Characterization of Mutations Associated with Streptomycin Resistance in Multidrug-Resistant Mycobacterium tuberculosis in Zambia
Abstract
:1. Introduction
2. Results
2.1. Correlation between Genotypes and STR Resistance
2.2. Mutations in rpsL
2.3. Mutations in rrs
2.4. Mutations in gidB
2.5. Association of Genotype and Mutations in rpsL, rrs and gidB
2.6. Molecular Determination of STR Resistance
3. Discussion
4. Materials and Methods
4.1. Samples and DST
4.2. DNA Extraction, PCR Amplification and Sequencing of rpsL, rrs, and gidB Genes
4.3. Spoligotyping
4.4. Statistical Analysis
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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Spoligotype | Streptomycin Resistant | Streptomycin Susceptible | Significance | ||||
---|---|---|---|---|---|---|---|
SIT | Clade | n = 91 | Proportion (%) | n = 47 | Proportion (%) | Odds Ratio (95%CI) | p Value |
21 | CAS1_Kili | 29 | 31.9 | 5 | 10.6 | 3.9 (1.4 to 11.0) | 0.009 |
59 | LAM11_ZWE | 21 | 23.1 | 8 | 17.0 | 1.5 (0.6–3.6) | 0.4096 |
20 | LAM1 | 4 | 4.4 | 13 | 27.7 | 0.1 (0.04–0.39) | 0.0005 |
815 | LAM11_ZWE | 10 | 11.0 | 3 | 6.4 | 1.8 (0.5–6.9) | 0.39 |
53 | T1 | 8 | 8.8 | 4 | 8.5 | 1.0 (0.3–3.6) | 0.96 |
Orphan | LAM11_ZWE | 4 | 4.4 | 1 | 2.1 | ||
137 | X2 | 3 | 3.3 | 4 | 8.5 | ||
52 | T2 | 3 | 3.3 | 2 | 4.3 | ||
Orphan | H1 | 2 | 2.2 | 2 | 4.3 | ||
42 | LAM9 | 1 | 1.1 | 2 | 4.3 | ||
4 | H3/T1 | 0 | 0.0 | 1 | 2.1 | ||
Orphan | EAI | 2 | 2.2 | 0 | 0.0 | ||
34 | S | 1 | 1.1 | 0 | 0.0 | ||
50 | H3 | 1 | 1.1 | 0 | 0.0 | ||
73 | T | 0 | 0.0 | 1 | 2.1 | ||
317 | T2 | 1 | 1.1 | 0 | 0.0 | ||
811 | LAM11_ZWE | 1 | 1.1 | 0 | 0.0 | ||
2173 | LAM11_ZWE | 0 | 0.0 | 1 | 2.1 |
rpsL (DNA) | RpsL (Protein) | rrs | gidB (DNA) | GidB (Protein) | STR Resistant | STR Susceptible |
---|---|---|---|---|---|---|
A128G | K43R | 21 | 0 | |||
A263G | K88R | 8 | 0 | |||
A262C | K88Q | 1 | 0 | |||
A514C | 3 | 0 | ||||
C517T | 2 | 0 | ||||
C517T | C548T | A183V | 1 | 0 | ||
A906G | G211C | G71R | 2 | 0 | ||
A907C | 3 | 0 | ||||
25_88del | 9fs | 1 | 0 | |||
T64C | Y22H | 3 | 2 | |||
98delG | 34fs | 3 | 1 | |||
G109A | G37R | 3 | 1 | |||
112delC | 39fs | 4 | 1 | |||
C223T | P75S | 1 | 0 | |||
G227A | G76D | 1 | 0 | |||
T242C | I81T | 1 | 0 | |||
T298C | F100L | 1 | 1 | |||
347delG | 117fs | 5 | 2 | |||
T371G | V124G | 5 | 1 | |||
C401A | A134E | 1 | 0 | |||
G412C | A138P | 3 | 1 | |||
C447G | S149R | 0 | 1 | |||
T455C | L152S | 2 | 0 | |||
G469C | G157R | 2 | 0 | |||
575_576delGC | 193fs | 2 | 0 | |||
T611A, C612A | 204 Stop | 4 | 1 | |||
No mutations | 8 | 35 |
rpsL (DNA) | RpsL (Protein) | rrs | gidB (DNA) | GidB (Protein) | CAS | LAM | H | T | S | X | EAI |
