TB-ISATEST: a Diagnostic LAMP Assay for Differentiation of Mycobacterium tuberculosis

Capa

Citar

Texto integral

Acesso aberto Acesso aberto
Acesso é fechado Acesso está concedido
Acesso é fechado Somente assinantes

Resumo

Consumption, white plague, tuberculosis… Only relatively recently, this disease has ceased to be an absolutely death sentence for infected people, but problems of the spread and diagnosis of the disease are still relevant. This paper presents results of the development of a new loop isothermal amplification (LAMP) assay, named TB-ISATEST, which targeting the species-specific gene rv2341 for the differentiation of Mycobacterium tuberculosis from non-tuberculosis mycobacteria. The assay is applicable for quantitative analysis of genomic DNA and allows detecting tenfold difference in concentration. The results of amplification optimization using a unique two-stage protocol based on the method of orthogonal Taguchi matrices are presented for the first time. A theoretical interpretation of the high amplification efficiency values observed in the LAMP reaction is proposed. Limit of detection of the developed assay is 40 copies of genomic DNA per reaction and amplification requires 15 min. In terms of the combination of characteristics, the TB-ISATEST assay surpasses all the known ways for identifying M. tuberculosis by the LAMP method.

Sobre autores

F. Shirshikov

Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency; Mendeleev University of Chemical Technology

Autor responsável pela correspondência
Email: shrshkv@ya.ru
Russia, 119435, Moscow, ul. Malaya Pirogovskaya 1A; Russia, 125047, Moscow, Miusskaya pl. 9

J. Bespyatykh

Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency; Mendeleev University of Chemical Technology

Email: shrshkv@ya.ru
Russia, 119435, Moscow, ul. Malaya Pirogovskaya 1A; Russia, 125047, Moscow, Miusskaya pl. 9

