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Caraballo L, Rangel Y, Reyna-Bello A, Muñoz M, Figueroa-Espinosa R, Sanz-Rodriquez CE, Guerrero E, Loureiro CL, Liu Q, Takiff HE. Outbreak of Intermediate Species Leptospira venezuelensis Spread by Rodents to Cows and Humans in L. interrogans-Endemic Region, Venezuela. Emerg Infect Dis 2024; 30:1514-1522. [PMID: 39043385 PMCID: PMC11286060 DOI: 10.3201/eid3008.231562] [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] [Indexed: 07/25/2024] Open
Abstract
Leptospirosis is a common but underdiagnosed zoonosis. We conducted a 1-year prospective study in La Guaira State, Venezuela, analyzing 71 hospitalized patients who had possible leptospirosis and sampling local rodents and dairy cows. Leptospira rrs gene PCR test results were positive in blood or urine samples from 37/71 patients. Leptospira spp. were isolated from cultured blood or urine samples of 36/71 patients; 29 had L. interrogans, 3 L. noguchii, and 4 L. venezuelensis. Conjunctival suffusion was the most distinguishing clinical sign, many patients had liver involvement, and 8/30 patients with L. interrogans infections died. The Leptospira spp. found in humans were also isolated from local rodents; L. interrogans and L. venezuelensis were isolated from cows on a nearby, rodent-infested farm. Phylogenetic clustering of L. venezuelensis isolates suggested a recently expanded outbreak strain spread by rodents. Increased awareness of leptospirosis prevalence and rapid diagnostic tests are needed to improve patient outcomes.
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2
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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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3
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587687. [PMID: 38617210 PMCID: PMC11014503 DOI: 10.1101/2024.04.02.587687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
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 human complement system and the adaptations to avoid activation of the innate immune cells. 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, QC, Canada
| | - Luke B. Harrison
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, 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, QC, Canada
| | - Mathieu Picardeau
- Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
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4
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Hsu SH, Wu CT, Sun YJ, Chang MY, Li C, Ko YC, Chou LF, Yang CW. Crystal structure of Leptospira LSS_01692 reveals a dimeric structure and induces inflammatory responses through Toll-like receptor 2-dependent NF-κB and MAPK signal transduction pathways. FEBS J 2023; 290:4513-4532. [PMID: 37243454 DOI: 10.1111/febs.16874] [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: 02/23/2023] [Revised: 05/12/2023] [Accepted: 05/25/2023] [Indexed: 05/28/2023]
Abstract
Leptospirosis is a commonly overlooked zoonotic disease that occurs in tropical and subtropical regions. Recent studies have divided the Leptospira spp. into three groups based on virulence, including pathogenic, intermediate, and saprophytic species. Pathogenic species express a protein family with leucine-rich repeat (LRR) domains, which are less expressed or absent in nonpathogenic species, highlighting the importance of this protein family in leptospirosis. However, the role of LRR domain proteins in the pathogenesis of leptospirosis is still unknown and requires further investigation. In this study, the 3D structure of LSS_01692 (rLRR38) was obtained using X-ray crystallography at a resolution of 3.2 Å. The results showed that rLRR38 forms a typical horseshoe structure with 11 α-helices and 11 β-sheets and an antiparallel dimeric structure. The interactions of rLRR38 with extracellular matrix and cell surface receptors were evaluated using ELISA and single-molecule atomic force microscopy. The results showed that rLRR38 interacted with fibronectin, collagen IV, and Toll-like receptor 2 (TLR2). Incubating HK2 cells with rLRR38 induced two downstream inflammation responses (IL-6 and MCP-1) in the TLR2 signal transduction pathway. The TLR2-TLR1 complex showed the most significant upregulation effects under rLRR38 treatment. Inhibitors also significantly inhibited nuclear factor κB and mitogen-activated protein kinases signals transduction under rLRR38 stimulation. In conclusion, rLRR38 was determined to be a novel LRR domain protein in 3D structure and demonstrated as a TLR2-binding protein that induces inflammatory responses. These structural and functional studies provide a deeper understanding of the pathogenesis of leptospirosis.
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Affiliation(s)
- Shen-Hsing Hsu
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Che-Ting Wu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, Taiwan
| | - Yuh-Ju Sun
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, Taiwan
| | - Ming-Yang Chang
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chien Li
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yi-Ching Ko
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Li-Fang Chou
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chih-Wei Yang
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Nephrology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
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5
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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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Munson E, Lawhon SD, Burbick CR, Zapp A, Villaflor M, Thelen E. An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0028122. [PMID: 36533907 PMCID: PMC9945509 DOI: 10.1128/jcm.00281-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.
