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Chinchilla D, Nieves C, Gutiérrez R, Sordoillet V, Veyrier FJ, Picardeau M. Phylogenomics of Leptospira santarosai, a prevalent pathogenic species in the Americas. PLoS Negl Trop Dis 2023; 17:e0011733. [PMID: 37917733 PMCID: PMC10645364 DOI: 10.1371/journal.pntd.0011733] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/14/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Leptospirosis is a complex zoonotic disease mostly caused by a group of eight pathogenic species (L. interrogans, L. borgpetersenii, L. kirschneri, L. mayottensis, L. noguchii, L. santarosai, L. weilii, L. alexanderi), with a wide spectrum of animal reservoirs and patient outcomes. Leptospira interrogans is considered as the leading causative agent of leptospirosis worldwide and it is the most studied species. However, the genomic features and phylogeography of other Leptospira pathogenic species remain to be determined. METHODOLOGY/PRINCIPAL FINDINGS Here we investigated the genome diversity of the main pathogenic Leptospira species based on a collection of 914 genomes from strains isolated around the world. Genome analyses revealed species-specific genome size and GC content, and an open pangenome in the pathogenic species, except for L. mayottensis. Taking advantage of a new set of genomes of L. santarosai strains isolated from patients in Costa Rica, we took a closer look at this species. L. santarosai strains are largely distributed in America, including the Caribbean islands, with over 96% of the available genomes originating from this continent. Phylogenetic analysis showed high genetic diversity within L. santarosai, and the clonal groups identified by cgMLST were strongly associated with geographical areas. Serotype identification based on serogrouping and/or analysis of the O-antigen biosynthesis gene loci further confirmed the great diversity of strains within the species. CONCLUSIONS/SIGNIFICANCE In conclusion, we report a comprehensive genome analysis of pathogenic Leptospira species with a focus on L. santarosai. Our study sheds new light onto the genomic diversity, evolutionary history, and epidemiology of leptospirosis in America and globally. Our findings also expand our knowledge of the genes driving O-antigen diversity. In addition, our work provides a framework for understanding the virulence and spread of L. santarosai and for improving its surveillance in both humans and animals.
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Affiliation(s)
- Diana Chinchilla
- Centro Nacional de Referencia de Bacteriología, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), La Unión, Cartago, Costa Rica
| | - Cecilia Nieves
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, Québec, Canada
| | - Ricardo Gutiérrez
- Centro Nacional de Referencia de Bacteriología, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), La Unión, Cartago, Costa Rica
| | - Vallier Sordoillet
- Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
| | - Frédéric J. Veyrier
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, Québec, Canada
| | - Mathieu Picardeau
- Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
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Novel MLST sequence types of pathogenic Leptospira spp.: Opening the black box of animal leptospirosis in Brazil. Acta Trop 2019; 196:135-141. [PMID: 31121146 DOI: 10.1016/j.actatropica.2019.05.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 01/11/2023]
Abstract
In the current context of the emergence of certain infectious diseases and discussion of the One Health concept for many of these, the study of leptospirosis - both in domestic and wild hosts - cannot be neglected. The study of animal leptospirosis has evolved in recent years. It has been demonstrated that the human-animal-environment interface is more important than previously thought. In the present study, 35 strains of five pathogenic Leptospira species were isolated from different animal species in Brazil and characterized by rrs, secY, and Multilocus Sequence Typing (MLST) sequencing. Phylogenetic inferences were performed and the molecular diversity of the populations (intra- and inter-population levels) was evaluated. Among the five studied species, 18 different sequence types (STs) were found (22 new alleles and 11 new STs). eBURST analysis revealed two clonal complexes (CCs) and seven singletons. A high genetic diversity was demonstrated (H = 0.954 ± 0.017), mainly for the L. santarosai population (H = 0.942 ± 0.034, n = 20). The same strain was identified in different host species, as well as strains with zoonotic potential circulating in the country. Although the difficulty of culturing Leptospira strains is well known, the high variability of the strains found in Brazil highlights the importance of animals in maintaining the biological cycle of the bacterium in nature. Moreover, the selection of autochthonous strains for the development of vaccines becomes a challenge.
