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Article ; Online: Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.

Rasko, David A / Webster, Dale R / Sahl, Jason W / Bashir, Ali / Boisen, Nadia / Scheutz, Flemming / Paxinos, Ellen E / Sebra, Robert / Chin, Chen-Shan / Iliopoulos, Dimitris / Klammer, Aaron / Peluso, Paul / Lee, Lawrence / Kislyuk, Andrey O / Bullard, James / Kasarskis, Andrew / Wang, Susanna / Eid, John / Rank, David /

Redman, Julia C / Steyert, Susan R / Frimodt-Møller, Jakob / Struve, Carsten / Petersen, Andreas M / Krogfelt, Karen A / Nataro, James P / Schadt, Eric E / Waldor, Matthew K

The New England journal of medicine

2011 Volume 365, Issue 8, Page(s) 709–717

Abstract: ... a large number of cases of diarrhea caused by Shiga-toxin-producing E. coli have been reported--3167 ... notably more virulent than most of the Shiga-toxin-producing E. coli strains. Preliminary genetic ... within the enteroaggregative pathotype of E. coli.: Methods: We used third-generation, single-molecule, real-time DNA ...

Abstract	Background: A large outbreak of diarrhea and the hemolytic-uremic syndrome caused by an unusual serotype of Shiga-toxin-producing Escherichia coli (O104:H4) began in Germany in May 2011. As of July 22, a large number of cases of diarrhea caused by Shiga-toxin-producing E. coli have been reported--3167 without the hemolytic-uremic syndrome (16 deaths) and 908 with the hemolytic-uremic syndrome (34 deaths)--indicating that this strain is notably more virulent than most of the Shiga-toxin-producing E. coli strains. Preliminary genetic characterization of the outbreak strain suggested that, unlike most of these strains, it should be classified within the enteroaggregative pathotype of E. coli. Methods: We used third-generation, single-molecule, real-time DNA sequencing to determine the complete genome sequence of the German outbreak strain, as well as the genome sequences of seven diarrhea-associated enteroaggregative E. coli serotype O104:H4 strains from Africa and four enteroaggregative E. coli reference strains belonging to other serotypes. Genomewide comparisons were performed with the use of these enteroaggregative E. coli genomes, as well as those of 40 previously sequenced E. coli isolates. Results: The enteroaggregative E. coli O104:H4 strains are closely related and form a distinct clade among E. coli and enteroaggregative E. coli strains. However, the genome of the German outbreak strain can be distinguished from those of other O104:H4 strains because it contains a prophage encoding Shiga toxin 2 and a distinct set of additional virulence and antibiotic-resistance factors. Conclusions: Our findings suggest that horizontal genetic exchange allowed for the emergence of the highly virulent Shiga-toxin-producing enteroaggregative E. coli O104:H4 strain that caused the German outbreak. More broadly, these findings highlight the way in which the plasticity of bacterial genomes facilitates the emergence of new pathogens.
MeSH term(s)	Bacterial Typing Techniques ; Base Sequence ; Diarrhea/epidemiology ; Diarrhea/microbiology ; Disease Outbreaks ; Escherichia coli Infections/epidemiology ; Escherichia coli Infections/microbiology ; Feces/microbiology ; Female ; Genome, Bacterial ; Germany/epidemiology ; Hemolytic-Uremic Syndrome/epidemiology ; Hemolytic-Uremic Syndrome/microbiology ; Humans ; Middle Aged ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Shiga-Toxigenic Escherichia coli/classification ; Shiga-Toxigenic Escherichia coli/genetics ; Shiga-Toxigenic Escherichia coli/isolation & purification
Language	English
Publishing date	2011-07-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	207154-x
ISSN	1533-4406 ; 0028-4793
ISSN (online)	1533-4406
ISSN	0028-4793
DOI	10.1056/NEJMoa1106920
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Article ; Online: Re-Using existing datasets to analyze possible factors behind the spatial distribution of antimicrobial resistance and hepatitis E virus infection in German wildlife

Günther, Taras / Fuhrmann, Marcel / Kramer-Schadt, Stephanie / Tenhagen, Bernd-Alois / Johne, Reimar / Belik, Vitaly

2019

Keywords	Text ; ddc:610
Language	English
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Landscape and scale-dependent spatial niches of bats foraging above intensively used arable fields