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Affiliation(s)
- Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Claire R. Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Amanda Zapp
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Maia Villaflor
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Elizabeth Thelen
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
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7
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New Genetic Variants of Leptospira spp Characterized by MLST from Peruvian Isolates. J Trop Med 2022; 2022:4184326. [PMID: 36249734 PMCID: PMC9553527 DOI: 10.1155/2022/4184326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/26/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
Leptospirosis is a zoonotic disease caused by the genus Leptospira, presenting complex and dynamic epidemiology. To determine the genetic variability and its phylogenetic relationship of Leptospira spp isolates from three sources in Iquitos (Peruvian Amazon) from 2002 to 2013, seven MLST genes were analyzed to obtain the Sequence Type (ST) and these sequences were concatenated for phylogenetic analysis. The genetic relationship between STs was determined with the goeBURST algorithm and genetic diversity was determined using DnaSP. Of 51 isolates, 48 were pathogenic belonging to five different species: Leptospira interrogans Nascimento 2004, Leptospira santarosai Feil 2004, Leptospira noguchii Haake 2021, Leptospira borgpetersenii Levett 2021, and Leptospira kirschneri Levett 2021. Of 20 STs identified, 60% corresponded to new genotypes circulating only in Peru. The genotypes ST17, ST37, and ST301 were recorded in rodents and humans. A high intraspecific genetic diversity was demonstrated in L. noguchi. The goeBURST analysis revealed three clonal complexes (CCs) and 16 singletons. The STs were found to show high genetic variability and phylogenetic and goeBURST analysis determined that the genotypes found did not form specific groups according to the source of infection or origin, which confirms the zoonotic potential of these STs in an area highly endemic for leptospirosis.
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8
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Role of Diagnostics in Epidemiology, Management, Surveillance, and Control of Leptospirosis. Pathogens 2022; 11:pathogens11040395. [PMID: 35456070 PMCID: PMC9032781 DOI: 10.3390/pathogens11040395] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 12/12/2022] Open
Abstract
A One Health approach to the epidemiology, management, surveillance, and control of leptospirosis relies on accessible and accurate diagnostics that can be applied to humans and companion animals and livestock. Diagnosis should be multifaceted and take into account exposure risk, clinical presentation, and multiple direct and/or indirect diagnostic approaches. Methods of direct detection of Leptospira spp. include culture, histopathology and immunostaining of tissues or clinical specimens, and nucleic acid amplification tests (NAATs). Indirect serologic methods to detect leptospiral antibodies include the microscopic agglutination test (MAT), the enzyme-linked immunosorbent assay (ELISA), and lateral flow methods. Rapid diagnostics that can be applied at the point-of-care; NAAT and lateral flow serologic tests are essential for management of acute infection and control of outbreaks. Culture is essential to an understanding of regional knowledge of circulating strains, and we discuss recent improvements in methods for cultivation, genomic sequencing, and serotyping. We review the limitations of NAATs, MAT, and other diagnostic approaches in the context of our expanding understanding of the diversity of pathogenic Leptospira spp. Novel approaches are needed, such as loop mediated isothermal amplification (LAMP) and clustered regularly interspaced short palindromic repeats (CRISPR)-based approaches to leptospiral nucleic acid detection.
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9
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Korba AA, Lounici H, Kainiu M, Vincent AT, Mariet JF, Veyrier FJ, Goarant C, Picardeau M. Leptospira ainlahdjerensis sp. nov., Leptospira ainazelensis sp. nov., Leptospira abararensis sp. nov. and Leptospira chreensis sp. nov., four new species isolated from water sources in Algeria. Int J Syst Evol Microbiol 2021; 71. [PMID: 34914572 DOI: 10.1099/ijsem.0.005148] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Leptospira strains were isolated from freshwater sampled at four sites in Algeria and characterized by whole-genome sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The cells were spiral-shaped and motile. Phylogenetic and MALDI-TOF MS analyses showed that the strains can be clearly distinguished from the other described species in the genus Leptospira, therefore representing two novel species of the pathogen subclade P1 and two novel species of the saprophyte subclade S1. The names Leptospira ainlahdjerensis sp. nov. (type strain 201903070T=KIT0297T=CIP111912T), Leptospira ainazelensis sp. nov. (201903071T=KIT0298T=CIP111913T), Leptospira abararensis sp. nov. (201903074T=KIT0299T=CIP111914T) and Leptospira chreensis (201903075T=KIT0300T=CIP111915T) are proposed.
