Schaufler Lab

Our workgroup addresses factors that contribute to the success of antimicrobial-resistant bacteria with a focus on Enterobacteriaceae. This does not only include the characterization of resistance but also the in-depth investigation of virulence and fitness determinants. With geno- and phenotypic experiments including experimental (micro)-evolution, functional and phylogenetic genome analysis as well as biofilm formation assays it is our main goal to analyze, to better understand and to fight successful pandemic pathogens. In collaboration with others, we elucidate the occurrence and transmission of antimicrobial-resistant bacteria in humans, animals (including food products) and the environment in a One Health context and push towards identifying and validating innovative bacterial therapeutic targets to fight antimicrobial-resistant pathogens. We can only counteract the threat of antimicrobial-resistant bacteria in a holistic approach!

Group photo in Greifswald Wieck

Group photo on the ferry to Hiddensee. Photo: Katharina Schaufler / HIOH

Helmholtz Institute for One Health (HIOH)
c/o University Medicine Greifswald
Epidemiology and Ecology of Antimicrobial Resistance (GEAR)

Fleischmannstraße 42
17489 Greifswald

+49 3834 3916-200


University of Greifswald
Institute of Pharmacy/LPG
Pharmaceutical Microbiology

Friedrich-Ludwig-Jahn-Straße 17
17489 Greifswald

+49 3834 420 4869

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News

Research

Projects

T!Raum – One Health – MDR-DEKOL – Intestinal decolonization of multi-resistant pathogens through the combined use of natural substances, probiotics and vaccines

Our long-term goal in the MDR-DEKOL joint project is to develop pharmacological intervention measures to reduce multidrug-resistant (MDR) pathogens in the intestines of livestock and humans. Natural substances, probiotics and vaccines are combined to achieve intestinal decolonization. This leads to a reduction in the environmental impact of MDR pathogens and reduced contamination of animal foodstuffs. In the long term, it is also conceivable that the principle could be transferred to prophylactic (e.g. preoperative) decolonization of human patients.
The intestine is the natural habitat of many Gram-negative MDR pathogens, which means that they can spread quickly, e.g. throughout the entire animal population of a stable. The decolonization of these bacteria from livestock is therefore urgently needed. However, there are problems that are not easy to solve, and attempts based solely on the administration of prebiotics and probiotics have so far failed. In addition to high efficiency, a high selectivity in the reduction of MDR pathogens with a simultaneous low impact on the overall microbiome is required. Our solution to this problem is based on a combinatorial approach that targets specific success characteristics of MDR pathogens.
Based on synergistic effects through the use of natural substances (e.g. flavonoids) to reduce biofilm formation and thus the colonization of MDR pathogens in the intestine, the use of probiotics to increase competitive pressure in the intestine and vaccines against typical surface markers of MDR pathogens that they need to adhere to the intestinal epithelium (e.g. adhesins), decolonization should be made possible. The approach is therefore aimed at 1) reducing biofilm formation and thus the ability to adhere to the intestinal epithelium, 2) increasing the competitive pressure in the intestines of the animals by administering antibiotics and 3) strengthening the host's resistance to colonization through specific antibody formation against MDR pathogens after vaccination.

T!Raum – One Health – Citizen science project with pupils to monitor zoonotic reservoirs and antibiotic resistance using flies (CIFLY)

The primary project objective is the development and evaluation of an educational measure to integrate the One Health topic and experiential science into the curriculum involving local schools, research institutes and a professional Citizen Science (CS) platform (educational relevance) in the T!Raum One Health Region Western Pomerania.
The measure to be developed includes a sustainable CS project with pupils in which the influence of urbanization, agriculture and climate change on wildlife biodiversity (including zoonotic pathogen reservoirs) and antimicrobial resistance (AMR) in the environment will be investigated. Together with scientists, pupils will develop a fly-based monitoring system for wildlife and AMR in Western Pomerania-Greifswald (VG) based on the latest research results in the field of environmental DNA and bacteriology (practical relevance). Flies (order: Diptera) are used as samplers of DNA from wildlife and microorganisms (bacteria). Flies are particularly suitable for DNA collection as they are found in a variety of environments and feed in a variety of ways (e.g. on mammal droppings or carcasses) and can ingest DNA from a variety of sources.
The generated CS data should provide pupils and scientists with information on the geographical and temporal changes in the occurrence of zoonotic reservoirs and AMR along a gradient from rural to urban areas (biological, educational relevance) and enable a comparison of the genotypes of AMR of flies and humans (clinical relevance). The project aims to strengthen the pupils' general understanding of science, convey the basics of the One Health concept and generate scientific data in the process.

