Whole-genome sequencing and analysis of Chryseobacterium arthrosphaerae from Rana nigromaculata.
Chryseobacterium arthrosphaerae
Rana nigromaculata
Bioinformatics analysis
Whole-genome sequence
Journal
BMC microbiology
ISSN: 1471-2180
Titre abrégé: BMC Microbiol
Pays: England
ID NLM: 100966981
Informations de publication
Date de publication:
08 Mar 2024
08 Mar 2024
Historique:
received:
04
07
2023
accepted:
12
02
2024
medline:
9
3
2024
pubmed:
9
3
2024
entrez:
8
3
2024
Statut:
epublish
Résumé
Chryseobacterium arthrosphaerae strain FS91703 was isolated from Rana nigromaculata in our previous study. To investigate the genomic characteristics, pathogenicity-related genes, antimicrobial resistance, and phylogenetic relationship of this strain, PacBio RS II and Illumina HiSeq 2000 platforms were used for the whole genome sequencing. The genome size of strain FS91703 was 5,435,691 bp and GC content was 37.78%. A total of 4,951 coding genes were predicted; 99 potential virulence factors homologs were identified. Analysis of antibiotic resistance genes revealed that strain FS91703 harbored 10 antibiotic resistance genes in 6 categories and 2 multidrug-resistant efflux pump genes, including adeG and farA. Strain FS91703 was sensitive to β-lactam combination drugs, cephem, monobactam and carbapenems, intermediately resistant to phenicol, and resistant to penicillin, aminoglycosides, tetracycline, fluoroquinolones, and folate pathway inhibitors. Phylogenetic analysis revealed that strain FS91703 and C. arthrosphaerae CC-VM-7
Identifiants
pubmed: 38459435
doi: 10.1186/s12866-024-03223-6
pii: 10.1186/s12866-024-03223-6
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
80Subventions
Organisme : Zhejiang Provincial Science and Technology Cooperation Plan of "Three Rural Areas and Nine Rural Areas"
ID : 2022SNJF072
Organisme : Zhejiang Provincial Science and Technology Cooperation Plan of "Three Rural Areas and Nine Rural Areas"
ID : 2022SNJF072
Organisme : Zhejiang Provincial Science and Technology Cooperation Plan of "Three Rural Areas and Nine Rural Areas"
ID : 2022SNJF072
Organisme : Zhejiang Provincial Science and Technology Cooperation Plan of "Three Rural Areas and Nine Rural Areas"
ID : 2022SNJF072
Organisme : Zhejiang Provincial Science and Technology Cooperation Plan of "Three Rural Areas and Nine Rural Areas"
ID : 2022SNJF072
Organisme : Zhejiang Provincial Science and Technology Cooperation Plan of "Three Rural Areas and Nine Rural Areas"
ID : 2022SNJF072
Informations de copyright
© 2024. The Author(s).
Références
Genco M, Curtoni A, Bottino P, Scabini S, Corcione S, Vita D, et al. First case of Chryseobacterium gallinarum bloodstream infection: a diagnostic and therapeutic challenge for an emerging pathogen. New Microbiol. 2024;46(4):412–5.
pubmed: 38252054
Cai J, Wu JY, Pan YX, Wang M, Qi Y, Isolation. Identificaiton and drug resistance analysis of Chryseobacterium sp. from Pseudosciaena crocea. China Anim Husb Veterinary Med. 2022;49(3):1135–43.
Hu WJ, Song YH, Qin JC, Shi K, Yu WH, Liu Y, et al. Study on the change law and pathogenicity of postpartum bovine intrauterine flora. Hubei Agricultural Sci. 2014;53(7):4115–9.
Xie CB, Luo JR, Zhao QM, Yu H. The study on drug resistance and resistant genotype of Chryseobacterium indologens. Clin Chem Lab Med. 2019;16(1):20–6.
Jeong JJ, Lee YJ, Pathirajad M, Pathiraja B, Choi Ki D, Kim. Draft genome sequences of Chryseobacterium Lactis NCTC 11309 T islateed from milk, Chryseobacterium Oncorphychi 701B-08 T from rainbow trout, and Chryseobactium Viscerum 687B-08 T from diseased fish. Genome Announcements. 2018;6(26):e00628–18.
doi: 10.1128/genomeA.00628-18
pubmed: 29954917
pmcid: 6025947
Wang XY, Han YN, Jin S. Identification of indole-producing aureobacillus from Ophiocephalus Argus and analysis of characteristics of extracellular products. Sinica Acta Hydrobiolica Sinica. 2016;40(3):641–6.
He SX, Ma GQ, Niu WJ. Study on pathogenicity of a pathogenic bacterium from sturgeon in northern China. J Agricultural Sci Technol. 2019;21(4):96–103.