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Affiliation(s)
| | | | - Malia Kainiu
- Institut Pasteur de Nouvelle-Calédonie, Leptospirosis Research and Expertise Unit, Nouméa, New Caledonia
| | - Antony T Vincent
- INRS-Centre Armand-Frappier Santé-Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec, Canada
| | | | - Fréderic J Veyrier
- INRS-Centre Armand-Frappier Santé-Biotechnologie, Bacterial Symbionts Evolution, Laval, Quebec, Canada
| | - Cyrille Goarant
- Institut Pasteur de Nouvelle-Calédonie, Leptospirosis Research and Expertise Unit, Nouméa, New Caledonia
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10
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Abstract
The diagnosis of leptospirosis depends on specific laboratory tests because nonspecific and diverse clinical manifestations make clinical diagnosis difficult and it is easily confused with other infectious diseases in the tropics. Suitable laboratory diagnostic tests vary depending on the stage of the disease, requiring the combination of diagnostic tests using appropriate specimens at each disease stage.
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Affiliation(s)
- Nobuo Koizumi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan.
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11
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Munson E, Carroll KC. Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019. J Clin Microbiol 2021; 59:e01309-20. [PMID: 32967902 PMCID: PMC8111135 DOI: 10.1128/jcm.01309-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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12
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Pérez LJ, Lanka S, DeShambo VJ, Fredrickson RL, Maddox CW. A Validated Multiplex Real-Time PCR Assay for the Diagnosis of Infectious Leptospira spp.: A Novel Assay for the Detection and Differentiation of Strains From Both Pathogenic Groups I and II. Front Microbiol 2020; 11:457. [PMID: 32265882 PMCID: PMC7100377 DOI: 10.3389/fmicb.2020.00457] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/04/2020] [Indexed: 12/12/2022] Open
Abstract
Leptospirosis is recognized as the most globally widespread reemerging zoonosis and represents a serious threat for both human and animal health. Indeed, leptospirosis is linked to more than 60,000 human deaths per year and to incalculable economic burden as consequence of medical treatment costs and livestock loss. The increasing number of reports from species of pathogenic Leptospira spp. group II causing disease in both humans and animals constitutes an additional concern to the complex epidemiology of this zoonotic agent. Diagnostic methods based on qPCR have improved the diagnosis of Leptospira spp. in terms of cost, time, and reliability, but most of the validated assays fail to detect species from the pathogenic group II. Hence, the current study was aimed to develop and validate a novel multiplex qPCR to enable the specific and selective detection of the whole group of infectious Leptospira spp., including both pathogenic groups I and II and moreover, selectively discriminate between them. To fit the "fitness of purpose" for the specific detection of infectious Leptospira spp. and further discrimination between both pathogenic groups three target regions on the 16S RNA gene were selected. These targets facilitated a broad and selective spectrum for the detection of all infectious Leptospira spp. with the exclusion of all saprophytic groups and the novel clade of environmental Leptospira spp. The analytical sensitivity (ASe) showed by the new assay also enables a wide window of detection for the agent at different stages of infection since the assay was able to efficiently detect at 95% of confidence ∼5 leptospires/reaction. From the evaluation of the analytical specificity (ASp) by in silico and in vitro approaches, it was congruently revealed that the primers and probes selected only recognized the specific targets for which the assay was intended. Bayesian latent class analysis of performance of the new assay on 684 clinical samples showed values of diagnostic sensitivity of 99.8% and diagnostic specificity of 100%. Thus, from the evaluation of the analytical and diagnostic parameters, the new multiplex qPCR assay is a reliable method for the diagnosis of Leptospira spp.
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Affiliation(s)
- Lester J. Pérez
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana–Champaign, Urbana, IL, United States
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Saraswathi Lanka
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Vanessa J. DeShambo
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Richard L. Fredrickson
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Carol W. Maddox
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana–Champaign, Urbana, IL, United States
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13
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Caimi K, Ruybal P. Leptospira spp., a genus in the stage of diversity and genomic data expansion. INFECTION GENETICS AND EVOLUTION 2020; 81:104241. [PMID: 32061688 DOI: 10.1016/j.meegid.2020.104241] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/09/2020] [Accepted: 02/10/2020] [Indexed: 12/14/2022]
Abstract
Leptospirosis is a widespread global zoonotic bacterial disease with a noteworthy human-animal-ecosystem interface. The disease presents different clinical manifestations and a high mortality and morbidity rates in humans and animals throughout the world. Characterization and correct classification of Leptospira isolates is essential for a better understanding the epidemiological properties of the disease. In the last ten years, molecular typing tools have been developed and applied to this field. These methods together with the availability of hundreds of new whole genome sequences that belong to known and new described species are shaping the understanding and structure of the entire genus.
