Mutation of Gyra Gene Found In Mycobacterium Leprae From Leprosy Patient In West Papua and Papua, Indonesia

Yustinus  Maladan; Hana Krismawati; Rosana Agus; Hotma M.L. Hutapea; Ratna Tanjung; Vatim Dwi Cahyani; Muhammad Fajri Rokhmad; Arli Aditya Parikesit

doi:10.22146/ijp.848

Yustinus Maladan Center for Papua Health Research and Development, Jl. Kesehatan No. 48, Jayapura, 99111, Indonesia
Hana Krismawati Center for Papua Health Research and Development, Jl. Kesehatan No. 48, Jayapura, 99111, Indonesia
Rosana Agus Biology Department, Mathematics and Natural Science Faculty, Hasunddin University, Jl Perintis Kemerdekaan No. 10, Makassar 90245, Indonesia
Hotma M.L. Hutapea Center for Papua Health Research and Development, Jl. Kesehatan No. 48, Jayapura, 99111, Indonesia
Ratna Tanjung Center for Papua Health Research and Development, Jl. Kesehatan No. 48, Jayapura, 99111, Indonesia
Vatim Dwi Cahyani Center for Papua Health Research and Development, Jl. Kesehatan No. 48, Jayapura, 99111, Indonesia
Muhammad Fajri Rokhmad Center for Papua Health Research and Development, Jl. Kesehatan No. 48, Jayapura, 99111, Indonesia
Arli Aditya Parikesit Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia

Keywords: Leprosy, gyrA, ofloxacin, Mycobacterium leprae

Abstract

Cases of leprosy in Indonesia are still high, especially in the provinces of West Papua, North Maluku and Papua. Drug resistance surveillance and typing strains of Mycobacterium leprae are useful molecular tools for leprosy control especially in the three Provinces. The purpose of this study was to identify mutations in the gyrA M. leprae gene obtained from leprosy patients in the provinces of West Papua and Papua on a molecular basis. M. leprae samples obtained from leprosy patients were extracted and continued with PCR and sequencing in the M. leprae gyrA gene. The sequencing results are aligned with M. leprae TN sequences to identify mutations. The phylogenetic tree was constructed using Mega 7 to get the M. leprae gyrA cluster. The RNAalifold server was employed to generate the conserved 2D structure for the gyrA MSAs. Six variants were found in the gyrA M. leprae obtained from the provinces of West Papua and Papua. The six variants are H71R, K73R, D95G, A101T, R107W, A127V. The existence of mutations in the gyrA M. leprae gene found in this study can be information in the treatment of leprosy in Papua if using Ofloxacin as an alternative treatment. Based on phylogenetic analysis found there are three distinct clusters of gyrA gene. The five variants are H71R, K73R, A101T, R107W, A127V are new variant of gyrA M. leprae. The D95G variant has been confirmed to cause resistance to Fluoroquinolone by in vitro methods, while the H71R, K73R, A101T, R107W, A127V variants are new variants whose effects on the fluoroquinolone are unknown. Thus, further analysis is needed to study the effects of the five variants on ofloxacin.

References

Akand EH., Downard KM., 2017. Mutational analysis employing a phylogenetic mass tree approach in a study of the evolution of the influenza virus. Mol Phylogenet Evol. 112: 209–217.

Bernhart SH., Hofacker IL., Will S., Gruber AR., Stadler PF., 2008. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics. 9: 474.

Cambau E., Chauffour-Nevejans A., Tejmar-Kolar L., Matsuoka M., Jarlier V., 2012. Detection of antibiotic resistance in leprosy using GenoType LepraeDR, a novel ready-to-use molecular test. PLoS Negl Trop Dis. 6: 1-7.

Cambau E., Perani E., Guillemin I., Jamet P., Ji B., 1997. Multidrug-resistance to dapsone, rifampicin, and ofloxacin in Mycobacterium leprae. Lancet. 349: 103–104.

Cambau E., Saunderson P., Matsuoka M., Cole ST., Kai M., Suffys P., Rosa PS., Williams D., Gupta UD., Lavania M., et al., 2018. Antimicrobial resistance in leprosy: results of the first prospective open survey conducted by a WHO surveillance network for the period 2009–15. Clin Microbiol Infect. 24: 1305–1310.

Chen Y., Liang W., Yang S., Wu N., Gao H., Sheng J., Yao H., Wo J., Fang Q., Cui D., et al., 2013. Human infections with the emerging avian influenza A H7N9 virus from wet market poultry: clinical analysis and characterisation of viral genome. Lancet. 381: 1916–25.

Chokkakula S., Chen Zhiming, Wang L., Jiang H., Chen Y., Shi Y., Zhang W., Gao W., Yang J., Li J., et al., 2019. Molecular surveillance of antimicrobial resistance and transmission pattern of Mycobacterium leprae in Chinese leprosy patients. Emerg Microbes Infect. 8: 1479–1489.