Kämpfer P, Arun A, Young CC, Chen WM, Sridhar KR, Rekha PD. Chryseobacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaeramagna Attems. Int J Syst Evol MicroBiol. 2010;60:1765–9.
doi: 10.1099/ijs.0.016840-0
pubmed: 19749032
Liang CY, Yang CH, Lai CH, Huang YH, Lin JN. Genomic features, comparative genomic analysis, and antimicrobial susceptibility patterns of Chryseobacterium arthrosphaerae strain ED882-96 isolated in Taiwan. Genes. 2019;10:309.
doi: 10.3390/genes10040309
pubmed: 31010035
pmcid: 6523182
Im JHM, Kim D, Jin JM, Kim EY, Park YK, Kwon HY, et al. Chryseobacterium arthrosphaerae ventriculitis a case report. Medicine. 2020;99(34):e21751.
doi: 10.1097/MD.0000000000021751
pubmed: 32846799
pmcid: 7447447
Zhu LH, Yin XL, Shi YF, Pi XE. Identification and antibacterial activity against Elizabethkingia miricola of Bacillus sp. ZL397. Feed Industry. 2023. https://link.cnki.net/urlid/21.1169.S.20231117.1720.006 .
Chen LW, Zhang MM, Zhang JN, Huang L, Zhao L, Xu X, et al. Synergism of sodA, sodB and KatG in Aeromonas hydrophila under antioxidative stress. J Fisheries China. 2021;45(1):136–46.
Medrano DCL, Vega GA, Ruiz BE, Abel M, Mayra C. Moonlight protein induce protection in a mouse model against Candida species. Microb Pathog. 2018;3(124):21–9.
doi: 10.1016/j.micpath.2018.08.024
Han ZQ, Cui ZJ. Reversible methionine residue oxidation in signalling proteins and methionine sulfoxide reductases. Acta Biophys Sin. 2012;26(10):861–79.
Gao HJ, Cheng GY, Wang YL, Ning J, Chen T, Li J, et al. Research progress of the mainly bacterial efflux pumps and related regulator. Chin J Anim Veterinary Sci. 2017;48(11):2023–33.
Zhang KH, Zuo LL, Xu X, Wang Y. Study on the mRNA expression of active efflux system gene adeFGH of multi-drug resistant Acinetobacter baumannii. China Mod Doctor. 2018;56(32):5–12.
Xiong F, Mou YZ. Detection of gene mutation locus and analysis of resistant substrate in multiple resistances system of Neisseria gonorrhoeae. Sichuan Med J. 2014;35(8):952–4.
Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 2016;13(12):1050.
doi: 10.1038/nmeth.4035
pubmed: 27749838
pmcid: 5503144
Hunt M, Silva ND, Otto TD, Julian P, Jacqueline A, Simon R. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 2015;16(1):294.
doi: 10.1186/s13059-015-0849-0
pubmed: 26714481
pmcid: 4699355
Tarailo-Graovac M, Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protocols Bioinf. 2009;4:1–14.
Akhter S, Aziz RK, Edwards RA. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity-and composition-based strategies. Nucleic Acids Res. 2012;40(16):e126.
doi: 10.1093/nar/gks406
pubmed: 22584627
pmcid: 3439882
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25(5):955–64.
doi: 10.1093/nar/25.5.955
pubmed: 9023104
pmcid: 146525
Lagesen K, Hallin P, Rødland EA, Staerfeldt H, Rognes T, Ussery H. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100–8.
doi: 10.1093/nar/gkm160
pubmed: 17452365
pmcid: 1888812
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res. 2003;31(1):439–41.
doi: 10.1093/nar/gkg006
pubmed: 12520045
pmcid: 165453
Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 2011;39:W316–22.
doi: 10.1093/nar/gkr483
pubmed: 21715386
pmcid: 3125809
Cantarel BL, Coutinho PM, Rancurel C, Thomas B, Vincent L, Bernard H. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 2008;37(suppl1):D233–8.
pubmed: 18838391
pmcid: 2686590
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.
doi: 10.1038/nmeth.3176
pubmed: 25402007
Sean R. A new generation of homology search tools based on probabilistic inference. Genome Inf. 2009;23:205–11.
Winnenburg R, Baldwin TK, Urban M, Rawlings C, Köhler J, Hammond-Kosack KE. PHI-base: a new database for pathogen host interactions. Nucleic Acids Res. 2006;34(suppl1):D459–64.
doi: 10.1093/nar/gkj047
pubmed: 16381911
Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 2005;33(suppl1):D325–8.
pubmed: 15608208
Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 2017;45(D1):D566–73.
doi: 10.1093/nar/gkw1004
pubmed: 27789705
Altschul SF, Gish W, Miller, et al. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
doi: 10.1016/S0022-2836(05)80360-2
pubmed: 2231712
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19(9):1639–45.
doi: 10.1101/gr.092759.109
pubmed: 19541911
pmcid: 2752132
Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing. Wayne, PA, USA: Clinical and Laboratory Standards Institute; 2020.
Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4(4):406–25.
pubmed: 3447015
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870–4.
doi: 10.1093/molbev/msw054
pubmed: 27004904
pmcid: 8210823
Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA. 2009;106:19126–31.
doi: 10.1073/pnas.0906412106
pubmed: 19855009
pmcid: 2776425
Lee I, Kim YO, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol MicroBiol. 2015;66:1100–3.
doi: 10.1099/ijsem.0.000760
pubmed: 26585518
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics. 2013. https://doi.org/10.1186/1471-2105-14-60 .
doi: 10.1186/1471-2105-14-60
pubmed: 23432962
pmcid: 3665452