Innovative Diagnostic Pipelines for One Health Surveillance

Cooperation partners: University Medicine Greifswald, FLI Riems

The project goal is the co-estimation and investigation of pathogen distribution, host exposure and bacterial genomic and phenotypic diversity that will provide important insights into the ecological processes governing the circulation of pathogens at the human/domestic/wildlife interface, especially in the context of longitudinal monitoring efforts in Mecklenburg-Western Pomerania (MVP). Here, we assembled a coherent and comprehensive diagnostic pipeline based on innovative but stable technologies that we will specifically tailor to the One Health surveillance needs in the two regions where it will be active (Sub-Saharan Africa and MVP). This pipeline will constitute a very solid foundation for all future diagnostic activities at the Helmholtz Institute for One Health in Greifswald.

Wildlife disease monitoring in Mecklenburg-Western Pomerania (MVP) through an integrated One Health surveillance-response system (WiMoPOH)

Cooperation partners: FLI Riems

A systematic sampling framework will be established for the continuous collection of longitudinal data and biological samples from free-ranging wild boar, wild ruminants, and carnivores in the One Health context. The wildlife samples will be investigated for selected pathogens and antimicrobial resistances paving the ground for a systematic and longitudinal wildlife monitoring in Mecklenburg-Western Pomerania and beyond.

IFZO Fragmented Transformations – Sustainability in the Baltic Sea region: The ecosystem Baltic Sea as nucleus of a regional integrating sustainability transformation?

Antibiotics and resistant germs in the Baltic Sea

The IFZO sub-project on the entry of substances into the Baltic Sea and the spread of antibiotic-resistant E. coli aims to expand the scientific basis of the sustainability transformation in the Baltic Sea region in an area that has not yet been comprehensively investigated. In addition to investigating the change in behavior in the context of the Baltic Sea literacy concept, necessary gaps in knowledge must be closed in order to enable appropriate behavior. In close collaboration with the University Medicine Greifswald and the Friedrich Loeffler Institute, antibiotic residues and the presence and effects of antibiotic-resistant germs (ESBL-producing E. coli) are monitored along the route from the clinic via the sewage treatment plant to the Baltic Sea in accordance with the One Health approach. A consolidation of knowledge in this research field also serves as an important component for the transformation of the Baltic Sea area into a sustainable region.

DISPATch_MRGN – Disarming pathogens as a different strategy to fight antimicrobial-resistant Gram-negatives

The aim of this research project is to identify and investigate success features of pandemic, antibiotic-resistant Escherichia coli and Klebsiella pneumoniae in order to develop innovative anti-infectives strategies.
By using a wide range of methods that include bioinformatics, microbiology and pharmaceutical biology, we plan to turn our basic research directly into application transfer. In cooperation with internal and external experts from the aforementioned areas and the industry we expect to identify bacterial targets for alternative anti-infectives and to find suitable active compounds. This approach aims to disarm and thus fight infectious, Gram-negative pathogens. The spread of these germs is one of the biggest challenges to the global health system.

Completed projects

SORMAS goes One Health: Water-based Outbreak Prediction in Peri-Urban Africa (SORMAS-WOPPA)