Kramer-Schadt, Stephanie / Voigt, Christian

Ecological Processes, 6:24

2017

Abstract: ... surrounded by vegetation patches with a high degree of edge complexity (e.g., hedgerow ... surrounded by vegetation patches with a low degree of edge complexity (e.g., roundly shaped forest patch ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	INTRODUCTION: Bats are threatened by agricultural intensification, and although bat ecology in agricultural landscapes is in the focus of current research, the effects of interacting spatiotemporal factors on species-specific bat activity above farmland remain understudied. Our aim was to identify spatiotemporal factors and their interactions relevant for the activity of bat species above conventionally managed arable fields. METHODS: We repeatedly monitored relative bat activity above open arable fields in Germany using acoustic monitoring. We used site-related biotic and abiotic factors and landscape characteristics across five spatial scales, their combinations, and interactions to identify those factors which best explain variation in bat activity. RESULTS: Numerous interactions between landscape characteristics and the insect abundance affected bat activity above fields. For instance, Pipistrellus pipistrellus became more active with increasing insect abundance, but only above fields with a low proportion of woody vegetation cover in the surroundings. Additionally, the level of bat activity in summer depended on landscape characteristics. For example, the activity of Pipistrellus nathusii was relatively low in summer above fields that were surrounded by vegetation patches with a high degree of edge complexity (e.g., hedgerow). However, the activity remained at a relatively high level and did not differ between seasons above fields that were surrounded by vegetation patches with a low degree of edge complexity (e.g., roundly shaped forest patch). CONCLUSIONS: Our results revealed that landscape characteristics and their interactions with insect abundance affected bat activity above conventionally managed fields and highlighted the opportunistic foraging behavior of bats. To improve the conditions for bats in agricultural landscapes, we recommend re-establishing landscape heterogeneity to protect aquatic habitats and to increase arthropod availability.
Keywords	Conservation ; Agriculture ; AgroScapeLabs ; Ecosystem service ; European bat species ; Landscape ; Multi-scale habitat modeling
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article ; Online: Anti-correlated feature selection prevents false discovery of subpopulations in scRNAseq.

Tyler, Scott R / Lozano-Ojalvo, Daniel / Guccione, Ernesto / Schadt, Eric E

Nature communications

2024 Volume 15, Issue 1, Page(s) 699

Abstract: While sub-clustering cell-populations has become popular in single cell-omics, negative controls for this process are lacking. Popular feature-selection/clustering algorithms fail the null-dataset problem, allowing erroneous subdivisions of homogenous ... ...

Abstract	While sub-clustering cell-populations has become popular in single cell-omics, negative controls for this process are lacking. Popular feature-selection/clustering algorithms fail the null-dataset problem, allowing erroneous subdivisions of homogenous clusters until nearly each cell is called its own cluster. Using real and synthetic datasets, we find that anti-correlated gene selection reduces or eliminates erroneous subdivisions, increases marker-gene selection efficacy, and efficiently scales to millions of cells.
MeSH term(s)	Single-Cell Gene Expression Analysis ; Algorithms ; Cluster Analysis
Language	English
Publishing date	2024-01-24
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-43406-9
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Article: Wild inside: Urban wild boar select natural, not anthropogenic food resources

Gras, Pierre / Kramer-Schadt, Stephanie / Ortmann, Sylvia

PLOS ONE, 12(4):e0175127

2017

Abstract: ... in urban areas. Urban WB might use anthropogenic resources (e.g. garbage) if those are easier to exploit and more ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	Most wildlife species are urban avoiders, but some became urban utilizers and dwellers successfully living in cities. Often, they are assumed to be attracted into urban areas by easily accessible and highly energetic anthropogenic food sources. We macroscopically analysed stomachs of 247 wild boar (Sus scrofa, hereafter WB) from urban areas of Berlin and from the surrounding rural areas. From the stomach contents we determined as predictors of food quality modulus of fineness (MOF,), percentage of acid insoluble ash (AIA) and macronutrients such as amount of energy and percentage of protein, fat, fibre and starch. We run linear mixed models to test: (1) differences in the proportion of landscape variables, (2) differences of nutrients consumed in urban vs. rural WB and (3) the impact of landscape variables on gathered nutrients. We found only few cases of anthropogenic food in the qualitative macroscopic analysis. We categorized the WB into five stomach content categories but found no significant difference in the frequency of those categories between urban and rural WB. The amount of energy was higher in stomachs of urban WB than in rural WB. The analysis of landscape variables revealed that the energy of urban WB increased with increasing percentage of sealing, while an increased human density resulted in poor food quality for urban and rural WB. Although the percentage of protein decreased in areas with a high percentage of coniferous forests, the food quality increased. High percentage of grassland decreased the percentage of consumed fat and starch and increased the percentage of fibre, while a high percentage of agricultural areas increased the percentage of consumed starch. Anthropogenic food such as garbage might serve as fallback food when access to natural resources is limited. We infer that urban WB forage abundant, natural resources in urban areas. Urban WB might use anthropogenic resources (e.g. garbage) if those are easier to exploit and more abundant than natural resources. This study shows that access to natural resources still is mandatory and drives the amount of protein, starch, fat or fibre in wild boar stomachs in urban as well as rural environments.
Keywords	Agriculture ; Grasslands ; Food ; Forests ; Fats ; Starches ; Stomach ; Urban areas
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: Landscape Structures Affect Risk of Canine Distemper in Urban Wildlife

