Peer Review #1 of "Modeling the ecologic niche of plague in sylvan and domestic animal hosts to delineate sources of human exposure in the western United States (v0.3)" [peer_review]

R Harrigan
2015 unpublished
Plague has been established in the western United States (US) since 1900 following the west coast introduction of commensal rodents infected with Yersinia pestis via early industrial shipping. Over the last century, plague ecology has transitioned through cycles of widespread human transmission, urban domestic transmission among commensal rodents, and ultimately settled into the predominantly sylvan foci that remain today where it is maintained alternatively by enzootic and epizootic
more » ... pizootic transmission. While zoonotic transmission to humans is much less common in modern times, significant plague risk remains in parts of the western US. Moreover, risk to some threatened species that are part of the epizootic cycle can be quite substantive. This investigation attempted to predict the risk of plague across the western US by modeling the ecologic niche of plague in sylvan and domestic animals identified between 2000 and 2015. A Maxent machine learning algorithm was used to predict this niche based on climate, altitude, land cover, and the presence of an important enzootic species, Peromyscus maniculatus. This model demonstrated good predictive ability (AUC = 86%) and identified areas of high risk in central Colorado, north-central New Mexico, and southwestern and northeastern California. The presence of P. maniculatus, altitude, precipitation during the driest and wettest quarters, and distance to artificial surfaces, all contributed substantively to maximizing the gain function. These findings add to the known landscape epidemiology and infection ecology of plague in the western US and may suggest locations of particular risk to be targeted for wild and domestic animal intervention. PeerJ reviewing PDF | (2015:09:6705:2:0:NEW 18 Nov 2015) Manuscript to be reviewed 1 Modeling the ecologic niche of plague in sylvan and domestic animal hosts to delineate sources of 2 human exposure in the western United States. Abstract 35 Plague has been established in the western United States (US) since 1900 following the west coast 36 introduction of commensal rodents infected with Yersinia pestis via early industrial shipping. Over the 37 last century, plague ecology has transitioned through cycles of widespread human transmission, urban 38 domestic transmission among commensal rodents, and ultimately settled into the predominantly sylvan 39 foci that remain today where it is maintained alternatively by enzootic and epizootic transmission. While 40 zoonotic transmission to humans is much less common in modern times, significant plague risk remains 41 in parts of the western US. Moreover, risk to some threatened species that are part of the epizootic 42 cycle can be quite substantive. This investigation attempted to predict the risk of plague across the 43 western US by modeling the ecologic niche of plague in sylvan and domestic animals identified between 44 2000 and 2015. A Maxent machine learning algorithm was used to predict this niche based on climate, 45 altitude, land cover, and the presence of an important enzootic species, Peromyscus maniculatus. This 46 model demonstrated good predictive ability (AUC = 86%) and identified areas of high risk in central 47 Colorado, north-central New Mexico, and southwestern and northeastern California. The presence of P. 48 maniculatus, altitude, precipitation during the driest and wettest quarters, and distance to artificial 49 surfaces, all contributed substantively to maximizing the gain function. These findings add to the known 50 landscape epidemiology and infection ecology of plague in the western US and may suggest locations of 51 particular risk to be targeted for wild and domestic animal intervention. 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 PeerJ reviewing PDF | (2015:09:6705:2:0:NEW 18 Nov 2015) Manuscript to be reviewed 67 Introduction 68 Plague was introduced to North America in 1900 during the third major pandemic, which began in the 69 19 th century in China(Eskey and Haas 1940). Subsequently, the causative agent, Yersinia pestis, 70 established in several foci across the semiarid regions of the western United States (US) where it is now 71 maintained enzootically in large part by the deer mouse (Peromyscus maniculatus), with occasional 72 epizootic events in some key species such as prairie dogs (Cynomys spp) and ground squirrels 73 (Spermophilus spp.)(Eskey and Haas 1940; Gage and Kosoy 2005). Indeed, the geographic extent of the 74 western US delineates one of the largest concentrations of sylvan plague foci in the modern world. 75 Despite the extensive foci of Y. pestis in the US, there are far fewer zoonotic transmissions to humans 76 than occur in other geographic areas of significant plague foci, such as Madagascar or the Democratic 77 Republic of the Congo(Stenseth et al. 2008). Nevertheless, the median annual incident cases of plague in 78 the US was three (range 0 -17) between 2001 and 2012(Kwit et al. 2015; Adams et al. 2014). Most of 79 these human cases present as bubonic and can be quite severe, especially when not recognized and 80 treated promptly with appropriate antibiotic therapy. As such, the ability to quantify the risk of zoonotic 81 transmission from animals to humans across the region of established plague foci in the US remains a 82 current research imperative. Flea bite and contact with infected animals accounted for 39.5% and 83 60.1%, respectively, of all infection transmissions with known exposure history between 1965 and 84 2012(Kugeler et al. 2015). Moreover, while direct contact with wildlife is a recognized risk factor, plague 85 is also often transmitted to domestic pets following exposure to wildlife, which then pass on the 86 infection to their human caretakers(Craven et al. 1993). The importance of direct and indirect (via 87 domestic animals) contact with wildlife notwithstanding, locations of animal plague in the landscape, 88 which may act as conduits to zoonotic transmission of Y. pestis to humans, remain uncertain. Abiotic 89 factors such as climate conditions and land cover and land use are of particular interest in understanding 90 the distribution of animal plague. For example, relationships between animal plague occurrence and PeerJ reviewing PDF | (2015:09:6705:2:0:NEW 18 Nov 2015) Manuscript to be reviewed 91 climate have been described in the western US, but in areas of more limited geographic extent (Holt et 92 al. 2009; Eisen, Glass, et al. 2007; Eisen, Reynolds, et al. 2007) , while studies of land cover have focused 93 on sylvan host habitat without also considering proximity to developed land parcels (Eisen, Enscore, et 94 al. 2007). Equally important are biotic factors, such as the relative contribution of enzootic species (e.g. 95 P. maniculatus) to plague occurrence among epizootic species (e.g. Cynomys spp.) (Stenseth et al. 2008; 96 Gage and Kosoy 2005). Therefore, it would be useful to attempt to model the presence of animal plague 97 as a function of both abiotic and biotic features across the region. The current investigation sought to 98 predict the ecologic niche of epizootic plague based on the presence of plague in sylvan and domestic 99 animal hosts across all states west of the Mississippi River, and thereby identify spaces of potential 100 zoonotic plague transmission to humans. A machine learning approach was used to model the ecologic 101 niche as a function of climate, altitude, land cover, and the presence of the enzootic reservoir, P. 102 maniculatus.
doi:10.7287/peerj.1493v0.3/reviews/1 fatcat:5vwfweb22zdd7fxqn5zct537ym