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Affiliation(s)
- K Caimi
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - P Ruybal
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Paraguay 2155 Piso: 12, CABA 1121, Argentina
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14
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Abstract
Leptospira spp. are morphologically and phylogenetically unique bacteria that are ubiquitous in the environment. Pathogenic species are the agents of leptospirosis, an emerging zoonotic disease transmitted to both human and animals from the environment contaminated with the urine of reservoir animals. The taxonomy of Leptospira has recently undergone extensive revisions with the use of whole-genome sequences, thus expanding considerably the number of species.
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15
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Vieira AS, Di Azevedo MIN, D'Andrea PS, do Val Vilela R, Lilenbaum W. Neotropical wild rodents Akodon and Oligoryzomys (Cricetidae: Sigmodontinae) as important carriers of pathogenic renal Leptospira in the Atlantic forest, in Brazil. Res Vet Sci 2019; 124:280-283. [PMID: 31004919 DOI: 10.1016/j.rvsc.2019.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 03/20/2019] [Accepted: 04/07/2019] [Indexed: 01/08/2023]
Abstract
Leptospirosis is an important worldwide zoonosis, caused by a bacterium of the genus Leptospira. For a better understanding of the disease, it is relevant the application of the one health concept. The Atlantic Forest is considered a biodiversity hotspot, with a great endemism of species and despite its importance and proximity to urban areas, the potential role of its fauna as carriers of infectious agents is still poorly understood. Although it is well-known that rats and mice are key reservoirs of leptospires, particularly Rattus norvegicus, wild rodents have also been revealed as reservoirs of leptospiral strains. Thus, the purpose of this study was to investigate the role of the sigmodontine rodents from genera Akodon and Oligoryzomys as pathogenic Leptospira carriers in the Atlantic Forest. We studied 52 Akodon spp. and 15 Oligoryzomys spp. from three areas. Overall 30% were PCR-positive for pathogenic Leptospira, 27% (14/52) Akodon spp. and 40% (6/15) Oligoryzomys spp. DNA sequencing of LipL32 gene confirmed nine species as pathogenic Leptospira. This remarkable incidence of leptospiral carriage within wild genera emphasizes the role of these rodents as carriers of leptospires throughout in this environment.
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Affiliation(s)
- Anahi S Vieira
- Fluminense Federal University, Laboratory of Veterinary Bacteriology, Biomedical Institute, 101 Prof. Hernani Mello Street, Niterói, Rio de Janeiro, Brazil
| | - Maria Isabel N Di Azevedo
- Fluminense Federal University, Laboratory of Veterinary Bacteriology, Biomedical Institute, 101 Prof. Hernani Mello Street, Niterói, Rio de Janeiro, Brazil
| | - Paulo Sérgio D'Andrea
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil 4365, Rio de Janeiro, RJ 21040-360, Brazil
| | - Roberto do Val Vilela
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil 4365, Rio de Janeiro, RJ 21040-360, Brazil
| | - Walter Lilenbaum
- Fluminense Federal University, Laboratory of Veterinary Bacteriology, Biomedical Institute, 101 Prof. Hernani Mello Street, Niterói, Rio de Janeiro, Brazil.
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16
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Guglielmini J, Bourhy P, Schiettekatte O, Zinini F, Brisse S, Picardeau M. Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PLoS Negl Trop Dis 2019; 13:e0007374. [PMID: 31026256 PMCID: PMC6513109 DOI: 10.1371/journal.pntd.0007374] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/13/2019] [Accepted: 04/09/2019] [Indexed: 12/15/2022] Open
Abstract
Leptospira is a highly heterogeneous bacterial genus that can be divided into three evolutionary lineages and >300 serovars. The causative agents of leptospirosis are responsible of an emerging zoonotic disease worldwide. To advance our understanding of the biodiversity of Leptospira strains at the global level, we evaluated the performance of whole-genome sequencing (WGS) as a genus-wide strain classification and genotyping tool. Herein we propose a set of 545 highly conserved loci as a core genome MLST (cgMLST) genotyping scheme applicable to the entire Leptospira genus, including non-pathogenic species. Evaluation of cgMLST genotyping was undertaken with 509 genomes, including 327 newly sequenced genomes, from diverse species, sources and geographical locations. Phylogenetic analysis showed that cgMLST defines species, clades, subclades, clonal groups and cgMLST sequence types (cgST), with high precision and robustness to missing data. Novel Leptospira species, including a novel subclade named S2 (saprophytes 2), were identified. We defined clonal groups (CG) optimally using a single-linkage clustering threshold of 40 allelic mismatches. While some CGs such as L. interrogans CG6 (serogroup Icterohaemorrhagiae) are globally distributed, others are geographically restricted. cgMLST was congruent with classical MLST schemes, but had greatly improved resolution and broader applicability. Single nucleotide polymorphisms within single cgST groups was limited to <30 SNPs, underlining a potential role for cgMLST in epidemiological surveillance. Finally, cgMLST allowed identification of serogroups and closely related serovars. In conclusion, the proposed cgMLST strategy allows high-resolution genotyping of Leptospira isolates across the phylogenetic breadth of the genus. The unified genomic taxonomy of Leptospira strains, available publicly at http://bigsdb.pasteur.fr/leptospira, will facilitate global harmonization of Leptospira genotyping, strain emergence follow-up and novel collaborative studies of the epidemiology and evolution of this emerging pathogen.
