Sequencing Approaches for Understanding the Pathogenic Features in Leptospira Genome

Main Article Content

Ramyadevi Veerabahu
Vigneshwaran Ravishankar*
Eshaa Umashankar

Abstract

Leptospirosis is a zoonotic illness caused by a bacterial spirochaete belonging to the genus Leptospira that induces renal failure in humans. This bacterium has high pathogenicity and can even cause death. As a result, research into the pathogenic mechanism of this organism is essential. Sequencing can be performed to understand the evolution and characteristics of an organism. Sequencing technologies like Sanger sequencing, Illumina sequencing, and recent technologies like MinION nanopore sequencing can be performed to study the whole genome of leptospiral strains. Based on whole genome sequencing, pathogenic characteristics and pathways involved during disease infection can be investigated. Identification of pathogenic features in the whole genome of Leptospira sp. may enable certain gene modifications or the development of potential vaccines to eradicate the disease. This review is an overview of various sequencing approaches and highlights the comparison of genome features present in pathogenic leptospires and saprophytic leptospires.


Keywords: Leptospira; vaccine; sequencing; genome; Illumina


*Corresponding author: Tel.: (+91) -9994828885


                                             E-mail: rvigneswaran9490@yahoo.com

Article Details

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References

Shen, Y., Nie, J., Kuang, L., Zhang, J. and Li, H., 2021. DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables. Microbial Biotechnology, 14(2), 323-362.

Pareek, C.S., Smoczynski, R. and Tretyn, A., 2011. Sequencing technologies and genome sequencing. Journal of applied genetics, 52 (4), 413-435.

Verma, S. and Gazara, R.K., 2021. Next-generation sequencing: an expedition from workstation to clinical applications. In: K. Raza and N. Dey, eds. Translational Bioinformatics in Healthcare and Medicine. London: Academic Press, pp. 29-47.

Bambini, S. and Rappuoli, R., 2009. The use of genomics in microbial vaccine development. Drug Discovery Today, 14(5), 252-260.

Kukurba, K.R. and Montgomery, S.B., 2015. RNA sequencing and analysis. Cold Spring Harbor Protocols, 2015(11), 951-969.

Ungelenk, M., 2021. Sequencing approaches. In: T. Liehr, ed. Cytogenomics. London: Academic Press, pp. 87-122.

Maxam, A.M. and Gilbert, W., 1977. A new method for sequencing DNA. Proceedings of the National Academy of Sciences of the United States of America, 74(2), 560-564.

Lehmann, A.R., 1997. Technologies for Detection of DNA Damage and Mutations. Journal of Medical Genetics, 34(5), 438-438.

Vilgis, S. and Deigner, H.P., 2018. Sequencing in precision medicine. In: H.P. Deigner and M. Kohl, eds. Precision Medicine. London: Academic Press, pp. 79-101.

Borsting, C. and Morling, N., 2015. Next generation sequencing and its applications in forensic genetics. Forensic Science International Genetics, 18, 78-89.

Berg, P., 2014. Fred Sanger: a memorial tribute. Proceedings of the National Academy of Sciences of the United States of America, 111(3), 883-884.

Sanger, F. and Coulson, A.R., 1975. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of Molecular Bioliogy, 94(3), 441-448.

Sanger, F., Nicklen, S. and Coulson, A.R., 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 74(12), 5463-5467.

Wang, J., Jiang, Y., Vincent, M., Sun, Y., Yu, H., Wang, J., Bao, Q., Kong, H. and Hu, S., 2005. Complete genome sequence of bacteriophage T5. Virology, 332(1), 45-65.

Crossley, B.M., Bai, J., Glaser, A., Maes, R., Porter, E., Killian, M.L., Clement, T. and Toohey-Kurth, K., 2020. Guidelines for Sanger sequencing and molecular assay monitoring. Journal of Veterinary Diagnostic Investigation, 32(6), 767-775, DOI: 10.1177/1040638720905833.

Heather, J.M. and Chain, B., 2016. The sequence of sequencers: The history of sequencing DNA. Genomics, 107(1), 1-8.

Hood, L.E., Hunkapiller, M.W. and Smith, L.M., 1987. Automated DNA sequencing and analysis of the human genome. Genomics, 1(3), 201-212.

