Complete genome of a novel mycobacteriophage WXIN isolated in Wuhan, China.
Mycobacterium septicum
Complete genome
Mycobacteriophage
Journal
BMC genomic data
ISSN: 2730-6844
Titre abrégé: BMC Genom Data
Pays: England
ID NLM: 101775394
Informations de publication
Date de publication:
18 Jun 2024
18 Jun 2024
Historique:
received:
01
03
2024
accepted:
12
06
2024
medline:
19
6
2024
pubmed:
19
6
2024
entrez:
18
6
2024
Statut:
epublish
Résumé
The rising of antibiotic resistance has sparked a renewed interest in mycobacteriophage as alternative therapeutic strategies against mycobacterial infections. So far, the vast majority of mycobacteriophages have been isolated using the model species Mycobacterium smegmatis, implying an overwhelming majority of mycobacteriophages in the environment remain uncultured, unclassified, and their specific hosts and infection strategies are still unknown. This study was undertaken to isolate and characterize novel mycobacteriophages targeting Mycobacterium septicum. Here a novel mycobacteriophage WXIN against M. septicum was isolated from soil samples in Wuhan, China. Whole genome analysis indicates that the phage genome consists of 115,158 bp with a GC content of 61.9%. Of the 260 putative open reading frames, 46 may be associated with phage packaging, structure, lysis, lysogeny, genome modification/replication, and other functional roles. The limited genome-wide similarity, along with phylogenetic trees constructed based on viral proteome and orthologous genes show that phage WXIN represents a novel cluster distantly related to cluster J mycobacteriophages (genus Omegavirus). Overall, these results provide novel insights into the genomic properties of mycobacteriophages, highlighting the great genetic diversity of mycobacteriophages in relation to their hosts.
Identifiants
pubmed: 38890591
doi: 10.1186/s12863-024-01244-8
pii: 10.1186/s12863-024-01244-8
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
62Subventions
Organisme : Scientific Research Staring Foundation of Wuhan Polytechnic University
ID : 2022RZ052
Informations de copyright
© 2024. The Author(s).
Références
Dookie N, Ngema SL, Perumal R, Naicker N, Padayatchi N, Naidoo K. The changing paradigm of drug-resistant tuberculosis treatment: successes, pitfalls, and future perspectives. Clin Microbiol Rev. 2022;35(4):e0018019. https://doi.org/10.1128/cmr.00180-19 .
doi: 10.1128/cmr.00180-19
pubmed: 36200885
Suttle CA. Viruses in the sea. Nature. 2005;437(7057):356–61. https://doi.org/10.1038/nature04160 .
doi: 10.1038/nature04160
pubmed: 16163346
Little JS, Dedrick RM, Freeman KG, Cristinziano M, Smith BE, Benson CA, Jhaveri TA, Baden LR, Solomon DA, Hatfull GF. Bacteriophage treatment of disseminated cutaneous Mycobacterium chelonae infection. Nat Commun 2022, 13(1):2313. https://doi.org/10.1038/s41467-022-29689-4 .
Kortright KE, Chan BK, Koff JL, Turner PE. Phage therapy: a renewed Approach to combat antibiotic-resistant Bacteria. Cell Host Microbe. 2019;25(2):219–32. https://doi.org/10.1016/j.chom.2019.01.014 .
doi: 10.1016/j.chom.2019.01.014
pubmed: 30763536
Dedrick RM, Guerrero-Bustamante CA, Garlena RA, Russell DA, Ford K, Harris K, Gilmour KC, Soothill J, Jacobs-Sera D, Schooley RT, et al. Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus. Nat Med. 2019;25(5):730–3. https://doi.org/10.1038/s41591-019-0437-z .
doi: 10.1038/s41591-019-0437-z
pubmed: 31068712
pmcid: 6557439
Nick JA, Dedrick RM, Gray AL, Vladar EK, Smith BE, Freeman KG, Malcolm KC, Epperson LE, Hasan NA, Hendrix J et al. Host and pathogen response to bacteriophage engineered against Mycobacterium abscessus lung infection. Cell 2022, 185(11):1860–e18741812. https://doi.org/10.1016/j.cell.2022.04.024 .
McNerney R. TB: the return of the phage. A review of fifty years of mycobacteriophage research. Int J Tuberc Lung Dis. 1999;3(3):179–84.
pubmed: 10094316
Sparks IL, Derbyshire KM, Jacobs WR Jr., Morita YS. Mycobacterium smegmatis: the Vanguard of Mycobacterial Research. J Bacteriol. 2023;205(1):e0033722. https://doi.org/10.1128/jb.00337-22 .
doi: 10.1128/jb.00337-22
pubmed: 36598232
Go JR, Wengenack NL, Abu Saleh OM, Corsini Campioli C, Deml SM, Wilson JW. Mycobacterium septicum: a 6-Year clinical experience from a Tertiary Hospital and Reference Laboratory. J Clin Microbiol 2020, 58(12). https://doi.org/10.1128/JCM.02091-20 .
Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de bruijn graph. Bioinformatics. 2015;31(10):1674–6. https://doi.org/10.1093/bioinformatics/btv033 .
doi: 10.1093/bioinformatics/btv033
pubmed: 25609793
Söding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005. https://doi.org/10.1093/nar/gki408 . 33(Web Server issue):W244-248.
doi: 10.1093/nar/gki408
pubmed: 15980461
pmcid: 1160169
Wu H, Li W, Zeng C, Li J, Wu H. Complete genome of a novel mycobacteriophage WXIN isolated in Wuhan, China. Sci Data Bank. 2024. https://doi.org/10.57760/sciencedb.16539 .
doi: 10.57760/sciencedb.16539
Nishimura Y, Yoshida T, Kuronishi M, Uehara H, Ogata H, Goto S. ViPTree: the viral proteomic tree server. Bioinf 2017, 33(15):2379–80. https://doi.org/10.1093/bioinformatics/btx157 .
Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20(1):238. https://doi.org/10.1186/s13059-019-1832-y .
doi: 10.1186/s13059-019-1832-y
pubmed: 31727128
pmcid: 6857279
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37(5):1530–4. https://doi.org/10.1093/molbev/msaa015 .
doi: 10.1093/molbev/msaa015
pubmed: 32011700
pmcid: 7182206
Li W, Wu H, Li J, Zeng C, Li J, Wu H. Mycobacterium phage WXIN, complete genome. NCBI. 2023. https://identifiers.org/nucleotide:OR813930.
Wu H, Li W, Zeng C, Li J, Wu H. Genomic sequence of mycobacteriophage WXIN. NCBI. 2024. https://identifiers.org/ncbi/insdc.sra:SRP492847.