@article{brown_chen_ivanova_leekitcharoenphon_parsons_niedermeyer_gould_strules_mesa-cruz_kelly_et al._2023, title={Draft Genome Sequences of 158 Listeria monocytogenes Strains Isolated from Black Bears (Ursus americanus) in the United States}, volume={12}, ISSN={2576-098X}, url={http://dx.doi.org/10.1128/mra.00248-23}, DOI={10.1128/mra.00248-23}, abstractNote={ Listeria monocytogenes is responsible for severe foodborne disease and major economic losses, but its potential reservoirs in natural ecosystems remain poorly understood. Here, we report the draft genome sequences of 158 L. monocytogenes strains isolated from black bears ( Ursus americanus ) in the southeastern United States between 2014 and 2017. }, number={7}, journal={Microbiology Resource Announcements}, publisher={American Society for Microbiology}, author={Brown, Phillip and Chen, Yi and Ivanova, Mirena and Leekitcharoenphon, Pimlapas and Parsons, Cameron and Niedermeyer, Jeffrey and Gould, Nicholas and Strules, Jennifer and Mesa-Cruz, J. Bernardo and Kelly, Marcella J. and et al.}, editor={Rasko, DavidEditor}, year={2023}, month={Jul} } @article{brown_hernandez_parsons_chen_gould_deperno_niedermeyer_kathariou_2023, title={Tetracycline resistance in Listeria monocytogenes and L. innocua from wild black bears (Ursus americanus) in the United States is mediated by novel transposable elements}, volume={89}, ISSN={["1098-5336"]}, url={https://doi.org/10.1128/aem.01205-23}, DOI={10.1128/aem.01205-23}, abstractNote={ABSTRACT Listeria monocytogenes is a facultative intracellular foodborne pathogen and the causative agent of the severe disease listeriosis. It is found ubiquitously in the environment and exhibits innate resistance to certain antimicrobials, but acquired antimicrobial resistance remains relatively uncommon. Given the potentially dire health outcomes associated with listeriosis, acquisition of antimicrobial resistance (AMR) by this pathogen is of considerable public health concern. AMR in L. monocytogenes has been surveyed frequently in strains of clinical and food origin, but much less commonly in wildlife. We analyzed 158 strains of L. monocytogenes and 27 of non-pathogenic Listeria spp. isolated from wild black bears ( Ursus americanus ) for resistance to a panel of antimicrobials. AMR was uncommon and noted mostly for tetracycline. Tetracycline resistance was more common in Listeria innocua than in L. monocytogenes . All tetracycline-resistant L. monocytogenes strains belonged to sequence type ST1039 and harbored the Tn 916 -like tet (M) transposon Tn 916.1039 in a conserved chromosomal location. In contrast, three different tetracycline resistance elements, i.e., the tet (M) elements Tn 5801.UAM and Tn 5801.551 and the tet (S) element Tn 6000.205 , were identified among tetracycline-resistant strains of L. innocua . The greater prevalence and diversity of tetracycline resistance elements among bear-derived non-pathogenic Listeria strains suggest the potential of the latter to serve as reservoirs for retention and diversification of AMR determinants in this wildlife host and warrant their further monitoring and study. IMPORTANCE Listeria monocytogenes causes severe foodborne illness and is the only human pathogen in the genus Listeria . Previous surveys of AMR in Listeria focused on clinical sources and food or food processing environments, with AMR in strains from wildlife and other natural ecosystems remaining under-explored. We analyzed 185 sequenced strains from wild black bears ( Ursus americanus ) from the United States, including 158 and 27 L . monocytogenes and L. innocua , respectively. Tetracycline resistance was the most prevalent resistance trait. In L . monocytogenes, it was encountered exclusively in serotype 4b strains with the novel Tn 916 -like element Tn 916.1039 . In contrast, three distinct, novel tetracycline resistance elements (Tn 5801.UAM , Tn5801.551 , and Tn 6000.205 ) were identified in L. innocua . Interestingly, Tn5801.551 was identical to elements in L. monocytogenes from a major foodborne outbreak in the United States in 2011. The findings suggest the importance of wildlife and non-pathogenic Listeria species as reservoir for resistance elements in Listeria . }, number={11}, journal={Environmental Microbiology}, author={Brown, Phillip and Hernandez, Kevin and Parsons, Cameron and Chen, Yi and Gould, Nicholas and DePerno, Christopher S. and Niedermeyer, Jeffrey and Kathariou, Sophia}, editor={Dozois, Charles M.Editor}, year={2023}, month={Nov} } @article{puckett_davis_harper_wakamatsu_battu_belant_beyer_carpenter_crupi_davidson_et al._2023, title={Genetic architecture and evolution of color variation in American black bears}, volume={33}, ISSN={0960-9822}, url={http://dx.doi.org/10.1016/j.cub.2022.11.042}, DOI={10.1016/j.cub.2022.11.042}, abstractNote={

