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1. Comparison of Antimicrobial-Resistant Escherichia coli Isolates from Urban Raccoons and Domestic Dogs

   https://doi.org/10.1128/AEM.00484-21  

   Worsley-Tonks, Katherine E.; Gehrt, Stanley D.; Miller, Elizabeth A.; Singer, Randall S.; Bender, Jeff B.; Forester, James D.; McKenzie, Shane C.; Travis, Dominic A.; Johnson, Timothy J.; Craft, Meggan E. (July 2021, Applied and Environmental Microbiology)

   Elkins, Christopher A. (Ed.)

   ABSTRACT Wildlife can be exposed to antimicrobial-resistant bacteria (ARB) via multiple pathways. Spatial overlap with domestic animals is a prominent exposure pathway. However, most studies of wildlife-domestic animal interfaces have focused on livestock and little is known about the wildlife-companion animal interface. Here, we investigated the prevalence and phylogenetic relatedness of extended-spectrum cephalosporin-resistant (ESC-R) Escherichia coli from raccoons ( Procyon lotor ) and domestic dogs ( Canis lupus familiaris ) in the metropolitan area of Chicago, IL, USA. To assess the potential importance of spatial overlap with dogs, we explored whether raccoons sampled at public parks (i.e., parks where people and dogs could enter) differed in prevalence and phylogenetic relatedness of ESC-R E. coli to raccoons sampled at private parks (i.e., parks where people and dogs could not enter). Raccoons had a significantly higher prevalence of ESC-R E. coli (56.9%) than dogs (16.5%). However, the richness of ESC-R E. coli did not vary by host species. Further, core single-nucleotide polymorphism (SNP)-based phylogenetic analyses revealed that isolates did not cluster by host species, and in some cases displayed a high degree of similarity (i.e., differed by less than 20 core SNPs). Spatial overlap analyses revealed that ESC-R E. coli were more likely to be isolated from raccoons at public parks than raccoons at private parks, but only for parks located in suburban areas of Chicago, not urban areas. That said, ESC-R E. coli isolated from raccoons did not genetically cluster by park of origin. Our findings suggest that domestic dogs and urban/suburban raccoons can have a diverse range of ARB, some of which display a high degree of genetic relatedness (i.e., differ by less than 20 core SNPs). Given the differences in prevalence, domestic dogs are unlikely to be an important source of exposure for mesocarnivores in urbanized areas. IMPORTANCE Antimicrobial-resistant bacteria (ARB) have been detected in numerous wildlife species across the globe, which may have important implications for human and animal health. Wildlife can be exposed to ARB via numerous pathways, including via spatial overlap with domestic animals. However, the interface with domestic animals has mostly been explored for livestock and little is known about the interface between wild animals and companion animals. Our work suggests that urban and suburban wildlife can have similar ARB to local domestic dogs, but local dogs are unlikely to be a direct source of exposure for urban-adapted wildlife. This finding is important because it underscores the need to incorporate wildlife into antimicrobial resistance surveillance efforts, and to investigate whether certain urban wildlife species could act as additional epidemiological pathways of exposure for companion animals, and indirectly for humans. 

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2. Widespread exposure to SARS-CoV-2 in wildlife communities

   https://doi.org/10.1038/s41467-024-49891-w  

   Goldberg, Amanda_R; Langwig, Kate_E; Brown, Katherine_L; Marano, Jeffrey_M; Rai, Pallavi; King, Kelsie_M; Sharp, Amanda_K; Ceci, Alessandro; Kailing, Christopher_D; Kailing, Macy_J; et al (July 2024, Nature Communications)

   Abstract Pervasive SARS-CoV-2 infections in humans have led to multiple transmission events to animals. While SARS-CoV-2 has a potential broad wildlife host range, most documented infections have been in captive animals and a single wildlife species, the white-tailed deer. The full extent of SARS-CoV-2 exposure among wildlife communities and the factors that influence wildlife transmission risk remain unknown. We sampled 23 species of wildlife for SARS-CoV-2 and examined the effects of urbanization and human use on seropositivity. Here, we document positive detections of SARS-CoV-2 RNA in six species, including the deer mouse, Virginia opossum, raccoon, groundhog, Eastern cottontail, and Eastern red bat between May 2022–September 2023 across Virginia and Washington, D.C., USA. In addition, we found that sites with high human activity had three times higher seroprevalence than low human-use areas. We obtained SARS-CoV-2 genomic sequences from nine individuals of six species which were assigned to seven Pango lineages of the Omicron variant. The close match to variants circulating in humans at the time suggests at least seven recent human-to-animal transmission events. Our data support that exposure to SARS-CoV-2 has been widespread in wildlife communities and suggests that areas with high human activity may serve as points of contact for cross-species transmission. 

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3. Physiological and behavioral responses to anthropogenic stressors in a human-tolerant mammal

   https://doi.org/10.1093/jmammal/gyz134  

   Hammond, Talisin T; Vo, Minnie; Burton, Clara T; Surber, Lisa L; Lacey, Eileen A; Smith, Jennifer E (September 2019, Journal of Mammalogy)

   Hayes, Loren (Ed.)

