Persistent anthrax as a major driver of wildlife mortality in a tropical rainforest (original) (raw)

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Acknowledgements

We thank the authorities in Côte d’Ivoire for long-term support, especially the Ministry of the Environment and Forests, the Ministry of Research, the directorship of the TNP and the CSRS in Abidjan; and national authorities from all other countries for providing permissions for our research (MINFoF, MINRESI, the Service de la Conservation de la Réserve du Dja, Cameroon, in Central African Republic; the Ministère des Eaux et Fôrets, Chasse et Peche and the Ministère de l’Education Nationale, de l’Alphabetisation, de l’Enseignement Superieur, et de la Recherche, the Agence Nationale des Parcs Nationaux, Gabon; Centre National de la Recherche Scientifique et Technologique, Gabon; Direction des Eaux, Forêts et Chasses, Senegal; Forestry Development Authority, Liberia; Institut Congolais pour la Conservation de la Nature, Democratic Republic of the Congo; Ministère de l’Agriculture de l’Elevage et des Eaux et Forêts, Guinea; Instituto da Biodiversidade e das Áreas Protegidas (IBAP), Guinea-Bissau; Ministère de la Recherche Scientifique, Democratic Republic of the Congo; Ministère de le Recherche Scientifique et Technologique, Democratic Republic of the Congo; Nigeria National Park Service, Nigeria, Uganda National Council for Science and Technology, Ugandan Wildlife Authority, Uganda). We thank the WWF Central African Republic, T. Börding, T. Hicks, Y. Moebius, V. Sommer, K. Zuberbühler and M. Peeters for their logistical support; the field assistants A. Henlin, K. Albrechtova and A. Lang for the collection of samples in TNP; and the field assistants from all other sites for their support; S. Becker, T. Franz, S. Howaldt, A. Lander, P. Lochau, H. Nattermann and A. Schneider for the laboratory work; J. Hinzmann, A. Nitsche and J. Tesch for sequencing; P. Wojciech Dabrowski and T. Semmler from RKI, as well as G. Hamilton at Glasgow Polyomics, for bioinformatic support; and M. Kovacev-Wegener for administrative support. We thank the German Research Council DFG KL 2521/1-1 and the Sonnenfeld-Stiftung for funding; and the Max-Planck-Society and Krekeler Foundation for funding of the Pan African Programme.

Author information

Author notes

  1. Constanze Hoffmann and Fee Zimmermann: These authors contributed equally to this work.

Authors and Affiliations

  1. Robert Koch Institute, P3: “Epidemiology of Highly Pathogenic Microorganisms”, Seestraße 10–11, Berlin, 13353, Germany
    Constanze Hoffmann, Fee Zimmermann, Kathrin Nowak, Anja Blankenburg, Ariane Düx, Jan F. Gogarten, Siv Aina Leendertz, Floraine Léguillon, Therese Löhrich, Kevin Merkel, Sonja Metzger, Svenja Niedorf, Hélène De Nys, Andreas Sachse, Ulla Thiesen, Doris Wu, Sébastien Calvignac-Spencer & Fabian H. Leendertz
  2. Robert Koch Institute, ZBS 2: Centre for Biological Threats and Special Pathogens, Highly Pathogenic Microorganisms, Seestraße 10–11, Berlin, 13353, Germany
    Fee Zimmermann, Susann Dupke, Roland Grunow & Silke R. Klee
  3. Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
    Roman Biek
  4. Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, Leipzig, 04103, Germany
    Hjalmar Kuehl, Roger Mundry, Anthony Agbor, Samuel Angedakin, Mimi Arandjelovic, Gregory Brazolla, Katherine Corogenes, Tobias Deschner, Paula Dieguez, Karsten Dierks, Henk Eshuis, Yisa Ginath Yuh, Jan F. Gogarten, Anne-Céline Granjon, Sorrel Jones, Jessica Junker, Juan Lapuente, Kevin Lee, Therese Löhrich, Sergio Marrocoli, Amelia Meier, Mizuki Murai, Hélène De Nys, Joost van Schijndel, Doris Wu, Christophe Boesch & Roman M. Wittig
  5. LANADA/LCVB, Bingerville, 206, Côte d’Ivoire
    Emmanuel Couacy-Hymann
  6. World Health Organization, Geneva 27, 1211, Switzerland
    Pierre Formenty
  7. Chimbo Foundation, Amstel 49, Amsterdam, 1011 PW, The Netherlands
    Annemarie Goedmakers & Els Ton
  8. Department of Biology, McGill University, 855 Sherbrooke Street, West Montreal, H3A 2T7, Quebec, Canada
    Jan F. Gogarten
  9. Department of Anthropology, The Ohio State University, 4034 Smith Laboratory, 174 West 18th Avenue, Columbus, 43210, Ohio, USA
    Scott McGraw
  10. Lukuru Foundation, 1235 Avenue des Poids Lourds/Quartier de Kingabois, Kinshasa, Democratic Republic of the Congo
    John Hart
  11. Limbe Wildlife Centre, Limbe, Cameroon
    John Kiang
  12. Arizona State University, PO Box 872402, Tempe, 85287-2402, Arizona, USA
    Kevin Langergraber
  13. Wild Chimpanzee Foundation (WCF), Deutscher Platz 6, Leipzig, 04103, Germany
    Vera Leinert
  14. German Primate Center, Kellnerweg 4, Göttingen, 37077, Germany
    Kerstin Mätz-Rensing
  15. Robert Koch Institute, Seestraße 10–11, Berlin, 13353, Germany
    Lothar H. Wieler

