Molecular Characterisation of M. kansasii Isolates by Whole-Genome Sequencing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Preliminary Genotypic Identification Tests
2.2. Genome Sequencing
2.3. Dataset
2.4. Variant Calling
2.5. Phylogenetic Analysis
2.6. Identification of Mutations in Drug-Resistant Locus
3. Results
3.1. Identification by Molecular Methods
3.2. Subtype Classification
3.3. Association of Mutation with Drug Resistance
3.3.1. RIF and INH Resistance
3.3.2. EMB Resistance
3.3.3. Clarithromycin Resistance
3.3.4. Quinolone Resistance
3.3.5. Amikacin Resistance
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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S. No. | Lab No. | Resistance to Drugs by Phenotypic DST | Gene Mutations Comparison | Treatment Outcome | Alignment Coverage | |||
---|---|---|---|---|---|---|---|---|
MTB Genome | M. kansasii Genome | No. of Reads | Coverage | Mean Depth | ||||
1 | NT 08 | RIF/SXT/DOX | embB | No mutation | Died | 5,067,055 | 99.6502 | 38.1 |
2 | NT 09 | EMB | embB | No mutation | Cured | 4,350,931 | 99.7226 | 38.2 |
3 | NT 12 | CLR/DOX | embB, aftB | aftB | Cured | 4,199,386 | 98.8226 | 37.9 |
4 | NT 13 | RIF/SXT/DOX/AMK/LZD/CIP/EMB | embB, aftB | No mutation | Relapse | 4,701,856 | 98.8198 | 38.1 |
5 | NT 16 | No resistance | embB, eis | eis | Cured | 4,740,116 | 99.6771 | 37.9 |
6 | NT 22 | EMB | embB | embB | Cured | 4,626,353 | 99.3018 | 38 |
7 | NT 27 | DOX/EMB | embB | No mutation | Died | 4,862,099 | 99.9468 | 38 |
8 | NT 28 | SXT/DOX/ EMB | embB, eis | No mutation | Cured | 4,557,193 | 99.6895 | 38.1 |
9 | NT 35 | No resistance | aftB | No mutation | Cured | 3,844,920 | 99.3199 | 38.3 |
10 | NT 43 | CLR/RFB/RIF/SXT/AMK/ DOX | embB | No mutation | Cured | 4,094,943 | 99.6353 | 38.1 |
11 | NT 33 | No resistance | embB | No mutation | Cured | 4,372,578 | 99.6714 | 38.1 |
12 | NT 47 | EMB | No mutation | rrl | Cured | 1,856,345 | 99.5578 | 40.9 |
S. No. | Strain | Former kansasii Subtype | GenBank No. |
---|---|---|---|
1 | ATCC 12478 | (M. kansasii) I | NC_022663.1_I * |
2 | MK7 | (M. kansasii) I | GCA_900565995.1 |
3 | Kuro-I | (M. kansasii) I | GCA_014701265.1 |
4 | 12MK | (M. persicum) II | NZ_MWQA01000001.1_II * |
5 | 1010001469 | (M. persicum) II | LWCM00000000.1 |
6 | 3MK | (M. persicum) II | MWKX01.1 |
7 | MK142 | (M. pseudokansasii) III | NZ_UPHU01000001.1_III * |
8 | 732 | (M. pseudokansasii) III | JANZ01.1 |
9 | 174_15_11 | (M. pseudokansasii) III | NKRD01.152 |
10 | FDAARGOS_1613 | (M. ostraviense) IV | NZ_CP089224.1_IV * |
11 | 241/15 | (M. ostraviense) IV | GCA_002705925.1 |
12 | 1010001458 | (M. ostraviense) IV | GCA_001632895.1 |
13 | MK21 | (M. innocens) V | NZ_UPHQ01000197.1_V * |
14 | 49_11 | (M. innocens) V | NKRC01.1 |
15 | 1010001454 | (M. innocens) V | LWCH01.1 |
16 | MK41 | (M. attenuatum) VI | NZ_UPHT01000123.1_VI * |
17 | MK191 | (M. attenuatum) VI | UPHS01.1 |
18 | MK136 | (M. attenuatum) VI | UPHP01.1 |
Target Drug | Drug-Resistant Locus | Mutation in Comparison to MTB Reference Sequence | Mutation in Comparison to M. kansasii Reference Sequence |
---|---|---|---|
Amikacin | eis/MKAN_RS04925 | V301I | M293T |
E348D | V297I | ||
D352G | |||
Ethambutol | embB | S272N | L78M |
S565G | G130A | ||
Q853R | A159G | ||
A1007T | A259T | ||
Y737N | |||
aftB | S159A | V100A | |
I202V | V107A | ||
S238G | M127V | ||
R401H | A133V | ||
M491L | M192L | ||
V511A | F257L | ||
A516Q | M331V | ||
A524G | V339L | ||
Q561R | I354V | ||
K399R | |||
V393L | |||
L394S | |||
G412V | |||
E435D | |||
T515S | |||
I541L | |||
K603R | |||
S657P |
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Rajendran, P.; Padmapriyadarsini, C.; Nagarajan, N.; Samyuktha, R.; Govindaraju, V.; Golla, R.; Ashokkumar, S.; Shanmugam, S. Molecular Characterisation of M. kansasii Isolates by Whole-Genome Sequencing. Pathogens 2023, 12, 1249. https://doi.org/10.3390/pathogens12101249
Rajendran P, Padmapriyadarsini C, Nagarajan N, Samyuktha R, Govindaraju V, Golla R, Ashokkumar S, Shanmugam S. Molecular Characterisation of M. kansasii Isolates by Whole-Genome Sequencing. Pathogens. 2023; 12(10):1249. https://doi.org/10.3390/pathogens12101249
Chicago/Turabian StyleRajendran, Priya, Chandrasekaran Padmapriyadarsini, Naveenkumar Nagarajan, Roja Samyuktha, Vadivu Govindaraju, Radhika Golla, Shanmugavel Ashokkumar, and Sivakumar Shanmugam. 2023. "Molecular Characterisation of M. kansasii Isolates by Whole-Genome Sequencing" Pathogens 12, no. 10: 1249. https://doi.org/10.3390/pathogens12101249