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Isidro J, Escudero R, Luque-Larena JJ, Pinto M, Borges V, González-Martín-Niño R, Duarte S, Vieira L, Mougeot F, Vidal D, Herrera-Rodríguez D, Rodríguez-Pastor R, Herrero-Cófreces S, Jubete-Tazo F, Gomes JP, Lopes de Carvalho I. Strengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samples. Front Microbiol 2024; 14:1277468. [PMID: 38249473 PMCID: PMC10797068 DOI: 10.3389/fmicb.2023.1277468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/23/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Francisella tularensis is a highly infectious bacterium that causes the zoonotic disease tularemia. The development of genotyping methods, especially those based on whole-genome sequencing (WGS), has recently increased the knowledge on the epidemiology of this disease. However, due to the difficulties associated with the growth and isolation of this fastidious pathogen in culture, the availability of strains and subsequently WGS data is still limited. Methods To surpass these constraints, we aimed to implement a culture-free approach to capture and sequence F. tularensis genomes directly from complex samples. Biological samples obtained from 50 common voles and 13 Iberian hares collected in Spain were confirmed as positive for F. tularensis subsp. holarctica and subjected to a WGS target capture and enrichment protocol, using RNA oligonucleotide baits designed to cover F. tularensis genomic diversity. Results We obtained full genome sequences of F. tularensis from 13 animals (20.6%), two of which had mixed infections with distinct genotypes, and achieved a higher success rate when compared with culture-dependent WGS (only successful for two animals). The new genomes belonged to different clades commonly identified in Europe (B.49, B.51 and B.262) and subclades. Despite being phylogenetically closely related to other genomes from Spain, the detected clusters were often found in other countries. A comprehensive phylogenetic analysis, integrating 599 F. tularensis subsp. holarctica genomes, showed that most (sub)clades are found in both humans and animals and that closely related strains are found in different, and often geographically distant, countries. Discussion Overall, we show that the implemented culture-free WGS methodology yields timely, complete and high-quality genomic data of F. tularensis, being a highly valuable approach to promote and potentiate the genomic surveillance of F. tularensis and ultimately increase the knowledge on the genomics, ecology and epidemiology of this highly infectious pathogen.
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Affiliation(s)
- Joana Isidro
- Genomics and Bioinformatics Unit, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Raquel Escudero
- Reference and Research Laboratory on Special Pathogens, National Centre for Microbiology (CNM), Carlos II Health Institute (ISCIII), Madrid, Spain
| | - Juan José Luque-Larena
- Departamento de Ciencias Agroforestales, Instituto Universitario de Investigación en Gestión Forestal Sostenible (iuFOR), E.T.S. Ingenierías Agrarias, Universidad de Valladolid, Palencia, Spain
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rosa González-Martín-Niño
- Reference and Research Laboratory on Special Pathogens, National Centre for Microbiology (CNM), Carlos II Health Institute (ISCIII), Madrid, Spain
| | - Sílvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - François Mougeot
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC, UCLM, JCCM), Ciudad Real, Spain
| | - Dolors Vidal
- Área de Microbiología, Facultad de Medicina, Universidad de Catilla-La Mancha (UCLM), Ciudad Real, Spain
| | - Daniel Herrera-Rodríguez
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC, UCLM, JCCM), Ciudad Real, Spain
- Área de Microbiología, Facultad de Medicina, Universidad de Catilla-La Mancha (UCLM), Ciudad Real, Spain
| | - Ruth Rodríguez-Pastor
- Department of Parasitology, Veterinary Faculty, University of Zaragoza, Zaragoza, Spain, Zaragoza, Spain
- Departamento de Parasitología, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Silvia Herrero-Cófreces
- Departamento de Ciencias Agroforestales, Instituto Universitario de Investigación en Gestión Forestal Sostenible (iuFOR), E.T.S. Ingenierías Agrarias, Universidad de Valladolid, Palencia, Spain
| | - Fernando Jubete-Tazo
- Departamento de Ciencias Agroforestales, Instituto Universitario de Investigación en Gestión Forestal Sostenible (iuFOR), E.T.S. Ingenierías Agrarias, Universidad de Valladolid, Palencia, Spain
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Veterinary and Animal Research Center (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Isabel Lopes de Carvalho
- Emergency and Biopreparedness Unit, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
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Caminero-Saldaña C, Correa-Cuadros JP, Baños-Herrero A, Riquelme C, Pallavicini Y, Fernández-Villán M, Plaza J, Pérez-Sánchez R, Sánchez N, Mougeot F, Luque-Larena JJ, Jaksic FM, García-Ariza MC. Exploring the influence of density-dependence and weather on the spatial and temporal variation in common vole (Microtus arvalis) abundance in Castilla y León, NW Spain. PEST MANAGEMENT SCIENCE 2023. [PMID: 38153883 DOI: 10.1002/ps.7954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND The common vole has invaded the agroecosystems of northwestern Spain, where outbreaks cause important crop damage and management costs. Little is yet known about the factors causing or modulating vole fluctuations. Here, we used 11 years of vole abundance monitoring data in 40 sites to study density-dependence and weather influence on vole dynamics. Our objective was to identify the population dynamics structure and determine whether there is direct or delayed density-dependence. An evaluation of climatic variables followed, to determine whether they influenced vole population peaks. RESULTS First- and second-order outbreak dynamics were detected at 7 and 33 study sites, respectively, together with second-order variability in periodicity (2-3 to 4-5-year cycles). Vole population growth was explained by previous year abundance (mainly numbers in summer and spring) at 21 of the sites (52.5%), by weather variables at 11 sites (27.5%; precipitation or temperature in six and five sites, respectively), and by a combination of previous abundance and weather variables in eight sites (20%). CONCLUSIONS We detected variability in vole spatiotemporal abundance dynamics, which differs in cyclicity and period. We also found regional variation in the relative importance of previous abundances and weather as factors modulating vole fluctuations. Most vole populations were cyclical, with variable periodicity across the region. Our study is a first step towards the development of predictive modeling, by disclosing relevant factors that might trigger vole outbreaks. It improves decision-making processes within integrated management dealing with mitigation of the agricultural impacts caused by voles. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Constantino Caminero-Saldaña
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Observatorio de Plagas y Enfermedades Agrícolas, Valladolid, Spain
| | - Jennifer Paola Correa-Cuadros
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Ana Baños-Herrero
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Observatorio de Plagas y Enfermedades Agrícolas, Valladolid, Spain