Authors

  1. Constanze Hoffmann
  2. Fee Zimmermann
  3. Roman Biek
  4. Hjalmar Kuehl
  5. Kathrin Nowak
  6. Roger Mundry
  7. Anthony Agbor
  8. Samuel Angedakin
  9. Mimi Arandjelovic
  10. Anja Blankenburg
  11. Gregory Brazolla
  12. Katherine Corogenes
  13. Emmanuel Couacy-Hymann
  14. Tobias Deschner
  15. Paula Dieguez
  16. Karsten Dierks
  17. Ariane Düx
  18. Susann Dupke
  19. Henk Eshuis
  20. Pierre Formenty
  21. Yisa Ginath Yuh
  22. Annemarie Goedmakers
  23. Jan F. Gogarten
  24. Anne-Céline Granjon
  25. Scott McGraw
  26. Roland Grunow
  27. John Hart
  28. Sorrel Jones
  29. Jessica Junker
  30. John Kiang
  31. Kevin Langergraber
  32. Juan Lapuente
  33. Kevin Lee
  34. Siv Aina Leendertz
  35. Floraine Léguillon
  36. Vera Leinert
  37. Therese Löhrich
  38. Sergio Marrocoli
  39. Kerstin Mätz-Rensing
  40. Amelia Meier
  41. Kevin Merkel
  42. Sonja Metzger
  43. Mizuki Murai
  44. Svenja Niedorf
  45. Hélène De Nys
  46. Andreas Sachse
  47. Joost van Schijndel
  48. Ulla Thiesen
  49. Els Ton
  50. Doris Wu
  51. Lothar H. Wieler
  52. Christophe Boesch
  53. Silke R. Klee
  54. Roman M. Wittig
  55. Sébastien Calvignac-Spencer
  56. Fabian H. Leendertz

Contributions

C.H., F.Z., A.A., S.A., M.A., G.B., K.C., T.D., P.D., K.D., H.E., P.F., Y.G.Y., A.G., A.-C.G., S.McG., J.H., S.J., J.J., J.K., K.La., J.L., K.Le., F.L., V.L., T.L., S.Ma., A.M., S.Me., M.M., J.v.S., E.T. and D.W. collected flies, bones and associated field data. Necropsies on wildlife that was found dead were performed by F.Z., K.N., A.B., E.C.-H., A.D., P.F., S.A.L., T.L., S.Me., S.N., H.D.N. and F.H.L. and laboratory analyses were performed by C.H., F.Z., K.N., S.D., R.G., K.M.-R., K.M., S.Me., H.D.N., A.S., U.T., S.R.K., L.H.W., S.C.-S. and F.H.L. The data were analysed by C.H., F.Z., R.B., H.K., R.M. and S.C.-S. and the manuscript was prepared by C.H., F.Z., R.B., H.K., R.M., J.F.G., S.C.-S. and F.H.L. The manuscript was revised and approved by all authors. The study was supervised by C.B., R.M.W., S.C.-S. and F.H.L.

Corresponding author

Correspondence toFabian H. Leendertz.

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Competing interests

The authors declare no competing financial interests.

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Extended data figures and tables

Extended Data Figure 1 Necropsies performed since 1996.

The total number of necropsies performed per year in TNP from 1996 to 2015. Grey bars indicate the number of Bcbva-positive necropsies and are annotated with the associated proportion. In the years 2003 and 2010 only limited veterinary service was available at TNP owing to political insecurity in the region.

Extended Data Figure 2 Geographic location of Bcbva-positive carcasses in TNP.

Necropsies that tested Bcbva-positive in TNP since 2001. GPS data was available for 70 of all necropsies that tested positive (n = 81).