Shetty, P.J., Amirtharaj, F. and Shaik, N.A., 2019. Introduction to nucleic acid sequencing. In: N.A. Shaik, K.R. Hakeem, B. Banaganapalli and R. Elango, eds. Essentials of Bioinformatics. Volume I. Cham: Springer, pp. 97-126.

Nyrén, P. and Lundin, A., 1985. Enzymatic method for continuous monitoring of inorganic pyrophosphate synthesis. Analytical Biochemistry, 151(2), 504-509.

Gansauge, M.-T., Gerber, T., Glocke, I., Korlevic, P., Lippik, L., Nagel, S., Riehl, L.M., Schmidt, A. and Meyer, M., 2017. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Research, 45(10), 1-10.

Shendure, J. and Ji, H., 2008. Next-generation DNA sequencing. Nature Biotechnology, 26(10), 1135-1145.

Metzker, M.L., 2010. Sequencing technologies - the next generation. Nature Reviews Genetics, 11(1), 31-46.

Liu, L., Li, Y., Li, S., Hu, N., He, Y., Pong, R., Lin, D., Lu, L. and Law, M., 2012. Comparison of next-generation sequencing systems. Journal of Biomedicine and Biotechnology, 2012, DOI: 10.1155/2012/251364.

Schadt, E.E., Turner, S. and Kasarskis, A., 2010. A window into third-generation sequencing. Human Molecular Genetics, 19(2), 227-240.

Travers, K.J., Chin, C.S., Rank, D.R., Eid, J.S. and Turner, S.W., 2010. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Research, 38(15), DOI: 10.1093/nar/gkq543.

Koren, S., Harhay, G.P., Smith, T.P., Bono, J.L., Harhay, D.M., McVey, S.D., Radune, D., Bergman, N.H. and Phillippy, A.M., 2013. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology, 14(9), DOI: 10.1186/gb-2013-14-9-r101.

Petersen, L.M., Martin, I.W., Moschetti, W.E., Kershaw, C.M. and Tsongalis, G.J., 2019. Third-generation sequencing in the clinical laboratory: Exploring the advantages and challenges of nanopore sequencing. Journal of Clinical Microbiology, 58(1), 01315-01319.

Jain, M., Olsen, H.E., Paten, B. and Akeson, M., 2016. The Oxford nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biology, 17(1), DOI: 10.1186/s130593-16-1103-0.

Wang, Y., Zhao, Y., Bollas, A., Wang, Y. and Au, K.F., 2021. Nanopore sequencing technology, bioinformatics and applications. Nature Biotechnology, 39(11), 1348-1365.

De Coster, W., De Rijk, P., De Roeck, A., De Pooter, T., D'Hert, S., Strazisar, M., Sleegers, K. and Van Broeckhoven, C., 2019. Structural variants identified by Oxford nanopore PromethION sequencing of the human genome. Genome Research, 29(7), 1178-1187.

Hess, J.F., Kohl, T.A., Kotrová, M., Rönsch, K., Paprotka, T., Mohr, V., Hutzenlaub, T., Brüggemann, M., Zengerle, R., Niemann, S. and Paust, N., 2020. Library preparation for next generation sequencing: A review of automation strategies. Biotechnology Advances, 41, DOI: 10.1016/j.biotechadv.2020.107537.

Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.F., Dougherty, B.A., Merrick, J.M., McKenney, K., Sutton, G., FitzHugh, W., Fields, C., Gocayne, J.D., Scott, J., Shirley, R., Liu, L., Glodek, A., Kelley, J.M., Weidman, J.F., Phillips, C.A., Spriggs, T., Hedblom, E., Cotton, M.D., Utterback, T.R., Hanna, M.C., Nguyen, D.T., Saudek, D.M., Brandon, R.C., Fine, L.D., Fritchman, J.L., Fuhrmann, J.L., Geoghagen, N.S.M., Gnehm, C.L., McDonald, L.A., Small, K.V., Fraser, C.M., Smith, H.O. and Venter, J.C., 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae. Science, 269(5223), 496-512.

Fraser, C.M., Gocayne, J.D., White, O., Adams, M.D., Clayton, R.A., Fleischmann, R.D., Bult, C.J., Kerlavage, A.R., Sutton, G., Kelley, J.M., Fritchman, R.D., Weidman, J.F., Small, K.V., Sandusky, M., Fuhrmann, J., Nguyen, D., Utterback, T.R., Saudek, D.M., Phillips, C.A., Merrick, J.M., Tomb, J.F., Dougherty, B.A., Bott, K.F., Hu, P.C., Lucier, T.S., Peterson, S.N., Smith, H.O., Hutchison, C.A. and Venter, J.C., 1995. The minimal gene complement of Mycoplasma genitalium. Science, 270(5235), 397-403.

