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Giraud-Gatineau A, Nieves C, Harrison LB, Benaroudj N, Veyrier FJ, Picardeau M. Evolutionary insights into the emergence of virulent Leptospira spirochetes. PLoS Pathog 2024; 20:e1012161. [PMID: 39018329 DOI: 10.1371/journal.ppat.1012161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/29/2024] [Accepted: 06/24/2024] [Indexed: 07/19/2024] Open
Abstract
Pathogenic Leptospira are spirochete bacteria which cause leptospirosis, a re-emerging zoonotic disease of global importance. Here, we use a recently described lineage of environmental-adapted leptospires, which are evolutionarily the closest relatives of the highly virulent Leptospira species, to explore the key phenotypic traits and genetic determinants of Leptospira virulence. Through a comprehensive approach integrating phylogenomic comparisons with in vitro and in vivo phenotyping studies, we show that the evolution towards pathogenicity is associated with both a decrease of the ability to survive in the environment and the acquisition of strategies that enable successful host colonization. This includes the evasion of the mammalian complement system and the adaptations to avoid activation of the innate immune cells by the highly-virulent Leptospira species (also called P1+ species), unlike other species belonging to the phylogenetically related P1- and P2 groups, as well as saprophytes. Moreover, our analysis reveals specific genetic determinants that have undergone positive selection during the course of evolution in Leptospira, contributing directly to virulence and host adaptation as demonstrated by gain-of-function and knock-down studies. Taken together, our findings define a new vision on Leptospira pathogenicity, identifying virulence attributes associated with clinically relevant species, and provide insights into the evolution and emergence of these life-threatening pathogens.
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Affiliation(s)
| | - Cecilia Nieves
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, Canada
| | - Luke B Harrison
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, Canada
| | - Nadia Benaroudj
- 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, Canada
| | - Mathieu Picardeau
- Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
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Ca Ferreira L, de Fa Ferreira Filho L, V Cosate MR, Sakamoto T. Genetic structure and diversity of the rfb locus of pathogenic species of the genus Leptospira. Life Sci Alliance 2024; 7:e202302478. [PMID: 38514188 PMCID: PMC10958091 DOI: 10.26508/lsa.202302478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Leptospirosis is caused by pathogenic strains of the genus Leptospira and is considered the most widespread zoonotic bacterial disease. The genus is characterized by the large number of serology variants, which challenges developing effective serotyping methods and vaccines with a broad spectrum. Because knowledge on the genetic basis of the serological diversity among leptospires is still limited, we aimed to explore the genetic structure and patterns of the rfb locus, which is involved in the biosynthesis of lipopolysaccharides, the major surface antigen that defines the serovar in leptospires. Here, we used genomic data of 722 pathogenic samples and compared the gene composition of their rfb locus by hierarchical clustering. Clustering analysis showed that the rfb locus gene composition is species-independent and strongly associated with the serological classification. The samples were grouped into four well-defined classes, which cluster together samples either belonging to the same serogroup or from different serogroups but sharing serological affinity. Our findings can assist in the development of new strategies based on molecular methods, which can lead to better tools for serological identification in this zoonosis.
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Affiliation(s)
- Leonardo Ca Ferreira
- https://ror.org/04wn09761 Bioinformatics Multidisciplinary Environment (BioME), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Luiz de Fa Ferreira Filho
- https://ror.org/04wn09761 Departamento de Engenharia de Computação e Automação (DCA), Centro de Tecnologia (CT), Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Maria Raquel V Cosate
- UMass Chain Medical School, Nonhuman Primates Reagent Resources, Department of Medicine, University of Massachusetts, Worcester, MA, USA
| | - Tetsu Sakamoto
- https://ror.org/04wn09761 Bioinformatics Multidisciplinary Environment (BioME), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte, Natal, Brazil
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Hagedoorn NN, Maze MJ, Carugati M, Cash-Goldwasser S, Allan KJ, Chen K, Cossic B, Demeter E, Gallagher S, German R, Galloway RL, Habuš J, Rubach MP, Shiokawa K, Sulikhan N, Crump JA. Global distribution of Leptospira serovar isolations and detections from animal host species: A systematic review and online database. Trop Med Int Health 2024; 29:161-172. [PMID: 38351504 PMCID: PMC11076152 DOI: 10.1111/tmi.13965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
OBJECTIVES Leptospira, the spirochaete causing leptospirosis, can be classified into >250 antigenically distinct serovars. Although knowledge of the animal host species and geographic distribution of Leptospira serovars is critical to understand the human and animal epidemiology of leptospirosis, current data are fragmented. We aimed to systematically review, the literature on animal host species and geographic distribution of Leptospira serovars to examine associations between serovars with animal host species and regions and to identify geographic regions in need of study. METHODS Nine library databases were searched from inception through 9 March 2023 using keywords including Leptospira, animal, and a list of serovars. We sought reports of detection of Leptospira, from any animal, characterised by cross agglutinin absorption test, monoclonal antibody typing, serum factor analysis, or pulsed-field gel electrophoresis to identify the serovar. RESULTS We included 409 reports, published from 1927 through 2022, yielding data on 154 Leptospira serovars. The reports included data from 66 (26.5%) of 249 countries. Detections were from 144 animal host species including 135 (93.8%) from the class Mammalia, 5 (3.5%) from Amphibia, 3 (2.1%) from Reptilia, and 1 (0.7%) from Arachnida. Across the animal host species, Leptospira serovars that were detected in the largest number of animal species included Grippotyphosa (n = 39), Icterohaemorrhagiae (n = 29), Pomona (n = 28), Australis (n = 25), and Ballum (n = 25). Of serovars, 76 were detected in a single animal host species. We created an online database to identify animal host species for each serovar by country. CONCLUSIONS We found that many countries have few or no Leptospira serovars detected from animal host species and that many serovars were detected from a single animal species. Our study highlights the importance of efforts to identify animal host species of leptospirosis, especially in places with a high incidence of human leptospirosis. We provide an updated resource for leptospirosis researchers.