   Abstract As humans continue to alter natural habitats, many wild animals are facing novel suites of environmental stimuli. These changes, including increased human–wildlife interactions, may exert sublethal impacts on wildlife such as alterations in stress physiology and behavior. California ground squirrels (Otospermophilus beecheyi) occur in human-modified as well as more pristine environments, where they face a variety of anthropogenic and naturally occurring threats. This makes this species a valuable model for examining the effects of diverse challenges on the physiology and behavior of free-living mammals. To explore potential sublethal effects of habitat modification on O. beecheyi, we compared body masses, behaviors, and fecal glucocorticoid metabolite (FGM) levels for free-living squirrels in human-disturbed versus undisturbed habitats. Prior to these analyses, we validated the use of FGMs in this species by exposing captive O. beecheyi to pharmacological and handling challenges; both challenges produced significant increases in FGMs in the study animals. While FGM responses were repeatable within captive individuals, responses by free-living animals were more variable, perhaps reflecting a greater range of life-history traits and environmental conditions within natural populations of squirrels. Animals from our human-disturbed study site had significantly higher FGMs, significantly lower body masses, and were significantly less behaviorally reactive to humans than those from our more pristine study site. Thus, despite frequent exposure of California ground squirrels to human impacts, anthropogenic stressors appear to influence stress physiology and other phenotypic traits in this species. These findings suggest that even human-tolerant mammalian species may experience important sublethal consequences due to human modifications of natural habitats. 

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4. Detection of Echinococcus multilocularis in coyotes in Washington State, USA highlights need for increased global wildlife surveillance

   https://doi.org/10.1101/2025.08.26.672275  

   Hentati, Yasmine; Reese, Ellie; Curran, Claire; Miller, Erika M; Díaz-Morales, Dakeishla M; Kreling, Samantha ES; Verocai, Guilherme G; Prugh, Laura R; Schell, Christopher J; Wood, Chelsea L (August 2025, bioRxiv)

   Abstract Echinococcus multilocularisis a zoonotic cestode that uses canids as definitive hosts and rodents as intermediate hosts. In humans, this parasite is the causative agent of alveolar echinococcosis. Recently, its range has been expanding across the Northern Hemisphere, and it is increasingly detected in wild canids, domestic dogs, and humans across Canada and the United States. While this expansion has been documented in isolated studies across the continent, a lack of routine sampling in wildlife hinders our ability to anticipate and mitigate further spread ofE. multilocularis. We confirmed the presence ofE. multilocularisin Washington State, USA, using a combination of morphological and molecular techniques across carcasses and field-collected scats of coyotes (Canis latrans), this region’s most common wild canid. Morphological identification of adult worms was confirmed by next-generation sequencing. Over a third of all samples tested positive forE. multiloculariswhen all methodologies were combined. Sequencing revealed a haplotype ofE. multilocularismatching a documented haplotype originally of European origin in British Columbia, Canada. Our study provides the first confirmation ofE. multilocularisin a wild host on the west coast of the U.S and provides additional haplotype information crucial to tracking the geographical expansion of the parasite. We also provide a new next-generation sequencing primer targeting cestodes of canids. The difference in amplification between intestinal and fecal samples suggests that non-invasive fecal sampling using DNA metabarcoding—a popular method of helminth surveillance —may lead to underestimation of prevalence, hindering control measures. The global significance of these findings extends beyond North America;E. multilocularisis a major public health concern in Europe and Asia, where alveolar echinococcosis is increasingly diagnosed in humans. Our study highlights the urgent need for increased surveillance and improved diagnostic strategies worldwide, particularly in regions with significant human-wildlife contact. Author summaryParasites that are transmitted between wildlife, domestic animals, and people are an important part of global health. One such parasite isEchinococcus multilocularis, a small tapeworm of canids that can cause a severe, life-threatening disease in humans called alveolar echinococcosis. Many wild canid hosts of the parasite, such as coyotes, overlap significantly with domestic dogs, which facilitates transmission to humans. In Europe, Asia, and Arctic regions of North America,E. multilocularishas long been recognized as a major public health problem. In recent decades its range has expanded across the Northern Hemisphere, raising concern. In this study, we discoveredE. multilocularisin coyotes in a densely populated area of Washington State, USA — the first detection ofE. multilocularisin a wild host in the region. More than one-third of our coyote samples containedE. multilocularis, confirming that it is widespread in the area. Genetic testing showed that the strain we detected matched one previously found in Canada, originally from Europe. Our findings underscore the importance of monitoringE. multilocularisand other parasites in wildlife so that emerging public health threats can be detected early, reducing risk to people and pets. 

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5. Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel ( Sciurus carolinensis )

   https://doi.org/10.1111/mec.17230  

   Fusco, Nicole A.; Cosentino, Bradley J.; Gibbs, James P.; Allen, Maximilian L.; Blumenfeld, Alexander J.; Boettner, George H.; Carlen, Elizabeth J.; Collins, Merri; Dennison, Catherine; DiGiacopo, Devin; et al (December 2023, Molecular Ecology)

   Abstract Urbanization is a persistent and widespread driver of global environmental change, potentially shaping evolutionary processes due to genetic drift and reduced gene flow in cities induced by habitat fragmentation and small population sizes. We tested this prediction for the eastern grey squirrel (Sciurus carolinensis), a common and conspicuous forest‐dwelling rodent, by obtaining 44K SNPs using reduced representation sequencing (ddRAD) for 403 individuals sampled across the species' native range in eastern North America. We observed moderate levels of genetic diversity, low levels of inbreeding, and only a modest signal of isolation‐by‐distance. Clustering and migration analyses show that estimated levels of migration and genetic connectivity were higher than expected across cities and forested areas, specifically within the eastern portion of the species' range dominated by urbanization, and genetic connectivity was less than expected within the western range where the landscape is fragmented by agriculture. Landscape genetic methods revealed greater gene flow among individual squirrels in forested regions, which likely provide abundant food and shelter for squirrels. Although gene flow appears to be higher in areas with more tree cover, only slight discontinuities in gene flow suggest eastern grey squirrels have maintained connected populations across urban areas in all but the most heavily fragmented agricultural landscapes. Our results suggest urbanization shapes biological evolution in wildlife species depending strongly on the composition and habitability of the landscape matrix surrounding urban areas. 

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