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AG Willmann (Clinical Genomics in Healthcare associated Infections)


Research Focus

Healthcare associated infections pose a major threat to modern medicine and their reduction is of a high priority. Therefore, a deeper knowledge about pathogen factors that are involved in virulence, transmission and persistence as well as antimicrobial resistance mechanisms is urgently needed to reach that goal. However, the bright spectrum of infections and underlying pathogens as well as different patient conditions hamper classical epidemiological approaches. Clinical genomics uses novel sequencing techniques that can determine whole genomes of pathogens or even a genomic overview over populations of pathogens (metagenomics). First results display an enormous genetic variety, even for members of one bacterial species that can differ in hundreds of genes and are thus significantly more divergent than humans. We aim to investigate the involvement of such divergent genetic factors in virulence, transmission and persistence within a clinical context. Such factors could be important targets for novel agents to reduce pathogenicity and transmissibility of healthcare associated pathogens, thus reducing patient mortality and spreading of bacterial organisms in the hospital. Furthermore, such factors could be used as reliable prognosis marker to improve allocation of clinical resources. Another aim of our group focuses on the genetic evolution of pathogens under antibiotic stress and the emergence of antibiotic resistance mechanisms. Understanding these processes can help to design treatment strategies that minimize the risk of antimicrobial resistance development.



Group leader



Matthias Willmann, MD, MSc., DTM&H

Tel. +49 7071 29-81527






Aademic career


Since 2016


Consultant in Clinical Microbiology, Virology and Epidemiology of Infectious Diseases


Assistant professor and group leader “Clinical Genomics in Healthcare associated Infections”, Institute of Medical Microbiology and Hygiene, University of Tübingen (Chair: Ingo B. Autenrieth)




Career award (Förderpreis) of the Deutsche Gesellschaft für Hygiene und Mikrobiologie (DGHM)


Hygiene Prize of the Rudolf Schülke Foundation


Since 2011


Group leader “Clinical Microbiology and Epidemiology of Infectious Diseases”, Institute of Medical Microbiology and Hygiene, University of Tübingen (Chair: Ingo B. Autenrieth)




Trust Fund Award and research stay at the Malaria Research Centre, Kuching, Malaysian Borneo (Chair: Balbir Singh)


Diploma in Tropical Medicine and Hygiene (DTM&H), Royal College of Physicians, London


London School of Hygiene and Tropical Medicine, MSc Degree in Tropical Medicine and International Health


2009 – 2010


Residency in Infectious Diseases, Comprehensive Infectious Diseases Center, University of Ulm (Chair: Peter Kern)




MD Thesis "SNARE-Proteine im retrograden Transport vom Golgi-Komplex zum Endoplasmatischen Retikulum.", Max Planck Institute for Biophysical Chemistry, Department of Neurobiology, Göttingen (Chair: Reinhard Jahn)



Group members


Anna Klimek +49 7071 29-81530
Myriam Spazierer +49 7071 29-81530
Mumina Javed +49 7071 29-74636
Maximilian Heinrich +49 7071 29-74636
Viola Ueltzhöffer +49 7071 29-74636
Benedikt Jentzsch +49 7071 29-74636
Alexander-Thomas Moritz +49 7071 29-74636



Publications (selection)

Peter S, Oberhettinger P, Schuele L, Dinkelacker A, Vogel W, Dörfel D, Bezdan D, Ossowski S, Marschal M, Liese J, Willmann M. "Genomic characterisation of clinical and environmental Pseudomonas putida group strains and determination of their role in the transfer of antimicrobial resistance genes to Pseudomonas aeruginosa." BMC Genomics, 2017


Peter S, Bezdan D, Oberhettinger P, Vogel W, Dörfel D, Dick J, Marschal M, Liese J, Weidenmaier C, Autenrieth I, Ossowski S, Willmann M. "Whole genome sequencing enabled the detection of a colistin-resistant hypermutating citrobacter werkmanii strain harbouring a novel metallo-beta-lactamase VIM-48.", Int J Antimicrob Agents. 2018 


Dößelmann B, Willmann M, Steglich M, Bunk B, Nübel U, Peter S, Neher RA.“Rapid and consistent evolution of colistin resistance in XDR Pseudomonas aeruginosa during morbidostat culture.” Antimicrobial Agents and Chemotherapy, 2017

Marschal M, Bachmaier J, Autenrieth I, Oberhettinger P, Willmann M, Peter S. “Evaluation of the Accelerate Pheno System for Fast Identification and Antimicrobial Susceptibility Testing from Positive Blood Cultures in Bloodstream Infections Caused by Gram-Negative Pathogens.” Journal of Clinical Microbiology, 2017


Huson DH, Steel M, El-Hadidi M, Mitra S, Peter S, Willmann M. “A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples.” Journal of Biotechnology, 2017


