Tracking the Distribution of Brucella abortus in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16
Abstract
:1. Introduction
2. Materials and Methods
2.1. Origin of Bacterial Isolates
2.2. Brucella Isolation from Sample Materials and DNA Extraction
2.3. Whole Genome Sequencing and Bioinformatics Procedure of the Raw Reads
2.4. Species Determination
2.5. Core Genome SNP Genotyping
2.6. Calculation of Trees and Simpson’s Diversity Index
2.7. In Silico and Lab-Based MLVA
2.8. Comparison with Entries in Public Databases
2.9. Geographical Map
3. Results
3.1. Origin of Bacterial Isolates and Their Classification
3.2. Core Genome SNP Genotyping for B. abortus
3.3. Comparing B. abortus cgSNP Analysis to MLVA Genotyping
3.4. Strain Comparison with Public Database Entries
3.5. Comparison of the MLVA Results of PCR Based Fragment Analysis and In Silico Analysis
4. Discussion
5. 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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Holzer, K.; El-Diasty, M.; Wareth, G.; Abdel-Hamid, N.H.; Hamdy, M.E.R.; Moustafa, S.A.; Linde, J.; Bartusch, F.; Sayour, A.E.; Elbauomy, E.M.; et al. Tracking the Distribution of Brucella abortus in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16. Microorganisms 2021, 9, 1942. https://doi.org/10.3390/microorganisms9091942
Holzer K, El-Diasty M, Wareth G, Abdel-Hamid NH, Hamdy MER, Moustafa SA, Linde J, Bartusch F, Sayour AE, Elbauomy EM, et al. Tracking the Distribution of Brucella abortus in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16. Microorganisms. 2021; 9(9):1942. https://doi.org/10.3390/microorganisms9091942
Chicago/Turabian StyleHolzer, Katharina, Mohamed El-Diasty, Gamal Wareth, Nour H. Abdel-Hamid, Mahmoud E. R. Hamdy, Shawky A. Moustafa, Jörg Linde, Felix Bartusch, Ashraf E. Sayour, Essam M. Elbauomy, and et al. 2021. "Tracking the Distribution of Brucella abortus in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16" Microorganisms 9, no. 9: 1942. https://doi.org/10.3390/microorganisms9091942