One Health EJP Short Term Missions Awarded in 2019
STM 1: Training on the application of source attribution models
Institute: IZSLER, Italy
Place to visit: RIVM, the Netherlands
Duration: 1 week
One Health Thematic Area: Integration of microbiological, risk assessment and surveillance activities
What did Virginia Filipello achieve during her Short Term Mission?
The aim of the visit to the RIVM was to enhance source attribution skills through an ad hoc structured and supervised training, which included exercises with real data and validation of learnt competences. The need for this mission fell within the context of an ongoing process of updating the current routine surveillance of foodborne pathogens with sequence based techniques at IZSLER. IZSLER carries out surveillance plans for the most populous region of Italy, Lombardy, producing large amounts of data. Therefore, the integration of surveillance data with source attribution analyses, could be of great usefulness to improve the positive outcomes on the regional territory. During the mission the participant has been informed on the activities and research ongoing in the hosting institute, with the possibility to interact with other professionals and receive input for future collaborations. During the training the participant received a general introduction on source attribution approaches, with a special focus on source attribution based on microbial subtyping. The Dutch, Hald, Asymmetric Island and STRUCTURE models were included in the training, with particular reference to MLST and MLVA data. The use of WGS in source attribution studies was discussed as well. After each training session, the participant was engaged in consolidating the learnt topics through simulation of attribution with data on Listeria monocytogenes retrieved from public databases. During the staying, it was organised a seminar in which the participant had the possibility to introduce herself and her institute to professionals from the hosting institute to share some highlights about her research activity.
I am a veterinarian with a PhD in Food Safety, and currently a research scholar in the Lombardy Regional Animal Health and Food Safety Institute (IZSLER), in Italy. The aim of my visit to the RIVM was to enhance my source attribution skills, to become able to integrate surveillance data with source attribution analyses, and improve the outcomes of our activities on the regional territory. This experience has been very enriching and informative. Not only I had the chance to learn hands-on the topic of my mission, but I was also encouraged to interact with the other professionals working at the hosting institution (RIVM). During the staying I was informed on the activities and research ongoing at RIVM, and I had fruitful exchanges with other members of the staff and received input for future collaborations. The training itself has been very educational and focussed on resources most useful in my home institution. Most importantly, I was trained to work independently and with critique. Moreover, the supervisor gave me the possibility to introduce myself and my home institute to colleagues involved in epidemiology of foodborne diseases by organising a seminar in which I presented my current research, which was a genuinely motivating opportunity. I am thoroughly grateful to the OHEJP for having granted such a stimulating and professionalizing experience, and I am confident that the newly learnt competence will advance the positive impact of our ongoing surveillance activities. “
STM 2: Application of advanced epidemiological analytical methods for antimicrobial resistance data in Salmonella in pigs
Institute: VISAVET-UCM, Spain
Place to visit: Centre for Statistics, Hasselt University
Duration: 7 weeks
One Health Thematic Area: Skills development missions …..
What did Kendy Tzu-Yun Teng achieve during her Short Term Mission?
The short term mission took place at the Centre of Statistics, the University of Hasselt. The aim of the visit was to develop skills in analysing data on phenotypic antimicrobial resistance (AMR) to identify patterns among the occurrences of resistance of different antimicrobials in an attempt to better understand the interactions and dynamics in Salmonella of swine origin. Data containing AMR information on the minimum inhibitory concentration results of seven antimicrobials from a total of 1,150 Salmonella isolates in 2001-2013 were collected through the Spanish Veterinary Antimicrobial Resistance Surveillance Network programme and analysed during the STM. The antimicrobials included Cefotaxime, Chloramphenicol, Ciprofloxacin, Florfenicol, Gentamicin, Nalidixic acid and Tetracycline. Multiple techniques, including principal component analysis, multiple correspondence analysis, hierarchical clustering, and latent class analysis, were performed to detect potential patterns and clusters among the (categorised) minimum inhibitory concentration results for antimicrobials. Generalised estimating equations were conducted to examine the evolution of the proportion of the resistant strains of each of the seven antimicrobials. Additionally, the structures of relationships among the antimicrobials were examined by Bayesian network analysis. We also made an effort to develop new approaches to Bayesian network analysis in Stan. The work performed during this STM demonstrated useful analytical techniques to explore the interactions among AMR and associations between AMR and Salmonella serotypes. On the base of this action, development to explore AMR phenotypes continues to be carried on.
