Other information

Researcher (Tenure track)- Research Group for Genomic Epidemiology, DTU Food 

From February 2019 - Present

Postdoc - Research Group for Genomic Epidemiology, DTU Food 

From October 2014 – January 2019

PhD Degree - Research Group for Genomic Epidemiology, DTU Food

From 1^st January 2011 to 30^th September, 2014 

Visiting PhD student at Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK. June 2013 to September 2013

EliteForsk-rejsestipendier from Danish Ministry of Higher Education and Science. The award was for PhD’s research stay abroad. The price of the award was 300,000 DKK (February 2013)

- VILLUM Young Investigators 2017. I was one of the 30 candidates who reached the interview stage of the award process.

- The Danish Dairy Research Foundation 2019 for 2 year project on “Improving food safety using whole genome sequencing and machine learning”. The amount of the grant was 2,391,354 DKK [PI of the project].

- Arla Food amba acknowledges the above project to be of high relevant to the dairy industry and confirms to support the project by a total of 500,000 DKK over 3 years [PI of the project]. 

- Karl Pedersen and Hustrus Industrifond 2019 support 3 year project on “Identification of virulence level in Listeria monocytogenes using WGS and machine learning”. The amount of the grant was 1,906,153 DKK [PI of the project].

- EU Reference Laboratory for Antimicrobial Resistance (https://ec.europa.eu/food/ref-labs_en) 

- COMPARE - COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe (http://www.compare-europe.eu) 

- NNF16OC0021856: Novo nordisk fonden: In this project, I have been working on metagenomics analysis of sewage to characterize antimicrobial resistance from all around the world. 

- Fleming Fund Regional Grants for capacity building of reference center for whole genome sequencing in East Africa (Tanzania), South Africa and West Africa (Nigeria). 

Course:

Whole genome analysis in diagnostic microbiology (23259) at DTU Food (responsible and main teacher, 5 ECTS) http://kurser.dtu.dk/course/23259

Online courses:

Whole genome sequencing of bacterial genomes - tools and applications

https://www.coursera.org/learn/wgs-bacteria  (one of the 20 best online courses of 2017)

Antimicrobial resistance - theory and methods

https://www.coursera.org/learn/antimicrobial-resistance/

Metagenomics applied to surveillance of pathogens and antimicrobial resistance

https://www.coursera.org/learn/metagenomics

Invited lecture:

- Metagenomics data analysis workshop on 18^th – 20^th December 2019 at King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, Thailand. 

- GMI12 NGS workshop with almost 100 scientist participants from several countries on 10^th – 11^th June 2019 at Nanyang Technical University (NTU), Singapore.

Member of scientific committee: 

Conference: The impact of whole genome sequencing and analytical developments on improvement of food safety, 26^th – 28^th March 2018, Paris, France

Member of organizing committee: 

- WHO Workshop on whole genome sequencing analysis and antimicrobial resistance for microbiologists and epidemiologists. 4^th – 8^th April 2016, Bangkok, Thailand.

Invited speaker:

- 12^th Workshop of the EU Brucellosis National Reference Laboratiories, 19^th – 20^th September 2019, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Paris

- ECDC-EFSA 3^rd Joint Network Meeting on One Health Approach to Collaborative Response to Foodborne Disease Outbreaks in EU/EEA. 16^th – 17^th October 2017, EFSA, Parma, Italy.

- Tackling Antimicrobial Resistance in the Food Chain: An ASEAN-EU Partnership, 3^rd – 5^th  April 2017, Bangkok, Thailand. 

Ana Rita Bastos Rebelo (2018-2021), DTU. “Infectious diseases and whole genome sequencing”

Nanna Sophia Mucha Munck (2016-2019), DTU. “Source attribution modelling using data from whole genome sequencing”

Clementine Henri (2014-2017) University Paris-Est, Anses, Maisons-Alfort Laboratory for Food Safety, Maisons-Alfort, France. “Genomics of Listeria monocytogenes of food origin”

Achiraya Siriphap (2012-2016) Mahidol University, Bangkok, Thailand. “Characterization and genetic variation of Vibrio cholera isolated from clinical and environmental sources in Thailand”

Research areas

RESEARCH INTERESTES

My research interests are in whole genome sequencing typing and epidemiology, short and long time evolution in bacterial genomes and population structure of mainly food pathogens. Of scientific highlights were linking the evaluation of using WGS in sub-typing and outbreak detection of Salmonella enterica published in BMC Genomics; “Genomic variation in Salmonella enterica core genes for epidemiological typing” and PLOS One; “Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica” and the discovery of a virulent fragment unique to S. Typhimurium ST313 and S. Dublin published in PLOS One; “The role of the st313-td gene in virulence of Salmonella Typhimurium ST313”. In addition, a study on short-term evolution and global epidemiology of S. Typhimurium DT104 will soon be published in a peer reviewed international journal.

I am author of 11 peer-reviewed published in international refereed journals; 5 as first author.  I have conducted research with 53 scientists in 18 countries.