Integrated Pathogen–Host Analysis of Citrobacter braakii SCGY-1L: Genomic Determinants and Host Transcriptional Dynamics During Infection
Abstract
1. Introduction
2. Materials and Methods
2.1. Bacterial Isolation
2.2. Bacterial Identification and Phylogenetic Analysis
2.3. Physiological and Biochemical Characteristics, and Antibiotic Susceptibility
2.4. Bacterial Challenge and Histopathological Analysis
2.5. Bacterial Library Construction and Genome Sequencing
2.6. Genome Assembly and Gene Annotation
2.7. Construction of Genome Circle Diagrams and Gene Functional Analysis
2.8. Transcriptomic Analysis of Hosts Infected by Bacteria
2.9. Functional Annotation of Differentially Expressed Genes
2.10. Real-Time Quantitative PCR
3. Results
3.1. Isolation and Identification of C. braakii SCGY-1L Strain
3.2. Pathogenicity Analysis and Antibiotic Susceptibility Test
3.3. Histopathology
3.4. Data Statistics and Genome Assessment
3.5. Bacterial Gene Annotation
3.6. Bacterial Genomic Circos Plot Analysis
3.7. Carbohydrate-Active Enzymes Analysis
3.8. Pathogenicity-Associated Gene Analysis
3.9. Antibiotic Resistance Gene Analysis
3.10. Transcriptome Sequencing Data Statistics and Identification of Differentially Expressed Genes
3.11. GO and KEGG Enrichment Analysis of Differentially Expressed Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Target Gene | Forward Primer (5′-3′) | Reverse Primer (5′-3′) | Reference or Genebank Accession No. |
---|---|---|---|
cfa | GCGGTTACTGGAAAGATG | CGGCGATACTGAAATAGG | CP137123.1 |
viaB | TGTCGAGCAGATGGATGAGCAT | ACGGCTGAAGGTTACGGACCGA | CP183865.1 |
ompX | CTACGAATACGGCTCTGC | ATCGGTTCCTTCACTTACAC | CP016762 |
ureD | GCCAGATGTCACGCATAACG | GGCTGCCACTGCTGATAGAA | CP128207.1 |
ureE | TAACAGGCTTTGGCGAGTAGGA | CGCCTTGACCACGCTCACT | CP069787.1 |
ureF | ATGCCGCAGAGTTGGCTGTC | GGAGATTGGCTGGGTGAAAA | CP174029.1 |
ureG | AGGTTATCGCCACCGCTTTC | GGTTGCCCGCATACTGCT | CP137175.1 |
slt-II | CCGGATCCATGAAGTGTATATTATTTAAATGG | CCCGAATTCTCAGTCATTATTAAACTGCAC | [27] |
slt-LA | TTTACGATAGACTTCTCGAC | CACATATAAATTATTTCGCTC | [28] |
slt-ILA | CCCGGATCCATGAAGTGTATATTATTTAAATGG | CCCGAATTCTTATTTACCCGTTGTATATAAAAA | [28] |
Characteristic | C. braakii SCGY-1L | Characteristic | SCGY-1L |
---|---|---|---|
Glucose gas | + | Sorbose | + |
Citrate | + | Mannitol | + |
Arginine | + | Raffinose | + |
Alanine | + | KCN | + |
Aesculin | − | MR | + |
V-P test | − | H2S | + |
Lactose | + | Nitrate reduction | + |
Sucrose | + | ornithine decarboxylase | + |
Indole | - | lysine decarboxylase | − |
Maltose | + | Urea | − |
Antibiotic | Concentration (μg/piece) | Test Diameter of the Inhibition Zone (mm) | Sensitivity |
---|---|---|---|
Amikacin | 30 | 18 | I |
Gentamicin | 10 | 15 | I |
Kanamycin | 30 | 20 | S |
Neomycin | 30 | 16 | I |
Erythromycin | 15 | 0 | R |
Medemycin | 30 | 0 | R |
Norfloxacin | 10 | 25 | S |
Ofloxacin | 5 | 24 | S |
Ciprofloxacin | 5 | 28 | S |
Polymyxin B | 300 | 14 | S |
Clindamycin | 2 | 0 | R |
Furazolidone | 300 | 18 | S |
Tetracycline | 30 | 20 | S |
Doxycycline | 30 | 18 | S |
Minocycline | 30 | 14 | I |
Penicillin | 10 | 16 | R |
Oxacillin | 1 | 0 | R |
Ampicillin | 10 | 15 | I |
Carbenicillin | 100 | 27 | S |
Piperacillin | 100 | 22 | S |
Cephalexin | 30 | 21 | S |
Cefazolin | 30 | 26 | S |
Cefradine | 30 | 18 | I |
Cefuroxim | 30 | 22 | S |
Ceftazidime | 30 | 21 | S |
Ceftriaxone | 30 | 28 | S |
Cefoperazone | 75 | 25 | S |
Vancomycin | 30 | 0 | R |
Paediatric Compound Sulfamethoxazole Tablets | 23.75/1.25 | 24 | S |
Chloramphenicol | 30 | 27 | S |
Florfenicol | 30 | 22 | S |
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Wang, Z.; Zhou, T.; Gu, S.; Yao, J.; Liu, S.; Mao, J. Integrated Pathogen–Host Analysis of Citrobacter braakii SCGY-1L: Genomic Determinants and Host Transcriptional Dynamics During Infection. Microorganisms 2025, 13, 2310. https://doi.org/10.3390/microorganisms13102310
Wang Z, Zhou T, Gu S, Yao J, Liu S, Mao J. Integrated Pathogen–Host Analysis of Citrobacter braakii SCGY-1L: Genomic Determinants and Host Transcriptional Dynamics During Infection. Microorganisms. 2025; 13(10):2310. https://doi.org/10.3390/microorganisms13102310
Chicago/Turabian StyleWang, Zhixiu, Tingting Zhou, Shaoxuan Gu, Jiaqi Yao, Suli Liu, and Jiaming Mao. 2025. "Integrated Pathogen–Host Analysis of Citrobacter braakii SCGY-1L: Genomic Determinants and Host Transcriptional Dynamics During Infection" Microorganisms 13, no. 10: 2310. https://doi.org/10.3390/microorganisms13102310
APA StyleWang, Z., Zhou, T., Gu, S., Yao, J., Liu, S., & Mao, J. (2025). Integrated Pathogen–Host Analysis of Citrobacter braakii SCGY-1L: Genomic Determinants and Host Transcriptional Dynamics During Infection. Microorganisms, 13(10), 2310. https://doi.org/10.3390/microorganisms13102310