Bibliografia

  1. Pai M., Behr M.A., Dowdy D., Dheda K., Divangahi M., Boehme C.C., Ginsberg A., Swaminathan S., Spigelman M., Getahun H., Menzies D., Raviglione M. // Nat. Rev. Dis. Prim. 2016. V. 2. P. 16076. https://doi.org/10.1038/nrdp.2016.76
  2. Bhat Z.S., Rather M.A., Maqbool M., Ahmad Z. // Biomed. Pharmacother. 2018. V. 103. P. 1733–1747. https://doi.org/10.1016/j.biopha.2018.04.176
  3. Chakaya J., Petersen E., Nantanda R., Mungai B.N., Migliori G.B., Amanullah F., Lungu P., Ntoumi F., Kumarasamy N., Maeurer M., Zumla A. // Int. J. Infect. Dis. 2022. V. 124. P. S26–S29. https://doi.org/10.1016/j.ijid.2022.03.011
  4. Bagcchi S. // The Lancet Microbe. 2023. V. 4. P. e20. https://doi.org/10.1016/S2666-5247(22)00359-7
  5. Achtman M. // Annu. Rev. Microbiol. 2008. V. 62. P. 53–70. https://doi.org/10.1146/annurev.micro.62.081307.162832
  6. Riojas M.A., McGough K.J., Rider-Riojas C.J., Rastogi N., Hazbón M.H. // Int. J. Syst. Evol. Microbiol. 2018. V. 68. P. 324–332. https://doi.org/10.1099/ijsem.0.002507
  7. Gupta R.S., Lo B., Son J. // Front Microbiol. 2018. V. 9. P. 67. https://doi.org/10.3389/fmicb.2018.00067
  8. Meehan C.J., Barco R.A., Loh Y.E., Cogneau S., Rigouts L. // Int. J. Syst. Evol. Microbiol. 2021. V. 71. P. 004922. https://doi.org/10.1099/ijsem.0.004922
  9. Johansen M.D., Herrmann J.-L., Kremer L. // Nat. Rev. Microbiol. 2020. V. 18. P. 392–407. https://doi.org/10.1038/s41579-020-0331-1
  10. Galagan J.E. // Nat. Rev. Genet. 2014. V. 15. P. 307–320. https://doi.org/10.1038/nrg3664
  11. Gagneux S. // Nat. Rev. Microbiol. 2018. V. 16. P. 202–213. https://doi.org/10.1038/nrmicro.2018.8
  12. Merker M., Rasigade J.-P., Barbier M., Cox H., Feuerriegel S., Kohl T.A., Shitikov E., Klaos K., Gaudin C., Antoine R., Diel R., Borrell S., Gagneux S., Nikolayevskyy V., Andres S., Crudu V., Supply P., Niemann S., Wirth T. // Nat. Commun. 2022. V. 13. P. 5105. https://doi.org/10.1038/s41467-022-32455-1
  13. Chakravorty S., Simmons A.M., Rowneki M., Parmar H., Cao Y., Ryan J., Banada P.P., Deshpande S., Shenai S., Gall A., Glass J., Krieswirth B., Schumacher S.G., Nabeta P., Tukvadze N., Rodrigues C., Skrahina A., Tagliani E., Cirillo D.M., Davidow A., Denkinger C.M., Persing D., Kwiatkowski R., Jones M., Alland D. // mBio. 2017. V. 8. P. e00812-17. https://doi.org/10.1128/mBio.00812-17
  14. World Health Organization, 2021. WHO Consolidated Guidelines on Tuberculosis. Module 3: Diagnosis. Rapid Diagnostics for Tuberculosis Detection, 2021 Update. Geneva: World Health Organization, 2021. https://www.who.int/publications/i/item/9789240029415
  15. Gryadunov D.A., Shaskolskiy B.L., Nasedkina T.V., Rubina A.Y., Zasedatelev A.S. // Acta Naturae. 2018. V. 10. P. 4–18. https://doi.org/10.32607/20758251-2018-10-4-4-18
  16. Notomi T., Okayama H., Masubuchi H., Yonekawa T., Watanabe K., Amino N., Hase T. // Nucleic Acids Res. 2000. V. 28. P. e63. https://doi.org/10.1093/nar/28.12.e63
  17. Tomita N., Mori Y., Kanda H., Notomi T. // Nat. Protoc. 2008. V. 3. P. 877–882. https://doi.org/10.1038/nprot.2008.57
  18. Kaboev O.K., Luchkina L.A., Akhmedov A.T., Bekker M.L. // J. Bacteriol. 1981. V. 145. P. 21–26. https://doi.org/10.1128/jb.145.1.21-26.1981
  19. Tanner N.A., Evans T.C. // Curr. Protoc. Mol. Biol. 2014. V. 105. P. 15.14.1–15.14.14. https://doi.org/10.1002/0471142727.mb1514s105
