Genomic Features, Comparative Genomic Analysis, and Antimicrobial Susceptibility Patterns of Chryseobacterium arthrosphaerae Strain ED882-96 Isolated in Taiwan
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strain ED882-96
2.2. Species Identification Using 16S Ribosomal RNA Gene Sequencing
2.3. Phylogenetic Tree Based on 16S rRNA Gene Sequences
2.4. Whole-Genome Sequencing
2.5. Analysis of Genome Similarity
2.6. Genome Annotation and Function Analysis of Strain ED882-96
2.7. Antimicrobial Susceptibility and Antibiotic Resistance Genes
2.8. Type Strains of the Genus Chryseobacterium and Whole-Genome Sequences of C. arthrosphaerae
2.9. Comparative Analysis of COGs and KEGG
3. Results and Discussion
3.1. 16S rRNA-based Phylogenetic Relationship
3.2. Basic Data of Whole-Genome Sequencing of Strain ED882-96
3.3. Similarity of Whole Genomes
3.4. General Genomic Annotation
3.5. Orthologous Genes, GO, and KEGG of Strain ED882-96
3.6. Comparative Genomic Analysis of COGs and KEGG in Five C. arthrosphaerae Strains
3.7. Virulence Factors
3.8. Antimicrobial Resistance and Associated Genes
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Assembly and annotation | Chromosome | Plasmid |
---|---|---|
Total sequence length (bp) | 4,249,864 | 435,667 |
Number of contigs | 2 | 1 |
Contig N50 (bp) | 2,386,100 | 435,667 |
Contig L50 | 1 | 1 |
GC content (%) | 38.3 | 38.1 |
Number of subsystems | 191 | 29 |
Number of coding sequences | 5413 | 512 |
Number of rRNA | 6 | 3 |
Number of tRNA | 37 | 22 |
Antibiotic Group | Antibiotics | MIC | Interpretation |
---|---|---|---|
β-lactams, β-lactam/β-lactamase inhibitors | Piperacillin | >64 | R |
Piperacillin-tazobactam | >128/4 | R | |
Ticarcillin-clavulanic acid | >64/2 | R | |
Ceftazidime | >16 | R | |
Cefepime | >32 | R | |
Ceftriaxone | >32 | R | |
Aztreonam | >16 | R | |
Imipenem | >8 | R | |
Meropenem | >8 | R | |
Aminoglycosides | Gentamicin | >8 | R |
Tobramycin | >8 | R | |
Amikacin | >32 | R | |
Tetracyclines/glycylcycline | Tetracycline | >8 | R |
Minocycline | >8 | R | |
Tigecycline | >8 | R | |
Fluoroquinolones | Ciprofloxacin | >2 | R |
Levofloxacin | >8 | R | |
Folate pathway inhibitors | Trimethoprim-sulfamethoxazole | >4/76 | R |
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Liang, C.-Y.; Yang, C.-H.; Lai, C.-H.; Huang, Y.-H.; Lin, J.-N. Genomic Features, Comparative Genomic Analysis, and Antimicrobial Susceptibility Patterns of Chryseobacterium arthrosphaerae Strain ED882-96 Isolated in Taiwan. Genes 2019, 10, 309. https://doi.org/10.3390/genes10040309
Liang C-Y, Yang C-H, Lai C-H, Huang Y-H, Lin J-N. Genomic Features, Comparative Genomic Analysis, and Antimicrobial Susceptibility Patterns of Chryseobacterium arthrosphaerae Strain ED882-96 Isolated in Taiwan. Genes. 2019; 10(4):309. https://doi.org/10.3390/genes10040309
Chicago/Turabian StyleLiang, Chih-Yu, Chih-Hui Yang, Chung-Hsu Lai, Yi-Han Huang, and Jiun-Nong Lin. 2019. "Genomic Features, Comparative Genomic Analysis, and Antimicrobial Susceptibility Patterns of Chryseobacterium arthrosphaerae Strain ED882-96 Isolated in Taiwan" Genes 10, no. 4: 309. https://doi.org/10.3390/genes10040309