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Prager KC, Danil K, Wurster E, Colegrove KM, Galloway R, Kettler N, Mani R, McDonough RF, Sahl JW, Stone NE, Wagner DM, Lloyd-Smith JO. Detection of Leptospira kirschneri in a short-beaked common dolphin (Delphinus delphis delphis) stranded off the coast of southern California, USA. BMC Vet Res 2024; 20:266. [PMID: 38902706 PMCID: PMC11188202 DOI: 10.1186/s12917-024-04111-x] [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: 01/22/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Pathogenic Leptospira species are globally important zoonotic pathogens capable of infecting a wide range of host species. In marine mammals, reports of Leptospira have predominantly been in pinnipeds, with isolated reports of infections in cetaceans. CASE PRESENTATION On 28 June 2021, a 150.5 cm long female, short-beaked common dolphin (Delphinus delphis delphis) stranded alive on the coast of southern California and subsequently died. Gross necropsy revealed multifocal cortical pallor within the reniculi of the kidney, and lymphoplasmacytic tubulointerstitial nephritis was observed histologically. Immunohistochemistry confirmed Leptospira infection, and PCR followed by lfb1 gene amplicon sequencing suggested that the infecting organism was L.kirschneri. Leptospira DNA capture and enrichment allowed for whole-genome sequencing to be conducted. Phylogenetic analyses confirmed the causative agent was a previously undescribed, divergent lineage of L.kirschneri. CONCLUSIONS We report the first detection of pathogenic Leptospira in a short-beaked common dolphin, and the first detection in any cetacean in the northeastern Pacific Ocean. Renal lesions were consistent with leptospirosis in other host species, including marine mammals, and were the most significant lesions detected overall, suggesting leptospirosis as the likely cause of death. We identified the cause of the infection as L.kirschneri, a species detected only once before in a marine mammal - a northern elephant seal (Mirounga angustirostris) of the northeastern Pacific. These findings raise questions about the mechanism of transmission, given the obligate marine lifestyle of cetaceans (in contrast to pinnipeds, which spend time on land) and the commonly accepted view that Leptospira are quickly killed by salt water. They also raise important questions regarding the source of infection, and whether it arose from transmission among marine mammals or from terrestrial-to-marine spillover. Moving forward, surveillance and sampling must be expanded to better understand the extent to which Leptospira infections occur in the marine ecosystem and possible epidemiological linkages between and among marine and terrestrial host species. Generating Leptospira genomes from different host species will yield crucial information about possible transmission links, and our study highlights the power of new techniques such as DNA enrichment to illuminate the complex ecology of this important zoonotic pathogen.
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Affiliation(s)
- K C Prager
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Kerri Danil
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, 92037, USA
| | - Elyse Wurster
- Ocean Associates Inc. Under Contract to Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, 92037, USA
| | - Kathleen M Colegrove
- Zoological Pathology Program, University of Illinois College of Veterinary Medicine, 3300 Golf Rd, Brookfield, IL, 60513, USA
| | - Renee Galloway
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Diseases Control and Prevention, Atlanta, GA, 30333, USA
| | - Niesa Kettler
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, 48825, USA
| | - Rinosh Mani
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, 48825, USA
| | - Ryelan F McDonough
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Nathan E Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
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Helman SK, Tokuyama AFN, Mummah RO, Stone NE, Gamble MW, Snedden CE, Borremans B, Gomez ACR, Cox C, Nussbaum J, Tweedt I, Haake DA, Galloway RL, Monzón J, Riley SPD, Sikich JA, Brown J, Friscia A, Sahl JW, Wagner DM, Lynch JW, Prager KC, Lloyd-Smith JO. Pathogenic Leptospira are widespread in the urban wildlife of southern California. Sci Rep 2023; 13:14368. [PMID: 37658075 PMCID: PMC10474285 DOI: 10.1038/s41598-023-40322-2] [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: 03/29/2023] [Accepted: 08/08/2023] [Indexed: 09/03/2023] Open
Abstract
Leptospirosis, the most widespread zoonotic disease in the world, is broadly understudied in multi-host wildlife systems. Knowledge gaps regarding Leptospira circulation in wildlife, particularly in densely populated areas, contribute to frequent misdiagnoses in humans and domestic animals. We assessed Leptospira prevalence levels and risk factors in five target wildlife species across the greater Los Angeles region: striped skunks (Mephitis mephitis), raccoons (Procyon lotor), coyotes (Canis latrans), Virginia opossums (Didelphis virginiana), and fox squirrels (Sciurus niger). We sampled more than 960 individual animals, including over 700 from target species in the greater Los Angeles region, and an additional 266 sampled opportunistically from other California regions and species. In the five target species seroprevalences ranged from 5 to 60%, and infection prevalences ranged from 0.8 to 15.2% in all except fox squirrels (0%). Leptospira phylogenomics and patterns of serologic reactivity suggest that mainland terrestrial wildlife, particularly mesocarnivores, could be the source of repeated observed introductions of Leptospira into local marine and island ecosystems. Overall, we found evidence of widespread Leptospira exposure in wildlife across Los Angeles and surrounding regions. This indicates exposure risk for humans and domestic animals and highlights that this pathogen can circulate endemically in many wildlife species even in densely populated urban areas.