  20. Nagamine K., Hase T., Notomi T. // Mol. Cell. Probes. 2002. V. 16. P. 223–229. https://doi.org/10.1006/mcpr.2002.0415
  21. Yonekawa T., Watanabe H., Hosaka N., Semba S., Shoji A., Sato M., Hamasaki M., Yuki S., Sano S., Segawa Y., Notomi T. // Sci. Rep. 2020. V. 10. P. 5409. https://doi.org/10.1038/s41598-020-62109-5
  22. Moore K.J.M., Cahill J., Aidelberg G., Aronoff R., Bektaş A., Bezdan D., Butler D.J., Chittur S.V., Codyre M., Federici F., Tanner N.A., Tighe S.W., True R., Ware S.B., Wyllie A.L., Afshin E.E., Bendesky A., Chang C.B., Dela Rosa R., Elhaik E., Erickson D., Goldsborough A.S., Grills G., Hadasch K., Hayden A., Her S.Y., Karl J.A., Kim C.H., Kriegel A.J., Kunstman T., Landau Z., Land K., Langhorst B.W., Lindner A.B., Mayer B.E., McLaughlin L.A., McLaughlin M.T., Molloy J., Mozsary C., Nadler J.L., D’Silva M., Ng D., O’Connor D.H., Ongerth J.E., Osuolale O., Pinharanda A., Plenker D., Ranjan R., Rosbash M., Rotem A., Segarra J., Schürer S., Sherrill-Mix S., Solo-Gabriele H., To S., Vogt M.C., Yu A.D., Mason C.E., The gLAMP Consortium // J. Biomol. Tech. 2021. V. 32. P. 228–275. https://doi.org/10.7171/jbt.21-3203-017
  23. Shirshikov F.V., Bespyatykh J.A. // Russ. J. Bioorg. Chem. 2022. V. 48. P. 1159–1174. https://doi.org/10.1134/S106816202206022X
  24. Iwamoto T., Sonobe T., Hayashi K. // J. Clin. Microbiol. 2003. V. 41. P. 2616–2622. https://doi.org/10.1128/JCM.41.6.2616-2622.2003
  25. Boehme C.C., Nabeta P., Henostroza G., Raqib R., Rahim Z., Gerhardt M., Sanga E., Hoelscher M., Notomi T., Hase T., Perkins M.D. // J. Clin. Microbiol. 2007. V. 45. P. 1936–1940. https://doi.org/10.1128/JCM.02352-06
  26. Rakotosamimanana N., Lapierre S.G., Raharimanga V., Raherison M.S., Knoblauch A.M., Raherinandrasana A.H., Rakotoson A., Rakotonirina J., Rasolofo V. // BMC Infect. Dis. 2019. V. 19. P. 542. https://doi.org/10.1186/s12879-019-4198-6
  27. World Health Organization, 2016. The Use of Loop-Mediated Isothermal Amplification (TB-LAMP) for the Diagnosis of Pulmonary Tuberculosis. Geneva: World Health Organization, 2016. https://apps.who.int/iris/handle/10665/249154
  28. Gray C.M., Katamba A., Narang P., Giraldo J., Zamudio C., Joloba M., Narang R., Paramasivan C.N., Hillemann D., Nabeta P., Amisano D., Alland D., Cobelens F., Boehme C.C. // J. Clin. Microbiol. 2016. V. 54. P. 1984–1991. https://doi.org/10.1128/JCM.03036-15
  29. García-Basteiro A.L., DiNardo A., Saavedra B., Silva D.R., Palmero D., Gegia M., Migliori G.B., Duarte R., Mambuque E., Centis R., Cuevas L.E., Izco S., Theron G. // Pulmonology. 2018. V. 24. P. 73–85. https://doi.org/10.1016/j.rppnen.2017.12.002
  30. Neonakis I.K., Spandidos D.A., Petinaki E. // Eur. J. Clin. Microbiol. Infect. Dis. 2011. V. 30. P. 937–942. https://doi.org/10.1007/s10096-011-1195-0
  31. Yuan L., Li Y., Wang M., Ke Z., Xu W. // J. Infect. Chemother. 2014. V. 20. P. 86–92. https://doi.org/10.1016/j.jiac.2013.07.003
  32. Nagai K., Horita N., Yamamoto M., Tsukahara T., Nagakura H., Tashiro K., Shibata Y., Watanabe H., Nakashima K., Ushio R., Ikeda M., Narita A., Kanai A., Sato T., Kaneko T. // Sci. Rep. 2016. V. 6. P. 39090. https://doi.org/10.1038/srep39090
  33. Nliwasa M., MacPherson P., Chisala P., Kamdolozi M., Khundi M., Kaswaswa K., Mwapasa M., Msefula C., Sohn H., Flach C., Corbett E.L. // PLoS One. 2016. V. 11. P. e0155101. https://doi.org/10.1371/journal.pone.0155101
