A Data-driven Horizon Scan of Bacterial Pathogens at the Wildlife–livestock Interface

EcoHealth - Tập 19 - Trang 246-258 - 2022
Michelle V. Evans1,2,3, John M. Drake2,3
1MIVEGEC, Institut de Recherche pour le Développement, Montpellier, France
2Odum School of Ecology, University of Georgia, Athens, USA
3Center for Ecology of Infectious Diseases, University of Georgia, Athens, USA

Tóm tắt

Many livestock diseases rely on wildlife for the transmission or maintenance of the pathogen, and the wildlife–livestock interface represents a potential site of disease emergence for novel pathogens in livestock. Predicting which pathogen species are most likely to emerge in the future is an important challenge for infectious disease surveillance and intelligence. We used a machine learning approach to conduct a data-driven horizon scan of bacterial associations at the wildlife–livestock interface for cows, sheep, and pigs. Our model identified and ranked from 76 to 189 potential novel bacterial species that might associate with each livestock species. Wildlife reservoirs of known and novel bacteria were shared among all three species, suggesting that targeting surveillance and/or control efforts towards these reservoirs could contribute disproportionately to reducing spillover risk to livestock. By predicting pathogen-host associations at the wildlife–livestock interface, we demonstrate one way to plan for and prevent disease emergence in livestock.

Tài liệu tham khảo

Alberts, B., A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter. 2002. Introduction to Pathogens. Molecular Biology of the Cell. 4th edition. Albery GF, Eskew EA, Ross N, Olival KJ (2020) Predicting the global mammalian viral sharing network using phylogeography. Nature Communications 11:1–9 Antonovics J, Boots M, Ebert D, Koskella B, Poss M, Sadd BM (2013) The origin of specificity by means of natural selection: evolved and nonhost resistance in host-pathogen interactions. Evolution 67:1–9 Azhar EI, El-Kafrawy SA, Farraj SA, Hassan AM, Al-Saeed MS, Hashem AM, Madani TA (2014) Evidence for Camel-to-Human Transmission of MERS Coronavirus. New England Journal of Medicine 370:2499–2505 Becker DJ, Washburne AD, Faust CL, Mordecai EA, Plowright RK (2019a) The problem of scale in the prediction and management of pathogen spillover. Philosophical Transactions of the Royal Society b: Biological Sciences 374:20190224 Becker DJ, Washburne AD, Faust CL, Pulliam JRC, Mordecai EA, Lloyd-Smith JO, Plowright RK (2019b) Dynamic and integrative approaches to understanding pathogen spillover. Philosophical Transactions of the Royal Society b: Biological Sciences 374:20190014 Bivand, R., T. Keitt, and B. Rowlingson. 2021. rgdal: Bindings for the “geospatial” data abstraction library. Boyce MS, Vernier PR, Nielsen SE, Schmiegelow FKA (2002) Evaluating resource selection functions. Ecological Modelling 157:281–300 Carlson, C., M. Farrell, Z. Grange, B. Han, N. Mollentze, A. Phelan, A. Rasmussen, G. Albery, B. Bett, D. Brett-Major, L. Cohen, T. Dallas, E. Eskew, A. Fagre, K. Forbes, R. Gibb, S. Halabi, C. Hammer, R. Katz, J. Kindrachuk, R. Muylaert, F. Nutter, J. Ogola, K. Olival, M. Rourke, S. Ryan, N. Ross, S. Seifert, T. Sironen, C. Standley, K. Taylor, M. Venter, and P. Webala. 2021. Zoonotic Risk Technology Enters the Viral Emergence Toolkit. Preprints:2021040200. Causey D, Edwards SV (2008) Ecology of Avian Influenza Virus in Birds. The Journal of Infectious Diseases 197:S29–S33 Chamberlain S, Szocs E (2013) taxize - taxonomic search and retrieval in R. F1000Research 2:191 Chang CC, Chomel BB, Kasten RW, Heller RM, Ueno H, Yamamoto K, Bleich VC, Pierce BM, Gonzales BJ, Swift PK, Boyce WM, Jang SS, Boulouis HJ, Piémont Y, Rossolini GM, Riccio ML, Cornaglia G, Pagani L, Lagatolla C, Selan L, Fontana R (2000) Bartonella spp. isolated from wild and domestic ruminants in North America. Emerging Infectious Diseases 6:306–311 Chanter N (1997) Streptococci and enterococci as animal pathogens. Journal of Applied Microbiology 83:100S-109S Chen, T., and C. Guestrin. 