Gras, Pierre / Marescot, Lucile / Benhaiem, Sarah / Kramer-Schadt, Stephanie

Frontiers in Ecology and Evolution, 6:136

2018

Abstract: ... To assess the impact of urban landscape structure heterogeneity (e.g., richness) and shares of green and ... owing to a decrease in host density (e.g., less foxes or raccoons) or an absence of wildlife movement ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	Urbanization rapidly changes landscape structure worldwide, thereby enlarging the human-wildlife interface. The emerging urban structures should have a key influence on the spread and distribution of wildlife diseases such as canine distemper, by shaping density, distribution and movements of wildlife. However, little is known about the role of urban structures as proxies for disease prevalence. To guide management, especially in densely populated cities, assessing the role of landscape structures in hampering or promoting disease prevalence is thus of paramount importance. Between 2008 and 2013, two epidemic waves of canine distemper hit the urban red fox (Vulpes vulpes) population of Berlin, Germany. The directly transmitted canine distemper virus (CDV) causes a virulent disease infecting a range of mammals with high host mortality, particularly in juveniles. We extracted information about CDV serological state (seropositive or seronegative), sex and age for 778 urban fox carcasses collected by the state laboratory Berlin Brandenburg. To assess the impact of urban landscape structure heterogeneity (e.g., richness) and shares of green and gray infrastructures at different spatial resolutions (areal of 28 ha, 78 ha, 314 ha) on seroprevalence we used Generalized Linear Mixed-Effects Models with binomial distributions. Our results indicated that predictors derived at a 28 ha resolution were most informative for describing landscape structure effects (AUC = 0.92). The probability to be seropositive decreased by 66% (0.6 to 0.2) with an increasing share of gray infrastructure (40 to 80%), suggesting that urbanization might hamper CDV spread in urban areas, owing to a decrease in host density (e.g., less foxes or raccoons) or an absence of wildlife movement corridors in strongly urbanized areas. However, less strongly transformed patches such as close-to-nature areas in direct proximity to water bodies were identified as high risk areas for CDV transmission. Therefore, surveillance and disease control actions targeting urban wildlife or human-wildlife interactions should focus on such areas. The possible underlying mechanisms explaining the prevalence distribution may be increased isolation, the absence of alternative hosts or an abiotic environment, all impairing the ability of CDV to persist without a host.
Keywords	CDV ; Berlin ; canine distemper ; disease ; landscape structures ; red fox Vulpes vulpes ; richness ; urban wildlife
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: Adaptive responses of animals to climate change are most likely insufficient

Radchuk, Viktoriia / Hickler, Thomas / Wilting, Andreas / Courtiol, Alexandre / Kramer-Schadt, Stephanie

Nature Communications, 10:3109

2019

Abstract: ... but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin) Senckenberg Gesellschaft für Naturforschung Museum für Naturkunde Berlin
Abstract	Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.
Keywords	Conservation biology ; Climate-change ecology ; Evolutionary ecology
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: Robustness of Eco-Epidemiological Capture-Recapture Parameter Estimates to Variation in Infection State Uncertainty

Benhaiem, Sarah / Marescot, Lucile / Hofer, Heribert / East, Marion / Kramer-Schadt, Stephanie