Summary

Color variation is a frequent evolutionary substrate for camouflage in small mammals, but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus (U. americanus), exhibits a range of colors including the cinnamon morph, which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (p < 10−13). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 (TYRP1) that likely affects binding of the zinc cofactor, impairs protein localization, and results in decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36 kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos but is not fixed across the range.}, number={1}, journal={Current Biology}, publisher={Elsevier BV}, author={Puckett, Emily E. and Davis, Isis S. and Harper, Dawn C. and Wakamatsu, Kazumasa and Battu, Gopal and Belant, Jerrold L. and Beyer, Dean E., Jr. and Carpenter, Colin and Crupi, Anthony P. and Davidson, Maria and et al.}, year={2023}, month={Jan}, pages={86–97.e10} } @article{gould_powell_olfenbuttel_deperno_2021, title={Growth and reproduction by young urban and rural black bears}, volume={102}, ISSN={0022-2372 1545-1542}, url={http://dx.doi.org/10.1093/jmammal/gyab066}, DOI={10.1093/jmammal/gyab066}, abstractNote={AbstractHuman-dominated landscapes contain fragmented natural land cover interspersed throughout an urban matrix. Animals that occupy human-dominated landscapes often grow and reproduce differently than conspecifics. Female American black bears (Ursus americanus) produce litters for the first time usually at age 4 years; 2-year-olds rarely give birth. We visited winter bear dens and trapped bears in spring and summer to compare the reproductive output and weight of female black bears within the city limits of Asheville, North Carolina, and three forested rural sites in North Carolina and Virginia representative of the undeveloped habitat of Asheville. Urban yearling females weighed nearly double (45.0 kg ± 8.1 [± SD]; n = 36) that of yearling females from the three rural study sites (23.2 ± 8.5 [Pisgah], 23.6 ± 8.3 [Virginia SW], and 23.9 ± 9.7 [Virginia NW]; n = 95). Across all sites, hard mast production during the autumn, when females were cubs, did not affect their weights as yearlings. Seven of 12 (58%) 2-year-old urban bears produced 11 cubs (mean litter size = 1.6 ± 0.8), but no 2-year-old rural females produced cubs. Production of hard mast in the autumn, when females were yearlings, did not influence cub production by 2-year-old female bears at the urban site. We hypothesize that reproduction by 2-year-old bears is linked to the availability of anthropogenic food sources associated with urban environments. To inform population level management decisions, managers and researchers should quantify urban food sources and the effects on black bear life history. If high fecundity allows urban populations to sustain relatively high mortality rates, then urban bear populations may be source populations for surrounding, rural areas. Alternately, if reproduction in urban populations cannot match high time-specific or age-specific urban mortality rates, then urban populations may be sinks for the surrounding areas.}, number={4}, journal={Journal of Mammalogy}, publisher={Oxford University Press (OUP)}, author={Gould, Nicholas P and Powell, Roger and Olfenbuttel, Colleen and DePerno, Christopher S}, editor={Hopkins, JackEditor}, year={2021}, month={Jul}, pages={1165–1173} } @article{joslyn_charles_deperno_gould_nowak_praggastis_purvine_robinson_strules_whitney_2020, title={A Sheaf Theoretical Approach to Uncertainty Quantification of Heterogeneous Geolocation Information}, volume={20}, ISSN={1424-8220}, url={http://dx.doi.org/10.3390/s20123418}, DOI={10.3390/s20123418}, abstractNote={Integration of multiple, heterogeneous sensors is a challenging problem across a range of applications. Prominent among these are multi-target tracking, where one must combine observations from different sensor types in a meaningful and efficient way to track multiple