  34. Yu G., Shen Y., Zhong F., Ye B., Yang J., Chen G. // PLoS One. 2018. V. 13. P. e0199290. https://doi.org/10.1371/journal.pone.0199290
  35. Lok K.H., Benjamin W.H., Kimerling M.E., Pruitt V., Lathan M., Razeq J., Hooper N., Cronin W., Dunlap N.E. // Emerg. Infect. Dis. 2002. V. 8. P. 1310–1313. https://doi.org/10.3201/eid0811.020291
  36. Thierry D., Brisson-Noël A., Vincent-Lévy-Frébault V., Nguyen S., Guesdon J.L., Gicquel B. // J. Clin. Microbiol. 1990. V. 28. P. 2668–2673. https://doi.org/10.1128/jcm.28.12.2668-2673.1990
  37. Kechin A., Oscorbin I., Cherednichenko A., Khrapov E., Schwartz Y., Stavitskaya N., Filipenko M. // Arch. Microbiol. 2023. V. 205. P. 71. https://doi.org/10.1007/s00203-023-03410-5
  38. Alonso H., Samper S., Martín C., Otal I. // BMC Genomics. 2013. V. 14. P. 422. https://doi.org/10.1186/1471-2164-14-422
  39. Zhou L., Ma C., Xiao T., Li M., Liu H., Zhao X., Wan K., Wang R. // Front. Microbiol. 2019. V. 10. P. 1–10. https://doi.org/10.3389/fmicb.2019.01887
  40. Goig G.A., Torres-Puente M., Mariner-Llicer C., Villamayor L.M., Chiner-Oms Á., Gil-Brusola A., Borrás R., Comas Espadas I. // Bioinformatics. 2019. V. 36. P. 985–989. https://doi.org/10.1093/bioinformatics/btz729
  41. Shirshikov F. V., Pekov Y.A., Miroshnikov K.A. // PeerJ. 2019. V. 7. P. e6801. https://doi.org/10.7717/peerj.6801
  42. Abramovitch R.B., Rohde K.H., Hsu F.-F., Russell D.G. // Mol. Microbiol. 2011. V. 80. P. 678–694. https://doi.org/10.1111/j.1365-2958.2011.07601.x
  43. Gupta A. // FEMS Microbiol. Lett. 2009. V. 290. P. 45–53. https://doi.org/10.1111/j.1574-6968.2008.01400.x
  44. Morero M., Ramirez M.R., Oyhenart J. // Vet. Parasitol. 2021. V. 295. P. 109462. https://doi.org/10.1016/j.vetpar.2021.109462
  45. Shoushtari M., Salehi-Vaziri M., Roohvand F., Arashkia A., Jalali T., Azadmanesh K. // Biotechnol. Lett. 2021. V. 43. P. 2149–2160. https://doi.org/10.1007/s10529-021-03175-1
  46. Wang Y., Li J., Li S., Zhu X., Wang X., Huang J., Yang X., Tai J. // Microchim. Acta. 2021. V. 188. P. 347. https://doi.org/10.1007/s00604-021-04985-w
  47. Schneider L., Blakely H., Tripathi A. // Electrophoresis. 2019. V. 40. P. 2706–2717. https://doi.org/10.1002/elps.201900167
  48. Bio-Rad Laboratories Inc., 2006. Real-Time PCR Applications Guide. Bulletin 5279. P. 4–6. https://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_5279.pdf
  49. Ruijter J.M., Barnewall R.J., Marsh I.B., Szentirmay A.N., Quinn J.C., van Houdt R., Gunst Q.D., van den Hoff M.J.B. // Clin. Chem. 2021. V. 67. P. 829–842. https://doi.org/10.1093/clinchem/hvab052
  50. von Hippel P.H., Johnson N.P., Marcus A.H. // Biopolymers. 2013. V. 99. P. 923–954. https://doi.org/10.1002/bip.22347
  51. Cousins D.V., Bastida R., Cataldi A., Quse V., Redrobe S., Dow S., Duignan P., Murray A., Dupont C., Ahmed N., Collins D.M., Butler W.R., Dawson D., Rodríguez D., Loureiro J., Romano M.I., Alito A., Zumarraga M., Bernardelli A. // Int. J. Syst. Evol. Microbiol. 2003. V. 53. P. 1305–1314. https://doi.org/10.1099/ijs.0.02401-0
  52. Alexander K.A., Laver P.N., Michel A.L., Williams M., van Helden P.D., Warren R.M., Gey van Pittius N.C. // Emerg. Infect. Dis. 2010. V. 16. P. 1296–1299. https://doi.org/10.3201/eid1608.100314