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Affiliation(s)
- Sarah K Helman
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA.
| | - Amanda F N Tokuyama
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Riley O Mummah
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Nathan E Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Mason W Gamble
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Celine E Snedden
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Benny Borremans
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Wildlife Health Ecology Research Organization, San Diego, CA, USA
| | - Ana C R Gomez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Caitlin Cox
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Julianne Nussbaum
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Isobel Tweedt
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - David A Haake
- Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, USA
- The David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | - Javier Monzón
- Natural Science Division, Pepperdine University, Malibu, CA, USA
| | - Seth P D Riley
- Santa Monica Mountains National Recreation Area, National Park Service, Thousand Oaks, CA, USA
| | - Jeff A Sikich
- Santa Monica Mountains National Recreation Area, National Park Service, Thousand Oaks, CA, USA
| | - Justin Brown
- Santa Monica Mountains National Recreation Area, National Park Service, Thousand Oaks, CA, USA
| | - Anthony Friscia
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jessica W Lynch
- Institute for Society and Genetics, University of California, Los Angeles, CA, USA
| | - Katherine C Prager
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
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Menezes A, Takahashi S, Routledge I, Metcalf CJE, Graham AL, Hay JA. serosim: An R package for simulating serological data arising from vaccination, epidemiological and antibody kinetics processes. PLoS Comput Biol 2023; 19:e1011384. [PMID: 37578985 PMCID: PMC10449138 DOI: 10.1371/journal.pcbi.1011384] [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: 01/24/2023] [Revised: 08/24/2023] [Accepted: 07/24/2023] [Indexed: 08/16/2023] Open
Abstract
serosim is an open-source R package designed to aid inference from serological studies, by simulating data arising from user-specified vaccine and antibody kinetics processes using a random effects model. Serological data are used to assess population immunity by directly measuring individuals' antibody titers. They uncover locations and/or populations which are susceptible and provide evidence of past infection or vaccination to help inform public health measures and surveillance. Both serological data and new analytical techniques used to interpret them are increasingly widespread. This creates a need for tools to simulate serological studies and the processes underlying observed titer values, as this will enable researchers to identify best practices for serological study design, and provide a standardized framework to evaluate the performance of different inference methods. serosim allows users to specify and adjust model inputs representing underlying processes responsible for generating the observed titer values like time-varying patterns of infection and vaccination, population demography, immunity and antibody kinetics, and serological sampling design in order to best represent the population and disease system(s) of interest. This package will be useful for planning sampling design of future serological studies, understanding determinants of observed serological data, and validating the accuracy and power of new statistical methods.
