Abd-Allah IM, El-Housseiny GS, Alshahrani MY, El-Masry SS, Aboshanab KM, Hassouna NA (2022) An anti-MRSA phage from raw fish rinse: stability evaluation and production optimization. Front Cell Infect Microbiol 12:904531. https://doi.org/10.3389/fcimb.2022.904531

Article  CAS  PubMed  PubMed Central  Google Scholar 

Abd-Allah IM, El-Housseiny GS, Al-Agamy MH, Radwan HH, Aboshanab KM, Hassouna NA (2023) Statistical optimization of a podoviral anti-MRSA phage CCASU-L10 generated from an under sampled repository: chicken rinse. Front Cell Infect Microbiol 13:1149848. https://doi.org/10.3389/fcimb.2023.1149848

Article  CAS  PubMed  PubMed Central  Google Scholar 

Abdelaziz SM, Aboshanab KM, Yahia IS, Yassien MA, Hassouna NA (2021) Correlation between the antibiotic resistance genes and susceptibility to antibiotics among the carbapenem-resistant gram-negative pathogens. Antibiotics 10(3):255. https://doi.org/10.3390/antibiotics10030255

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alikhan N-F, Petty NK, Ben Zakour NL, Beatson SA (2011) BLAST ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12:402. https://doi.org/10.1186/1471-2164-12-402

Article  CAS  PubMed  PubMed Central  Google Scholar 

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2

Article  CAS  PubMed  Google Scholar 

Al-Zubidi M, Widziolek M, Court EK, Gains AF, Smith RE, Ansbro K, Alrafaie A, Evans C, Murdoch C, Mesnage S, Douglas CWI, Rawlinson A, Stafford GP (2019) Identification of novel bacteriophages with therapeutic potential that target Enterococcus faecalis. Infect Immun 87(11):e00512-e519. https://doi.org/10.1128/IAI.00512-19

Article  CAS  PubMed  PubMed Central  Google Scholar 

Arshadi M, Mahmoudi M, Motahar MS, Soltani S, Pourmand MR (2018) Virulence determinants and antimicrobial resistance patterns of vancomycin-resistant Enterococcus faecium isolated from different sources in Southwest Iran. Iran J Public Health 47:264–272

PubMed  PubMed Central  Google Scholar 

Besemer J (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618. https://doi.org/10.1093/nar/29.12.2607

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bolocan AS, Upadrasta A, de Almeida Bettio PH, Clooney AG, Draper LA, Ross RP, Hill C (2019) Evaluation of phage therapy in the context of Enterococcus faecalis and Its associated diseases. Viruses 11:366. https://doi.org/10.3390/v11040366

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bonenfant Q, Noé L, Touzet H (2023) Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming. Bioinform Adv 3(1):vbac085. https://doi.org/10.1093/bioadv/vbac085

Article  PubMed  Google Scholar 

Canfield GS, Chatterjee A, Espinosa J, Mangalea MR, Sheriff EK, Keidan M, McBride SW, McCollister BD, Hang HC, Duerkop BA (2021) Lytic bacteriophages facilitate antibiotic sensitization of Enterococcus faecium. Antimicrob Agents Chemother 65(5):e00143-e221. https://doi.org/10.1128/AAC.00143-21

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chatterjee A, Willett JLE, Nguyen UT, Monogue B, Palmer KL, Dunny GM, Duerkop BA (2020) Parallel genomics uncover novel enterococcal-bacteriophage interactions. Mbio 11(2):e03120-e3219. https://doi.org/10.1128/mBio.03120-19

Article  CAS  PubMed  PubMed Central  Google Scholar 

CLSI (2021) CLSI: performance standards for antimicrobial susceptibility testing. Clinical and Laboratory Standards Institute 2021. In: vol. M100-Ed31. https://clsi.org/media/z2uhcbmv/m100ed31_sample.pdf. Accessed 5 Feb 2025

de Azevedo RB, Manta MM, da Silva SM, Cavalcanti de Sá RAQ, de Souza NL, Melo Coutinho HD, da Silva MV, da Silva TD, dos Santos Correia MT, de Oliveira MBM (2023) Virulence factors and biofilm formation in vancomycin resistant Enterococcus faecalis and Enterococcus faecium; isolates in Brazil. Adv Microbiol 13:299–314. https://doi.org/10.4236/aim.2023.136019