---|---|---|---|---|---|---|---|---|---|---|---|
A128G | K43R | 16 | 2 | 1 | 1 | 1 | |||||
A263G | K88R | 4 | 1 | 3 | |||||||
A262C | K88Q | 1 | |||||||||
A514C | 3 | ||||||||||
C517T | 2 | ||||||||||
C517T | C548T | A183V | 1 | ||||||||
A906G | G330T | G71R | 2 | ||||||||
A907C | 3 | ||||||||||
25_88del | 9fs | 1 | |||||||||
T64C | Y22H | 5 | |||||||||
98delG | 34fs | 4 | |||||||||
G109A | G37R | 4 | |||||||||
112delC | 39fs | 5 | |||||||||
C223T | P75S | 1 | |||||||||
G227A | G76D | 1 | |||||||||
T242C | I81T | 1 | |||||||||
T298C | F100L | 2 | |||||||||
347delG | 117fs | 3 | 4 | ||||||||
T371G | V124G | 6 | |||||||||
C401A | A134E | 1 | |||||||||
G412C | A138P | 4 | |||||||||
C447G | S149R | 1 | |||||||||
T455C | L152S | 2 | |||||||||
G469C | G157R | 2 | |||||||||
575_576delGC | 193fs | 2 | |||||||||
T611A, C612A | 204 Stop | 5 | |||||||||
No mutations | 3 | 27 | 3 | 8 | 2 | ||||||
Total | 34 | 69 | 6 | 19 | 1 | 7 | 2 |
Correlation of Drug Resistance Genotype and Phenotype | ||||||||
---|---|---|---|---|---|---|---|---|
Susceptible | Resistant | Sensitivity (%) | Specificity (%) | PPV (%) | NPV (%) | |||
Mutation | No Mutation | Mutation | No Mutation | |||||
rpsL | 0 | 47 | 30 | 61 | 33.0 | 100 | 100 | 43.5 |
rrs | 0 | 47 | 11 | 80 | 12.1 | 100 | 100 | 37.0 |
gidB | 12 | 35 | 45 | 46 | 49.5 | 74.5 | 78.9 | 43.2 |
rrs or rpsL | 0 | 47 | 41 | 50 | 45.1 | 100 | 100 | 48.5 |
rpsL or rrs or gidB | 12 | 35 | 83 | 8 | 91.2 | 74.5 | 87.4 | 81.4 |
Gene | Primer Set | |
---|---|---|
rrs | Foward | GATGACGGCCTTCGGGTTGT |
Reverse | AGGCCACAAGGGAACGCCTA | |
rpsL | Foward | GGCCGACAAACAGAACGT |
Reverse | GTTCACCAACTGGGTGAC | |
gidB | Foward | CGCCGAGTCGTTGTGCT |
Reverse | AGCCTGGCCCGACCTTA |
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Bwalya, P.; Yamaguchi, T.; Solo, E.S.; Chizimu, J.Y.; Mbulo, G.; Nakajima, C.; Suzuki, Y. Characterization of Mutations Associated with Streptomycin Resistance in Multidrug-Resistant Mycobacterium tuberculosis in Zambia. Antibiotics 2021, 10, 1169. https://doi.org/10.3390/antibiotics10101169
Bwalya P, Yamaguchi T, Solo ES, Chizimu JY, Mbulo G, Nakajima C, Suzuki Y. Characterization of Mutations Associated with Streptomycin Resistance in Multidrug-Resistant Mycobacterium tuberculosis in Zambia. Antibiotics. 2021; 10(10):1169. https://doi.org/10.3390/antibiotics10101169
Chicago/Turabian StyleBwalya, Precious, Tomoyuki Yamaguchi, Eddie Samuneti Solo, Joseph Yamweka Chizimu, Grace Mbulo, Chie Nakajima, and Yasuhiko Suzuki. 2021. "Characterization of Mutations Associated with Streptomycin Resistance in Multidrug-Resistant Mycobacterium tuberculosis in Zambia" Antibiotics 10, no. 10: 1169. https://doi.org/10.3390/antibiotics10101169