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Affiliation(s)
- Julien Guglielmini
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France
| | - Pascale Bourhy
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
| | - Olivier Schiettekatte
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
- Université Paris Diderot, Ecole Doctorale BioSPC, Paris, France
| | - Farida Zinini
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Mathieu Picardeau
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
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17
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Masuzawa T, Saito M, Nakao R, Nikaido Y, Matsumoto M, Ogawa M, Yokoyama M, Hidaka Y, Tomita J, Sakakibara K, Suzuki K, Yasuda S, Sato H, Yamaguchi M, Yoshida SI, Koizumi N, Kawamura Y. Molecular and phenotypic characterization of Leptospira johnsonii sp. nov., Leptospira ellinghausenii sp. nov. and Leptospira ryugenii sp. nov. isolated from soil and water in Japan. Microbiol Immunol 2019; 63:89-99. [PMID: 30817029 DOI: 10.1111/1348-0421.12671] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/07/2019] [Accepted: 02/20/2019] [Indexed: 11/27/2022]
Abstract
In a previous study, 50 of 132 soil samples collected throughout Japan were found to be Leptospira-positive. In the present study, three strains identified in the collected specimens, three, E8, E18 and YH101, were found to be divergent from previously described Leptospira species according to 16S ribosomal RNA gene sequence analysis. These three strains have a helical shape similar to that of typical Leptospira and were not re-isolated from experimental mice inoculated with the cultured strains. Upon 16S ribosomal RNA gene sequence analysis, E8 was found to belong to the intermediate Leptospira species clade and E18 and YH101 to belong to the saprophytic Leptospira species clade. Based on analyses of genome-to-genome distances and average nucleotide identity in silico using whole genome sequences and DNA-DNA hybridization in vitro, these isolates were found to be distinct from previously described Leptospira species. Therefore, these three isolates represent novel species of the genus Leptospira for which the names Leptospira johnsonii sp. nov., (type strain E8 T , = JCM 32515 T = CIP111620 T ), Leptospira ellinghausenii sp. nov., (type strain E18 T , = JCM 32516 T = CIP111618 T ) and Leptospira ryugenii sp. nov., (type strain YH101 T , = JCM 32518 T = CIP111617 T ) are proposed.
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Affiliation(s)
- Toshiyuki Masuzawa
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba
| | - Mitsumasa Saito
- Department of Microbiology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka
| | - Ryo Nakao
- Laboratory of Parasitology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido
| | - Yasuhiko Nikaido
- Department of Microbiology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka
| | - Masahiro Matsumoto
- Department of Microbiology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka
| | - Midori Ogawa
- Department of Microbiology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka
| | - Mitsuru Yokoyama
- Shared-Use Research Center, University of Occupational and Environmental Health, Kitakyushu, Fukuoka
| | - Yusuke Hidaka
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka
| | - Junko Tomita
- Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Aichi
| | - Keiko Sakakibara
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba
| | - Kazushi Suzuki
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba
| | - Shima Yasuda
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba
| | - Hiroki Sato
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba
| | - Masaya Yamaguchi
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Chiba Institute of Science (CIS), Choshi, Chiba
| | - Shin-Ichi Yoshida
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka
| | - Nobuo Koizumi
- Department of Bacteriology I, National Institute of Infectious Diseases, Toyama, Tokyo, Japan
| | - Yoshiaki Kawamura
- Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Aichi
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18
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Geographical and temporal distribution of the residual clusters of human leptospirosis in China, 2005-2016. Sci Rep 2018; 8:16650. [PMID: 30413773 PMCID: PMC6226456 DOI: 10.1038/s41598-018-35074-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022] Open
Abstract
Human leptospirosis outbreaks still persistently occur in part of China, indicating that leptospirosis remains an important zoonotic disease in the country. Spatiotemporal pattern of the high-risk leptospirosis cluster and the key characteristics of high-risk areas for leptospirosis across the country are still poorly understood. Using spatial analytical approaches, we analyzed 8,158 human leptospirosis cases notified during 2005-2016 across China to explore the geographical distribution of leptospirosis hotspots and to characterize demographical, ecological and socioeconomic conditions of high-risk counties for leptospirosis in China. During the period studied, leptospirosis incidence was geographically clustered with the highest rate observed in the south of the Province of Yunnan. The degree of spatial clustering decreased over time suggesting changes in local risk factors. However, we detected residual high-risk counties for leptospirosis including counties in the southwest, central, and southeast China. High-risk counties differed from low-risk counties in terms of its demographical, ecological and socioeconomic characteristics. In high-risk clusters, leptospirosis was predominantly observed on younger population, more males and farmers. Additionally, high-risk counties are characterized by larger rural and less developed areas, had less livestock density and crops production, and located at higher elevation with higher level of precipitation compare to low-risk counties. In conclusion, leptospirosis distribution in China appears to be highly clustered to a discrete number of counties highlighting opportunities for elimination; hence, public health interventions should be effectively targeted to high-risk counties identified in this study.