| | - Carlos Riquelme
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Yesica Pallavicini
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Observatorio de Plagas y Enfermedades Agrícolas, Valladolid, Spain
| | - Mercedes Fernández-Villán
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Observatorio de Plagas y Enfermedades Agrícolas, Valladolid, Spain
| | - Javier Plaza
- Facultad de Ciencias Agrarias y Ambientales, Universidad de Salamanca, Salamanca, Spain
| | - Rodrigo Pérez-Sánchez
- Facultad de Ciencias Agrarias y Ambientales, Universidad de Salamanca, Salamanca, Spain
| | - Nilda Sánchez
- Facultad de Ciencias Agrarias y Ambientales, Universidad de Salamanca, Salamanca, Spain
| | - François Mougeot
- Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Juan José Luque-Larena
- Departamento de Ciencias Agroforestales (Zoología), ETSIIAA, Universidad de Valladolid, Palencia, Spain
- Instituto Universitario de Investigación en Gestión Forestal Sostenible (iuFOR), Palencia, Spain
| | - Fabián M Jaksic
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - María Carmen García-Ariza
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Observatorio de Plagas y Enfermedades Agrícolas, Valladolid, Spain
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Hušková J, Hušek J. Population Density of European Hare Predicts Risk of Tularemia Infection, Czech Republic, 2006-2022. Vector Borne Zoonotic Dis 2023; 23:615-618. [PMID: 37589998 DOI: 10.1089/vbz.2023.0027] [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: 08/18/2023] Open
Abstract
Background: Over 200 different animal species are susceptible to infection by tularemia, highly infectious disease caused by Francisella tularensis. Hares (Lepus sp.) and small rodents, such as common vole (Microtus arvalis), have been acknowledged as the most significant sources of human tularemia infection in most European countries. Our objective was to verify ability of these species in predicting incidence of human tularemia in a Central European country, the Czech Republic. Materials and Methods: We used 17 years of data on densities of European hare (Lepus europaeus) and common vole, and climate variability to test effects of these factors on temporal dynamics of tularemia incidence. The data were obtained from annual reports available from online e-repositories. Results: The analysis showed that 33% of the yearly variation in human tularemia incidence was explained solely by the abundance of European hare in the Czech Republic during 2007-2022. Density of common vole and North Atlantic Oscillation index, a measure of climate variability, did not significantly explain tularemia incidence. While hare population declined severely during 1993-2022, we did not detect any clear accompanied decrease in the prevalence of tularemia in humans and hares. Conclusion: Contrary to expectations, only hares proved capable in predicting yearly dynamics in human tularemia incidence in the Czech Republic. We call for continued monitoring of infection rates in hares and advocate the use of hunter estimates of hare abundance as a cheap and effective means of predicting the risk of tularemia.
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Affiliation(s)
- Jana Hušková
- Department of Microbiology, Regional Hospital Kolín, Kolín, Czech Republic
| | - Jan Hušek
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
- Department of Biology, University of Hradec Králové, Hradec Králové, Czech Republic
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Vole outbreaks may induce a tularemia disease pit that prevents Iberian hare population recovery in NW Spain. Sci Rep 2023; 13:3898. [PMID: 36890167 PMCID: PMC9995447 DOI: 10.1038/s41598-023-30651-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/27/2023] [Indexed: 03/10/2023] Open
Abstract
Iberian hare populations have suffered severe declines during recent decades in Spain. Between 1970 and 1990s, a rapid increase in irrigation crop surface in NW Spain (Castilla-y-León region) was followed by a common vole massive range expansion and complete colonization of lowland irrigated agricultural landscapes from mountainous habitats. The subsequent large cyclic fluctuations in abundance of colonizing common voles have contributed to a periodic amplification of Francisella tularensis, the etiological agent that causes human tularemia outbreaks in the region. Tularemia is a fatal disease to lagomorphs, so we hypothesize that vole outbreaks would lead to disease spill over to Iberian hares, increasing prevalence of tularemia and declines among hare populations. Here we report on the possible effects that vole abundance fluctuations and concomitant tularemia outbreaks had on Iberian hare populations in NW Spain. We analysed hare hunting bag data for the region, which has been recurrently affected by vole outbreaks between 1996 and 2019. We also compiled data on F. tularensis prevalence in Iberian hares reported by the regional government between 2007 and 2016. Our results suggest that common vole outbreaks may limit the recovery of hare populations by amplifying and spreading tularemia in the environment. The recurrent rodent-driven outbreaks of tularemia in the region may result in a "disease pit" to Iberian hares: at low host densities, the rate of population growth in hares is lower than the rate at which disease-induced mortality increases with increased rodent host density, therefore, keeping hare populations on a low-density equilibrium. We highlight future research needs to clarify tularemia transmission pathways between voles and hares and confirm a disease pit process.
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Buhler K, Bouchard É, Elmore S, Samelius G, Jackson J, Tomaselli M, Fenton H, Alisauskas R, Jenkins E. Tularemia above the Treeline: Climate and Rodent Abundance Influences Exposure of a Sentinel Species, the Arctic Fox ( Vulpes lagopus), to Francisella tularensis. Pathogens 2022; 12:pathogens12010028. [PMID: 36678376 PMCID: PMC9861794 DOI: 10.3390/pathogens12010028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Tularemia is a zoonotic disease found throughout most of the northern hemisphere that may experience range expansion with warming temperatures. Rodents and lagomorphs are reservoirs for the disease, and outbreaks of tularemia often follow peaks in their abundance. As small mammals dominate the diet of arctic foxes (Vulpes lagopus), we determined whether they may serve as sentinels by identifying antibodies in live-captured and harvested foxes from northern Canada. Overall seroprevalence was 2% (CI95 1-2%) in 176 foxes harvested in 2018-2019 compared to 17% (CI95 12-22%) of 230 foxes captured live in 2011-2021. Prevalence was at an all-time high in 2018, following a peak in vole abundance in 2017. Antibodies were identified in fox pups born in 2018 and 2019, suggesting that F. tularensis was actively transmitted during the summers. High precipitation during the summer, increased snow cover and colder temperatures in May, and a higher abundance of voles were all associated with increased seroprevalence in live-captured foxes. Thus, exposure to F. tularensis is largely mediated through climate and rodent populations in the Canadian Arctic, and arctic foxes are useful sentinels for F. tularensis in northern ecosystems. Further studies should investigate whether infection impacts arctic fox survival and reproductive success in the circumpolar North.
