Isolation and characterization of Yersinia phage fMtkYen3-01.
Journal
Archives of virology
ISSN: 1432-8798
Titre abrégé: Arch Virol
Pays: Austria
ID NLM: 7506870
Informations de publication
Date de publication:
19 Oct 2024
19 Oct 2024
Historique:
received:
15
05
2024
accepted:
29
08
2024
medline:
19
10
2024
pubmed:
19
10
2024
entrez:
19
10
2024
Statut:
epublish
Résumé
Yersinia enterocolitica causes yersiniosis, the third most common gastrointestinal infection in humans throughout Europe. The emergence of multidrug resistance and the lack of effective new antibiotics have drawn attention to phage therapy as a treatment option. Here, we report the complete genome sequence of phage fMtkYen3-01, which infects Y. enterocolitica serotype O:3 strains. This phage has a genome 40,415 bp in length with 45.1% GC content and 49 predicted genes. fMtkYen3-01 infected 9.5% of the 42 Y. enterocolitica strains tested and showed stability at 25-40 °C, as well as pH 5.0-10.0. These results suggest the therapeutic potential of this phage.
Identifiants
pubmed: 39425798
doi: 10.1007/s00705-024-06149-6
pii: 10.1007/s00705-024-06149-6
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
226Subventions
Organisme : Shota Rustaveli National Science Foundation
ID : PHDF-21-2176
Organisme : Research Council of Finland
ID : #346772
Informations de copyright
© 2024. The Author(s).
Références
The European Union One Health 2020 Zoonoses Report—2021. EFSA J Wiley Online Lib. https://doi.org/10.2903/j.efsa.2021.6971
Šumilo D, Love NK, Manuel R, Dabke G, Paranthaman K, Jenkins C, McCarthy ND (2023) Forgotten but not gone: Yersinia infections in England, 1975 to 2020. Eurosurveillance 28(14):2200516. https://doi.org/10.2807/1560-7917.ES.2023.28.14.2200516
doi: 10.2807/1560-7917.ES.2023.28.14.2200516
pubmed: 37022213
pmcid: 10283466
Dey A (2020) Annual epidemiological report for 2020
Leon-Velarde CG, Kropinski AM, Chen S, Abbasifar A, Griffiths MW, Odumeru JA (2014) Complete genome sequence of bacteriophage vB_YenP_AP5 which infects Yersinia enterocoliticaof serotype O:3. Virol J 11(1):1–14. https://doi.org/10.1186/1743-422X-11-188
doi: 10.1186/1743-422X-11-188
Mäki-Ikola O, Heesemann J, Toivanen A, Granfors K (1997) High frequency of Yersinia antibodies in healthy populations in Finland and Germany. Rheumatol Int 16(6):227–229. https://doi.org/10.1007/BF01375653
doi: 10.1007/BF01375653
pubmed: 9106932
Rosner BM, Werber D, Höhle M, Stark K (2013) Clinical aspects and self-reported symptoms of sequelae of Yersinia enterocolitica infections in a population-based study, Germany 2009–2010. BMC Infect Dis 13:236. https://doi.org/10.1186/1471-2334-13-236
doi: 10.1186/1471-2334-13-236
pubmed: 23701958
pmcid: 3669037
Laanto E, Mäkelä K, Hoikkala V, Ravantti JJ, Sundberg L-R (2020) Adapting a phage to combat phage resistance. Antibiotics 9(6):291. https://doi.org/10.3390/antibiotics9060291
doi: 10.3390/antibiotics9060291
pubmed: 32486059
pmcid: 7345892
Almeida GMF, Sundberg L-R (2020) The forgotten tale of Brazilian phage therapy. Lancet Infect Dis 20(5):e90–e101. https://doi.org/10.1016/S1473-3099(20)30060-8
doi: 10.1016/S1473-3099(20)30060-8
pubmed: 32213334
Myelnikov D (2018) An alternative cure: the adoption and survival of bacteriophage therapy in the USSR, 1922–1955. J Hist Med Allied Sci 73(4):385–411. https://doi.org/10.1093/jhmas/jry024
doi: 10.1093/jhmas/jry024
pubmed: 30312428
pmcid: 6203130
Żaczek M, Weber-Dąbrowska B, Międzybrodzki R, Łusiak-Szelachowska M, Górski A (2020) Phage therapy in Poland—a centennial journey to the first ethically approved treatment facility in Europe. Front Microbiol. https://doi.org/10.3389/fmicb.2020.01056/full
doi: 10.3389/fmicb.2020.01056/full
pubmed: 32973726
pmcid: 7466739
Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT (2023) Phage therapy: from biological mechanisms to future directions. Cell 186(1):17–31. https://doi.org/10.1016/j.cell.2022.11.017
doi: 10.1016/j.cell.2022.11.017
pubmed: 36608652
pmcid: 9827498
Clokie MRJ, Kropinski AM, editors (2009) Bacteriophages. In: Walker JM (ed.) Methods in molecular biology. Humana Press, Totowa. https://doi.org/10.1007/978-1-60327-164-6
Patpatia S, Schaedig E, Dirks A, Paasonen L, Skurnik M, Kiljunen S (2022) Rapid hydrogel-based phage susceptibility test for pathogenic bacteria. Front Cell Infect Microbiol. https://doi.org/10.3389/fcimb.2022.1032052
doi: 10.3389/fcimb.2022.1032052
pubmed: 36569196
pmcid: 9771388