Jorge, S., Kremer, F.S., Oliveira, N.R.d., Navarro, G.d.O.S.V., Guimarães, A.M., Sanchez, C.D., Woloski, R.D.D.S., Ridieri, K.F., Campos, V.F., Pinto, L.d.S. and Dellagostin, O.A., 2018. Whole-genome sequencing of Leptospira interrogans from southern Brazil: genetic features of a highly virulent strain. Memorias do Instituto Oswaldo Cruz, 113(2), 80-86.

Nascimento, A.L., Verjovski-Almeida, S., Van Sluys, M.A., Monteiro-Vitorello, C.B., Camargo, L.E., Digiampietri, L.A., Harstkeerl, R.A., Ho, P.L., Marques, M.V., Oliveira, M.C., Setubal, J.C., Haake, D.A. and Martins, E.A., 2004. Genome features of Leptospira interrogans serovar Copenhageni. Brazilian Journal of Medical and Biological Research, 37(4), 459-477.

Guglielmini, J., Bourhy, P., Schiettekatte, O., Zinini, F., Brisse, S. and Picardeau, M., 2019. Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PLoS Neglected Tropical Diseases, 13(4), DOI: 10.1371/journal.pntd.0007374.

Fraga, T.R., Carvalho, E., Isaac, L. and Barbosa, A.S., 2015. Leptospira and Leptospirosis. In: Y.-W. Tang, M. Sussman, D. Liu, I. Poxton and J. Schwartzman, eds. Molecular Medical Microbiology. Boston: Academic Press, pp. 1973-1990.

Xu, Y., Zheng, H., Zhang, Y., Wang, Y., Zhang, J., Li, Z., Cui, S., Xin, X., Ye, Q., Chang, Y.F. and Wang, J., 2017. Genomic analysis of a new serovar of Leptospira weilii serogroup Manhao. Frontiers in Microbiology, 8, DOI: 10.3389/fmicb.2017.00149.

He, P., Sheng, Y.Y., Shi, Y.Z., Jiang, X.G., Qin, J.H., Zhang, Z.M., Zhao, G.P. and Guo, X.K., 2007. Genetic diversity among major endemic strains of Leptospira interrogans in China. BMC Genomics, 8, DOI: 10.1186/1471-2164-8-204.

Evangelista, K.V. and Coburn, J., 2010. Leptospira as an emerging pathogen: a review of its biology, pathogenesis and host immune responses. Future Microbiology, 5(9), 1413-1425.

Picardeau, M., Bulach, D.M., Bouchier, C., Zuerner, R.L., Zidane, N., Wilson, P.J., Creno, S., Kuczek, E.S., Bommezzadri, S., Davis, J.C., McGrath, A., Johnson, M.J., Boursaux-Eude, C., Seemann, T., Rouy, Z., Coppel, R.L., Rood, J.I., Lajus, A., Davies, J.K., Médigue, C. and Adler, B., 2008. Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis. PloS ONE, 3(2), DOI: 10.1371/journal.pone.0001607.

Ristow, P., Bourhy, P., Kerneis, S., Schmitt, C., Prevost, M.C., Lilenbaum, W. and Picardeau, M., 2008. Biofilm formation by saprophytic and pathogenic leptospires. Microbiology, 154(5), 1309-1317.

Picardeau, M., 2018. Toolbox of molecular techniques for studying Leptospira spp. Current Topics in Microbiology and Immunology, 415, 141-162.

Wei, Y., Silke, J.R. and Xia, X., 2019. An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria. Scientific Reports, 9(1), DOI: 10.1038/s41598-019-39369-x.

Vincent, A.T., Schiettekatte, O., Goarant, C., Neela, V.K., Bernet, E., Thibeaux, R., Ismail, N., Mohd Khalid, M.K.N., Amran, F., Masuzawa, T., Nakao, R., Amara Korba, A., Bourhy, P., Veyrier, F.J. and Picardeau, M., 2019. Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics. PLoS Neglected Tropical Diseases, 13(5), DOI: 10.1371/journal.pntd.0007270.

