Occupancy modeling for improved accuracy and understanding of pathogen prevalence and dynamics

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  Colvin, Michael E ^a,b   Peterson, James T ^a   Kent, Michael L ^a   Schreck, Carl B ^a  

^a OREGON STATE UNIVERSITY   (United States)

^b MISSISSIPPI STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL TISSUE; ARTICLE; COMMUNITY DYNAMICS; DIAGNOSTIC TEST; ECHINOSTOMA; HISTOLOGY; INFECTION RATE; MICROBIOLOGY; MICROORGANISM DETECTION; MYXOZOA; NANOPHYETUS SALMINCOLA; NONHUMAN; OCCUPANCY MODEL; ONCORHYNCHUS TSHAWYTSCHA; PARVICAPSULA MINIBICORNIS; PREVALENCE; PROBABILITY; RENIBACTERIUM SALMONINARUM; SAMPLE SIZE; SENSITIVITY ANALYSIS; STATISTICAL ANALYSIS; STATISTICAL MODEL; TISSUE DISTRIBUTION; ANIMAL; BIOLOGICAL MODEL; HOST PATHOGEN INTERACTION; MICROCOCCACEAE; MICROFLORA; PARASITOLOGY; PATHOGENICITY; SALMONINE; TREMATODE;

NANOPHYETUS; ONCORHYNCHUS TSHAWYTSCHA; PARVICAPSULA MINIBICORNIS; RENIBACTERIUM SALMONINARUM;

ANIMALS; HOST-PATHOGEN INTERACTIONS; MICROBIOTA; MICROCOCCACEAE; MODELS, BIOLOGICAL; SALMON; TREMATODA;

EID: 84928914702     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0116605     Document Type: Article

References (57)