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19
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First Release of the Bacterial Biobank of the Urban Environment (BBUE). Microbiol Resour Announc 2018; 7:MRA01201-18. [PMID: 30533746 PMCID: PMC6256582 DOI: 10.1128/mra.01201-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/02/2018] [Indexed: 12/28/2022] Open
Abstract
Metagenomics is providing a broad overview of bacterial functional diversity; however, culturing and biobanking are still essential for microbiology. Here, we present the Bacterial Biobank of the Urban Environment (BBUE), a sizable culture collection for long-term storage and characterization of the microbiota associated with urban environments relevant for public health. Metagenomics is providing a broad overview of bacterial functional diversity; however, culturing and biobanking are still essential for microbiology. Here, we present the Bacterial Biobank of the Urban Environment (BBUE), a sizable culture collection for long-term storage and characterization of the microbiota associated with urban environments relevant for public health.
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20
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Abstract
Leptospirosis is a worldwide zoonotic disease determined by pathogenic spirochetes of the genus Leptospira. The control of bovine leptospirosis involves several measures including antibiotic treatment of carriers. Despite its importance, few studies regarding antimicrobial susceptibility of strains from bovine origin have been conducted. The aim of this study was to determine the in vitro susceptibility of Leptospira strains obtained from cattle in Rio de Janeiro, Brazil, against the main antibiotics used in bovine veterinary practice. A total of 23 Leptospira spp. strains were investigated for minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs) using broth macrodilution. At the species level, there were not differences in MIC susceptibility except for tetracycline (P < 0.05). Nevertheless, at the serogroup level, differences in MIC were observed among Sejroe strains, mainly for ceftiofur, doxycycline and in MBC for streptomycin (P < 0.05). One strain presented MBC values above maximum plasmatic concentration described for streptomycin and was classified as presenting reduced susceptibility. Efficacy of antimicrobial therapy on bovine leptospirosis could be compromised due to occurrence of infection by Leptospira strains presenting reduced susceptibility.
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21
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Jaeger LH, Pestana CP, Carvalho-Costa FA, Medeiros MA, Lilenbaum W. Characterization of the clonal subpopulation Fiocruz L1-130 of Leptospira interrogans in rats and dogs from Brazil. J Med Microbiol 2018; 67:1361-1367. [DOI: 10.1099/jmm.0.000806] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Lauren Hubert Jaeger
- 1Laboratory of Veterinary Bacteriology, Department of Microbiology and Parasitology, Universidade Federal Fluminense, Niterói, RJ, Brazil
- 2Laboratory of Epidemiology and Molecular Systematics, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | | | - Filipe Anibal Carvalho-Costa
- 2Laboratory of Epidemiology and Molecular Systematics, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | | | - Walter Lilenbaum
- 1Laboratory of Veterinary Bacteriology, Department of Microbiology and Parasitology, Universidade Federal Fluminense, Niterói, RJ, Brazil
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22
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Long-term preservation of Leptospira spp.: challenges and prospects. Appl Microbiol Biotechnol 2018; 102:5427-5435. [PMID: 29736823 DOI: 10.1007/s00253-018-9047-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 10/17/2022]
Abstract
Preservation of leptospiral cultures is tantamount to success in leptospiral diagnostics, research, and development of preventive strategies. Each Leptospira isolate has imperative value not only in disease diagnosis but also in epidemiology, virulence, pathogenesis, and drug development studies. As the number of circulating leptospires is continuously increasing and congruent with the importance to retain their original characteristics and properties, an efficient long-term preservation is critically needed to be well-established. However, the preservation of Leptospira is currently characterized by difficulties and conflicting results mainly due to the biological nature of this organism. Hence, this review seeks to describe the efforts in developing efficient preservation methods, to discover the challenges in preserving this organism and to identify the factors that can contribute to an effective long-term preservation of Leptospira. Through the enlightenment of the previous studies, a potentially effective method has been suggested. The article also attempts to evaluate novel strategies used in other industrial and biotechnological preservation efforts and consider their potential application to the conservation of Leptospira spp.