Wendel AF, Kaase M, Autenrieth IB, Peter S, Oberhettinger P, Rieber H, Pfeffer K, MacKenzie CR, Willmann M. „Protracted Regional Dissemination of GIM-1-Producing Serratia marcescens in Western Germany.” Antimicrobial Agents and Chemotherapy, 2017


Willmann M, Peter S. “Translational metagenomics and the human resistome: confronting the menace of the new millennium.” Journal of Molecular Medicine, 2017

Zipperer A, Konnerth MC, Laux C, Berscheid A, Janek D, Weidenmaier C, Burian M, Schilling NA, Slavetinsky C, Marschal M, Willmann M, Kalbacher H, Schittek B, Brötz-Oesterhelt H, Grond S, Peschel A & Krismer B „Human commensals produce a novel antibiotic that impairs pathogen colonization.” Nature, 2016


Hamprecht A, Rohde AM, Behnke M, Feihl S, Gastmeier P, Gebhardt F, Kern WV, Knobloch JK, Mischnik A, Obermann B, Querbach C, Peter S, Schneider C, Schröder W, Schwab F, Tacconelli E, Wiese-Posselt M, Wille T, Willmann M, Seifert H, Zweigner J; DZIF-ATHOS Study Group. „Colonization with third-generation cephalosporin-resistant Enterobacteriaceae on hospital admission: prevalence and risk factors.” Journal of Antimicrobial Chemotherapy, 2016


Willmann M, El-Hadidi M, Huson DH, Schütz M, Weidenmaier C, Autenrieth IB, Peter S. „Antibiotic selection pressure determination through sequence-based metagenomics. Antimicrobial Agents and Chemotherapy, 2015


Willmann M, Bezdan D, Zapata L, Susak H, Vogel W, Schröppel K, Liese J, Weidenmaier C, Autenrieth IB, Ossowski S, Peter S. "Analysis of a long-term outbreak of extensively drug-resistant Pseudomonas aeruginosa: a molecular epidemiological study." Journal of Antimicrobial Chemotherapy, 2015


Buhl M, Peter S, Willmann M. “Prevalence and risk factors associated with colonization and infection of extensively drug-resistant Pseudomonas aeruginosa: a systemic review.” Expert Review of Anti-infective Therapy, 2015


Willmann M, Klimek AM, Vogel W, Liese J, Marschal M, Autenrieth IB, Peter S, Buhl M: "Clinical and treatment-related risk factors for nosocomial colonisation with extensively drug-resistant Pseudomonas aeruginosa in a haematological patient population: a matched case control study." BMC Infectious Diseases, 2014


Ahmed AM, Pinheiro MM, Divis PC, Siner A, Zainudin R, Wong IT, Lu CW, Singh-Khaira SK, Millar SB, Lynch S, Willmann M, Singh B, Krishna S, Cox-Singh J. Disease progression in Plasmodium knowlesi malaria is linked to variation in invasion gene family members. PLoS Neglected Tropical Diseases, 2014


Peter S, Wolz C, Kaase M, Marschal M, Schulte B, Vogel W, Autenrieth I, Willmann M. Emergence of Citrobacter freundii carrying IMP-8 metallo-β-lactamase in Germany. New Microbes and New Infections, 2014


Peter S, Lacher A, Marschal M, Hölzl F, Buhl M, Autenrieth I, Kaase M, Willmann M. Evaluation of phenotypic detection methods for metallo-β-lactamases (MBLs) in clinical isolates of Pseudomonas aeruginosa.“ European Journal of Clinical Microbiology & Infectious Diseases, 2014


Willmann M, Kuebart I, Marschal M, Schröppel K, Vogel W, Flesch I, Markert U, Autenrieth IB, Hölzl F, Peter S: "Effect of metallo-beta-lactamase production and multidrug resistance on clinical outcomes in patients with Pseudomonas aeruginosa bloodstream infection: a retrospective cohort study." BMC Infectious Diseases, 2013


Willmann M, Marschal M, Hölzl F, Schröppel K, Autenrieth IB, Peter S: "Time series analysis as a tool to predict the impact of antimicrobial restriction in antibiotic stewardship programs using the example of multidrug-resistant Pseudomonas aeruginosa." Antimicrobial Agents and Chemotherapy, 2013 


Willmann M, Kuebart I, Vogel W, Flesch I, Markert U, Marschal M, Schröppel K, Autenrieth IB, Hölzl F, Peter S: "Time to positivity as prognostic tool in patients with Pseudomonas aeruginosa bloodstream infection." Journal of Infection, 2013


Willmann M, Ahmed A, Siner A, Wong IT, Woon LC, Singh B, Krishna S, Cox-Singh J. Laboratory markers of disease severity in Plasmodium knowlesi infection: a case control study. Malaria Journal, 2013


Verrier SE, Willmann M, Wenzel D, Winter U, von Mollard GF, Söling HD. Members of a mammalian SNARE complex interact in the endoplasmic reticulum in vivo and are found in COPI vesicles. European Journal of Cell Biology, 2008






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