Cooperation partners: HZI Braunschweig, FLI Riems, Africa

The One Health approach is highly relevant for solving challenges in the different disciplines of human- and animal health. Multiple countries use the Surveillance Outbreak Response Management and Analysis System (SORMAS) successfully for the surveillance of human pathogens. SORMAS is a mobile eHealth system that organizes and facilitates disease control and outbreak management in addition to disease surveillance and epidemiological analysis. Yet, current infectious disease surveillance systems generally employ strategies to monitor communicable diseases at a time point when they already occur in a given population and management is applied to fight the emerging outbreak. It would strengthen SORMAS further to include One Health aspects and to target microorganisms that have the potential to impact human and animal health at the source of infection before a disease establishes. While environmental water samples have already been used to monitor biodiversity as well as terrestrial and aquatic pathogens, data are rarely linked to veterinary and public health surveillance systems. Water samples provide an easy-to-handle matrix for laboratory analyses, they accumulate microbes that circulate at the human-domestic livestock-wildlife interface often before disease outbreaks are reported and combine early detection with reliable and standardized laboratory-based investigations. Even the resistome can be monitored. Since all microorganisms share the presence of nucleic acids, it is obvious that the application of high-throughput sequencing methods provides new and promising avenues for public and veterinary health monitoring. While metagenomics from environmental DNA (eDNA) do not provide information about disease progression or biological relevance, they offer an unbiased and comprehensive insight into the diversity of microbes in a given ecosystem. An automated monitoring and subsequent management of water sources in peri-urban Africa would tackle diseases before they manifest in humans or animals. In this study, we aim for the conceptualisation of the incorporation of environmental signals into SORMAS. Since the software has already been integrated into the national public health surveillance system in Ghana, we team up with our long-term collaborator at the Kumasi Centre of Collaborative Research in Tropical Medicine (KCCR) at the Kwame Nkrumah University of Science and Technology (KNUST), Dr. A. Sylverken. Our objectives are a) the conceptualization of the incorporation of environmental signals into SORMAS serving public and veterinary health outbreak prevention and b) establishing baseline data and novel insights into the depth of microbial diversity and candidate pathogens for epidemics in peri-urban Africa with the goal to use those data for consequent surveillance of water sources.

KEAnI – Holistic system for the rapid establishment of an antibiogram for nosocomial infections

Subproject: Development and validation of a blood culture method in a microfluidic scale

Bacterial infectious agents that cause sepsis must be diagnosed, defined and treated in the shortest time possible. The therapeutic success depends largely on diagnostic speed. KEAnI focuses on the development of a technology for the rapid establishment of an antibiogram for nosocomial infections. In cooperation with two SMEs (MEDIPAN GmbH and GA Generic Assays GmbH), the University Hospital Greifswald and the Brandenburg University of Technology Cottbus-Senftenberg, a rapid antibiotic resistance test for sepsis patients will be developed in this project. This enables the direct transfer of research knowledge into therapeutic and economic utilization and application on patients.

Reduction of environmental pollution by antibiotic-resistant bacteria via gut decolonization of animals and humans using combined pre- and probiotic interventions (PreProBiotics)

Cooperation partners: HZI Braunschweig, University Medicine Greifswald, FLI Riems

Multi-drug-resistant pathogens (MDR) have been identified as an increasing threat to humans and animals worldwide. Besides the identification and development of new antibiotic compounds, the exploration of alternative strategies not requiring the use of antibiotics gains considerable importance. Among these potential alternatives, microbiota-based decolonization approaches have delivered promising preliminary results. However, decolonization of Gram-positive MDR bacteria is seemingly easier to achieve than decolonization of multi-drug-resistant Gram-negatives. Also promising are specific natural compounds possibly exhibiting significant antibacterial activity such as polyphenols and tannins. The combination of these plant-based compounds with probiotic bacterial species could help to decolonize the gut of animals with MDR pathogens and facilitate the reestablishment of colonization resistance. We aim to identify microbiota consortia that successfully compete with MDR bacteria in the gut lumen and plant compounds that elicit bactericidal activity against MDR pathogens and thus, in combination, enable decolonization of these pathogens. Using stool samples of wild and matching farm animals (e.g wild duck vs. brood duck; ruminants vs. dairy cattle; wild boar vs. fattening pig) we first aim to assess the level of colonization resistance (CR) against MDR pathogens by spiking stool samples with marked MDR bacteria such as ESBL-producing E. coli, carbapenem-resistant K. pneumoniae and MRSA and screen the proportion of MDR bacteria by selective plating of stool samples on antibiotic plates. In parallel, stool samples of the same animals will be spiked with both bioactive plant-based natural compounds (phenols and tannins) and assessed for their levels of CR using the same in vitro stool assays. Second, we aim to isolate specific competing probiotic strains from "MDR-clearing" samples, and third, evaluate these new therapeutics to decolonize the gut of MDR carrying farm animals including in-depth whole-genome sequence and initial mode-of-action analysis of selected bacterial strains.