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Affiliation(s)
- Arthur Menezes
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Saki Takahashi
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Isobel Routledge
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - C. Jessica E. Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Princeton School of Public and International Affairs, Princeton University, Princeton, New Jersey, United States of America
| | - Andrea L. Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - James A. Hay
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
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Cruz JS, Nery N, Sacramento GA, Victoriano R, Montenegro ALS, Santana JO, Costa F, Ko AI, Reis MG, Wunder EA. Biannual and Quarterly Comparison Analysis of Agglutinating Antibody Kinetics on a Subcohort of Individuals Exposed to Leptospira interrogans in Salvador, Brazil. Front Med (Lausanne) 2022; 9:862378. [PMID: 35492362 PMCID: PMC9048256 DOI: 10.3389/fmed.2022.862378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
IntroductionLeptospirosis is a zoonosis with a worldwide spread that leads to clinical manifestations ranging from asymptomatic infection to a life-threatening disease. The immune response is predominantly humoral mediated limited to the infecting serovar. Individuals living in an area endemic for leptospirosis are often exposed to an environment contaminated with leptospires and there is a paucity of information on naturally acquired immunity. In the present study, we evaluated the kinetics of agglutinating antibodies in individuals from an endemic area for leptospirosis in Salvador, Brazil comparing two different intersample collection times.MethodsBetween 2017–2018, we carried out a biannual prospective cohort with 2,086 individuals living in an endemic area for leptospirosis in Salvador, Brazil. To compare agglutinating antibody kinetics using microscopic agglutination test (MAT) with different collection times, a subcohort of 72 individuals with quarterly follow-up was carried out in parallel.ResultsThe results revealed that using a shorter time for intersample collection led to the detection of a higher number of infections and reinfection events. Furthermore, we observed a higher rate of titer decay indicating partial and short protection. However, there was no indication of major changes in risk factors for the disease.ConclusionsWe evaluated antibody kinetics among residents of an endemic area for leptospirosis comparing two sample collection times. The constant exposure to the contaminated environment increases the risk for leptospirosis infection with reinfection events being more common than expected. This indicates that the burden of leptospirosis might be underestimated by serological surveys, and further studies are necessary to better characterize the humoral response after infection.
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Affiliation(s)
- Jaqueline S. Cruz
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
| | - Nivison Nery
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil
| | | | - Renato Victoriano
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil
| | - Albino L. S. Montenegro
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
| | - Juliet O. Santana
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
- Departamento de Geografia, Instituto de Geociências, Universidade Federal da Bahia, Salvador, Brazil
| | - Federico Costa
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States
| | - Albert I. Ko
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States
| | - Mitermayer G. Reis
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States
- Departamento de Medicina e Patologia Legal, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
| | - Elsio A. Wunder
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States
- *Correspondence: Elsio A. Wunder Jr.
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5
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Borremans B, Gamble A, Prager KC, Helman SK, McClain AM, Cox C, Savage V, Lloyd-Smith JO. Quantifying antibody kinetics and RNA detection during early-phase SARS-CoV-2 infection by time since symptom onset. eLife 2020; 9:e60122. [PMID: 32894217 PMCID: PMC7508557 DOI: 10.7554/elife.60122] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/04/2020] [Indexed: 01/03/2023] Open
Abstract
Understanding and mitigating SARS-CoV-2 transmission hinges on antibody and viral RNA data that inform exposure and shedding, but extensive variation in assays, study group demographics and laboratory protocols across published studies confounds inference of true biological patterns. Our meta-analysis leverages 3214 datapoints from 516 individuals in 21 studies to reveal that seroconversion of both IgG and IgM occurs around 12 days post-symptom onset (range 1-40), with extensive individual variation that is not significantly associated with disease severity. IgG and IgM detection probabilities increase from roughly 10% at symptom onset to 98-100% by day 22, after which IgM wanes while IgG remains reliably detectable. RNA detection probability decreases from roughly 90% to zero by day 30, and is highest in feces and lower respiratory tract samples. Our findings provide a coherent evidence base for interpreting clinical diagnostics, and for the mathematical models and serological surveys that underpin public health policies.
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Affiliation(s)
- Benny Borremans
- Ecology and Evolutionary Biology Department, University of California, Los AngelesLos AngelesUnited States
- I-BioStat, Data Science Institute, Hasselt UniversityHasseltBelgium
- Evolutionary Ecology Group, University of AntwerpAntwerpBelgium
| | - Amandine Gamble
- Ecology and Evolutionary Biology Department, University of California, Los AngelesLos AngelesUnited States
| | - KC Prager
- Ecology and Evolutionary Biology Department, University of California, Los AngelesLos AngelesUnited States
| | - Sarah K Helman
- Ecology and Evolutionary Biology Department, University of California, Los AngelesLos AngelesUnited States
| | | | - Caitlin Cox
- Ecology and Evolutionary Biology Department, University of California, Los AngelesLos AngelesUnited States
| | - Van Savage
- Ecology and Evolutionary Biology Department, University of California, Los AngelesLos AngelesUnited States
- Biomathematics Department, University of California, Los AngelesLos AngelesUnited States
| | - James O Lloyd-Smith
- Ecology and Evolutionary Biology Department, University of California, Los AngelesLos AngelesUnited States
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