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23
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Thibeaux R, Girault D, Bierque E, Soupé-Gilbert ME, Rettinger A, Douyère A, Meyer M, Iraola G, Picardeau M, Goarant C. Biodiversity of Environmental Leptospira: Improving Identification and Revisiting the Diagnosis. Front Microbiol 2018; 9:816. [PMID: 29765361 PMCID: PMC5938396 DOI: 10.3389/fmicb.2018.00816] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/10/2018] [Indexed: 01/24/2023] Open
Abstract
Leptospirosis is an important environmental disease and a major threat to human health causing at least 1 million clinical infections annually. There has recently been a growing interest in understanding the environmental lifestyle of Leptospira. However, Leptospira isolation from complex environmental samples is difficult and time-consuming and few tools are available to identify Leptospira isolates at the species level. Here, we propose a polyphasic isolation and identification scheme, which might prove useful to recover and identify environmental isolates and select those to be submitted to whole-genome sequencing. Using this approach, we recently described 12 novel Leptospira species for which we propose names. We also show that MALDI-ToF MS allows rapid and reliable identification and provide an extensive database of Leptospira MALDI-ToF mass spectra, which will be valuable to researchers in the leptospirosis community for species identification. Lastly, we also re-evaluate some of the current techniques for the molecular diagnosis of leptospirosis taking into account the extensive and recently revealed biodiversity of Leptospira in the environment. In conclusion, we describe our method for isolating Leptospira from the environment, confirm the usefulness of mass spectrometry for species identification and propose names for 12 novel species. This also offers the opportunity to refine current molecular diagnostic tools.
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Affiliation(s)
- Roman Thibeaux
- Leptospirosis Research and Expertise Unit, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Noumea, New Caledonia
| | - Dominique Girault
- Leptospirosis Research and Expertise Unit, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Noumea, New Caledonia
| | - Emilie Bierque
- Leptospirosis Research and Expertise Unit, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Noumea, New Caledonia
| | - Marie-Estelle Soupé-Gilbert
- Leptospirosis Research and Expertise Unit, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Noumea, New Caledonia
| | - Anna Rettinger
- Bacteriology and Mycology, Institute for Infectious Diseases and Zoonoses, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Munich, Germany
| | - Anthony Douyère
- Institut des Sciences Exactes et Appliquées, Plateau MET/MEB, Université de la Nouvelle-Calédonie, Noumea, New Caledonia
| | - Michael Meyer
- Institut des Sciences Exactes et Appliquées, Plateau MET/MEB, Université de la Nouvelle-Calédonie, Noumea, New Caledonia
| | - Gregorio Iraola
- Bioinformatics Unit, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Mathieu Picardeau
- Biology of Spirochetes Unit, Institut Pasteur, National Reference Centre and WHO Collaborating Center for Leptospirosis, Paris, France
| | - Cyrille Goarant
- Leptospirosis Research and Expertise Unit, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Noumea, New Caledonia
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24
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Schneider AG, Casanovas-Massana A, Hacker KP, Wunder EA, Begon M, Reis MG, Childs JE, Costa F, Lindow JC, Ko AI. Quantification of pathogenic Leptospira in the soils of a Brazilian urban slum. PLoS Negl Trop Dis 2018; 12:e0006415. [PMID: 29624576 PMCID: PMC5906024 DOI: 10.1371/journal.pntd.0006415] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/18/2018] [Accepted: 03/27/2018] [Indexed: 12/29/2022] Open
Abstract
Background Leptospirosis is an important zoonotic disease that causes considerable morbidity and mortality globally, primarily in residents of urban slums. While contact with contaminated water plays a critical role in the transmission of leptospirosis, little is known about the distribution and abundance of pathogenic Leptospira spp. in soil and the potential contribution of this source to human infection. Methods/Principal findings We collected soil samples (n = 70) from three sites within an urban slum community endemic for leptospirosis in Salvador, Brazil. Using qPCR of Leptospira genes lipl32 and 16S rRNA, we quantified the pathogenic Leptospira load in each soil sample. lipl32 qPCR detected pathogenic Leptospira in 22 (31%) of 70 samples, though the median concentration among positive samples was low (median = 6 GEq/g; range: 4–4.31×102 GEq/g). We also observed heterogeneity in the distribution of pathogenic Leptospira at the fine spatial scale. However, when using 16S rRNA qPCR, we detected a higher proportion of Leptospira-positive samples (86%) and higher bacterial concentrations (median: 4.16×102 GEq/g; range: 4–2.58×104 GEq/g). Sequencing of the qPCR amplicons and qPCR analysis with all type Leptospira species revealed that the 16S rRNA qPCR detected not only pathogenic Leptospira but also intermediate species, although both methods excluded saprophytic Leptospira. No significant associations