Leskinen K, Tuomala H, Wicklund A, Horsma-Heikkinen J, Kuusela P, Skurnik M, Kiljunen S (2017) Characterization of vB_SauM-fRuSau02, a twort-like bacteriophage isolated from a therapeutic phage cocktail. Viruses 9(9):258. https://doi.org/10.3390/v9090258
doi: 10.3390/v9090258
pubmed: 28906479
pmcid: 5618024
Cooper C J, Denyer S P, Maillard J-Y (2011) Rapid and quantitative automated measurement of bacteriophage activity against cystic fibrosis isolates of Pseudomonas aeruginosa. J Appl Microbiol 110(3):631–640. https://doi.org/10.1111/j.1365-2672.2010.04928.x
Leon-Velarde CG, Happonen L, Pajunen M, Leskinen K, Kropinski AM, Mattinen L, Rajtor M, Zur J, Smith D, Chen S et al (2016) Yersinia enterocolitica-specific infection by bacteriophages TG1 and ϕR1-RT is dependent on temperature-regulated expression of the phage host receptor OmpF. Appl Environ Microbiol 82(17):5340–5353. https://doi.org/10.1128/AEM.01594-16
doi: 10.1128/AEM.01594-16
pubmed: 27342557
pmcid: 4988191
Pinta E, Li Z, Batzilla J, Pajunen M, Kasanen T, Rabsztyn K, Rakin A, Skurnik M (2012) Identification of three oligo-/polysaccharide-specific ligases in Yersinia enterocolitica. Mol Microbiol 83(1):125–136. https://doi.org/10.1111/j.1365-2958.2011.07918.x
doi: 10.1111/j.1365-2958.2011.07918.x
pubmed: 22053911
Kiljunen S, Hakala K, Pinta E, Huttunen S, Pluta P, Gador A, Lönnberg H, Skurnik M (2005) Yersiniophage ϕR1-37 is a tailed bacteriophage having a 270 kb DNA genome with thymidine replaced by deoxyuridine. Microbiology 151(12):4093–4102. https://doi.org/10.1099/mic.0.28265-0
doi: 10.1099/mic.0.28265-0
pubmed: 16339954
Skurnik M, Hyytiäinen H, Happonen LJ, Kiljunen S, Datta N, Mattinen L, Williamson K, Kristo P, Szeliga M, Kalin-Mänttäri L et al (2012) Characterization of the genome, proteome, and structure of yersiniophage phi R1–37. J Virol 86(23):12625–12642. https://doi.org/10.1128/JVI.01783-12
doi: 10.1128/JVI.01783-12
pubmed: 22973030
pmcid: 3497697
Garneau JR, Depardieu F, Fortier L-C, Bikard D, Monot M (2017) PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data. Sci Rep 7(1):8292. https://doi.org/10.1038/s41598-017-07910-5
doi: 10.1038/s41598-017-07910-5
pubmed: 28811656
pmcid: 5557969
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9(1):75. https://doi.org/10.1186/1471-2164-9-75
doi: 10.1186/1471-2164-9-75
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucl Acids Res. 36(suppl_2):W5–W9. https://doi.org/10.1093/nar/gkn201
doi: 10.1093/nar/gkn201
pubmed: 18440982
pmcid: 2447716
Zimmermann L, Stephens A, Nam S-Z, Rau D, Kübler J, Lozajic M, Gabler F, Söding J, Lupas AN, Alva V (2018) A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J Mol Biol 430(15):2237–2243. https://doi.org/10.1016/j.jmb.2017.12.007 . (Computation Resources for Molecular Biology)
doi: 10.1016/j.jmb.2017.12.007
pubmed: 29258817
HMMER|Bioinformatics Toolkit. https://toolkit.tuebingen.mpg.de/tools/hmmer . Accessed 8 Oct 2023
Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS (2016) PHASTER: a better, faster version of the PHAST phage search tool. Nucl Acids Res 44(W1):W16-21. https://doi.org/10.1093/nar/gkw387
doi: 10.1093/nar/gkw387
pubmed: 27141966
pmcid: 4987931
Chan PP, Lin BY, Mak AJ, Lowe TM (2021) tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucl Acids Res. 49(16):9077–9096. https://doi.org/10.1093/nar/gkab688
doi: 10.1093/nar/gkab688
pubmed: 34417604
pmcid: 8450103
Nishimura Y, Yoshida T, Kuronishi M, Uehara H, Ogata H, Goto S (2017) ViPTree: the viral proteomic tree server. Bioinformatics 33(15):2379–2380. https://doi.org/10.1093/bioinformatics/btx157
doi: 10.1093/bioinformatics/btx157
pubmed: 28379287
Rangel-Pineros G, Millard A, Michniewski S, Scanlan D, Sirén K, Reyes A, Petersen B, Clokie MRJ, Sicheritz-Pontén T (2021) From trees to clouds: PhageClouds for fast comparison of ∼640,000 phage genomic sequences and host-centric visualization using genomic network graphs. PHAGE. 2(4):194–203. https://doi.org/10.1089/phage.2021.0008
doi: 10.1089/phage.2021.0008
pubmed: 36147515
pmcid: 9041511
Moraru C, Varsani A, Kropinski AM (2020) VIRIDIC—a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses 12(11):1268. https://doi.org/10.3390/v12111268
doi: 10.3390/v12111268
pubmed: 33172115
pmcid: 7694805
Salem M, Skurnik M (2018) Genomic characterization of sixteen Yersinia enterocolitica-infecting podoviruses of pig origin. Viruses 10(4):174. https://doi.org/10.3390/v10040174
doi: 10.3390/v10040174
pubmed: 29614052
pmcid: 5923468