Suitability of the virulence factor for siderophore production as a strategy in the fight against resistant bacteria

Association of North German Universities

 

Subclinical bovine mastitis: Significance of the teat canal microbiome and its interrelation with constituents of the human microbiota (NO-MASTITIS)

Cooperation partners: HZI Braunschweig, University Medicine Greifswald, FLI Riems

Bovine subclinical mastitis is the most frequent disease of dairy cows and associated with high economic losses, however, its pathogenesis is not sufficiently understood. Breaching the mammary epithelium in the teat canal (TC) by pathogenic microorganisms followed by intra-mammary infection is the main cause of mastitis. Yet, this is physiologically prevented by a diverse range of TC-colonizing commensal bacteria allowing to resist colonization by pathogens. However, we hypothesize that routine contacts with human microbiota during milking processes may lead to dysbiosis that negatively affect the protecting TC ecosystem. Moreover, antibiotic treatment, disinfection and feed supplements favor co-selection of antibiotic-, biocide- and heavy metal-resistant strains, which may serve as hidden reservoir for (multi-)drug resistant organisms (MDROs). Fitting into the one-health-concept, we will extensively analyze the TC microbiota of healthy and diseased dairy cows by culturomic and genomic approaches to clarify the SM pathogenesis and to analyze the spread of antibiotic-, metal-, and biocide resistances in dairy farming. This pilot project will provide the basis for mastitis prevention and future comparative investigations on the TC microbiota under different husbandry and hygienic conditions and on its interaction with the barn and pasture environment.

Team

Prof. Dr. Katharina Schaufler, PhD
Prof. Dr. Katharina Schaufler, PhD ORCID iD icon

Head of lab (CV)

Room A6.2.21 (HIOH)

+49 3834 3916-200

Elias Eger
Dr. Elias Eger ORCID iD icon

Research associate

Room A6.0.28 (HIOH)

+49 3834 3916-211

Alexandra Dürwald
Dr. Alexandra Dürwald

Research associate

Room A6.0.17 (HIOH)

+49 3834 3916-215

Kumar Siddharth Singh
Dr. Kumar Siddharth Singh

Research associate

Room A6.0.28 (HIOH)

+49 3834 3916-216

Madeleine Paditz
Madeleine Paditz

Assistant / Research associate

Room A6.0.17 (HIOH)

+49 3834 3916-213

Michael Schwabe
Michael Schwabe

Bioinformatician

Room A6.0.28 (HIOH)

+49 3834 3916-212

Sara-Lucia Wawrzyniak
Sara-Lucia Wawrzyniak

Technical assistant

Room A6.0.29 (HIOH)

+49 3834 3916-214

Stefan Heiden
Stefan Heiden ORCID iD icon

Bioinformatician

Room A6.0.28 (HIOH)

+49 3834 3916-210

Dennis Karnatz
Dennis Karnatz

Technical assistant

Room A6.0.29 (HIOH)

+49 3834 3916-217

Jana Brendecke
Jana Brendecke

PhD student

Room 117 (Institute of Pharmacy)

+49 3834 420 4947

Xènia Camprubí-Márquez
Xènia Camprubí-Márquez

PhD student

Room 117 (Institute of Pharmacy)

+49 3834 420 4947

Thaddäus Echelmeyer
Thaddäus Echelmeyer

PhD student

Room 113 (Institute of Pharmacy)

+49 3834 420 4855

Phillip Lübcke
Phillip Lübcke

PhD student

Room 113 (Institute of Pharmacy)

+49 3834 420 4855

Justus Müller
Justus Müller

PhD student

Room 113 (Institute of Pharmacy)

+49 3834 420 4855

Sebastian Paschen
Sebastian Paschen

PhD student

 

 

Lena-Sophie Swiatek
Lena-Sophie Swiatek

PhD student

Room 113 (Institute of Pharmacy)

+49 3834 420 4855

Markus Ellmann

Diploma student

 

 

Maximilian Baeß

Student assistant

 

 

Linus Hübner

Student assistant

 

 

Fynn Meller
Fynn Meller

Student assistant

 

 

Robin Michael
Robin Michael

Student assistant

 

 

Max Sittner
Max Sittner

Student assistant

 

 