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Affiliation(s)
- Kayla Buhler
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
- Correspondence:
| | - Émilie Bouchard
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
- Research Group on Epidemiology of Zoonoses and Public Health (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Stacey Elmore
- Division of Natural Sciences, University of Maine Fort Kent, 23 University Drive, Fort Kent, MA 04743, USA
| | - Gustaf Samelius
- Snow Leopard Trust, 4649 Sunnyside Ave North, Suite 325, Seattle, WA 98103, USA
| | - Jessica Jackson
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Matilde Tomaselli
- Canadian High Arctic Research Station, Polar Knowledge Canada, 1 Uvajuq Road, P.O. Box 2150, Cambridge Bay, NU X0B 0C0, Canada
| | - Heather Fenton
- Government of The Northwest Territories, Department of Environment and Natural Resources, 5th Floor Scotiabank Centre, P.O. Box 1320, Yellowknife, NT X1A 2P9, Canada
- Australian Wildlife Health Registry, Taronga Zoo, P.O. Box 20, Mosman, NSW 2088, Australia
| | - Ray Alisauskas
- Prairie and Northern Wildlife Research Centre, Wildlife Research Division, Environment and Climate Change Canada, 115 Perimeter Road, Saskatoon, SK S7N 0X4, Canada
- Department of Biology, University of Saskatchewan, Science Place, Saskatoon, SK S7N 5E2, Canada
| | - Emily Jenkins
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
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Roos D, Caminero-Saldaña C, Elston D, Mougeot F, García-Ariza MC, Arroyo B, Luque-Larena JJ, Revilla FJR, Lambin X. From pattern to process? Dual travelling waves, with contrasting propagation speeds, best describe a self-organised spatio-temporal pattern in population growth of a cyclic rodent. Ecol Lett 2022; 25:1986-1998. [PMID: 35908289 PMCID: PMC9543711 DOI: 10.1111/ele.14074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/19/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022]
Abstract
The dynamics of cyclic populations distributed in space result from the relative strength of synchronising influences and the limited dispersal of destabilising factors (activators and inhibitors), known to cause multi‐annual population cycles. However, while each of these have been well studied in isolation, there is limited empirical evidence of how the processes of synchronisation and activation–inhibition act together, largely owing to the scarcity of datasets with sufficient spatial and temporal scale and resolution. We assessed a variety of models that could be underlying the spatio‐temporal pattern, designed to capture both theoretical and empirical understandings of travelling waves using large‐scale (>35,000 km2), multi‐year (2011–2017) field monitoring data on abundances of common vole (Microtus arvalis), a cyclic agricultural rodent pest. We found most support for a pattern formed from the summation of two radial travelling waves with contrasting speeds that together describe population growth rates across the region.
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Affiliation(s)
- Deon Roos
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK.,Área de Plagas, Instituto Tecnológico Agrario de Castilla-y-León (ITACyL), Valladolid, Spain
| | | | - David Elston
- Biomathematics & Statistics Scotland, Aberdeen, UK
| | - François Mougeot
- Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | | | - Beatriz Arroyo
- Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Juan José Luque-Larena
- Dpto. Ciencias Agroforestales, ETSIIAA, Universidad de Valladolid, Palencia, Spain.,Instituto Universitario de Investigación en Gestión Forestal Sostenible, Palencia, Spain
| | | | - Xavier Lambin
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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Graves TA, Yarnall MJ, Johnston AN, Preston TM, Chong GW, Cole EK, Janousek WM, Cross PC. Eyes on the herd: Quantifying ungulate density from satellite, unmanned aerial systems, and GPScollar data. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2600. [PMID: 35343018 DOI: 10.1002/eap.2600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 10/01/2021] [Accepted: 10/13/2021] [Indexed: 06/14/2023]
Abstract
Novel approaches to quantifying density and distributions could help biologists adaptively manage wildlife populations, particularly if methods are accurate, consistent, cost-effective, rapid, and sensitive to change. Such approaches may also improve research on interactions between density and processes of interest, such as disease transmission across multiple populations. We assess how satellite imagery, unmanned aerial system (UAS) imagery, and Global Positioning System (GPS) collar data vary in characterizing elk density, distribution, and count patterns across times with and without supplemental feeding at the National Elk Refuge (NER) in the US state of Wyoming. We also present the first comparison of satellite imagery data with traditional counts for ungulates in a temperate system. We further evaluate seven different aggregation metrics to identify the most consistent and sensitive metrics for comparing density and distribution across time and populations. All three data sources detected higher densities and aggregation locations of elk during supplemental feeding than non-feeding at the NER. Kernel density estimates (KDEs), KDE polygon areas, and the first quantile of interelk distances detected differences with the highest sensitivity and were most highly correlated across data sources. Both UAS and satellite imagery provide snapshots of density and distribution patterns of most animals in the area at lower cost than GPS collars. While satellite-based counts were lower than traditional counts, aggregation metrics matched those from UAS and GPS data sources when animals appeared in high contrast to the landscape, including brown elk against new snow in open areas. UAS counts of elk were similar to traditional ground-based counts on feed grounds and are the best data source for assessing changes in small spatial extents. Satellite, UAS, or GPS data can provide appropriate data for assessing density and changes in density from adaptive management actions. For the NER, where high elk densities are beneath controlled airspace, GPS collar data will be most useful for evaluating how management actions, including changes in the dates of supplemental feeding, influence elk density and aggregation across large spatial extents. Using consistent and sensitive measures of density may improve research on the drivers and effects of density within and across a wide range of species.
