Comparative De Novo and Pan-Genome Analysis of MDR Nosocomial Bacteria Isolated from Hospitals in Jeddah, Saudi Arabia
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethical Approvement
2.2. Clinical Specimens
2.3. Isolation and Identification of MDR Bacteria
2.4. Amplification of 16S rRNA Gene, Sequencing, and Phylogenetic Analysis
2.5. Whole Genome Sequencing and Analysis Workflow
2.6. De Novo Assembly of MDR Bacterial Sequences
2.7. Pan-Genome Analysis
2.7.1. Calculation of Mash Distances and ANI
2.7.2. Profiling of Virulence and Antibiotic Resistance Genes
3. Statistical Analysis
4. Results
4.1. Identification of Isolated Bacteria
4.2. Identification Based on 16S rRNA Gene and Whole Genome Sequencing
4.3. Phylogenetic Tree of the Seven Selected MDR Bacteria
4.4. Detection of MDR Genes
5. Discussion
6. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample ID | Index 5 | Index 7 |
---|---|---|
Pseudomonas_1 | CTAGGCAA | CTCACCAA |
K_pneumoniae_3 | CTGTATTA | ATATGGAT |
K_pneumoniae_6 | TCACGCCG | GCGCAAGC |
E_coli_7 | ACTTACAT | AAGATACT |
S_aureus_9 | GTCCGTGC | GGAGCGTC |
S_aureus_10 | AAGGTACC | ATGGCATG |
S_aureus_12 | GGAACGTT | GCAATGCA |
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Alghamdi, M.; Al-Judaibi, E.; Al-Rashede, M.; Al-Judaibi, A. Comparative De Novo and Pan-Genome Analysis of MDR Nosocomial Bacteria Isolated from Hospitals in Jeddah, Saudi Arabia. Microorganisms 2023, 11, 2432. https://doi.org/10.3390/microorganisms11102432
Alghamdi M, Al-Judaibi E, Al-Rashede M, Al-Judaibi A. Comparative De Novo and Pan-Genome Analysis of MDR Nosocomial Bacteria Isolated from Hospitals in Jeddah, Saudi Arabia. Microorganisms. 2023; 11(10):2432. https://doi.org/10.3390/microorganisms11102432
Chicago/Turabian StyleAlghamdi, Molook, Effat Al-Judaibi, Mohammed Al-Rashede, and Awatif Al-Judaibi. 2023. "Comparative De Novo and Pan-Genome Analysis of MDR Nosocomial Bacteria Isolated from Hospitals in Jeddah, Saudi Arabia" Microorganisms 11, no. 10: 2432. https://doi.org/10.3390/microorganisms11102432
APA StyleAlghamdi, M., Al-Judaibi, E., Al-Rashede, M., & Al-Judaibi, A. (2023). Comparative De Novo and Pan-Genome Analysis of MDR Nosocomial Bacteria Isolated from Hospitals in Jeddah, Saudi Arabia. Microorganisms, 11(10), 2432. https://doi.org/10.3390/microorganisms11102432