google Scholar 

  26. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T et al (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206–D214. https://doi.org/10.1093/nar/gkt1226

    Article  CAS  PubMed  Google Scholar 

  27. Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537–539. https://doi.org/10.1093/bioinformatics/bti054

    Article  CAS  PubMed  Google Scholar 

  28. 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. https://doi.org/10.1093/bioinformatics/btr703

    Article  CAS  PubMed  Google Scholar 

  29. Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y et al (2005) VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 33:D325-328. https://doi.org/10.1093/nar/gki008

    Article  CAS  PubMed  Google Scholar 

  30. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A et al (2020) CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 48:D517–D525. https://doi.org/10.1093/nar/gkz935

    Article  CAS  PubMed  Google Scholar 

  31. Lowe TM, Chan PP (2016) tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44:W54-57. https://doi.org/10.1093/nar/gkw413

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027. https://doi.org/10.1093/molbev/msab120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Sullivan MJ, Petty NK, Beatson SA (2011) Easyfig: a genome comparison visualizer. Bioinformatics 27:1009–1010. https://doi.org/10.1093/bioinformatics/btr039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Wang Y, Wang W, Lv Y, Zheng W, Mi Z, Pei G et al (2014) Characterization and complete genome sequence analysis of novel bacteriophage IME-EFm1 infecting Enterococcus faecium. J Gen Virol 95:2565–2575. https://doi.org/10.1099/vir.0.067553-0

    Article  CAS  PubMed  Google Scholar 

  35. Arias CA, Murray BE (2012) The rise of the Enterococcus: beyond vancomycin resistance. Nat Rev Microbiol 10:266–278. https://doi.org/10.1038/nrmicro2761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Cattoir V, Giard JC (2014) Antibiotic resistance in Enterococcus faecium clinical isolates. Expert Rev Anti Infect Ther 12:239–248. https://doi.org/10.1586/14787210.2014.870886

    Article  CAS  PubMed  Google Scholar 

  37. Turner D, Kropinski AM, Adriaenssens EM (2021) A roadmap for genome-based phage taxonomy. Viruses. https://doi.org/10.3390/v13030506

    Article  PubMed  PubMed Central  Google Scholar 

  38. Rigvava S, Kusradze I, Tchgkonia I, Karumidze N, Dvalidze T, Goderdzishvili M (2022) Novel lytic bacteriophage vB_GEC_EfS_9 against Enterococcus faecium. Virus Res 307:198599. https://doi.org/10.1016/j.virusres.2021.198599

    Article  CAS  PubMed  Google Scholar 

  39. Xing S, Zhang X, Sun Q, Wang J, Mi Z, Pei G et al (2017) Complete genome sequence of a novel, virulent Ahjdlikevirus bacteriophage that infects Enterococcus faecium. Arch Virol 162:3843–3847. https://doi.org/10.1007/s00705-017-3503-1

    Article  CAS  PubMed  Google Scholar 

  40. Tian F, Li J, Nazir A, Tong Y (2021) Bacteriophage—a promising alternative measure for bacterial biofilm control. Infect Drug Resist 14:205–217. https://doi.org/10.2147/IDR.S290093

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Holmberg A, Rasmussen M (2016) Mature biofilms of Enterococcus faecalis and Enterococcus faecium are highly resistant to antibiotics. Diagn Microbiol Infect Dis 84:19–21. https://doi.org/10.1016/j.diagmicrobio.2015.09.012

    Article  CAS  PubMed  Google Scholar 

  42. Mi L, Liu Y, Wang C, He T, Gao S, Xing S et al (2019) Identification of a lytic Pseudomonas aeruginosa phage depolymerase and its anti-biofilm effect and bactericidal contribution to serum. Virus Genes 55:394–405. https://doi.org/10.1007/s11262-019-01660-4

    Article  CAS  PubMed  Google Scholar 

  43. Guo Z, Huang J, Yan G, Lei L, Wang S, Yu L et al (2017) Identification and characterization of Dpo42, a novel depolymerase derived from the Escherichia coli phage vB_EcoM_ECOO78. Front Microbiol 8:1460. https://doi.org/10.3389/fmicb.2017.01460

    Article  PubMed  PubMed Central  Google Scholar 

  44. Topka-Bielecka G, Dydecka A, Necel A, Bloch S, Nejman-Falenczyk B, Wegrzyn G et al (2021) Bacteriophage-derived depolymerases against bacterial biofilm. Antibiotics (Basel). https://doi.org/10.3390/antibiotics10020175

    Article  PubMed  Google Scholar 

  45. Kunz Coyne AJ, Stamper K, Kebriaei R, Holger DJ, El Ghali A, Morrisette T et al (2022) Phage cocktails with daptomycin and ampicillin eradicates biofilm-embedded multidrug-resistant Enterococcus faecium with preserved phage susceptibility. Antibiotics (Basel). https://doi.org/10.3390/antibiotics11091175

    Article  PubMed  Google Scholar 

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Funding

This work was supported by the Science & Technology Fundamental Resources Investigation Program (Grant No.2022FY101100) and the Research Fund of Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province (FB19-06).

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Author notes

  1. Qianyu Qu and Tao Chen have contributed equally to this work and share the first authorship.

Authors and Affiliations

  1. West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China

    Qianyu Qu, Penggang He & Peibin Zeng

  2. Medical Laboratory, Xindu District People’s Hospital of Chengdu, Chengdu, China

    Tao Chen

  3. Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China

    Huaixin Geng & Guangxin Luan

Authors
  1. Qianyu Qu
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  2. Tao Chen
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  3. Penggang He
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  4. Huaixin Geng
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  5. Peibin Zeng
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  6. Guangxin Luan
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Contributions

GL and PZ contributed to the design of the study. TC provides the bacterial strains used in this study. QQ, PH, and HG were involved in data acquisition. QQ and TC analyzed and interpreted the data. QQ wrote the first manuscript. PZ and GL critically revised the manuscript for important intellectual content. All authors approved the final version to be submitted.

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Correspondence to Peibin Zeng or Guangxin Luan.

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Qu, Q., Chen, T., He, P. et al. Isolation and characterization of a novel lytic bacteriophage vB_Efm_LG62 infecting Enterococcus faecium. Virus Genes 59, 763–774 (2023). https://doi.org/10.1007/s11262-023-02016-9

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  • DOI: https://doi.org/10.1007/s11262-023-02016-9

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