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Affiliation(s)
- Tabitha A Graves
- U.S. Geological Survey, Northern Rocky Mountain Science Center, West Glacier, Montana, USA
| | - Michael J Yarnall
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, USA
| | - Aaron N Johnston
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, USA
| | - Todd M Preston
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, USA
| | - Geneva W Chong
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Jackson, Wyoming, USA
| | - Eric K Cole
- National Elk Refuge, U.S. Fish and Wildlife Service, National Elk Refuge, Jackson, Wyoming, USA
| | - William M Janousek
- U.S. Geological Survey, Northern Rocky Mountain Science Center, West Glacier, Montana, USA
| | - Paul C Cross
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, USA
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8
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Herrero-Cófreces S, Mougeot F, Lambin X, Luque-Larena JJ. Linking Zoonosis Emergence to Farmland Invasion by Fluctuating Herbivores: Common Vole Populations and Tularemia Outbreaks in NW Spain. Front Vet Sci 2021; 8:698454. [PMID: 34458354 PMCID: PMC8397442 DOI: 10.3389/fvets.2021.698454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
The expansion and intensification of agriculture are driving profound changes in ecosystems worldwide, favoring the (re)emergence of many human infectious diseases. Muroid rodents are a key host group for zoonotic infectious pathogens and frequently invade farming environments, promoting disease transmission and spillover. Understanding the role that fluctuating populations of farm dwelling rodents play in the epidemiology of zoonotic diseases is paramount to improve prevention schemes. Here, we review a decade of research on the colonization of farming environments in NW Spain by common voles (Microtus arvalis) and its public health impacts, specifically periodic tularemia outbreaks in humans. The spread of this colonizing rodent was analogous to an invasion process and was putatively triggered by the transformation and irrigation of agricultural habitats that created a novel terrestrial-aquatic interface. This irruptive rodent host is an effective amplifier for the Francisella tularensis bacterium during population outbreaks, and human tularemia episodes are tightly linked in time and space to periodic (cyclic) variations in vole abundance. Beyond the information accumulated to date, several key knowledge gaps about this pathogen-rodent epidemiological link remain unaddressed, namely (i) did colonizing vole introduce or amplified pre-existing F. tularensis? (ii) which features of the “Francisella—Microtus” relationship are crucial for the epidemiology of tularemia? (iii) how virulent and persistent F. tularensis infection is for voles under natural conditions? and (iv) where does the bacterium persist during inter-epizootics? Future research should focus on more integrated, community-based approaches in order to understand the details and dynamics of disease circulation in ecosystems colonized by highly fluctuating hosts.
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Affiliation(s)
- Silvia Herrero-Cófreces
- Dpto. Ciencias Agroforestales, Escuela Técnica Superior de Ingenierías Agrarias, Universidad de Valladolid, Palencia, Spain.,Instituto Universitario de Investigación en Gestión Forestal Sostenible, Universidad de Valladolid, Palencia, Spain
| | - François Mougeot
- Grupo de Gestión de Recursos Cinegéticos y Fauna Silvestre, Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Xavier Lambin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Juan José Luque-Larena
- Dpto. Ciencias Agroforestales, Escuela Técnica Superior de Ingenierías Agrarias, Universidad de Valladolid, Palencia, Spain.,Instituto Universitario de Investigación en Gestión Forestal Sostenible, Universidad de Valladolid, Palencia, Spain
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9
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FREQUENT LEPTOSPIRA SPP. DETECTION BUT ABSENCE OF TULA ORTHOHANTAVIRUS IN MICROTUS SPP. VOLES, NORTHWESTERN SPAIN. J Wildl Dis 2021; 57:733-742. [PMID: 34320644 DOI: 10.7589/jwd-d-20-00109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 04/09/2021] [Indexed: 11/20/2022]
Abstract
The common vole (Microtus arvalis) is a major agricultural pest in Europe and is a reservoir for several zoonotic agents, such as Leptospira spp. and Tula orthohantavirus (TULV). However, little is known about the occurrence of those pathogens in voles from Spain, where the species has largely expanded its distribution range in the past decades, causing agricultural pests and zoonotic diseases. For a molecular survey, 580 common voles and six Lusitanian pine voles (Microtus lusitanicus) were collected in 26 localities from four provinces of northwestern Spain. We assessed the presence of Leptospira spp. DNA in kidney tissue by PCR targeting the lipL32 gene, detecting a prevalence of 7.9% (95% confidence interval, 5.9-10.4) for common voles and of 33.3% (95% confidence interval, 4.3-77.7) for Lusitanian pine voles. We identified Leptospira kirschneri in 24 animals and Leptospira borgpetersenii in two animals, using secY gene-specific PCR. We analyzed environmental and demographic factors (such as age class, weight, and sex) and population dynamics data for their potential effect on the Leptospira spp. prevalence in those voles. The Leptospira spp. DNA detection rate in common voles increased significantly with maximum air temperature, vole weight, and amount of accumulated rainfall during the 90 d before capture and within the peak phase of the population cycle. We assessed the presence of TULV in lung tissue of 389 voles by reverse-transcription PCR, with no positive results. The absence of TULV might be explained by the evolutionary isolation of the common vole in Spain. The detection of two Leptospira genomospecies underlines the necessity for further typing efforts to understand the epidemiology of leptospiral infection in the common vole and the potential risk for human health in Spain.
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Tularemia Outbreaks in Spain from 2007 to 2020 in Humans and Domestic and Wild Animals. Pathogens 2021; 10:pathogens10070892. [PMID: 34358042 PMCID: PMC8308475 DOI: 10.3390/pathogens10070892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/01/2021] [Accepted: 07/12/2021] [Indexed: 11/25/2022] Open
Abstract
In this study, tularemia outbreaks associated with humans and several domestic and wild animals (Iberian hares, wild rabbits, voles, mice, grey shrews, sheep, dogs, foxes, wolves, ticks, and river crayfish) are reported in Spain from 2007 to 2020. Special attention was paid to the outbreaks in humans in 2007–2009 and 2014–2015, when the most important waves occurred. Moreover, positive rates of tularemia in lagomorphs were detected in 2007–2010, followed by negative results in 2011–2013, before again returning to positive rates in 2014 and in 2017 and in 2019–2020. Lagomorphs role in spreading Francisella tularensis in the epidemiological chain could not be discarded. F. tularensis is described for the first time infecting the shrew Crocidura russula worldwide, and it is also reported for the first time infecting wild rabbits (Oryctolagus cuniculus) in Spain. Serological positives higher than 0.4% were seen for sheep only from 2007–2009 and again in 2019, while serological rates greater than 1% were revealed in dogs in 2007–2008 and in wild canids in 2016. F. tularensis were detected in ticks in 2009, 2014–2015, 2017, and 2019. Lastly, negative results were achieved for river crayfish and also in environmental water samples from 2007 to 2020.