Frontiers in veterinary science, 5:197

2018

Abstract: ... infection state uncertainty (i.e., the proportion of U) from 20 to 90%, and (2) heterogeneity ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	Estimating eco-epidemiological parameters in free-ranging populations can be challenging. As known individuals may be undetected during a field session, or their health status uncertain, the collected data are typically “imperfect”. Multi-event capture-mark-recapture (MECMR) models constitute a substantial methodological advance by accounting for such imperfect data. In these models, animals can be “undetected” or “detected” at each time step. Detected animals can be assigned an infection state, such as “susceptible” (S), “infected” (I), or “recovered” (R), or an “unknown” (U) state, when for instance no biological sample could be collected. There may be heterogeneity in the assignment of infection states, depending on the manifestation of the disease in the host or the diagnostic method. For example, if obtaining the samples needed to prove viral infection in a detected animal is difficult, this can result in a low chance of assigning the I state. Currently, it is unknown how much uncertainty MECMR models can tolerate to provide reliable estimates of eco-epidemiological parameters and whether these parameters are sensitive to heterogeneity in the assignment of infection states. We used simulations to assess how estimates of the survival probability of individuals in different infection states and the probabilities of infection and recovery responded to (1) increasing infection state uncertainty (i.e., the proportion of U) from 20 to 90%, and (2) heterogeneity in the probability of assigning infection states. We simulated data, mimicking a highly virulent disease, and used SIR-MECMR models to quantify bias and precision. For most parameter estimates, bias increased and precision decreased gradually with state uncertainty. The probabilities of survival of I and R individuals and of detection of R individuals were very robust to increasing state uncertainty. In contrast, the probabilities of survival and detection of S individuals, and the infection and recovery probabilities showed high biases and low precisions when state uncertainty was >50%, particularly when the assignment of the S state was reduced. Considering this specific disease scenario, SIR-MECMR models are globally robust to state uncertainty and heterogeneity in state assignment, but the previously mentioned parameter estimates should be carefully interpreted if the proportion of U is high.
Keywords	SIR model ; assignment probability ; bias ; multi-event capture-mark-recapture ; simulation ; state uncertainty ; partial observation ; precision
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: Editorial: Streaming inflammation: From damage to healing and resilience-Volume II.

Devchand, Pallavi R / Schadt, Eric E / FitzGerald, Garret A

Frontiers in pharmacology

2023 Volume 14, Page(s) 1185593

Language	English
Publishing date	2023-03-24
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2023.1185593
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Article: Relevance of Indirect Transmission for Wildlife Disease Surveillance

http://orcid.org/0000-0002-8853-7202 / Kramer-Schadt, Stephanie / Thulke, Hans-Hermann

Frontiers in veterinary science, 3:110

2016

Abstract: ... by the transmission potential per infectious host (i.e., basic reproductive number R0) and the spatial transmission ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	Epidemiological models of infectious diseases are essential tools in support of risk assessment, surveillance design, and contingency planning in public and animal health. Direct pathogen transmission from host to host is an essential process of each host–pathogen system and respective epidemiological modeling concepts. It is widely accepted that numerous diseases involve indirect transmission (IT) through pathogens shed by infectious hosts to their environment. However, epidemiological models largely do not represent pathogen persistence outside the host explicitly. We hypothesize that this simplification might bias management-related model predictions for disease agents that can persist outside their host for a certain time span. We adapted an individual-based, spatially explicit epidemiological model that can mimic both transmission processes. One version explicitly simulated indirect pathogen transmission through a contaminated environment. The second version simulated direct host-to-host transmission only. We aligned the model variants by the transmission potential per infectious host (i.e., basic reproductive number R0) and the spatial transmission kernel of the infection to allow unbiased comparison of predictions. The quantitative model results are provided for the example of surveillance plans for early detection of foot-and-mouth disease in wild boar, a social host. We applied systematic sampling strategies on the serological status of randomly selected host individuals in both models. We compared between the model variants the time to detection and the area affected prior to detection, measures that strongly influence mitigation costs. Moreover, the ideal sampling strategy to detect the infection in a given time frame was compared between both models. We found the simplified, direct transmission model to underestimate necessary sample size by up to one order of magnitude but to overestimate the area put under control measures. Thus, the model predictions underestimated surveillance efforts but overestimated mitigation costs. We discuss parameterization of IT models and related knowledge gaps. We conclude that the explicit incorporation of IT mechanisms in epidemiological modeling may reward by adapting surveillance and mitigation efforts.
Keywords	FMD ; contingency planning ; environmental transmission ; indirect transmission ; individual-based ; simulation model ; wild boar ; wildlife surveillance
Language	English
Document type	Article
Database	Repository for Life Sciences

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