Ricaldi, J.N., Fouts, D.E., Selengut, J.D., Harkins, D.M., Patra, K.P., Moreno, A., Lehmann, J.S., Purushe, J., Sanka, R., Torres, M., Webster, N.J., Vinetz, J.M. and Matthias, M.A., 2012. Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. PLoS Neglected Tropical Diseases, 6(10), DOI: 10.137/journal.pntd.000 1853.

Fouts, D.E., Matthias, M.A., Adhikarla, H., Adler, B., Amorim-Santos, L., Berg, D.E., Bulach, D., Buschiazzo, A., Chang, Y.-F., Galloway, R.L., Haake, D.A., Haft, D.H., Hartskeerl, R., Ko, A.I., Levett, P.N., Matsunaga, J., Mechaly, A.E., Monk, J.M., Nascimento, A.L.T., Nelson, K.E., Palsson, B., Peacock, S.J., Picardeau, M., Ricaldi, J.N., Thaipandungpanit, J., Wunder, E.A., Jr., Yang, X.F., Zhang, J.-J. and Vinetz, J.M., 2016. What makes a bacterial species pathogenic?: Comparative genomic analysis of the genus Leptospira. PLoS Neglected Tropical Diseases, 10(2), DOI: 10.137/journal.pntd.0004403.

Ramli, S.R., Moreira, G.M.S.G., Zantow, J., Goris, M.G.A., Nguyen, V.K., Novoselova, N., Pessler, F. and Hust, M., 2019. Discovery of Leptospira spp. seroreactive peptides using ORFeome phage display. PLoS Neglected Tropical Diseases, 13(1), DOI: 10.137/journal.pntd.0007131.

Sudhakara, P., Sellamuthu, I. and Aruni, A.W., 2019. Bacterial sialoglycosidases in virulence and pathogenesis. Pathogens, 8(1), DOI: 10.3390/pathogens8010039.

Louwen, R., Staals, R.H.J., Endtz, H.P., van Baarlen, P. and van der Oost, J., 2014. The role of CRISPR-Cas systems in virulence of pathogenic bacteria. Microbiology and Molecular Biology Reviews, 78(1), 74-88.

Handing, J.W., Ragland, S.A., Bharathan, U.V. and Criss, A.K., 2018. The MtrCDE efflux pump contributes to survival of Neisseria gonorrhoeae from human neutrophils and their antimicrobial components. Frontiers in Microbiology, 9, DOI: 10.3389/fmicb.2018.02688.

Hsu, S.H. and Yang, C.W., 2022. Insight into the Structure, Functions, and Dynamics of the Leptospira Outer Membrane Proteins with the Pathogenicity. Membranes (Basel), 12(3), DOI: 10.3390/membranes12030300.

Ramli, S.R., Bunk, B., Spröer, C., Geffers, R., Jarek, M., Bhuju, S., Goris, M., Mustakim, S. and Pessler, F., 2021. Complete genome sequencing of Leptospira interrogans isolates from Malaysia reveals massive genome rearrangement but high conservation of virulence-associated genes. Pathogens, 10(9), DOI: 10.3390/pathogens10091198.

Chou, L.F., Chen, Y.T., Lu, C.W., Ko, Y.C., Tang, C.Y., Pan, M.J., Tian, Y.C., Chiu, C.H., Hung, C.C. and Yang, C.W., 2012. Sequence of Leptospira santarosai serovar Shermani genome and prediction of virulence-associated genes. Gene, 511(2), 364-370.

Scheibye-Alsing, K., Hoffmann, S., Frankel, A., Jensen, P., Stadler, P.F., Mang, Y., Tommerup, N., Gilchrist, M.J., Nygård, A.B., Cirera, S., Jørgensen, C.B., Fredholm, M. and Gorodkin, J., 2009. Sequence assembly. Computational Biology and Chemistry, 33(2), 121-136.

Chou, L.-F., Chen, T.-W., Ko, Y.-C., Pan, M.-J., Tian, Y.-C., Chiu, C.-H., Tang, P., Hung, C.-C. and Yang, C.-W., 2014. Potential impact on kidney infection: a whole-genome analysis of Leptospira santarosai serovar Shermani. Emerging Microbes and Infection, 3(1), DOI: 10.1038/emi.2014.78.