2016. XGBoost: A Scalable Tree Boosting System. Pages 785–794 Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. Association for Computing Machinery, New York, NY, USA. Clark L, Hall J (2006) Avian Influenza in Wild Birds: Status as Reservoirs, and Risks to Humans and Agriculture. Ornithological Monographs 60:3–29 Cleaveland S, Laurenson MK, Taylor LH (2001) Diseases of humans and their domestic mammals: pathogen characteristics, host range and the risk of emergence. Philosophical Transactions of the Royal Society of London. Series b, Biological Sciences 356:991–999 Coimbra NDR, Goes-Neto A, Azevedo V, Ouangraoua A (2020) Reconstructing the phylogeny of Corynebacteriales while accounting for horizontal gene transfer. Genome Biology and Evolution 12:381–395 Cooke RSC, Bates AE, Eigenbrod F (2019) Global trade-offs of functional redundancy and functional dispersion for birds and mammals. Global Ecology and Biogeography 28:484–495 Dallas TA, Becker DJ (2021) Taxonomic resolution affects host−parasite association model performance. Parasitology 148:584–590 Dallas T, Park AW, Drake JM (2017) Predictability of helminth parasite host range using information on geography, host traits and parasite community structure. Parasitology 144:200–205 Daszak, P., R. Plowright, J. Epstein, J. Pulliam, S. Abdul Rahman, H. Field, A. Jamaluddin, S. Sharifah, C. Smith, K. Olival, S. Luby, K. Halpin, A. Hyatt, A. Cunningham, and Henipavirus Ecology Research Group. 2006. The emergence of Nipah and Hendra virus: pathogen dynamics across a wildlife–livestock-human continuum. Page in S. K. Collinge and C. Ray, editors. Disease Ecology. Oxford University Press. Davis DS, Elzer PH (2002) Brucella vaccines in wildlife. Veterinary Microbiology 90:533–544 Elith J, Leathwick JR (2009) Species Distribution Models: Ecological Explanation and Prediction Across Space and Time. Annual Review of Ecology, Evolution, and Systematics 40:677–697 Elith J, Leathwick JR, Hastie T (2008) A working guide to boosted regression trees. Journal of Animal Ecology 77:802–813 Epstein JH, Field HE, Luby S, Pulliam JRC, Daszak P (2006) Nipah virus: Impact, origins, and causes of emergence. Current Infectious Disease Reports 8:59–65 Evans MV, Dallas TA, Han BA, Murdock CC, Drake JM (2017) Data-driven identification of potential Zika virus vectors. eLife 6:e22053 Federhen S (2012) The NCBI Taxonomy database. Nucleic Acids Research 40:D136–D143 Food and Agriculture Organization of the United Nations. 2022. FAOSTAT: Statistics Database. Gibb, R., G. F. Albery, D. J. Becker, L. Brierley, R. Connor, T. A. Dallas, E. A. Eskew, M. J. Farrell, A. L. Rasmussen, S. J. Ryan, A. Sweeny, C. J. Carlson, and T. Poisot. 2021. Data proliferation, reconciliation, and synthesis in viral ecology. bioRxiv:2021.01.14.426572. Gilbert M, Nicolas G, Cinardi G, Van Boeckel TP, Vanwambeke SO, Wint GRW, Robinson TP (2018) Global distribution data for cattle, buffaloes, horses, sheep, goats, pigs, chickens and ducks in 2010. Scientific Data 5:180227 Godfroid J (2017) Brucellosis in livestock and wildlife: zoonotic diseases without pandemic potential in need of innovative one health approaches. Archives of Public Health 75:1–6 Gortazar C, Diez-Delgado I, Barasona JA, Vicente J, De La Fuente J, Boadella M (2015) The wild side of disease control at the wildlife–livestock-human interface: A review. Frontiers in Veterinary Science 1:1–12 Han, B. A., A. M. Kramer, and J. M. Drake. 