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Affiliation(s)
| | - Michael J. Maze
- Centre for International Health, University of Otago, Dunedin, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Manuela Carugati
- Division of Infectious Diseases, Duke University Medical Center, Durham, United States of America
| | | | - Kathryn J. Allan
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Kevin Chen
- Infectious Diseases Department, Te Whatu Ora Hauora a Toi Bay of Plenty
| | - Brieuc Cossic
- College of Veterinary Medicine, Ithaca, NY, United States of America
| | - Elena Demeter
- College of Veterinary Medicine, Ithaca, NY, United States of America
| | - Sarah Gallagher
- Health Sciences Library, University of Otago, Dunedin, New Zealand
| | - Richard German
- Health Sciences Library, University of Otago, Dunedin, New Zealand
| | - Renee L. Galloway
- Bacterial Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Josipa Habuš
- Faculty of Veterinary Medicine, University of Zagreb
| | - Matthew P. Rubach
- Division of Infectious Diseases, Duke University Medical Center, Durham, United States of America
- Duke Global Health Institute, Duke University, Durham, NC, United States of America
- Kilimanjaro Christian Medical University College, Tumaini University, Moshi, Tanzania
| | - Kanae Shiokawa
- School of Veterinary Medicine, Ross University, St Kitts
| | - Nadezhda Sulikhan
- Federal Scientific Center of East Asia Terrestrial Biodiversity, FEB Russian Academy of Sciences, Vladivostok, Russia
| | - John A. Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand
- Division of Infectious Diseases, Duke University Medical Center, Durham, United States of America
- Duke Global Health Institute, Duke University, Durham, NC, United States of America
- Kilimanjaro Christian Medical University College, Tumaini University, Moshi, Tanzania
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Senavirathna I, Jayasundara D, Warnasekara J, Kappagoda C, Agampodi S. Levels of Cytokines in Leptospirosis Patients with Different Serovars and rfb Locus. J Interferon Cytokine Res 2024; 44:80-93. [PMID: 38377491 PMCID: PMC10880283 DOI: 10.1089/jir.2023.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 11/21/2023] [Indexed: 02/22/2024] Open
Abstract
Leptospirosis has a wide spectrum of clinical manifestations ranging from mild to severe disease. The cytokine response is considered one of the key drivers for this varying manifestation. The different cytokine response observed in patients with leptospirosis could be due to the variation of infecting serovars. Since the rfb locus codes for the lipopolysaccharide synthesis of the bacterial cell wall, which also determines the serovar, this locus may play a role in driving a specific cytokine response in the host. We investigated 12 commonly used cytokine profiles in serum samples of culture, microscopic agglutination test (MAT), or polymerase chain reaction (PCR)-positive patients with leptospirosis. The sequences of the rfb locus in culture-positive samples were generated from whole genome sequencing and serovar status was drawn from original data published. Isolated cultures were subjected to whole genome sequencing using the PacBio RS II system, and the resulting data were used to determine the species. The recovered genomic data were annotated with the Rapid Annotation using Subsystem Technology (RAST) subsystem, and the rfb locus was extracted. The cytokine analysis was carried out using the Qiagen human ELISA kit. Eighteen samples were found to be positive by culture, while the other 7 samples were positive by PCR or MAT. Infections from Leptospira interrogans serovar Autumnalis (5), Pyrogens (3), Icterohaemorrhagiae (1) Leptospira borgpetersenii (all 7 samples clustered in same clonal group with serovar status not determined), Leptospira weilii (1 with serovar status not determined), and Leptospira kirschneri serovar Grippotyphosa (1) were included in the analysis. Three patients [infected with Leptospira interrogansserovar Autumnalis (2) and Pyrogens (1)] and 2 MAT-positive patients (highest titer against serovar Bratislava of L.interrognas) were reported to have severe clinical manifestations, while the rest had mild to moderate symptoms. Although the serum cytokine concentration of patients with severe clinical manifestation was comparatively higher, a statistically significant difference was observed only for interleukin (IL)-1β (P < 0.05). IL-10/tumor necrosis factor-alpha (TNF-α) ratio was high in patients with severe complications. In general, patients infected with L. interrogans showed higher concentration of cytokines compared to L. borgpetersenii.
