[논문]Comparative genome characterization of Leptospira interrogans from mild and severe leptospirosis patients

Anuntakarun, Songtham; Sawaswong, Vorthon; Jitvaropas, Rungrat; Praianantathavorn, Kesmanee; Poomipak, Witthaya; Suputtamongkol, Yupin; Chirathaworn, Chintana; Payungporn, Sunchai

doi:10.5808/gi.21037

[국내논문] Comparative genome characterization of Leptospira interrogans from mild and severe leptospirosis patients 원문보기

Genomics & informatics, v.19 no.3, 2021년, pp.31.1 - 31.9

Anuntakarun, Songtham (Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University) , Sawaswong, Vorthon (Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University) , Jitvaropas, Rungrat (Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University) , Praianantathavorn, Kesmanee (Department of Biochemistry, Faculty of Medicine, Chulalongkorn University) , Poomipak, Witthaya (Research Affairs, Faculty of Medicine, Chulalongkorn University) , Suputtamongkol, Yupin (Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University) , Chirathaworn, Chintana (Department of Microbiology, Faculty of Medicine, Chulalongkorn University) , Payungporn, Sunchai (Department of Biochemistry, Faculty of Medicine, Chulalongkorn University)

Abstract ▼ AI-Helper

Leptospirosis is a zoonotic disease caused by spirochetes from the genus Leptospira. In Thailand, Leptospira interrogans is a major cause of leptospirosis. Leptospirosis patients present with a wide range of clinical manifestations from asymptomatic, mild infections to severe illness involving organ failure. For better understanding the difference between Leptospira isolates causing mild and severe leptospirosis, illumina sequencing was used to sequence genomic DNA in both serotypes. DNA of Leptospira isolated from two patients, one with mild and another with severe symptoms, were included in this study. The paired-end reads were removed adapters and trimmed with Q30 score using Trimmomatic. Trimmed reads were constructed to contigs and scaffolds using SPAdes. Cross-contamination of scaffolds was evaluated by ContEst16s. Prokka tool for bacterial annotation was used to annotate sequences from both Leptospira isolates. Predicted amino acid sequences from Prokka were searched in EggNOG and David gene ontology database to characterize gene ontology. In addition, Leptospira from mild and severe patients, that passed the criteria e-value < 10e-5 from blastP against virulence factor database, were used to analyze with Venn diagram. From this study, we found 13 and 12 genes that were unique in the isolates from mild and severe patients, respectively. The 12 genes in the severe isolate might be virulence factor genes that affect disease severity. However, these genes should be validated in further study.

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표/그림 (6)

표 Table 1. Characteristics of mild and severe data and de novo assembly
그림 Fig. 1. Comparison of clusters of orthologous groups of proteins between mild and severe strains.
그림 Fig. 2. Comparison of virulence factor genes between mild and severe strains. (A) Venn diagram analysis between mild and severe strains in chromosome 1. (B) Venn diagram analysis between mild and severe strains in chromosome 2. (C) Comparison region of predicted virulence factor genes in each chromosome of both mild and severe strains (M_1: chromosome 1 in mild strain, M_2: chromosome 2 in mild strain, S_1: chromosome 1 in severe strain and S_2 chromosome 2 in severe strain; Yellow stripe in the black bar: region of virulence factor genes).
표 Table 2. Description of predicted virulence factor genes in mild strains
그림 Fig. 3. Comparison of lipoprotein predicted genes between mild and severe strains. The class of prediction from LipoP 1.0 was separated into four groups including cytoplasmic, signal peptide, N-terminal transmembrane helix, and lipoprotein signal peptide.
표 Table 3. Description of predicted virulence factor genes in severe strains

참고문헌 (38)

Bharti AR, Nally JE, Ricaldi JN, Matthias MA, Diaz MM, Lovett MA, et al. Leptospirosis: a zoonotic disease of global importance. Lancet Infect Dis 2003;3:757-771.

상세보기
Adler B, de la Pena Moctezuma A. Leptospira and leptospirosis. Vet Microbiol 2010;140:287-296.

상세보기
Picardeau M, Bulach DM, Bouchier C, Zuerner RL, Zidane N, Wilson PJ, et al. Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis. PLoS One 2008;3:e1607.

상세보기
Xu Y, Zhu Y, Wang Y, Chang YF, Zhang Y, Jiang X, et al. Whole genome sequencing revealed host adaptation-focused genomic plasticity of pathogenic Leptospira. Sci Rep 2016;6:20020.

상세보기
Weimer BC. 100K Pathogen Genome Project. Genome Announc 2017;5:e00594-17.

상세보기
Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 2005;33:D325-D328.

상세보기
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114-2120.

상세보기
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455-477.

상세보기
Lee I, Chalita M, Ha SM, Na SI, Yoon SH, Chun J. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017;67:2053-2057.

상세보기
Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. ACT: the Artemis Comparison Tool. Bioinformatics 2005;21:3422-3423.