  53. Esteban J., Muñoz-Egea M.C. // Tuberculosis and Nontuberculous Mycobacterial Infections / Ed. David Schlossberg. Washington, DC: ASM Press, 2017. P. 754. https://doi.org/10.1128/microbiolspec.TNMI7-0021-2016
  54. Ngabonziza J.C.S., Loiseau C., Marceau M., Jouet A., Menardo F., Tzfadia O., Antoine R., Niyigena E.B., Mulders W., Fissette K., Diels M., Gaudin C., Duthoy S., Ssengooba W., André E., Kaswa M.K., Habimana Y.M., Brites D., Affolabi D., Mazarati J.B., de Jong B.C., Rigouts L., Gagneux S., Meehan C.J., Supply P. // Nat. Commun. 2020. V. 11. P. 2917. https://doi.org/10.1038/s41467-020-16626-6
  55. Panda A., Drancourt M., Tuller T., Pontarotti P. // Sci. Rep. 2018. V. 8. P. 14817. https://doi.org/10.1038/s41598-018-33261-w
  56. Eldholm V., Balloux F. // Trends Microbiol. 2016. V. 24. P. 637–648. https://doi.org/10.1016/j.tim.2016.03.007
  57. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. // J. Mol. Biol. 1990. V. 215. P. 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
  58. Szklarczyk D., Gable A.L., Lyon D., Junge A., Wyder S., Huerta-Cepas J., Simonovic M., Doncheva N.T., Morris J.H., Bork P., Jensen L.J., von Mering C. // Nucleic Acids Res. 2019. V. 47. P. D607–D613. https://doi.org/10.1093/nar/gky1131
  59. Chitale P., Lemenze A.D., Fogarty E.C., Shah A., Grady C., Odom-Mabey A.R., Johnson W.E., Yang J.H., Eren A.M., Brosch R., Kumar P., Alland D. // Nat. Commun. 2022. V. 13. P. 7068. https://doi.org/10.1038/s41467-022-34853-x
  60. Lu J., Johnston A., Berichon P., Ru K., Korbie D., Trau M. // Sci. Rep. 2017. V. 7. P. 41328. https://doi.org/10.1038/srep41328
  61. Dwight Z., Palais R., Wittwer C.T. // Bioinformatics. 2011. V. 27. P. 1019–1020. https://doi.org/10.1093/bioinformatics/btr065
  62. Zuker M. // Nucleic Acids Res. 2003. V. 31. P. 3406–3415. https://doi.org/10.1093/nar/gkg595
  63. Kerpedjiev P., Hammer S., Hofacker I.L. // Bioinformatics. 2015. V. 31. P. 3377–3379. https://doi.org/10.1093/bioinformatics/btv372
  64. Popenda M., Szachniuk M., Antczak M., Purzycka K.J., Lukasiak P., Bartol N., Blazewicz J., Adamiak R.W. // Nucleic Acids Res. 2012. V. 40. P. e112. https://doi.org/10.1093/nar/gks339
  65. Sehnal D., Bittrich S., Deshpande M., Svobodová R., Berka K., Bazgier V., Velankar S., Burley S.K., Koča J., Rose A.S. // Nucleic Acids Res. 2021. V. 49. P. W431–W437. https://doi.org/10.1093/nar/gkab314
  66. Shitikov E.A., Bespyatykh J.A., Ischenko D.S., Alexeev D.G., Karpova I.Y., Kostryukova E.S., Isaeva Y.D., Nosova E.Y., Mokrousov I.V., Vyazovaya A.A., Narvs-kaya O.V., Vishnevsky B.I., Otten T.F., Zhuravlev V.Iu., Yablonsky P.K., Ilina E.N., Govorun V.M. // PLoS One. 2014. V. 9. P. e84971. https://doi.org/10.1371/journal.pone.0084971
  67. Bustin S.A., Benes V., Garson J.A., Hellemans J., Huggett J., Kubista M., Mueller R., Nolan T., Pfaffl M.W., Shipley G.L., Vandesompele J., Wittwer C.T. // Clin. Chem. 2009. V. 55. P. 611–622. https://doi.org/10.1373/clinchem.2008.112797

Arquivos suplementares

Arquivos suplementares
Ação
1. JATS XML
Baixar
2.

Baixar (363KB)
Metadados
3.

Baixar (271KB)
Metadados
4.

Baixar (192KB)
Metadados
5.

Baixar (93KB)
Metadados
6.

Baixar (191KB)
Metadados
7.

Baixar (155KB)
Metadados

Declaração de direitos autorais © Ф.В. Ширшиков, Ю.А. Беспятых, 2023

Este site utiliza cookies

Ao continuar usando nosso site, você concorda com o procedimento de cookies que mantêm o site funcionando normalmente.

Informação sobre cookies