Alumni

03/2020-12/2023 Katharina Sydow (PhD student)
01/2022-06/2022 Hildegard Kieninger (Master student - Pharmacy, University of Basel)
11/2021-04/2022 Eva-Marie Gottschlich (Diploma student - Pharmacy, University of Greifswald)
05/2021-10/2021 Marielle Domke (Diploma student - Pharmacy, University of Greifswald)
11/2020-04/2021 Hannah Kalinowski, Justus Müller, Phillip Lübcke, Chiara Monaco (Diploma students - Pharmacy, University of Greifswald)
11/2019-04/2020 Fabian Zillen (Diploma student - Pharmacy, University of Greifswald)
05/2019-10/2019 Lena Nikolaus (Diploma student - Pharmacy, University of Greifswald)
05/2019-10/2019 Lina Csechala (Bachelor student - Biochemistry, University of Greifswald)
11/2018-04/2019 Julia Müller (Diploma student - Pharmacy, University of Greifswald)

Curriculum Vitae

Prof. Dr. Katharina Schaufler, PhD

Positions

Since 08/2023 Head of the department "Epidemiology and Ecology of Antimicrobial Resistance" (GEAR) at the Helmholtz Institute for One Health (HIOH), Greifswald, Germany
W3 Professor at University Medicine Greifswald, Germany
05/2021-07/2023 Professor at Kiel University, Institute of Infection Medicine, Kiel, Germany
Since 11/2020 Group leader of the BMBF junior research group "DISPATch_MRGN"
01/2019-10/2020 Junior professor of Pharmaceutical Microbiology at the Institute of Pharmacy, Pharmaceutical Biology, University of Greifswald, Germany
09/2018–12/2018 Postdoctoral fellow, Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Germany
02/2017–07/2018 Postdoctoral fellow, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, USA; Supervisor: Michael S. Gilmore, MD PhD
08/2016–09/2016 Intern (scientific management), Young Academy Berlin, Germany
05/2012–07/2016 Graduate student and research assistant, Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Germany; Supervisor: Lothar H. Wieler, DVM PhD

Degrees & Education

11/2019 Veterinary Specialist for Microbiology
12/2016 PhD (summa cum laude); Supervisor: Lothar H. Wieler, DVM PhD
Title: "Functional plasmid analysis of ESBL-producing Escherichia coli of pandemic sequence types ST131 and ST648"
06/2016 Dr. med. vet. (summa cum laude); Supervisor: Lothar H. Wieler, DVM PhD
Title: "Molecular analysis of ESBL-producing Escherichia coli from different habitats discloses insights into phylogeny, clonal relationships and transmission scenarios"
05/2013–06/2016 Member of the Graduate Program "Biomedical Sciences", Dahlem Research School (DRS), Berlin
08/2014–03/2016 Member of the Berlin-Hyderabad Research Training School on Infectious Diseases and Genetic-Functional Epidemiology (BRIDGE)
03/2012 Veterinary State Examination, License to Practice Veterinary Medicine
09/2008–06/2009 Veterinary medicine studies, Universidad Complutense de Madrid, Spain
10/2006–03/2012 Veterinary medicine studies, Justus-Liebig-Universität Gießen, Germany

Honors & Awards

09/2023 Sponsorship award by the German Society for Hygiene and Microbiology (DGHM)
11/2021 Postdoctoral Award for Hygiene and Microbiology by the Robert Koch Foundation
10/2020 Anton Mayr Prize awarded by the German Veterinary Medical Society (DVG)
01/2020 Young Ambassador for the American Society for Microbiology (ASM)
09/2018–12/2018 Feodor Lynen-Return Fellowship awarded by the Alexander von Humboldt-Foundation
02/2017–07/2018 Feodor Lynen-Postdoctoral Fellowship awarded by the Alexander von Humboldt-Foundation
09/2016 Dissertation Prize awarded by the German Society for Hygiene and Microbiology (DGHM)
07/2015 Travel Grant awarded by the German Academic Exchange Service (DAAD) to carry out a lecture tour in the United States (Columbia University, New York, and University of Maryland, Baltimore)
12/2012–06/2015 Doctoral Fellowship awarded by the SONNENFELD-Foundation and DRS
05/2014 Poster Prize awarded by the program committee of the German Veterinary Medical Society (DVG)
10/2013 Conference Attendance Grant awarded by the program committee of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID)
03/2013 Conference Attendance Grant awarded by the Academy for Animal Health (AfT)

Publications

Preprints

Peer-reviewed

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013