Extended Data Figure 3 Effect of mammalian DNA content on anthrax positivity in flies.

Shown is the probability of Bcbva positivity (PA) as a function of the amount of mammalian DNA (copies) found in a fly. The amount of mammal DNA was binned (bin width of 0.25) and the area of the points depicts the number of flies (range, 1–206) in the respective bins. The dashed line indicates the fitted model and the dotted lines the 95% confidence interval.

Extended Data Figure 4 Effect of season on anthrax positivity in flies.

The probability of Bcbva positivity (PA) over the course of a year (binned in 10-day periods) is shown. The area of the points depicts the number of flies in the respective 10-day period. The dashed line indicates the fitted model and the dotted lines the 95% confidence interval.

Extended Data Figure 5 Maximum clade credibility tree based on chromosomal sequences of Bcbva isolates from TNP (Côte d’Ivoire, n = 124) and Grebo (Liberia, n = 2).

One sequence per host (mammals or flies, two divergent isolates for fly 600) was included and the final alignment of variant sites measured 298 bp. The size of the nodes represents posterior probability values. The location of the root received a posterior probability of 1.

Extended Data Figure 6 Maximum likelihood tree for sub-Saharan Bcbva strains.

Maximum likelihood tree based on chromosomal sequences of Bcbva strains from Côte d’Ivoire, Cameroon, Central African Republic and Liberia. The alignment of variant sites measured 1,016 bp. Bootstrap values are shown above the branches and the scale bar indicates substitution per chromosomal site. The tree was rooted using TempEst version 1.5.

Extended Data Figure 7 Fly snapshot sampling scheme.

For the fly snapshot, flies were caught following a 2 × 2-km grid system within and outside the research area within 19 days. In total 908 snapshot flies were analysed.

Extended Data Figure 8 Genetic and geographic distances of Bcbva isolates from the fly snapshot.

a, Maximum likelihood tree based on chromosomal sequences of Bcbva isolates from the 19-day fly snapshot. Each dot represents one fly isolate. Colours were chosen to illustrate the distribution of genetically clustering isolates on the map presented in b. The final alignment of variant sites measured 123 bp. Bootstrap values are shown above all internal branches. The tree was rooted using the ‘best-fit’ option in Path-O-Gen version 1.2. The scale bar shows substitutions per site. b, Geographic origin of Bcbva isolates collected during the fly snapshot. Colours correspond to maximum likelihood tree in a. Large circles represent two isolates.

Extended Data Figure 9 Box plot of genetic and mean geographic distances.

Bcbva isolates from TNP were binned by relative genetic distance (bin size = 0.03, approximately 2.5 SNPs).The two most genetically distant isolates received a value of 1 and all other distances were scaled accordingly. Diamonds indicate the geographic distance means of the groups. To examine variation within genetic lineages, we analysed isolates with low genetic distance (maximum relative genetic distance <0.5, marked in blue) and their mean geographic distance. For low genomic distances, the linear regression of geographic distances on genetic distances has an _R_2 of 0.72 and a slope coefficient that differs significantly from zero (Student’s _t_-test, P = 4 × 10−5).

Extended Data Figure 10 Fly species composition based on generalized mixed Yule-coalescent model (GMYC) analysis.

a–c, Fly species composition for three sites with known Bcbva occurrence: TNP, Côte d’Ivoire (a); Dja Faunal Reserve, Cameroon (b); Dzanga-Sangha Protected Areas, Central African Republic (c). The proportions of flies per site (%) belonging to a single fly species identified with GMYC models are shown. Different colours indicate different taxonomic fly families.

Supplementary information

Supplementary Information

This file contains a detailed method section as well as additional tables (Tables S1-10) and figures (Fig. S1-8). (PDF 2638 kb)

Supplementary Table 1

This file contains results that were derived from the analyses of flies caught in TNP analyzed in this study. The file includes results from PCR and culture as well as flymeal analysis results for a selection of flies. (XLSX 148 kb)

Supplementary Table 2

This file contains results of fly meal analysis with taxonomic assignment at genus level. The file provides the number of sequences per amplicon assigned at genus level. (XLSX 97 kb)

Supplementary Table 3

This file contains results of fly meal analysis with taxonomic assignment at order level. The file provides the number of sequences per amplicon assigned at order level. (XLSX 24 kb)

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Hoffmann, C., Zimmermann, F., Biek, R. et al. Persistent anthrax as a major driver of wildlife mortality in a tropical rainforest.Nature 548, 82–86 (2017). https://doi.org/10.1038/nature23309

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