It was a great stay at the Centre for Statistics, Hasselt University, working with Prof Marc Aerts and Dr Stijn Jaspers. We worked together to apply readily available analytical methods and to explore potential techniques for data on phenotypic antimicrobial resistance (AMR). This action intended to enrich the current WP4 in NOVA project and introduced methods that can be regularly applied to phenotypic AMR data. We chose the Centre for Statistics at Hasselt University because of their abundance in the experience of working with AMR data for the past years. This short term mission also allowed us to extend connection to institutes external to OHEJP and to form new collaboration. Besides the benefits at the project and institute level, I as a researcher also benefited greatly. I got to learn more analytical methods that can be applied to not just phenotypic AMR data but also surveillance, epidemiological and experiential data. Furthermore, we were and still are working on the potential of improving one of the current approaches. This short term mission was my first stay at a statistics research centre, giving me very different and positive stimuli, and I had been really enjoyed it. Thanks to OHJEP for giving me this opportunity!
STM 3: Training in bioinformatics to study the dynamics of E.coli in laying hens: Training on the application of source attribution models
Institute: VISAVET-UCM, Spain
Place to visit: DTU, Denmark
Duration: 4 weeks
One Health Thematic Area: Skills development missions
What did Irene Aldea Ramos achieve during her Short Term Mission?
I visited the Technical University of Denmark with the aim of improving my bioinformatics knowledge. The National Food Institute of DTU is part of the Centre of Genomic Epidemiology which has several web services for the analysis of whole genome sequences. During this month, I have been learning to perform phylogenetic analysis based on the whole DNA sequences. We have worked in the construction of phylogenetic trees with both programs of the Centre of Genomic Epidemiology and with other web-available programs. We also analysed resistance genes and how they move between bacteria. To do this, we tried to describe the genetic context of the genes and also to rebuild the mobile genetic elements. I have learned now not only how to use some tools for the search of this mobile genetic elements but also how to read the results properly. They have also helped me to further analyse the data I already had and they have given me some guidelines and ideas for the work that I can do next, as well as to relate the results that I obtain with the objectives of my project. During the staying I also had the opportunity to attend some sessions of a course in which we were taught to use some tools for the analysis of WGS data.
Knowledge about the dynamics of Antimicrobial Resistant bacteria transmission is one of the main objectives of my project, and for this the tools for bioinformatics analysis are really useful to me. During this stay I have been taught a lot about the use of these tools.
In the time that I have been in the DTU I have not only learned a lot, but I also have met colleagues from other parts of the world who work on similar tasks and with whom I have been able to chat and share ideas and impressions. I really had the opportunity to live a motivating experience both academically and personally. It is enriching to know other places with different cultures and different way of working. Therefore, I would like to thank OHEJP for the grant and members of the DTU for helping me and making me feel comfortable in an unknown place during the month the stay lasted. By last, I strongly recommend visiting Copenhagen and, especially, the DTU.
STM 4: Skills development focused on development of a framework for reporting outbreak investigations using consumer purchase data
Institute: FHI, Norway
Place to visit: SSI, Denmark
Duration: 1 week
One Health Thematic Area: Skills development missions; Integration of microbiological, risk assessment and surveillance activities; Harmonisation of diagnostics tests, platforms and research tools
What did Solveig Jore acheive during her Short Term Mission?
During this week of short term-mission, we worked on developing a framework for reporting outbreak investigations using consumer purchase data. We also looked at the current and previous use of purchase data and the potential future use. We worked on a description of “best practice” for using purchase data with the aim of harmonising the use of this kind of surveillance data amongst the European countries. In addition, we started drafting an opinion paper describing the method and existing barriers for the benefit of new users and with the hope that these barriers eventually can be overcome.
Great stay at the Statens Serum Institute (SSI) where the purpose of this scientific mission was to develop a framework for reporting outbreak investigations using consumer purchase data. We looked at the past, present and possible future use of consumer purchase data and aimed at making a description of best practice, which is a task under WP2 in the NOVA project. Development of “best practice” for using purchase data is important in order to harmonise the use of this kind of surveillance data amongst the European countries. In addition, we started drafting an opinion paper describing the method and existing barriers for the benefit of new users and with the hope that these barriers eventually can be overcome, and we worked on developing an opinion paper on the use of consumer purchase data. SSI has previous experience with using consumer purchase data in several outbreak investigations they have done earlier and it was very useful to become a part of their team for a week and work together with the highly skilled epidemiologists on developing the use of this tool further. I really enjoyed the new contacts I got during my short-term mission and the excellent collaboration we had during my stay at the SSI. I highly recommend a stay at both the Institute and Denmark, and particular Copenhagen.