Biochip-Based Identification of Mycobacterial Species in Russia
Abstract
1. Introduction
2. Results
2.1. The Development of Biochip Test for Species Identification
2.2. The Spectra of Mycobacterium Species Identified in Clinical Isolates
2.3. Regional Variation of Mycobacterial Species
2.4. Whole-Genome Sequencing of Novel Mycobacterial Species
3. Discussion
4. Materials and Methods
4.1. Biochip Design and Fabrication
4.2. Processing of Clinical Isolates
4.3. Phylogenetic Analysis and Target Sequencing
4.4. Whole-Genome Sequencing and Bioinformatic Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Cluster or Complex | Growth Rate | Species in Cluster | Total Cases | Cases with Repeated Isolation |
---|---|---|---|---|
M. avium | slow | 6 | 1135 | 306 |
M. chelonae-abscessus | rapid | 3 | 177 | 38 |
M. lentiflavum | slow | 4 | 159 | 17 |
M. fortuitum | rapid | 6 | 141 | 15 |
M. gastri-kansasii | slow | 4 | 98 | 45 |
M. asiaticum-gordonae | slow | 3 | 86 | 6 |
M. tuberculosis | slow | 1 | 68 | - |
M. malmoense | slow | 2 | 25 | 6 |
M. xenopi | slow | 1 | 22 | 5 |
M. mucogenicum | rapid | 4 | 17 | 4 |
M. terrae | slow | 9 | 8 | 0 |
M. neoaurum | rapid | 3 | 7 | 0 |
M. szulgai | slow | 1 | 6 | 3 |
M. aurum | rapid | 3 | 5 | 3 |
M. chubuense | rapid | 1 | 4 | 1 |
M. shimodei | slow | 3 | 4 | 1 |
M. scrofulaceum | slow | 3 | 4 | 2 |
M. litorale | rapid | 1 | 4 | 1 |
M. duvalii | rapid | 2 | 3 | 0 |
M. interjectum | slow | 2 | 3 | 0 |
M. talmoniae | slow | 1 | 2 | 0 |
M. triviale | slow | 1 | 1 | 0 |
M. bohemicum | slow | 1 | 1 | 0 |
M. tokaiense | rapid | 1 | 1 | 0 |
M. elephantis | rapid | 1 | 1 | 1 |
(M. mageritense) | rapid | 1 | 6 | 1 |
Cluster | Isolate | Sample | Reference | Total Cases | Cases with Repeated Isolation |
---|---|---|---|---|---|
M. aurum | SMC-8 | SAMN20167551 | - | 2 | 1 |
M. mucogenicum | 21IE208 | SAMN31811490 | - | 4 | 3 |
M. mucogenicum | TY81 | SAMD00239442 | - | 1 | |
M. terrae | CSUR_Q5927 * | SAMN32979486 | - | 1 | |
M. asiaticum | CTRI_14-8773 | SAMN04123344 | [52] | 5 | 1 |
Strain Name | pU-009 | pV-006 | pR-1184 |
---|---|---|---|
Proposed name | M. moscowiensis | M. sibiricum | M. petersburgensis |
Genome accession | GCA_041287095.1 | GCA_041287115.1 | GCA_041287235.1 |
Assembly (bp) | 5,730,899 | 5,120,508 | 5,944,740 |
GC (%) | 68.44 | 68.01 | 66.1 |
Genes | 5538 | 4963 | 5632 |
CDSs | 5486 | 4906 | 5578 |
Pseudo Genes | 109 | 94 | 83 |
RNA | 52 | 57 | 54 |
Closest species | M. talmoniae | M. duvalii | M. lentiflavum |
ANI (%) | 92.11 | 84.20 | 91.60 |
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Zimenkov, D.; Zhuravlev, V.; Ushtanit, A.; Filippova, M.; Semenova, U.; Solovieva, N.; Sviridenko, M.; Khakhalina, A.; Safonova, S.; Makarova, M.; et al. Biochip-Based Identification of Mycobacterial Species in Russia. Int. J. Mol. Sci. 2024, 25, 13200. https://doi.org/10.3390/ijms252313200
Zimenkov D, Zhuravlev V, Ushtanit A, Filippova M, Semenova U, Solovieva N, Sviridenko M, Khakhalina A, Safonova S, Makarova M, et al. Biochip-Based Identification of Mycobacterial Species in Russia. International Journal of Molecular Sciences. 2024; 25(23):13200. https://doi.org/10.3390/ijms252313200
Chicago/Turabian StyleZimenkov, Danila, Vyacheslav Zhuravlev, Anastasia Ushtanit, Marina Filippova, Uliana Semenova, Natalia Solovieva, Maria Sviridenko, Anastasia Khakhalina, Svetlana Safonova, Marina Makarova, and et al. 2024. "Biochip-Based Identification of Mycobacterial Species in Russia" International Journal of Molecular Sciences 25, no. 23: 13200. https://doi.org/10.3390/ijms252313200
APA StyleZimenkov, D., Zhuravlev, V., Ushtanit, A., Filippova, M., Semenova, U., Solovieva, N., Sviridenko, M., Khakhalina, A., Safonova, S., Makarova, M., Gordeeva, E., Guselnikova, E., Schwartz, Y., Stavitskaya, N., & Yablonsky, P. (2024). Biochip-Based Identification of Mycobacterial Species in Russia. International Journal of Molecular Sciences, 25(23), 13200. https://doi.org/10.3390/ijms252313200