targets. Because different sensors have differing error models, we seek a theoretically justified quantification of the agreement among ensembles of sensors, both overall for a sensor collection, and also at a fine-grained level specifying pairwise and multi-way interactions among sensors. We demonstrate that the theory of mathematical sheaves provides a unified answer to this need, supporting both quantitative and qualitative data. Furthermore, the theory provides algorithms to globalize data across the network of deployed sensors, and to diagnose issues when the data do not globalize cleanly. We demonstrate and illustrate the utility of sheaf-based tracking models based on experimental data of a wild population of black bears in Asheville, North Carolina. A measurement model involving four sensors deployed among the bears and the team of scientists charged with tracking their location is deployed. This provides a sheaf-based integration model which is small enough to fully interpret, but of sufficient complexity to demonstrate the sheaf’s ability to recover a holistic picture of the locations and behaviors of both individual bears and the bear-human tracking system. A statistical approach was developed in parallel for comparison, a dynamic linear model which was estimated using a Kalman filter. This approach also recovered bear and human locations and sensor accuracies. When the observations are normalized into a common coordinate system, the structure of the dynamic linear observation model recapitulates the structure of the sheaf model, demonstrating the canonicity of the sheaf-based approach. However, when the observations are not so normalized, the sheaf model still remains valid.}, number={12}, journal={Sensors}, publisher={MDPI AG}, author={Joslyn, Cliff A. and Charles, Lauren and DePerno, Chris and Gould, Nicholas and Nowak, Kathleen and Praggastis, Brenda and Purvine, Emilie and Robinson, Michael and Strules, Jennifer and Whitney, Paul}, year={2020}, month={Jun}, pages={3418} } @article{westmoreland_stoskopf_sheppard_deperno_gould_olfenbuttel_maggi_2019, title={Detection and Prevalence of Babesia spp. in American Black Bears (Ursus americanus) from Eastern and Western North Carolina, USA}, volume={55}, ISSN={0090-3558}, url={http://dx.doi.org/10.7589/2018-06-164}, DOI={10.7589/2018-06-164}, abstractNote={Blood samples collected from American black bears ( Ursus americanus) in eastern and western North Carolina, US, were analyzed for piroplasms. Piroplasmids were detected in 17% (23/132) of the animals surveyed. We detected a Babesia spp. previously identified in North American raccoons ( Procyon lotor) and a maned wolf ( Chrysocyon brachyurus); prevalence was 22% (14/64) and 13% (9/68) in the mountain and coastal black bear populations, respectively. The presence of the same Babesia species in black bears, raccoons, and a maned wolf suggests piroplasms may not be host specific.}, number={3}, journal={Journal of Wildlife Diseases}, publisher={Wildlife Disease Association}, author={Westmoreland, Lori S. H. and Stoskopf, Michael K. and Sheppard, Erica and DePerno, Christopher S. and Gould, Nicholas P. and Olfenbuttel, Colleen and Maggi, Ricardo G.}, year={2019}, month={Jul}, pages={678} } @article{parsons_niedermeyer_gould_brown_strules_parsons_bernardo mesa‐cruz_kelly_hooker_chamberlain_et al._2020, title={Listeria monocytogenes at the human–wildlife interface: black bears ( Ursus americanus ) as potential vehicles for Listeria}, volume={13}, ISBN={1751-7915}, ISSN={1751-7915 1751-7915}, url={http://dx.doi.org/10.1111/1751-7915.13509}, DOI={10.1111/1751-7915.13509}, abstractNote={SummaryListeria monocytogenes is the causative agent of the foodborne illness listeriosis, which can result in severe symptoms and death in susceptible humans and other animals. L. monocytogenes is ubiquitous in the environment and isolates from food and food processing, and clinical sources have been extensively characterized. However, limited information is available on L. monocytogenes from wildlife, especially from urban or suburban settings. As urban and suburban areas are expanding worldwide, humans are increasingly encroaching into wildlife habitats, enhancing the frequency of human–wildlife contacts and associated pathogen transfer events. We investigated the prevalence and characteristics of L. monocytogenes in 231 wild black bear capture events between 2014 