2016a. Global Patterns of Zoonotic Disease in Mammals. Trends in Parasitology:1–13. Han BA, Majumdar S, Calmon FP, Glicksberg BS, Horesh R, Kumar A, Perer A, von Marschall EB, Wei D, Mojsilović A, Varshney KR (2019) Confronting data sparsity to identify potential sources of Zika virus spillover infection among primates. Epidemics 27:59–65 Han BA, Schmidt JP, Alexander LW, Bowden SE, Hayman DTS, Drake JM (2016b) Undiscovered bat hosts of Filoviruses. PLoS Neglected Tropical Diseases 10:e0004815-e4910 Han BA, Schmidt JP, Bowden SE, Drake JM (2015) Rodent reservoirs of future zoonotic diseases. Proceedings of the National Academy of Sciences 112:7039–7044 Hassell JM, Begon M, Ward MJ, Fèvre EM (2017) Urbanization and Disease Emergence: Dynamics at the Wildlife–Livestock–Human Interface. Trends in Ecology & Evolution 32:55–67 Hijmans, R. 2020. raster: Geographic data analysis and modeing. IUCN. 2021. The IUCN Red List of Threatened Species. Jones KE, Patel NG, Levy MA, Storeygard A, Balk D, Gittleman JL, Daszak P (2008) Global trends in emerging infectious diseases. Nature 451:990–993 Keating KA, Cherry S (2004) Use and Interpretation of Logistic Regression in Habitat-Selection Studies. The Journal of Wildlife Management 68:774–789 Knight-Jones TJD, Rushton J (2013) The economic impacts of foot and mouth disease – What are they, how big are they and where do they occur? Preventive Veterinary Medicine 112:161–173 Kock RA, Wamwayi HM, Rossiter PB, Libeau G, Wambwa E, Okori J, Shiferaw FS, Mlengeya TD (2006) Re-infection of wildlife populations with rinderpest virus on the periphery of the Somali ecosystem in East Africa. Preventive Veterinary Medicine 75:63–80 Lancaster T, Imbens G (1996) Case-control studies with contaminated controls. Journal of Econometrics 71:145–160 Liu C, Newell G, White M (2015) On the selection of thresholds for predicting species occurrence with presence-only data. Ecology and Evolution 6:337–348 Logan NAY (1988) 1988. Bacillus species of medical and veterinary importance. Journal of Medical Microbiology 25:157–165 Luis AD, O’Shea TJ, Hayman DTS, Wood JLN, Cunningham AA, Gilbert AT, Mills JN, Webb CT (2015) Network analysis of host–virus communities in bats and rodents reveals determinants of cross-species transmission. Ecology Letters 18:1153–1162 Majewska AA, Huang T, Han B, Drake JM (2021) Predictors of zoonotic potential in helminths. Philosophical Transactions of the Royal Society B: Biological Sciences 376:20200356 Miller RS, Farnsworth ML, Malmberg JL (2013) Diseases at the livestock–wildlife interface: Status, challenges, and opportunities in the United States. Preventive Veterinary Medicine 110:119–132 Morens DM, Holmes EC, Davis AS, Taubenberger JK (2011) Global rinderpest eradication: Lessons learned and why humans should celebrate too. The Journal of Infectious Diseases 204:502–505 Morse SS (1995) Factors in the emergence of infectious diseases. Emerging Infectious Diseases 1:7–15 Narrod C, Zinsstag J, Tiongco M (2012) A One Health Framework for Estimating the Economic Costs of Zoonotic Diseases on Society. EcoHealth 9:150–162 Nenzén HK, Araújo MB (2011) Choice of threshold alters projections of species range shifts under climate change. Ecological Modelling 222:3346–3354 Olival KJ, Hosseini PR, Zambrana-Torrelio C, Ross N, Bogich TL, Daszak P (2017) Host and viral traits predict zoonotic spillover from mammals. Nature 546:646–650 Olsen SC (2010) Brucellosis in the United States: Role and significance of wildlife reservoirs. Vaccine 28:F73–F76 Olson DM, Dinerstein E, Wikramanayake ED, Burgess ND, Powell GVN, Underwood EC, D’amico JA, Itoua I, Strand HE, Morrison JC, Loucks CJ, Allnutt TF, Ricketts TH, Kura Y, Lamoreux JF, Wettengel WW, Hedao P, Kassem KR (2001) Terrestrial ecoregions of the world: A new map of life on earth. BioScience 51:933–938 Pacifici M, Santini L, Marco MD, Baisero D, Francucci L, Marasini GG, Visconti P, Rondinini C (2013) Generation Length for Mammals. Nature Conservation 5:89–94 Paradis E, Schliep K (2019) ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35:526–528 Pearson RG, Raxworthy CJ, Nakamura M, Townsend Peterson A (2006) Predicting species distributions from small numbers of occurrence records: a test case using cryptic geckos in Madagascar. Journal of Biogeography 34:102–117 Pebesma E (2018) Simple features for R: Standardized support for spatial vector data. The R Journal 10:439–446 Perry BD, Grace D, Sones K (2013) Current drivers and future directions of global livestock disease dynamics. Proceedings of the National Academy of Sciences 110:20871–20877 Prager KC, Mazet JAK, Dubovi EJ, Frank LG, Munson L, Wagner AP, Woodroffe R (2012) Rabies virus and canine distemper virus in wild and domestic carnivores in northern Kenya: Are domestic dogs the reservoir? EcoHealth 9:483–498 R Core Team (2018) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing Rhyan JC, Nol P, Quance C, Gertonson A, Belfrage J, Harris L, Straka K, Robbe-Austerman S (2013) Transmission of Brucellosis from Elk to Cattle and Bison, Greater Yellowstone Area, USA, 2002–2012. Emerging Infectious Diseases 19:1992–1995 Rota CT, Millspaugh JJ, Kesler DC, Lehman CP, Rumble MA, Jachowski CMB (2013) A re-evaluation of a case–control model with contaminated controls for resource selection studies. Journal of Animal Ecology 82:1165–1173 Royle JA, Chandler RB, Yackulic C, Nichols JD (2012) Likelihood analysis of species occurrence probability from presence-only data for modelling species distributions. Methods in Ecology and Evolution 3:545–554 Schatz AM, Park AW (2021) Host and parasite traits predict cross-species parasite acquisition by introduced mammals. Proceedings of the Royal Society b: Biological Sciences 288:20210341 Schumaker BA, Peck DE, Kauffman ME (2012) Brucellosis in the Greater Yellowstone area: disease management at the wildlife– livestock interface. Human-Wildlife Interactions 6:48–63 Shaw LP, Wang AD, Dylus D, Meier M, Pogacnik G, Dessimoz C, Balloux F (2020) The phylogenetic range of bacterial and viral pathogens of vertebrates. Molecular Ecology 29:3361–3379 Siembieda JL, Kock RA, McCracken TA, Newman SH (2011) The role of wildlife in transboundary animal diseases. Animal Health Research Reviews 12:95–111 Sowani H, Kulkarni M, Zinjarde S (2018) An insight into the ecology, diversity and adaptations of Gordonia species. Critical Reviews in Microbiology 44:393–413 Spalding MD, Fox HE, Allen GR, Davidson N, Ferdaña ZA, Finlayson M, Halpern BS, Jorge MA, Lombana A, Lourie SA, Martin KD, McManus E, Molnar J, Recchia CA, Robertson J (2007) Marine ecoregions of the world: A bioregionalization of coastal and shelf areas. BioScience 57:573–583 Stephens PR, Pappalardo P, Huang S, Byers JE, Farrell MJ, Gehman A, Ghai RR, Haas SE, Han B, Park AW, Schmidt JP, Altizer S, Ezenwa VO, Nunn CL (2017) Global Mammal Parasite Database version 2.0. Ecology 98:1476–1476 Upham NS, Esselstyn JA, Jetz W (2019) Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLOS Biology 17:e3000494 Vinderola G, Ouwehand AC, Salminen S, von Wright A (eds) (2019) Lactic Acid Bacteria: Microbiological and Functional Aspects, 5th edn. Boca Raton: CRC Press Ward G, Hastie T, Barry S, Elith J, Leathwick JR (2009) Presence-Only Data and the EM Algorithm. Biometrics 65:554–563 Wardeh M, Risley C, McIntyre MK, Setzkorn C, Baylis M (2015) Database of host-pathogen and related species interactions, and their global distribution. Scientific Data 2:150049 Wiethoelter AK, Beltrán-Alcrudo D, Kock R, Mor SM (2015) Global trends in infectious diseases at the wildlife–livestock interface. Proceedings of the National Academy of Sciences 112:9662–9667 Wilman H, Belmaker J, Simpson J, de la Rosa C, Rivadeneira MM, Jetz W (2014) EltonTraits 1.0: Species-level foraging attributes of the world’s birds and mammals. Ecology 95:2027–2027 Winter DJ (2017) rentrez: an R package for the NCBI eUtils API. The R Journal 9:520–526 Woodroffe R, Donnelly CA, Cox DR, Gilks P, Jenkins HE, Johnston WT, Le Fevre AM, Bourne FJ, Cheeseman CL, Clifton-Hadley RS, Gettinby G, Hewinson RG, McInerney JP, Mitchell AP, Morrison WI, Watkins GH (2009) Bovine Tuberculosis in cattle and badgers in localized culling areas. Journal of Wildlife Diseases 45:128–143 World Organization for Animal Health. 2021. Terrestrial Animal Health Code. Zhang T, Yu B (2005) Boosting with early stopping: Convergence and consistency. The Annals of Statistics 33:1538–1579