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Janousek WM, Graves TA, Berman EE, Chong GW, Cole EK, Dewey SR, Johnston AN, Cross PC. Human activities and weather drive contact rates of wintering elk. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.13818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- William M. Janousek
- United States Geological Survey Northern Rocky Mountain Science Center West Glacier MT USA
| | - Tabitha A. Graves
- United States Geological Survey Northern Rocky Mountain Science Center West Glacier MT USA
| | - Ethan E. Berman
- United States Geological Survey Northern Rocky Mountain Science Center West Glacier MT USA
| | - Geneva W. Chong
- United States Geological Survey Northern Rocky Mountain Science Center Bozeman MT USA
| | - Eric K. Cole
- United States Fish and Wildlife Service Jackson WY USA
| | - Sarah R. Dewey
- National Park Service Grand Teton National Park Moose WY USA
| | - Aaron N. Johnston
- United States Geological Survey Northern Rocky Mountain Science Center Bozeman MT USA
| | - Paul C. Cross
- United States Geological Survey Northern Rocky Mountain Science Center Bozeman MT USA
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Ahmad F, Farooq A, Ghani Khan MU, Shabbir MZ, Rabbani M, Hussain I. Identification of Most Relevant Features for Classification of Francisella tularensis using Machine Learning. Curr Bioinform 2021. [DOI: 10.2174/1574893615666200219113900] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Francisella tularensis is a stealth pathogen fatal for animals and humans.
Ease of its propagation, coupled with high capacity for ailment and death makes it a potential
candidate for biological weapon.
Objective:
Work related to the pathogen’s classification and factors affecting its prolonged
existence in soil is limited to statistical measures. Machine learning other than conventional
analysis methods may be applied to better predict epidemiological modeling for this soil-borne
pathogen.
Methods:
Feature-ranking algorithms namely; relief, correlation and oneR are used for soil
attribute ranking. Moreover, classification algorithms; SVM, random forest, naive bayes, logistic
regression and MLP are used for classification of the soil attribute dataset for Francisella
tularensis positive and negative soils.
Results:
Feature-ranking methods concluded that clay, nitrogen, organic matter, soluble salts, zinc,
silt and nickel are the most significant attributes while potassium, phosphorous, iron, calcium,
copper, chromium and sand are the least contributing risk factors for the persistence of the
pathogen. However, clay is the most significant and potassium is the least contributing attribute.
Data analysis suggests that feature-ranking using relief produced classification accuracy of 84.35%
for multilayer perceptron; 82.99% for linear regression; 80.27% for SVM and random forest; and
78.23% for naive bayes, which is better than other ranking methods. MLP outperforms other
classifiers by generating an accuracy of 84.35%, 82.99% and 81.63% for feature-ranking using
relief, correlation and oneR algorithms, respectively.
Conclusion:
These models can significantly improve accuracy and can minimize the risk of
incorrect classification. They further help in controlling epidemics and thereby minimizing the
socio-economic impact on the society.
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Affiliation(s)
- Fareed Ahmad
- Department of Computer Science and Engineering, Faculty of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Amjad Farooq
- Department of Computer Science and Engineering, Faculty of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Muhammad Usman Ghani Khan
- Department of Computer Science and Engineering, Faculty of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | | | - Masood Rabbani
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Irshad Hussain
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
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Herrero-Cófreces S, Flechoso MF, Rodríguez-Pastor R, Luque-Larena JJ, Mougeot F. Patterns of flea infestation in rodents and insectivores from intensified agro-ecosystems, Northwest Spain. Parasit Vectors 2021; 14:16. [PMID: 33407813 PMCID: PMC7789319 DOI: 10.1186/s13071-020-04492-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/19/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Fleas frequently infest small mammals and play important vectoring roles in the epidemiology of (re)emerging zoonotic disease. Rodent outbreaks in intensified agro-ecosystems of North-West Spain have been recently linked to periodic zoonotic diseases spillover to local human populations. Obtaining qualitative and quantitative information about the composition and structure of the whole flea and small mammal host coexisting communities is paramount to understand disease transmission cycles and to elucidate the disease-vectoring role of flea species. The aims of this research were to: (i) characterise and quantify the flea community parasiting a small mammal guild in intensive farmlands in North-West Spain; (ii) determine and evaluate patterns of co-infection and the variables that may influence parasitological parameters. METHODS We conducted a large-scale survey stratified by season and habitat of fleas parasitizing the small mammal host guild. We report on the prevalence, mean intensity, and mean abundance of flea species parasitizing Microtus arvalis, Apodemus sylvaticus, Mus spretus and Crocidura russula. We also report on aggregation patterns (variance-to-mean ratio and discrepancy index) and co-infection of hosts by different flea species (Fager index) and used generalized linear mixed models to study flea parameter variation according to season, habitat and host sex. RESULTS Three flea species dominated the system: Ctenophthalmus apertus gilcolladoi, Leptopsylla taschenbergi and Nosopsyllus fasciatus. Results showed a high aggregation pattern of fleas in all hosts. All host species in the guild shared C. a. gilcolladoi and N. fasciatus, but L. taschenbergi mainly parasitized mice (M. spretus and A. sylvaticus). We found significant male-biased infestation patterns in mice, seasonal variations in flea abundances for all rodent hosts (M. arvalis, M. spretus and A. sylvaticus), and relatively lower infestation values for voles inhabiting alfalfas. Simultaneous co-infections occurred in a third of all hosts, and N. fasciatus was the most common flea co-infecting small mammal hosts. CONCLUSIONS The generalist N. fasciatus and C. a. gilcolladoi dominated the flea community, and a high percentage of co-infections with both species occurred within the small mammal guild. Nosopsyllus fasciatus may show higher competence of inter-specific transmission, and future research should unravel its role in the circulation of rodent-borne zoonoses.