1. Starliper CE, Schill WB (2011) Columnaris disease, coldwater disease, and bacterial gill disease. In: Woo PTK, Bruno DW, editors. Fish diseases and disorders, volume 3: viral, bacterial and fungal Infections. 2nd ed. Cambridge, MA: CABI International. pp. 606-631.
2. Kock RA, Woodford MH, Rossiter PB (2010) Disease risks associated with the translocation of wildlife. Revue Scientifique Et Technique-Office International Des Epizooties 29: 329-350. PMID: 20919586
3. Cunningham AA (1996) Disease risks of wildlife translocations. Conservation Biology 10: 349-353.
4. Leighton FA (2002) Health risk assessment of the translocation of wild animals. Revue Scientifique Et Technique De L Office International Des Epizooties 21: 187-195.
5. Nehring RB, Walker PG (1996) Whirling disease in the wild: the new reality in the intermountain West. Fisheries 21: 28-30.
6. Vincent ER (1996) Whirling disease and wild trout: The Montana experience. Fisheries 21: 32-34.
7. Hiner M, Moffitt CM (2001) Variation in infections of Myxobolus cerebralis in field-exposed cutthroat and rainbow trout in Idaho. Journal of Aquatic Animal Health 13: 124-132.
8. Allen TJ (1986) Evaluation of movements, harvest rate, vulnerability and survival of translocated racoons in southern West Virginia. Transactions of the Northeastern Section of the Wildlife Society 43: 64.
9. Anthony JA, Childs JE, Glass GE, Korch GW, Ross L, et al. (1990) Land-Use Associations and Changes in Population Indexes of Urban Raccoons during a Rabies Epizootic. Journal of Wildlife Diseases 26: 170-179. PMID: 2338721
10. Warner RE (1968) The role of introduced disease in the extinction of the endemic Hawaiian avifauna. The Condor 70: 101-120.
11. Adams MJ, Chelgren ND, Reinitz D, Cole RA, Rachowicz LJ, et al. (2010) Using occupancy models to understand the distribution of an amphibian pathogen, Batrachochytrium dendrobatidis. Ecological Applications 20: 289-302. PMID: 20349848
12. Hanna SE, Connor CJ, Wang HH (2005) Real-time polymerase chain reaction for the food microbiologist: Technologies, applications, and limitations. Journal of Food Science 70: R49-R53.
13. Meyer CP, Paulay G (2005) DNA barcoding: Error rates based on comprehensive sampling. Plos Biology 3: 2229-2238.
14. Wilcox TM, McKelvey KS, Young MK, Jane SF, Lowe WH, et al. (2013) Robust Detection of Rare Species Using Environmental DNA: The Importance of Primer Specificity. Plos One 8. doi: 10.1371/ journal.pone.0082806 PMID: 24482673
15. Rodnick KJ, St.-Hilaire S, Battiprolu PK, Seiler SM, Kent ML, et al. (2008) Habitat Selection Influences Sex Distribution, Morphology, Tissue Biochemistry, and Parasite Load of Juvenile Coho Salmon in the West Fork Smith River, Oregon. Transactions of the American Fisheries Society 137: 1571-1590.
16. Kent ML, Traxler GS, Kieser D, Richard J, Dawe SC, et al. (1998) Survey of salmonid pathogens in ocean-caught fishes in British Columbia, Canada. Journal of Aquatic Animal Health 10: 211-219.
17. Kent M, Benda S, St-Hilaire S, Schreck CB (2013) Sensitivity and specificity of histology for diagnoses of four common pathogens and detection of non-target pathogens in adult Chinook salmon in freshwater. Journal of Veterinary Diagnostic Investigation 25: 341-351. doi: 10.1177/1040638713482124 PMID: 23536613
18. Ferguson JA, St-Hilaire S, Peterson TS, Rodnick KJ, Kent ML (2011) Survey of parasites in threatened stocks of coho salmon (Oncorhynchus kisutch) in Oregon by examination of wet tissues and histology. Journal of Parasitology 97: 1085-1098. doi: 10.1645/GE-2757.1 PMID: 21668345
19. Blaustein AR, Romansic JM, Scheessele EA, Han BA, Pessier AP, et al. (2005) Interspecific variation in susceptibility of frog tadpoles to the pathogenic fungus Batracbochytrium dendrobatidis. Conservation Biology 19: 1460-1468.
20. Saksida SM, Marty GD, Jones SRM, Manchester HA, Diamond CL, et al. (2012) Parasites and hepatic lesions among pink salmon, Oncorhynchus gorbuscha (Walbaum), during early seawater residence. Journal of Fish Diseases 35: 137-151. doi: 10.1111/j.1365-2761.2011.01330.x PMID: 22233513
21. Koponen K, Myers MS, Ritola O, Huuskonen SE, Lindstrom-Seppa P (2001) Histopathology of feral fish from a PCB-Contaminated freshwater lake. Ambio 30: 122-126. PMID: 11436658
22. Stentiford GD, Longshaw M, Lyons BP, Jones G, Green M, et al. (2003) Histopathological biomarkers in estuarine fish species for the assessment of biological effects of contaminants. Marine Environmental Research 55: 137-159. PMID: 12502035
23. NRC, (National Research Council) (2008) Brucellosis in the Greater Yellowstone Area. Washington, DC: The National Academy Press.
24. NRC, (National Research Council) (2011) Guide for the care and use of laboratory animals. Washington, DC: The National Academy Press.
25. Greiner M, Gardner IA (2000) Application of diagnostic tests in veterinary epidemiologic studies. Preventive Veterinary Medicine 45: 43-59. PMID: 10802333
26. Tamhane A (2008) Matched-sample analysis: Sensitivity, specificity, and P values. Clinical Infectious Diseases 46: 474-475. doi: 10.1086/524893 PMID: 18181745
27. AFS-FHS, (American Fisheries Society-Fish Health Section), (2010) AFS-FHS blue book: suggested procedures for the detection and identification of certain finfish and shellfish pathogens. Bethesda, MD: American Fisheries Society.
28. Courcoul A, Moyen JL, Brugere L, Faye S, Henault S, et al. (2014) Estimation of Sensitivity and Specificity of Bacteriology, Histopathology and PCR for the Confirmatory Diagnosis of Bovine Tuberculosis Using Latent Class Analysis. Plos One 9. doi: 10.1371/journal.pone.0115916 PMID: 25551830