were identified between the presence of pathogenic Leptospira DNA and environmental characteristics (vegetation, rat activity, distance to an open sewer or a house, or soil clay content), though samples with higher soil moisture content showed higher prevalences. Conclusion/Significance This is the first study to successfully quantify the burden of pathogenic Leptospira in soil from an endemic region. Our results support the hypothesis that soil may be an under-recognized environmental reservoir contributing to transmission of pathogenic Leptospira in urban slums. Consequently, the role of soil should be considered when planning interventions aimed to reduce the burden of leptospirosis in these communities. Leptospirosis is a globally distributed zoonotic disease that disproportionately affects vulnerable populations in urban slums. The disease is transmitted by direct contact with water, soil, or mud that has been contaminated with infected urine shed from chronically infected animals. Despite the critical role the environment plays in the epidemiology of the disease, the contribution of soil to the transmission cycle remains largely undescribed. Herein, we investigated the distribution of pathogenic Leptospira in soil samples from an endemic urban slum in Brazil. We found pathogenic Leptospira in nearly one-third of the soil samples, predominantly in low concentrations (<5×102 GEq/g). However, we observed considerable variation in the distribution and concentration of the pathogen at the fine spatial scale within the slum. Our results indicate that soil is likely an important additional environmental reservoir of pathogenic Leptospira in urban slums and prevention strategies should consider soil to help prevent the transmission of the disease in similar settings.
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Affiliation(s)
- Andrew G. Schneider
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
- * E-mail: (ACM); (AIK)
| | - Kathryn P. Hacker
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Bahia, Brazil
| | - Elsio A. Wunder
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Bahia, Brazil
| | - Mike Begon
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Mitermayer G. Reis
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Bahia, Brazil
| | - James E. Childs
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
| | - Federico Costa
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Bahia, Brazil
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Janet C. Lindow
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Bahia, Brazil
| | - Albert I. Ko
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Bahia, Brazil
- * E-mail: (ACM); (AIK)
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25
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Thibeaux R, Iraola G, Ferrés I, Bierque E, Girault D, Soupé-Gilbert ME, Picardeau M, Goarant C. Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence. Microb Genom 2018; 4. [PMID: 29310748 PMCID: PMC5857368 DOI: 10.1099/mgen.0.000144] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Despite recent advances in our understanding of the genomics of members of the genus Leptospira, little is known on how virulence has emerged in this heterogeneous bacterial genus as well as on the lifestyle of pathogenic members of the genus Leptospira outside animal hosts. Here, we isolated 12 novel species of the genus Leptospira from tropical soils, significantly increasing the number of known species to 35 and finding evidence of highly unexplored biodiversity in the genus. Extended comparative phylogenomics and pan-genome analyses at the genus level by incorporating 26 novel genomes, revealed that, the traditional leptospiral ‘pathogens’ cluster, as defined by their phylogenetic position, can be split in two groups with distinct virulence potential and accessory gene patterns. These genomic distinctions are strongly linked to the ability to cause or not severe infections in animal models and humans. Our results not only provide new insights into virulence evolution in the members of the genus Leptospira, but also lay the foundations for refining the classification of the pathogenic species.
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Affiliation(s)
- Roman Thibeaux
- 1Institut Pasteur in New Caledonia, Institut Pasteur International Network, Leptospirosis Research and Expertise Unit, Noumea, New Caledonia
| | | | - Ignacio Ferrés
- 2Institut Pasteur Montevideo, Bioinformatics Unit, Uruguay
| | - Emilie Bierque
- 1Institut Pasteur in New Caledonia, Institut Pasteur International Network, Leptospirosis Research and Expertise Unit, Noumea, New Caledonia
| | - Dominique Girault
- 1Institut Pasteur in New Caledonia, Institut Pasteur International Network, Leptospirosis Research and Expertise Unit, Noumea, New Caledonia
| | - Marie-Estelle Soupé-Gilbert
- 1Institut Pasteur in New Caledonia, Institut Pasteur International Network, Leptospirosis Research and Expertise Unit, Noumea, New Caledonia
| | - Mathieu Picardeau
- 3Institut Pasteur, Unité de Biologie des Spirochètes, 28 rue du docteur Roux, 75724 Paris Cedex 15, France
| | - Cyrille Goarant
- 1Institut Pasteur in New Caledonia, Institut Pasteur International Network, Leptospirosis Research and Expertise Unit, Noumea, New Caledonia
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