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Affiliation(s)
- Silvia Herrero-Cófreces
- Dpto. Ciencias Agroforestales, ETSIIAA, Universidad de Valladolid, Avda. de Madrid 44, 34004 Palencia, Spain
- Instituto Universitario de Investigación en Gestión Forestal Sostenible, Palencia, Spain
| | - Manuel Fabio Flechoso
- Dpto. Ciencias Agroforestales, ETSIIAA, Universidad de Valladolid, Avda. de Madrid 44, 34004 Palencia, Spain
- Dpto. Biología Animal (Zoología), Universidad de Salamanca, Campus Unamuno S/N, 37007 Salamanca, Spain
| | - Ruth Rodríguez-Pastor
- Dpto. Ciencias Agroforestales, ETSIIAA, Universidad de Valladolid, Avda. de Madrid 44, 34004 Palencia, Spain
- Instituto Universitario de Investigación en Gestión Forestal Sostenible, Palencia, Spain
| | - Juan José Luque-Larena
- Dpto. Ciencias Agroforestales, ETSIIAA, Universidad de Valladolid, Avda. de Madrid 44, 34004 Palencia, Spain
- Instituto Universitario de Investigación en Gestión Forestal Sostenible, Palencia, Spain
| | - François Mougeot
- Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain
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Lauret V, Delibes-Mateos M, Mougeot F, Arroyo-Lopez B. Understanding conservation conflicts associated with rodent outbreaks in farmland areas. AMBIO 2020; 49:1122-1133. [PMID: 31542887 PMCID: PMC7067974 DOI: 10.1007/s13280-019-01256-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/26/2019] [Accepted: 09/03/2019] [Indexed: 05/15/2023]
Abstract
Rodent outbreaks affect many farmland areas worldwide and the negative environmental impacts of control campaigns cause intense social tensions. In such conservation conflicts, understanding stakeholders' viewpoints is critical to promote ecologically sustainable management. We used Q-methodology, a framework standing between qualitative and quantitative social research, to investigate human subjectivity and understand conflicts caused by rodent outbreaks in Spain. We interviewed farmers, conservationists, hunters, and governmental agencies, and identified five main discourses about the origins and consequences of the conflictive situation. Finding sustainable management is impaired by opposing views about causes and consequences of vole outbreaks and their management, which are at the root of the conflict. Social tensions will likely remain until the underlying conflicts between people holding different views are also managed. Decision-making should therefore focus on mitigating underlying conflicts. Using trained independent mediators would help the effective resolution of conservation conflicts caused by rodent outbreaks and their management.
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Affiliation(s)
- Valentin Lauret
- CEFE, Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
- Instituto de Investigación en Recursos Cinegéticos (IREC), CSIC-UCLM-JCCM, Ciudad Real, Spain
- Département de Biologie, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Miguel Delibes-Mateos
- Instituto de Estudios Sociales Avanzados (IESA-CSIC), Córdoba, Spain
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - François Mougeot
- Instituto de Investigación en Recursos Cinegéticos (IREC), CSIC-UCLM-JCCM, Ciudad Real, Spain
| | - Beatriz Arroyo-Lopez
- Instituto de Investigación en Recursos Cinegéticos (IREC), CSIC-UCLM-JCCM, Ciudad Real, Spain
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15
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Rodríguez-Pastor R, Mougeot F, Vidal MD, Jado I, González-Martín-Niño RM, Escudero R, Luque-Larena JJ. Zoonotic Bacteria in Fleas Parasitizing Common Voles, Northwestern Spain. Emerg Infect Dis 2019; 25:1423-1425. [PMID: 31211940 PMCID: PMC6590758 DOI: 10.3201/eid2507.181646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We detected Francisella tularensis and Bartonella spp. in fleas parasitizing common voles (Microtus arvalis) from northwestern Spain; mean prevalence was 6.1% for F. tularensis and 51% for Bartonella spp. Contrasted vector–host associations in the prevalence of these bacteria suggest that fleas have distinct roles in the transmission cycle of each pathogen in nature.
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Hemati M, Khalili M, Rohani M, Sadeghi B, Esmaeili S, Ghasemi A, Mahmoudi A, Gyuranecz M, Mostafavi E. A serological and molecular study on Francisella tularensis in rodents from Hamadan province, Western Iran. Comp Immunol Microbiol Infect Dis 2019; 68:101379. [PMID: 31733511 DOI: 10.1016/j.cimid.2019.101379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/27/2019] [Accepted: 10/29/2019] [Indexed: 01/11/2023]
Abstract
INTRODUCTION AND PURPOSE Tularemia is a zoonotic disease, the most important hosts of which are rodents. Endemic regions and reservoirs of F. tularensis are not well-researched areas in Iran. The present study aimed to study F. tularensis infection in the rodent populations of western Iran. MATERIALS AND METHODS Samples were collected in different areas of Kabudar Ahang County in Hamadan province (west of Iran) from 2014 to 2017. Tularemia serological and molecular tests were conducted using the tube agglutination test and Real-time PCR method tracking the ISFtu2 gene. Positive serum samples were evaluated for cross-reactivity with brucellosis. RESULTS A total of 433 rodents, collected from 33 localities, were included in the study. The most abundant species belonged to the Persian jird (Meriones persicus; 75.5%), and Libyan jird (Meriones libycus; 10.1%). Among the studied samples, three (0.74 %) were seropositive and five (1.15%) were PCR positive. Seropositive samples were two M. persicus and one M. libycus, and PCR positive rodents were four M. persicus and one M. vinogradovi. Tularemia seropositive samples showed no cross-reactivity with brucellosis. CONCLUSION Given the presence of infection in rodents with tularemia agent in the studied area, it is crucial to elucidate the risks of rodent exposure to tularemia for physicians, health personnel and the general population.
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Affiliation(s)
- Majid Hemati
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mohammad Khalili
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahdi Rohani
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Kabudar Ahang, Hamadan, Iran; Department of Microbiology, Pasteur Institute of Iran, Tehran, Iran
| | - Balal Sadeghi
- Food Hygiene and Public Health Department, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Saber Esmaeili
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Kabudar Ahang, Hamadan, Iran; Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Ahmad Ghasemi
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Kabudar Ahang, Hamadan, Iran; Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Ahmad Mahmoudi
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Kabudar Ahang, Hamadan, Iran; Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Miklós Gyuranecz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary; Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary
| | - Ehsan Mostafavi
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Kabudar Ahang, Hamadan, Iran; Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran.
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17
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Weather influences M. arvalis reproduction but not population dynamics in a 17-year time series. Sci Rep 2019; 9:13942. [PMID: 31558762 PMCID: PMC6763496 DOI: 10.1038/s41598-019-50438-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 09/12/2019] [Indexed: 01/14/2023] Open
Abstract
Rodent outbreaks have plagued European agriculture for centuries, but continue to elude comprehensive explanation. Modelling and empirical work in some cyclic rodent systems suggests that changes in reproductive parameters are partly responsible for observed population dynamics. Using a 17-year time series of Microtus arvalis population abundance and demographic data, we explored the relationship between meteorological conditions (temperature and rainfall), female reproductive activity, and population growth rates in a non-cyclic population of this grassland vole species. We found strong but complex relationships between female reproduction and climate variables, with spring female reproduction depressed after cold winters. Population growth rates were, however, uncorrelated with either weather conditions (current and up to three months prior) or with female reproduction (number of foetuses per female and/or proportion of females reproductively active in the population). These results, coupled with age-structure data, suggest that mortality, via predation, disease, or a combination of the two, are responsible for the large multi-annual but non-cyclic population dynamics observed in this population of the common vole.