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Swiercz A, Frohmberg W, Kierzynka M, Wojciechowski P, Zurkowski P, Badura J, Laskowski A, Kasprzak M, Blazewicz J. GRASShopPER-An algorithm for de novo assembly based on GPU alignments. PLoS One 2018; 13:e0202355. [PMID: 30114279 PMCID: PMC6095601 DOI: 10.1371/journal.pone.0202355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/01/2018] [Indexed: 12/14/2022] Open
Abstract
Next generation sequencers produce billions of short DNA sequences in a massively parallel manner, which causes a great computational challenge in accurately reconstructing a genome sequence de novo using these short sequences. Here, we propose the GRASShopPER assembler, which follows an approach of overlap-layout-consensus. It uses an efficient GPU implementation for the sequence alignment during the graph construction stage and a greedy hyper-heuristic algorithm at the fork detection stage. A two-part fork detection method allows us to identify repeated fragments of a genome and to reconstruct them without misassemblies. The assemblies of data sets of bacteria Candidatus Microthrix, nematode Caenorhabditis elegans, and human chromosome 14 were evaluated with the golden standard tool QUAST. In comparison with other assemblers, GRASShopPER provided contigs that covered the largest part of the genomes and, at the same time, kept good values of other metrics, e.g., NG50 and misassembly rate.
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Affiliation(s)
- Aleksandra Swiercz
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
- * E-mail:
| | - Wojciech Frohmberg
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
| | - Michal Kierzynka
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
- Poznań Supercomputing and Networking Center, Poznań, Poland
| | - Pawel Wojciechowski
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
| | - Piotr Zurkowski
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
| | - Jan Badura
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
| | - Artur Laskowski
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
| | - Marta Kasprzak
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
| | - Jacek Blazewicz
- Institute of Computing Science, Poznań University of Technology, Poznań, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- European Centre for Bioinformatics and Genomics, Poznań, Poland
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Grassmann AA, Souza JD, McBride AJA. A Universal Vaccine against Leptospirosis: Are We Going in the Right Direction? Front Immunol 2017; 8:256. [PMID: 28337203 PMCID: PMC5343615 DOI: 10.3389/fimmu.2017.00256] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/21/2017] [Indexed: 12/22/2022] Open
Abstract
Leptospirosis is the most widespread zoonosis in the world and a neglected tropical disease estimated to cause severe infection in more than one million people worldwide every year that can be combated by effective immunization. However, no significant progress has been made on the leptospirosis vaccine since the advent of bacterins over 100 years. Although protective against lethal infection, particularly in animals, bacterin-induced immunity is considered short term, serovar restricted, and the vaccine can cause serious side effects. The urgent need for a new vaccine has motivated several research groups to evaluate the protective immune response induced by recombinant vaccines. Significant protection has been reported with several promising outer membrane proteins, including LipL32 and the leptospiral immunoglobulin-like proteins. However, efficacy was variable and failed to induce a cross-protective response or sterile immunity among vaccinated animals. As hundreds of draft genomes of all known Leptospira species are now available, this should aid novel target discovery through reverse vaccinology (RV) and pangenomic studies. The identification of surface-exposed vaccine candidates that are highly conserved among infectious Leptospira spp. is a requirement for the development of a cross-protective universal vaccine. However, the lack of immune correlates is a major drawback to the application of RV to Leptospira genomes. In addition, as the protective immune response against leptospirosis is not fully understood, the rational use of adjuvants tends to be a process of trial and error. In this perspective, we discuss current advances, the pitfalls, and possible solutions for the development of a universal leptospirosis vaccine.
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Affiliation(s)
- André Alex Grassmann
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas , Pelotas , Brazil
| | - Jéssica Dias Souza
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas , Pelotas , Brazil
| | - Alan John Alexander McBride
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas, Pelotas, Brazil; Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Ministry of Health, Salvador, Brazil
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Kremer FS, Eslabão MR, Jorge S, Oliveira NR, Labonde J, Santos MNP, Monte LG, Grassmann AA, Cunha CEP, Forster KM, Moreno LZ, Moreno AM, Campos VF, McBride AJA, Pinto LS, Dellagostin OA. Draft genome of the Leptospira interrogans strains, Acegua, RCA, Prea, and Capivara, obtained from wildlife maintenance hosts and infected domestic animals. Mem Inst Oswaldo Cruz 2016; 111:280-3. [PMID: 27074260 PMCID: PMC4830120 DOI: 10.1590/0074-02760160010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/03/2016] [Indexed: 01/22/2023] Open
Abstract
In the present paper, we announce new draft genomes of four Leptospira interrogans strains named Acegua, RCA, Prea, and Capivara. These strains were isolated in the state of Rio Grande do Sul, Brazil, from cattle, dog, Brazilian guinea pig, and capybara, respectively.
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Affiliation(s)
- Frederico S Kremer
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - Marcus R Eslabão
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - Sérgio Jorge
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - Natasha R Oliveira
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - Julia Labonde
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - Monize N P Santos
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - Leonardo G Monte
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - André A Grassmann
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - Carlos E P Cunha
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - Karine M Forster
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | | | | | - Vinicius F Campos
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - Alan J A McBride
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - Luciano S Pinto
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
| | - Odir A Dellagostin
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brasil
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