상세보기
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068-2069.

상세보기
Huerta-Cepas J, Szklarczyk D, Heller D, Hernandez-Plaza A, Forslund SK, Cook H, et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019;47:D309-D314.

상세보기
Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, et al. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol 2007;8:R183.

상세보기
Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017;45:D353-D361.

상세보기
Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A. Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci 2003;12:1652-1662.

상세보기
Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016;44:W16-W21.

상세보기
Farrar J, Hotez P, Junghanss T, Kang G, Lalloo D, White N, et al. Manson's Tropical Diseases. Oxford: Saunders, 2013.
The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nat Genet 2000;25:25-29.

상세보기
Fortier LC, Sekulovic O. Importance of prophages to evolution and virulence of bacterial pathogens. Virulence 2013;4:354-365.

상세보기
Kurilung A, Keeratipusana C, Suriyaphol P, Hampson DJ, Prapasarakul N. Correction to: Genomic analysis of Leptospira interrogans serovar Paidjan and Dadas isolates from carrier dogs and comparative genomic analysis to detect genes under positive selection. BMC Genomics 2019;20:246.

상세보기
Turner D, Ackermann HW, Kropinski AM, Lavigne R, Sutton JM, Reynolds DM. Comparative analysis of 37 Acinetobacter bacteriophages. Viruses 2017;10:5.
Kovacs-Simon A, Titball RW, Michell SL. Lipoproteins of bacterial pathogens. Infect Immun 2011;79:548-561.

상세보기
Kumari SR, Kadam K, Badwaik R, Jayaraman VK. LIPOPREDICT: bacterial lipoprotein prediction server. Bioinformation 2012;8:394-398.

상세보기
Samoilov AE, Stoyanova NA, Tokarevich NK, Evengard B, Zueva EV, Panferova YA, et al. Lethal outcome of leptospirosis in southern Russia: characterization of Leptospira interrogans isolated from a deceased teenager. Int J Environ Res Public Health 2020;17:4238.
Senevirathna I, Jayasundara D, Lefler JP, Chaiboonm KL, Warnasekara J, Agampodi S, et al. Complete genome sequence of Leptospira interrogans strains FMAS_KW1, FMAS_KW2 and FMAS_AW1 isolated from leptospirosis patients from Karawanalla and Awissawella, Sri Lanka. J Genomics 2020;8:49-52.

상세보기
Llanes A, Prakoso D, Restrepo CM, Rajeev S. Complete genome sequence of a virulent Leptospira interrogans serovar Copenhageni strain, assembled with a combination of nanopore and Illumina reads. Microbiol Resour Announc 2020;9:e00200-20.

상세보기
Plaut AG. The IgA1 proteases of pathogenic bacteria. Annu Rev Microbiol 1983;37:603-622.

상세보기
Mistry D, Stockley RA. IgA1 protease. Int J Biochem Cell Biol 2006;38:1244-1248.
Krause KM, Serio AW, Kane TR, Connolly LE. Aminoglycosides: an overview. Cold Spring Harb Perspect Med 2016;6:a027029.

상세보기
Faine S, Adler B, Bolin C, Perolat P. "Leptospira" and leptospirosis. 2nd ed. Melbourne: MediSci, 1999.
Kobayashi Y. Clinical observation and treatment of leptospirosis. J Infect Chemother 2001;7:59-68.
Du Y, Li T, Wang YG, Xia H. Identification and functional analysis of dTDP-glucose-4,6-dehydratase gene and its linked gene cluster in an aminoglycoside antibiotics producer of Streptomyces tenebrarius H6. Curr Microbiol 2004;49:99-107.
Hood MI, Skaar EP. Nutritional immunity: transition metals at the pathogen-host interface. Nat Rev Microbiol 2012;10:525-537.

상세보기
Zeinert R, Martinez E, Schmitz J, Senn K, Usman B, Anantharaman V, et al. Structure-function analysis of manganese exporter proteins across bacteria. J Biol Chem 2018;293:5715-5730.

상세보기
Lisher JP, Giedroc DP. Manganese acquisition and homeostasis at the host-pathogen interface. Front Cell Infect Microbiol 2013;3:91.

상세보기
Saier MH Jr. Molecular phylogeny as a basis for the classification of transport proteins from bacteria, archaea and eukarya. Adv Microb Physiol 1998;40:81-136.
Lambert A, Picardeau M, Haake DA, Sermswan RW, Srikram A, Adler B, et al. FlaA proteins in Leptospira interrogans are essential for motility and virulence but are not required for formation of the flagellum sheath. Infect Immun 2012;80:2019-2025.

상세보기
Cheng C, Wang H, Ma T, Han X, Yang Y, Sun J, et al. Flagellar basal body structural proteins FlhB, FliM, and FliY are required for flagellar-associated protein expression in Listeria monocytogenes. Front Microbiol 2018;9:208.

상세보기

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