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Roos D, Caminero Saldaña C, Arroyo B, Mougeot F, Luque-Larena JJ, Lambin X. Unintentional effects of environmentally-friendly farming practices: Arising conflicts between zero-tillage and a crop pest, the common vole ( Microtus arvalis). AGRICULTURE, ECOSYSTEMS & ENVIRONMENT 2019; 272:105-113. [PMID: 30774172 PMCID: PMC6360522 DOI: 10.1016/j.agee.2018.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/18/2018] [Accepted: 11/17/2018] [Indexed: 05/27/2023]
Abstract
Common voles are a main European facultative, fossorial, farmland rodent pest that can greatly reduce crop yields during population outbreaks. Crop protection against common voles is a complex task that requires the consideration of a set of preventive and control measures within an integrated pest management strategy. A possible option could be to modify farming practices to reduce the availability of refuges for rodents and the damage to crops that they subsequently cause. Farming, however, must simultaneously meet multiple goals including the reduction of the carbon (C) emissions, soil erosion and water use, and the improvement of soil quality. Crop establishment through conservation agriculture strategies, like zero-tillage, would reduce crop management investment, but is also promoted in many regions to reduce C emissions and increase soil organic matter. It could, however, create favourable refuge habitats for fossorial rodent crop pests, like common voles, benefitting from reduced soil disturbance between crop rotations and thus increasing burrow persistence. Assessing the impact that tillage practices, their interaction with different crops and the influence of proximity to potential common vole sources, have on common vole occupancy could provide a valuable tool within an integrated management strategy. Using a 2-ha experimental field with 62 plots 180 m2 (each roughly matching common vole home range size) located experimental plots in north-western Spain, we tested how tillage practices, crop type (wheat, barley, vetch, Narbonne vetch, pea and fallow) and distances from possible colonization sources affect field use by common vole during low population density conditions. Our results show that tillage practices have more influence on common vole occurrence (zero tillage > reduced and conventional tillage) than other aspects such as crop type thus supporting the hypothesis that tillage practices play a key role in common vole habitat use.
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Affiliation(s)
- Deon Roos
- School of Biological Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
- Área de Plagas, Instituto Tecnológico Agrario de Castilla y León (ITACyL), Ctra. Burgos km 119, 47071, Valladolid, Spain
| | - Constantino Caminero Saldaña
- Área de Plagas, Instituto Tecnológico Agrario de Castilla y León (ITACyL), Ctra. Burgos km 119, 47071, Valladolid, Spain
| | - Beatriz Arroyo
- Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - François Mougeot
- Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - Juan José Luque-Larena
- Dpto. Ciencias Agroforestales, ETSIIAA, Universidad de Valladolid, Avda. de Madrid 44, 34004, Palencia, Spain
- Instituto Universitario de Investigación en Gestión Forestal Sostenible, Palencia, Spain
| | - Xavier Lambin
- School of Biological Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
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Zoonotic pathogens in fluctuating common vole (Microtus arvalis) populations: occurrence and dynamics. Parasitology 2018; 146:389-398. [PMID: 30246665 DOI: 10.1017/s0031182018001543] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Diseases and host dynamics are linked, but their associations may vary in strength, be time-lagged, and depend on environmental influences. Where a vector is involved in disease transmission, its dynamics are an additional influence, and we often lack a general understanding on how diseases, hosts and vectors interact. We report on the occurrence of six zoonotic arthropod-borne pathogens (Anaplasma, Bartonella, Borrelia, Coxiella, Francisella and Rickettsia) in common voles (Microtus arvalis) throughout a population fluctuation and how their prevalence varies according to host density, seasonality and vector prevalence. We detected Francisella tularensis and four species of Bartonella, but not Anaplasma, Borrelia, Coxiella or Rickettsia. Bartonella taylorii and B. grahamii prevalence increased and decreased with current host (vole and mice) density, respectively, and increased with flea prevalence. Bartonella doshiae prevalence decreased with mice density. These three Bartonella species were also more prevalent during winter. Bartonella rochalimae prevalence varied with current and previous vole density (delayed-density dependence), but not with season. Coinfection with F. tularensis and Bartonella occurred as expected from the respective prevalence of each disease in voles. Our results highlight that simultaneously considering pathogen, vector and host dynamics provide a better understanding of the epidemiological dynamics of zoonoses in farmland rodents.
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Valerio M, López-Medrano F, Regalado-Artamendi I, Muñoz P, Aguado JM, Bouza E. A patient with a rapidly lethal pneumonia after a visit to a touristic area in rural Leon (Spain). REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2018; 31:367-373. [PMID: 29953175 PMCID: PMC6172680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Maricela Valerio
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Francisco López-Medrano
- Unit of Infectious Diseases, University Hospital 12 de Octubre. Madrid, Spain. Instituto de Investigación Biomédica i+12, Madrid, Spain,Medicine Department, School of Medicine, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | | | - Patricia Muñoz
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain
| | - José María Aguado
- Unit of Infectious Diseases, University Hospital 12 de Octubre. Madrid, Spain. Instituto de Investigación Biomédica i+12, Madrid, Spain,Medicine Department, School of Medicine, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Emilio Bouza
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,Medicine Department, School of Medicine, Universidad Complutense de Madrid (UCM), Madrid, Spain,CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain
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21
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Pilo P. Phylogenetic Lineages of Francisella tularensis in Animals. Front Cell Infect Microbiol 2018; 8:258. [PMID: 30109216 PMCID: PMC6079424 DOI: 10.3389/fcimb.2018.00258] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 07/11/2018] [Indexed: 12/24/2022] Open
Abstract
Tularemia is a zoonotic disease caused by the facultative intracellular bacterium Francisella tularensis. This microorganism can infect a plethora of animal species and its ecology is particularly complex. Much research was performed to understand its biology but many questions are still open, especially concerning the life cycle of this bacterium in the environment related to physical and biological parameters. Numerous animals are major hosts of F. tularensis but precise reservoir species are not yet well defined. Moreover, the exact range of species susceptible to tularemia is not clear and is complicated by the differences in virulence and ecology observed among the subspecies of F. tularensis. Indeed, different life cycles in nature, including the animal species concerned, were previously described for F. tularensis subsp. tularensis and F. tularensis subsp. holarctica. Recently, molecular techniques showing adequate discrimination between strains were developed, leading to the possibility to investigate links between phylogenetic lineages and infection in animals. New perspectives in research are now possible thanks to the information available and the simplicity of the molecular procedures. Current studies are unfolding the evolution of F. tularensis and these developments will lead to the elucidation of geographical and ecological differences observed by veterinarians, microbiologists and conservation biologists. However, systematic, coordinated collection of data and extensive sampling are important to efficiently assemble the findings of future research.
