On estimating the spatial distribution of Yersinia pestis in the United States using a wide-ranging sentinel species and spatial statistics with sampling considerations Restricted; Files Only
Buller, Ian (Spring 2019)
Abstract
Plague is a highly consequential disease caused by the bacterium Yersinia pestis that infects multiple mammal host species, including humans providing a concern for public health and conservation. However, the precise locations where the disease is transmitted within the United States remain unknown and uncertain. While human cases are rare in the United States, plague is maintained within small mammal populations, namely wild rodents, and their flea vectors; therefore, plague surveillance systems typically focus on monitoring animal species, but are often faced with administrative, logistical, and biological challenges. In collaboration with plague surveillance agencies, I aim to: 1) identify sources of data uncertainties and bias in plague surveillance systems, 2) predict the spatial distribution of enzootic plague in the western United States, and 3) evaluate the association between enzootic plague and historical human plague cases in the United States. I collate an extensive set of human, animal, and environmental information and discuss the quality of these data. I develop an ecological niche modeling method that uses climatological variables and coyote (Canis latrans) specimens tested for exposure to Y. pestis to predict the spatial distribution of enzootic plague in California and the western United States, even in areas that have not historically been monitored for plague activity. I identify areas of the United States that are sensitive to some types of data uncertainty and bias, including positional uncertainty in the sampling location of coyote specimens and sampling effort bias of agencies that monitor plague activity. Finally, I use a spatial statistical framework, integrated nested Laplace approximation, to estimate historical human plague risk across the western United States and demonstrate that enzootic plague is positively associated with human plague risk at the county level (relative risk: 1.20; 95% credibility interval: 1.16 – 1.24). I work closely with plague surveillance agencies, so my results will have immediate impact on plague surveillance such as prioritizing future laboratory testing. I close by proposing future directions, including tangible advancements to the developed method to test biogeographical hypotheses and applications to other disease systems and fields of science.
Table of Contents
Abstract
Acknowledgements
1 Introduction .................... 1
1.1 Yersinia pestis: Plague .................... 3
1.2 Dissertation aims .................... 6
1.3 References .................... 8
2 Surveillance data for Yersinia pestis in the United States .................... 13
2.1 Introduction .................... 13
2.2 Cataloging data sources .................... 14
2.2.1 Human data .................... 14
2.2.2 Animal data .................... 16
2.2.3 Environmental data .................... 20
2.3 Cataloging data quality .................... 21
2.3.1 Quality of human data .................... 21
2.3.2 Quality of animal data .................... 22
2.3.3 Quality of environmental data .................... 29
2.4 Summary .................... 30
2.5 References .................... 31
2.6 Appendices .................... 36
2.6.1 Appendix A: Panels .................... 36
2.6.2 Appendix B: Tables .................... 39
2.6.3 Appendix C: Figures .................... 44
3 Examining spatial patterns in principal component space to identify suitable habitat for enzootic plague transmission in California, U.S.A. ... 54
3.1 Introduction .................... 54
3.2 Data and methods .................... 56
3.2.1 Wildlife disease data .................... 56
3.2.2 Environmental data processing .................... 57
3.2.3 Spatial analysis in the principal component space .................... 58
3.3 Results .................... 64
3.4 Discussion .................... 65
3.5 References .................... 72
3.6 Appendices .................... 77
3.6.1 Appendix A: Panels .................... 77
3.6.2 Appendix B: Tables .................... 79
3.6.3 Appendix C: Figures .................... 81
4 Monte Carlo assessment of the effect of positional uncertainty in animal-based plague surveillance: A case study in California, U.S.A. ... 99
4.1 Introduction .................... 99
4.2 Data and methods .................... 102
4.2.1 Surveillance data and classification of positional uncertainty .................... 102
4.2.2 Environmental data processing .................... 104
4.2.3 Statistical methods .................... 105
4.3 Results .................... 106
4.3.1 Stratified by geocode confidence level .................... 107
4.3.2 Spatially displaced permutations .................... 108
4.4 Discussion .................... 109
4.5 References .................... 115
4.6 Appendices .................... 119
4.6.1 Appendix A: Panels .................... 119
4.6.2 Appendix B: Tables .................... 120
4.6.3 Appendix C: Figures .................... 124
5 Combining multiple animal-based surveillance systems to predict the spatial distribution of enzootic plague in the western United States ... 144
5.1 Introduction .................... 144
5.2 Data and methods .................... 146
5.2.1 Coyote location and plague exposure data ....................147
5.2.2 Independently observed coyotes ....................148
5.2.3 Statistical methods .................... 150
5.3 Results .................... 154
5.3.1 Spatial distribution of enzootic plague in the western United States .................... 154
5.3.2 Spatial sampling effort of plague surveillance in the United States .................... 155
5.3.3 Spatial distribution of enzootic plague in western United States accounting for spatial sampling effort ... 156
5.4 Discussion .................... 156
5.5 References .................... 163
5.6 Appendices .................... 168
5.6.1 Appendix A: Panels .................... 168
5.6.2 Appendix B: Tables .................... 170
5.6.3 Appendix C: Figures .................... 175
6 Associating human risk with the spatial distribution of enzootic plague in the western United States ... 197
6.1 Introduction .................... 197
6.2 Data and methods .................... 199
6.2.1 Human data collation .................... 199
6.2.2 Environmental data processing .................... 200
6.2.3 Statistical methods .................... 203
6.3 Results .................... 206
6.4 Discussion .................... 209
6.5 References .................... 215
6.6 Appendices .................... 218
6.6.1 Appendix A: Panels .................... 218
6.6.2 Appendix B: Tables .................... 219
6.6.3 Appendix C: Figures .................... 225
7 Discussion and Future Directions .................... 243
7.1 Summary .................... 243
7.2 Future Directions .................... 244
7.3 Broader Impact .................... 248
7.4 References .................... 250
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