and 2017 in urban and suburban sites in North Carolina, Georgia, Virginia and United States, with samples derived from 183 different bears. Of the 231 captures, 105 (45%) yielded L. monocytogenes either alone or together with other Listeria. Analysis of 501 samples, primarily faeces, rectal and nasal swabs for Listeria spp., yielded 777 isolates, of which 537 (70%) were L. monocytogenes. Most L. monocytogenes isolates exhibited serotypes commonly associated with human disease: serotype 1/2a or 3a (57%), followed by the serotype 4b complex (33%). Interestingly, approximately 50% of the serotype 4b isolates had the IVb‐v1 profile, associated with emerging clones of L. monocytogenes. Thus, black bears may serve as novel vehicles for L. monocytogenes, including potentially emerging clones. Our results have significant public health implications as they suggest that the ursine host may preferentially select for L. monocytogenes of clinically relevant lineages over the diverse listerial populations in the environment. These findings also help to elucidate the ecology of L. monocytogenes and highlight the public health significance of the human–wildlife interface.}, number={3}, journal={Microbial Biotechnology}, publisher={Wiley}, author={Parsons, Cameron and Niedermeyer, Jeff and Gould, Nicholas and Brown, Phillip and Strules, Jennifer and Parsons, Arielle W. and Bernardo Mesa‐Cruz, J. and Kelly, Marcella J. and Hooker, Michael J. and Chamberlain, Michael J. and et al.}, editor={Brown, PhillipEditor}, year={2020}, month={May}, pages={706–721} } @article{sasmal_gould_schuler_chang_thachil_strules_olfenbuttel_datta_deperno_2019, title={LEPTOSPIROSIS IN URBAN AND SUBURBAN AMERICAN BLACK BEARS (URSUS AMERICANUS) IN WESTERN NORTH CAROLINA, USA}, volume={55}, ISSN={["1943-3700"]}, DOI={10.7589/2017-10-263}, abstractNote={Abstract: American black bear (Ursus americanus) populations in North Carolina, US have recovered significantly in recent decades and now occupy much of western North Carolina, including urbansuburban areas. We used the black bear as a potential sentinel for leptospirosis, a bacterial zoonotic disease caused by Leptospira spp., which is maintained by domestic and wild mammals. We determined whether Leptospira spp. were present across a gradient of housing densities in the urban and suburban black bear population in and around Asheville, North Carolina using serologic and molecular surveys. We collected blood from captured black bears (n=94) and kidneys and bladders from carcasses (n=19). We tested a total of 96 (47 females, 47 males, and 2 unknown) serum samples by microscopic agglutination test (MAT) and had positive results (titer .1:100) for L. kirschneri serovar Grippotyphosa (L. Grippotyphosa) in 4 females (8%) and 5 males (10%). No other serovars showed elevated titers in MAT. We tested a total of 125 samples using PCR (n=96 serum, n=20 kidney, and n=9 bladders) and obtained positive results from one serum (1%), one kidney (5%), and one bladder (11%). The presence of Leptospira spp. in black bears occupying an urban and suburban landscape may indicate a more extensive occurrence of the bacteria among animals in the study region because black bears are the top carnivore in that ecosystem. Potential threats of widespread contamination during natural events such as flood or drought must be considered.}, number={1}, journal={JOURNAL OF WILDLIFE DISEASES}, author={Sasmal, Indrani and Gould, Nicholas P. and Schuler, Krysten L. and Chang, Yung-Fu and Thachil, Anil and Strules, Jennifer and Olfenbuttel, Colleen and Datta, Shubham and DePerno, Christopher S.}, year={2019}, month={Jan}, pages={74–83} } @article{funk_lovich_hohenlohe_hofman_morrison_sillett_ghalambor_maldonado_rick_day_et al._2016, title={Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)}, volume={25}, ISSN={["1365-294X"]}, DOI={10.1111/mec.13605}, abstractNote={AbstractThe evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction‐site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome‐wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.}, number={10}, journal={MOLECULAR ECOLOGY}, author={Funk, W. Chris and Lovich, Robert E. and Hohenlohe, Paul A. and Hofman, Courtney A. and Morrison, Scott A. and Sillett, T. Scott and Ghalambor, Cameron K. and Maldonado, Jesus E. and Rick, Torben C. and Day, Mitch D. and et al.}, year={2016}, month={May}, pages={2176–2194} }