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Affiliation(s)
- Indika Senavirathna
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
- Department of Biochemistry, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Dinesha Jayasundara
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
- Department of Microbiology, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Janith Warnasekara
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
- Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Chamila Kappagoda
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Suneth Agampodi
- International Vaccine Institute, Seoul, Republic of Korea
- Department of Internal Medicine, School of Medicine, Yale University, New Haven, California, USA
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Senavirathna I, Jayasundara D, Warnasekara J, Matthias MA, Vinetz JM, Agampodi S. Complete genome sequences of twelve strains of Leptospira interrogans isolated from humans in Sri Lanka. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105462. [PMID: 37301334 DOI: 10.1016/j.meegid.2023.105462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/31/2023] [Accepted: 06/04/2023] [Indexed: 06/12/2023]
Abstract
Leptospirosis, a major zoonotic disease caused by pathogenic Leptospira spp. is recognized globally as an emerging zoonotic disease. Whole-genome sequencing reveals hidden messages about Leptospira's pathogenesis. We used Single Molecule Real-Time (SMRT) sequencing to obtain complete genome sequences of twelve L. interrogans isolates from febrile patients from Sri Lanka for a comparative whole genome sequencing study. The sequence data generated 12 genomes with a coverage greater than X600 with sizes ranging from 4.62 Mb to 5.16 Mb, and a G + C content ranging from 35.00% to 35.42%. The total number of coding sequences predicted by the NCBI (National Center for Biotechnology Information) genome assembly platform ranged from 3845 to 4621 for the twelve strains. Leptospira serogroup with similar-sized LPS biosynthetic loci that belonged to the same clade had a close relationship in the phylogenetic analysis. Nonetheless, variations in the genes encoding sugar biosynthesis were found in the serovar determinant region (rfb locus). Type I and Type III CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems were found in all of the strains. Genome BLAST Distance Phylogeny of these sequences allowed for detailed genomic strain typing. These findings may help us better understand the pathogenesis, develop a tools for early diagnosis, comparative genomic analysis and evolution of Leptospira.
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Affiliation(s)
- Indika Senavirathna
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Sri Lanka; Department of Biochemistry, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Sri Lanka.
| | - Dinesha Jayasundara
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Sri Lanka; Department of Microbiology, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka
| | - Janith Warnasekara
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Sri Lanka; Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Sri Lanka
| | - Michael A Matthias
- Section of Infectious Disease, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Joseph M Vinetz
- Section of Infectious Disease, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Suneth Agampodi
- Section of Infectious Disease, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA; International Vaccine Institute, Seoul, Republic of Korea
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Pětrošová H, Mikhael A, Culos S, Giraud-Gatineau A, Gomez AM, Sherman ME, Ernst RK, Cameron CE, Picardeau M, Goodlett DR. Lipid A structural diversity among members of the genus Leptospira. Front Microbiol 2023; 14:1181034. [PMID: 37303810 PMCID: PMC10248169 DOI: 10.3389/fmicb.2023.1181034] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Lipid A is the hydrophobic component of bacterial lipopolysaccharide and an activator of the host immune system. Bacteria modify their lipid A structure to adapt to the surrounding environment and, in some cases, to evade recognition by host immune cells. In this study, lipid A structural diversity within the Leptospira genus was explored. The individual Leptospira species have dramatically different pathogenic potential that ranges from non-infectious to life-threatening disease (leptospirosis). Ten distinct lipid A profiles, denoted L1-L10, were discovered across 31 Leptospira reference species, laying a foundation for lipid A-based molecular typing. Tandem MS analysis revealed structural features of Leptospira membrane lipids that might alter recognition of its lipid A by the host innate immune receptors. Results of this study will aid development of strategies to improve diagnosis and surveillance of leptospirosis, as well as guide functional studies on Leptospira lipid A activity.
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Affiliation(s)
- Helena Pětrošová
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- University of Victoria Genome British Columbia Proteomics Center, University of Victoria, Victoria, BC, Canada
| | - Abanoub Mikhael
- University of Victoria Genome British Columbia Proteomics Center, University of Victoria, Victoria, BC, Canada
| | - Sophie Culos
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | | | - Alloysius M. Gomez
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Matthew E. Sherman
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, United States
| | - Robert K. Ernst
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, United States
| | - Caroline E. Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, United States
| | - Mathieu Picardeau
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Biology of Spirochetes Unit, Paris, France
| | - David R. Goodlett
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- University of Victoria Genome British Columbia Proteomics Center, University of Victoria, Victoria, BC, Canada
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