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Correlating genetic mutations with isoniazid phenotypic levels of resistance in Mycobacterium tuberculosis isolates from patients with drug-resistant tuberculosis in a high burden setting

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Abstract

We analysed mutations in katG, inhA and rpoB genes, and isoniazid phenotypic resistance levels in Mycobacterium tuberculosis isolates from drug-resistant TB patients from São Paulo state, Brazil. Isolates resistant to the critical concentration of isoniazid in MGIT (0.1 µg/mL) were screened for mutations in katG 315 codon, inhA promoter region and rpoB RRDR by MTBDRplus assay and subjected to determination of isoniazid resistance levels by MGIT 960. Discordances were resolved by Sanger sequencing. Among the 203 isolates studied, 109 (54%) were isoniazid-monoresistant, 47 (23%) MDR, 29 (14%) polydrug-resistant, 12 (6%) pre-XDR and 6 (3%) XDR. MTBDRplus detected isoniazid mutations in 75% (153/203) of the isolates. Sequencing of the entire katG and inhA genes revealed mutations in 18/50 wild-type isolates by MTBDRplus (10 with novel mutations), resulting in a total of 32/203 (16%) isolates with no mutations detected. 81/83 (98%) isolates with katG 315 mutations alone had intermediate resistance. Of the 66 isolates with inhA C-15T mutation alone, 51 (77%) showed low-level, 14 (21%) intermediate and 1 (2%) high-level resistance. 5/6 (83%) isolates with mutations in both katG and inhA had high-level resistance. Inferred mutations corresponded to 22% (16/73) of all mutations found in rpoB. Mutations detected in katG regions other than codon 315 in this study might be potential new isoniazid resistance markers and could explain phenotypic resistance in some isolates without katG and inhA classic mutations. In our setting, 16% of isoniazid-resistant isolates, some with high-level resistance, presented no mutations either in katG or inhA.

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Data availability

The datasets generated and analysed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

The authors thank the technical assistance and support provided by the staff of Núcleo de Tuberculose e Micobacterioses and Centro de Bacteriologia of IAL, as well as the TB laboratory network from São Paulo for the valuable partnership.

Funding

This work was supported in part by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) [grants numbers 2012/51756–5 and 2017/16082–7].

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Authors and Affiliations

  1. Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), Av. Dr. Arnaldo, 351, 9º andar, São Paulo, SP, 01246-000, Brazil

    Juliana Maira Watanabe Pinhata, Angela Pires Brandao, Flávia de Freitas Mendes, Lucilaine Ferrazoli & Rosângela Siqueira de Oliveira

  2. Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, RJ, 21040-360, Brazil

    Angela Pires Brandao

  3. Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz (FIOCRUZ), Av. Prof. Moraes Rego, s/n, Cidade Universitária, Recife, PE, 50740-465, Brazil

    Michelle Christiane da Silva Rabello

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  1. Juliana Maira Watanabe Pinhata
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  2. Angela Pires Brandao
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  3. Flávia de Freitas Mendes
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  4. Michelle Christiane da Silva Rabello
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  5. Lucilaine Ferrazoli
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  6. Rosângela Siqueira de Oliveira
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Contributions

JMWP and RSO conceived the study and designed the experiments; JMWP and FFM performed and analysed MTBDRplus tests; JMWP, APB and MCSR performed and analysed gene sequencing; JMWP collected laboratory data; JMWP and RSO analysed the data; JMWP wrote the draft; and JMWP, RSO, APB and LF reviewed and edited the draft. All authors read and approved the final manuscript and agreed to be responsible for all aspects of the work.

Corresponding author

Correspondence to Juliana Maira Watanabe Pinhata.

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This study was approved by Adolfo Lutz Institute Ethics Committee (Plataforma Brasil no. 1.473.145).

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The authors declare no competing interests.

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Pinhata, J.M.W., Brandao, A.P., Mendes, F.d.F. et al. Correlating genetic mutations with isoniazid phenotypic levels of resistance in Mycobacterium tuberculosis isolates from patients with drug-resistant tuberculosis in a high burden setting. Eur J Clin Microbiol Infect Dis 40, 2551–2561 (2021). https://doi.org/10.1007/s10096-021-04316-0

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