Article  CAS  Google Scholar 

De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C (2018) NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34:2666–2669. https://doi.org/10.1093/bioinformatics/bty149

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dreyer A, Lenz C, Groß U, Bohne W, Zautner AE (2024) Comparative analysis of proteomic adaptations in Enterococcus faecalis and Enterococcus faecium after long term bile acid exposure. BMC Microbiol 24:110. https://doi.org/10.1186/s12866-024-03253-0

Article  CAS  PubMed  PubMed Central  Google Scholar 

El-Atrees DM, El-Kased RF, Abbas AM, Yassien MA (2022) Characterization and anti-biofilm activity of bacteriophages against urinary tract Enterococcus faecalis isolates. Sci Rep 12:13048. https://doi.org/10.1038/s41598-022-17275-z

Article  CAS  PubMed  PubMed Central  Google Scholar 

EVREA-Phage (2024) EVREA-phage: phage therapy against Enterococcus faecium. In: German Center for infection research. https://www.dzif.de/en/projekt/evrea-phage. Accessed 10 Feb 2025

Fahmy N, Abdel-Gawad A, Rezk G, Mahmoud E (2021) Characterization of Enterococci isolated from intensive care unit (ICU); Distribution of virulence markers, virulence genes and antibiotic resistance pattern. Microbes Infect Diss 2(4):725–735. https://doi.org/10.21608/mid.2021.76391.1158

Article  CAS  Google Scholar 

Fiore E, Van Tyne D, Gilmore MS (2019) Pathogenicity of enterococci. Microbiol Spectr 7(4):1–23. https://doi.org/10.1128/microbiolspec.GPP3-0053-2018

Article  Google Scholar 

Hallajzadeh M, Mojtahedi A, Amirmozafari N, Pirhajati Mahabadi V (2020) Characterizing a lytic bacteriophage infecting methicillin-resistant Staphylococcus aureus (MRSA) isolated from burn patients. Arch Clin Infect Dis 15(1):1–13. https://doi.org/10.5812/archcid.91634

Article  CAS  Google Scholar 

Hashem YA, Abdelrahman KA, Aziz RK (2021) Phenotype-genotype correlations and distribution of key virulence factors in Enterococcus faecalis isolated from patients with urinary tract infections. Infect Drug Resist 14:1713–1723. https://doi.org/10.2147/IDR.S305167

Article  PubMed  PubMed Central  Google Scholar 

Hegstad K, Giske CG, Haldorsen B, Matuschek E, Schønning K, Leegaard TM, Kahlmeter G, Sundsfjord A (2014) Performance of the EUCAST disk diffusion method, the CLSI agar screen method, and the vitek 2 automated antimicrobial susceptibility testing system for detection of clinical isolates of Enterococci with low- and medium-level VanB-type vancomycin resistance: a multicenter study. J Clin Microbiol 52:1582–1589. https://doi.org/10.1128/JCM.03544-13

Article  CAS  PubMed  PubMed Central  Google Scholar 

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 

Hyman P (2019) Phages for phage therapy: isolation, characterization, and host range breadth. Pharmaceuticals 12:35. https://doi.org/10.3390/ph12010035

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jett BD, Huycke MM, Gilmore MS (1994) Virulence of enterococci. Clin Microbiol Rev 7:462–478. https://doi.org/10.1128/CMR.7.4.462

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kabwe M, Meehan-Andrews T, Ku H, Petrovski S, Batinovic S, Chan HT, Tucci J (2021) Lytic bacteriophage EFA1 modulates HCT116 colon cancer cell growth and upregulates ROS production in an Enterococcus faecalis co-culture system. Front Microbiol 12:650849. https://doi.org/10.3389/fmicb.2021.650849

Article  PubMed  PubMed Central  Google Scholar 

Khalifa L, Shlezinger M, Beyth S, Houri-Haddad Y, Coppenhagen-Glazer S, Beyth N, Hazan R (2016) Phage therapy against Enterococcus faecalis in dental root canals. J Oral Microbiol 8:32157. https://doi.org/10.3402/jom.v8.32157