29. Williams CJ, Moffitt CM (2005) Estimation of pathogen prevalence in pooled samples using maximum likelihood methods and open-source software. Journal of Aquatic Animal Health 17: 386-391.
30. Williams CJ, Moffitt CM (2010) Estimation of fish and wildlife disease prevalence from imperfect diagnostic tests on pooled samples with varying pool sizes. Ecological Informatics 5: 273-280.
31. Lachish S, Gopalaswamy AM, Knowles SCL, Sheldon BC (2012) Site-occupancy modelling as a novel framework for assessing test sensitivity and estimating wildlife disease prevalence from imperfect diagnostic tests. Methods in Ecology and Evolution 3: 339-348.
32. Thompson KG (2007) Use of site occupancy models to estimate prevalence of Myxobolus cerebralis infection in trout. Joural of Aquatic Animal Health 19: 8-13. doi: 10.1577/H06-016.1 PMID: 18236627
33. McClintock BT, Nichols JD, Bailey LL, MacKenzie DI, Kendall WL, et al. (2010) Seeking a second opinion: uncertainty in disease ecology. Ecology Letters 13: 659-674. doi: 10.1111/j.1461-0248.2010.01472.x PMID: 20426794
34. Miller DAW, Talley BL, Lips KR, Grant EH (2012) Estimating patterns and drivers of infection prevalence and intensity when detection is imperfect and sampling error occurs. Methods in Ecology and Evolution 3: 850-859.
35. NMFS, (National Marine Fisheries Service) (1999) Endangered and threatened species: threatened status for three Chinook salmon evolutionarily significant units (ESUs) in Washington and Oregon, and endangered status for one Chinook salmon ESU in Washington. Federal Register 64: 14308-14328.
36. Schreck CB, Kent ML, Colvin ME, Benda S, Sharpe C, et al. (2013) Potential causes and managemant of prespawn mortality in adult upper Willamette River spring Chinook. Annual Report to for the US Army Corps of Engineers, Portland District.
37. Luna LG (1968) Manual of histologic staining methods of the Armed Forces Institute of Pathology. New York: McGraw-Hill Book Company.
38. Link WA, Barker RJ (2009) Bayesian inference: with ecological applications. San Francisco: Academic Press.
39. Lunn DJ, Thomas A, Best N, Spiegelhalter D (2000) WinBUGS - a Bayesian modelling framework: concepts, structure, and extensibility. Statistics and Computing 10: 325-337.
40. Gelman A, Rubin DB (1992) Inference from iterative simulation using multiple sequences. Statistical Science 7: 457-511.
41. Gelman A, Hill J (2007) Data analysis using regression and multilevel/hierarchical models. Cambridge; New York: Cambridge; New York: Cambridge University Press. doi: 10.1093/jxb/erm028 PMID: 25506957
42. R Development Core Team (2010) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
43. Sturtz S, Ligges U., Gelman A (2005) R2WinBUGS: a package for running WinBUGS from R. Journal of Statistical Software 12: 1-16.
44. Kendall WL, White GC (2009) A cautionary note on substituting spatial subunits for repeated temporal sampling in studies of site occupancy. Journal of Applied Ecology 46: 1182-1188.
45. Guillera-Arroita G (2011) Impact of sampling with replacement in occupancy studies with spatial replication. Methods in Ecology and Evolution 2: 401-406.
46. Nichols JD, Bailey LL, O'Connell AF, Talancy NW, Grant EHC, et al. (2008) Multi-scale occupancy estimation and modelling using multiple detection methods. Journal of Applied Ecology 45: 1321-1329.
47. Pascho RJ, Goodrich TD, McKibben CL (1997) Evaluation by enzyme-linked immunosorbent assay (ELISA) of Renibacterium salmoninarum bacterins affected by persistence of bacterial antigens. Journal of Aquatic Animal Health 9: 99-107.
48. MacKenzie DI, Nichols JD, Lachman GB, Droege S, Royle JA, et al. (2002) Estimating site occupancy rates when detection probabilities are less than one. Ecology 83: 2248-2255.
49. Mackenzie DI, Royle JA (2005) Designing occupancy studies: general advice and allocating survey effort. Journal of Applied Ecology 42: 1105-1114.
50. Guillera-Arroita G, Ridout MS, Morgan BJT (2010) Design of occupancy studies with imperfect detection. Methods in Ecology and Evolution 1: 131-139.
51. Guillera-Arroita G, Lahoz-Monfort JJ (2012) Designing studies to detect differences in species occupancy: power analysis under imperfect detection. Methods in Ecology and Evolution 3: 860-869.
52. Poulin R (2013) Explaining variability in parasite aggregation levels among host samples. Parasitology 140: 541-546. doi: 10.1017/S0031182012002053 PMID: 23343821
53. Jacobson KC, Teel D, Van Doornik DM, Casillas E (2008) Parasite-associated mortality of juvenile Pacific salmon caused by the trematode Nanophyetus salmincola during early marine residence. Marine Ecology-Progress Series 354: 235-244.
54. Chen PC, Liu SC, Liu HI, Chen TW, Chiang KS (2011) Probability of detecting nematode infestations for quarantine sampling with imperfect extraction efficacy. Journal of Nematology 43: 16-24. PMID: 22791911
55. Cooch E, Conn P, Ellner S, Dobson A, Pollock K (2012) Disease dynamics in wild populations: modeling and estimation: a review. Journal of Ornithology 152: 485-509.
56. Guillera-Arroita G, Lahoz-Monfort JJ, McKenzie DI, Wintle BA, McCarthy MA (In press) Ignoring imperfect detection in biological surveys is dangerous: a response to 'Fitting and Interpreting Occupancy Models'. PLoS ONE. doi: 10.1371/journal.pone.0117679 PMID: 25626018
57. Shea CP, Peterson JT, Conroy MJ, Wisniewski JM (2012) Evaluating the influence of land use, drought and reach isolation on the occurrence of freshwater mussel species in the lower Flint River Basin, Georgia (U.S.A.). Freshwater Biology: 382-395. doi: 10.1182/asheducation-2012.1.382 PMID: 23233608