Ahmed, N., Devi, S.M., Valverde Mde, L., Vijayachari, P., Machang'u, R.S., Ellis, W.A. and Hartskeerl, R.A., 2006. Multilocus sequence typing method for identification and genotypic classification of pathogenic Leptospira species. Annals of Clinical Microbiology and Antimicrobials, 5, DOI: 10.1186/1476-0711-5-28.

Chin, V.K., Lee, T.Y., Lim, W.F., wan Shahriman, Y.W.Y., Syafinaz, A.N., Zamberi, S., Maha, A., 2018. Leptospirosis in human: Biomarkers in host immune responses. Microbiological Research, 207, 108-115.

Wagenaar, J.F., Goris, M.G., Gasem, M.H., Isbandrio, B., Moalli, F., Mantovani, A., Boer, K.R., Hartskeerl, R.A., Garlanda, C. and van Gorp, E.C., 2009. Long pentraxin PTX3 is associated with mortality and disease severity in severe Leptospirosis. Journal of Infection, 58(6), 425-432.

Lindow, J.C., Wunder, E.A., Jr., Popper, S.J., Min, J.N., Mannam, P., Srivastava, A., Yao, Y., Hacker, K.P., Raddassi, K., Lee, P.J., Montgomery, R.R., Shaw, A.C., Hagan, J.E., Araújo, G.C., Nery, N., Jr., Relman, D.A., Kim, C.C., Reis, M.G. and Ko, A.I., 2017. Correction: Cathelicidin insufficiency in patients with fatal leptospirosis. PLoS Pathogens, 13(9), DOI: 10.1371/journalppat.1006646.

Hauk, P., Macedo, F., Romero, E.C., Vasconcellos, S.A., de Morais, Z.M., Barbosa, A.S. and Ho, P.L., 2008. In LipL32, the major leptospiral lipoprotein, the C terminus is the primary immunogenic domain and mediates interaction with collagen IV and plasma fibronectin. Infection and immunity, 76(6), 2642-2650.

Philip, N., Jani, J., Azhari, N.N., Sekawi, Z. and Neela, V.K., 2021. In vivo and in silico virulence analysis of Leptospira species isolated from environments and rodents in leptospirosis outbreak areas in Malaysia. Frontiers in Microbiology, 12, DOI: 10.3389/fmicb.2021.753328.

Narayanavari, S.A., Lourdault, K., Sritharan, M., Haake, D.A. and Matsunaga, J., 2015. Role of sph2 Gene Regulation in Hemolytic and Sphingomyelinase Activities Produced by Leptospira interrogans. PLoS Neglected Tropical Diseases, 9(8), DOI: 10.1371/journal.pntd.0003952.

Murray, G.L., Srikram, A., Henry, R., Puapairoj, A., Sermswan, R.W. and Adler, B., 2009. Leptospira interrogans requires heme oxygenase for disease pathogenesis. Microbes and Infection, 11(2), 311-314.

Guernier, V., Allan, K.J. and Goarant, C., 2018. Advances and challenges in barcoding pathogenic and environmental Leptospira. Parasitology, 145(5), 595-607.

Ghazaei, C., 2018. Pathogenic Leptospira: Advances in understanding the molecular pathogenesis and virulence. Open Veterinary Journal, 8(1), 13-24.

Haake, D.A. and Matsunaga, J., 2021. Leptospiral immunoglobulin-like domain proteins: roles in virulence and immunity. Frontiers in Immunology, 11, DOI: 10.3389/fimmu.2020.579907.

Herman, H.S., Mehta, S., Cárdenas, W.B., Stewart-Ibarra, A.M. and Finkelstein, J.L., 2016. Micronutrients and leptospirosis: A review of the current evidence. PLoS Neglected Tropical Diseases, 10(7), DOI: 10.137/journal.pntd.0004652.

Kumar, S., Lata, K.S., Sharma, P., Bhairappanavar, S.B., Soni, S. and Das, J., 2019. Inferring pathogen-host interactions between Leptospira interrogans and Homo sapiens using network theory. Scientific Reports, 9(1), DOI: 10.1038/s41598-018-38329-1.

Eshghi, A., Henderson, J., Trent, M.S. and Picardeau, M., 2015. Leptospira interrogans lpxD homologue is required for thermal acclimatization and virulence. Infection and Immunity, 83(11), 4314-4321.

Ko, A.I., Goarant, C. and Picardeau, M., 2009. Leptospira: the dawn of the molecular genetics era for an emerging zoonotic pathogen. Nature Reviews Microbiology, 7(10), 736-747.