Gruber AR., Lorenz R., Bernhart SH., Neuböck R., Hofacker IL., 2008. The Vienna RNA websuite. Nucleic Acids Res. 36.

Hargrave J., Wallace T., Lush D., 2010. Guidelines for the Control of Leprosy in the Northern Territory. 3rd ed. Northern Territory: Centre for Disease Control.

Hofacker IL., Fekete M., Stadler PF., 2002. Secondary Structure Prediction for Aligned RNA Sequences. J Mol Biol. 319: 1059–1066.

Hofacker IL., Stadler PF., 1999. Automatic detection of conserved base pairing patterns in RNA virus genomes. Comput Chem. 23: 401–14.
Kai M., Phuc NHN., Nguyen HA., Pham THBD., Nguyen KH., Miyamoto Y., Maeda Y., Fukutomi Y., Nakata N., Matsuoka M., et al., 2011. Analysis of Drug-Resistant Strains of Mycobacterium leprae in an Endemic Area of Vietnam. Clin Infect Dis. 52: 127–132.

Kumar S., Stecher G., Tamura K., 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 33: 1870–1874.

Li W., Matsuoka M., Kai M., Thapa P., Khadge S., Hagge DA., Brennan PJ., Vissa V., 2012. Real-Time PCR and High-Resolution Melt Analysis for Rapid Detection of Mycobacterium leprae Drug Resistance Mutations and Strain Types. J Clin Microbiol.50: 742–753.

Lorenz R., Bernhart SH., Höner zu Siederdissen C., Tafer H., Flamm C., Stadler PF., Hofacker IL., 2011. ViennaRNA Package 2.0. Algorithms Mol Biol. 6: 26.

Maeda S., Matsuoka M., Nakata N., Kai M., Maeda Y., Hashimoto K., Kimura H., Kobayashi K., Kashiwabara Y., 2001. Multidrug Resistant Mycobacterium leprae from Patients with Leprosy. Antimicrob Agents Chemother. 45: 3635–3639.

Maladan Y., Krismawati H., Hutapea HML., Oktavian A., Fatimah R., Widodo., 2019. A new Mycobacterium leprae dihydropteroate synthase variant (V39I) from Papua, Indonesia. Heliyon. 5: e01279.

Matrat S., Cambau E., Jarlier V., Aubry A., 2008. Are all the DNA gyrase mutations found in Mycobacterium leprae clinical strains involved in resistance to fluoroquinolones? Antimicrob Agents Chemother. 52: 745–747.

Parikesit AA., 2018. The Construction of Two and Three Dimensional Molecular Models for the miR-31 and Its Silencer as the Triple Negative Breast Cancer Biomarkers. Online J Biol Sci. 18: 424–431.

Parikesit AA., Nurdiansyah R., 2020. The Predicted Structure for the Anti-Sense siRNA of the RNA Polymerase Enzyme (RdRp) gene of the SARS-CoV-2. Ber Biol. 19: 97–108.

Shepard CC., 1960. The experimental disease that follows the injection of human leprosy bacilli into foot-pads of mice. J Exp Med. 112:445–454.

Thompson JD., Gibson TJ., Higgins DG., 2002. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics. Chapter 2: Unit 2.3.

Veziris N., Chauffour A., Escolano S., Henquet S., Matsuoka M., Jarlier V., Aubry A., 2013. Resistance of M. leprae to Quinolones: A Question of Relativity? PLoS Negl Trop Dis. 7: 1-6

WHO., 2017a. A Guide for Surveillance of Antimicrobial Resistance in Leprosy. E. A. Cooreman/leprosy, New Delhi.

WHO., 2017b. Leprosy elimination. http://www.who.int/lep/mdt/en/.

WHO., 2018. Guidelines for the Diagnosis, Treatment and Prevention of Leprosy, New Delhi.

WHO., 2020. Global leprosy (Hansen disease) update, 2019: time to step-up prevention initiatives. Wkly Epidemiol Rec. 95: 417–440.

Willby M., Sikes RD., Malik S., Metchock B., Posey JE., 2015. Correlation between GyrA substitutions and ofloxacin, levofloxacin, and moxifloxacin cross-resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother. 59: 5427–5434.

Williams DL., Gillis TP., 2012a. Drug-resistant leprosy : Monitoring and Current Status. Lepr Rev. 83: 269–281.

Yokoyama K., Kim H., Mukai T., Matsuoka M., Nakajima C., Suzuki Y., 2012. Amino acid substitutions at position 95 in GyrA can add fluoroquinolone resistance to Mycobacterium leprae. Antimicrob Agents Chemother. 56: 697–702.

You E-Y., Kang TJ., Kim S-K., Lee S-B., Chae G-T., 2005. Mutations in genes related to drug resistance in Mycobacterium leprae isolates from leprosy patients in Korea. J Infect. 50:6–11.