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Affiliation(s)
- Paola Pilo
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
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Mostafavi E, Ghasemi A, Rohani M, Molaeipoor L, Esmaeili S, Mohammadi Z, Mahmoudi A, Aliabadian M, Johansson A. Molecular Survey of Tularemia and Plague in Small Mammals From Iran. Front Cell Infect Microbiol 2018; 8:215. [PMID: 30042927 PMCID: PMC6048195 DOI: 10.3389/fcimb.2018.00215] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/07/2018] [Indexed: 12/04/2022] Open
Abstract
Introduction: Plague and tularemia are zoonoses and their causative bacteria are circulating in certain regions of Iran. This study was conducted to investigate potential disease reservoirs amongst small wildlife species in different regions of Iran. Methods: Rodents, insectivores and hares from 17 different provinces of the country were collected in 2014 and 2015. Samples were taken from the spleens of the animals and Real-time PCR was applied to detect nucleic acid sequences that are specific to Francisella tularensis and Yersinia pestis, respectively. Results: Among 140 collected rodents, 25 distinct species were identified out of which five were the most common: Microtus paradoxus (21% out of 140 rodents), Apodemus witherbyi (12%), Microtus irani (11%), Mus musculus (11%) and Microtus socialis (10%). Seventeen insectivores were collected and identified as Crocidura suaveolens (82%) and C. leucodon (18%). Fifty-one hares were collected and identified as Lepus europaeus (57%), Lepus tolai (14%) and Lepus sp. (29%). Three out of 140 explored rodents (1.91%) were positive for F. tularensis, an A. witherbyi, a Mus musculus domesticus, and a Chionomys nivalis collected from Golestan, Khuzestan and Razavi Khorasan provinces, respectively. Two hares (3.92%) were F. tularensis-positive, a L. europaeus from Khuzestan and a Lepus sp. from the Sistan and Baluchistan province. None of the tested animals were positive for Y. pestis. Conclusion: This is the first report of direct detection of F. tularensis in mammals of Iran and the first-time observation of the agent in a snow vole, C. nivalis worldwide. The results indicate that tularemia is more widespread in Iran than previously reported including the Northeast and Southwestern parts of the country. Future studies should address genetic characterization of F. tularensis positive DNA samples from Iran to achieve molecular subtyping and rule out assay cross-reactivity with near neighbor Francisella species.
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Affiliation(s)
- Ehsan Mostafavi
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Kabudar Ahang, Iran.,Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Ahmad Ghasemi
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Kabudar Ahang, Iran.,Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran.,Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahdi Rohani
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Kabudar Ahang, Iran.,Department of Microbiology, Pasteur Institute of Iran, Tehran, Iran
| | - Leila Molaeipoor
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran.,Department of Epidemiology, School of Public Health, Iran University of Medical Sciences, Tehran, Iran.,Student Research Committee, Faculty of Public Health Branch, Iran University of Medical Sciences, Tehran, Iran
| | - Saber Esmaeili
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Kabudar Ahang, Iran.,Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran.,Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zeinolabedin Mohammadi
- Rodentology Research Department, Applied Animal Institute, Ferdowsi University of Mashhad, Mashhad, Iran.,Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmad Mahmoudi
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Kabudar Ahang, Iran.,Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran.,Rodentology Research Department, Applied Animal Institute, Ferdowsi University of Mashhad, Mashhad, Iran.,Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mansour Aliabadian
- Rodentology Research Department, Applied Animal Institute, Ferdowsi University of Mashhad, Mashhad, Iran.,Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Anders Johansson
- Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
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Romairone J, Jiménez J, Luque-Larena JJ, Mougeot F. Spatial capture-recapture design and modelling for the study of small mammals. PLoS One 2018; 13:e0198766. [PMID: 29879211 PMCID: PMC5991742 DOI: 10.1371/journal.pone.0198766] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/24/2018] [Indexed: 11/18/2022] Open
Abstract
Spatial capture-recapture modelling (SCR) is a powerful analytical tool to estimate density and derive information on space use and behaviour of elusive animals. Yet, SCR has been seldom applied to the study of ecologically keystone small mammals. Here we highlight its potential and requirements with a case study on common voles (Microtus arvalis). First, we address mortality associated with live-trapping, which can be high in small mammals, and must be kept minimal. We designed and tested a nest box coupled with a classic Sherman trap and show that it allows a 5-fold reduction of mortality in traps. Second, we address the need to adjust the trapping grid to the individual home range to maximize spatial recaptures. In May-June 2016, we captured and tagged with transponders 227 voles in a 1.2-ha area during two monthly sessions. Using a Bayesian SCR with a multinomial approach, we estimated: (1) the baseline detection rate and investigated variation according to sex, time or behaviour (aversion/attraction after a previous capture); (2) the parameter sigma that describes how detection probability declines as a function of the distance to an individual´s activity centre, and investigated variation according to sex; and (3) density and population sex-ratio. We show that reducing the maximum distance between traps from 12 to 9.6m doubled spatial recaptures and improved model predictions. Baseline detection rate increased over time (after overcoming a likely aversion to entering new odourless traps) and was greater for females than males in June. The sigma parameter of males was twice that of females, indicating larger home ranges. Density estimates were of 142.92±38.50 and 168.25±15.79 voles/ha in May and June, respectively, with 2–3 times more females than males. We highlight the potential and broad applicability that SCR offers and provide specific recommendations for using it to study small mammals like voles.
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Affiliation(s)
- Juan Romairone
- Dpto. Ciencias Agroforestales, Escuela Técnica Superior de Ingenierías, Universidad de Valladolid, Avda. De Madrid, Palencia, Spain.,Instituto Universitario de Investigación en Gestión Forestal Sostenible (iuFOR), Avda. De Madrid, Palencia, Spain
| | - José Jiménez
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ronda de Toledo, Ciudad Real, Spain
| | - Juan José Luque-Larena
- Dpto. Ciencias Agroforestales, Escuela Técnica Superior de Ingenierías, Universidad de Valladolid, Avda. De Madrid, Palencia, Spain.,Instituto Universitario de Investigación en Gestión Forestal Sostenible (iuFOR), Avda. De Madrid, Palencia, Spain
| | - François Mougeot
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ronda de Toledo, Ciudad Real, Spain
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