Contact

Email:    monika(at)mimuw.edu.pl

Phone: +48 22 55 44 456
Fax:     +48 22 55 44 300

Affiliation:
University of Warsaw,
Faculty of Mathematics, Informatics and Mechanics,
Institute of Applied Mathematics and Mechanics

ul. Banacha 2
02-097 Warsaw
POLAND
National Science Centre grant (Unisono: 2016/22/Z/ST1/00690) entitled "Effectiveness of infection control strategies against intra- and inter-hospital transmission of MultidruG-resistant Enterobacteriaceae – insights from a multi-level mathematical NeTwork model" within JPI-EC-AMR (Joint Programming Initiative on Antimicrobial Resistance) network joint co-funded call “To unravel the dynamics of transmission and selection of antimicrobial resistance (AMR) at genetic, bacterial, animal, human, societal, and environmental levels, in order to design and evaluate preventive and intervening measures for controlling resistance”.

Project information:


ACRONYM: EMerGE-NeT
Title: Effectiveness of infection control strategies against intra- and inter-hospital transmission of MultidruG-resistant Enterobacteriaceae – insights from a multi-level mathematical NeTwork model
Keywords: Network modelling, multidrug-resistant Enterobacteriaceae, transmission dynamics, infection control, healthcare network
Realization period: 2017-2020 (extended till 2021)
Budget: Polish team 1 047 068 PLN


Consortium members:

  1. Helmholtz Centre for Infection Research/Department for Epidemiology, Germany (Mikolajczyk, Rafael)
  2. Charité- University Medicine Berlin/Institute of Hygiene and Environmental Medicine, Germany (Gastmeier, Petra)
  3. Nicolaus Copernicus University/Dept. of Microbiology, Poland (Deptula, Aleksander)
  4. UMC Utrecht/Julius Centre for Health Sciences & Primary Care, Netherlands (Kretzschmar, Mirjam)
  5. Rabin Medical Center, Beilinson Hospital/Dept. of Medicine, Israel (Leibovici, Leonard)
  6. Hospital Universitario Virgen Macarena Sevilla./Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Spain (López Cortés, L. Eduardo)
  7. University of Warsaw/Institute of Applied Mathematics and Mechanics, Poland (Piotrowska, Monika J.)

Warsaw team:


Short description:

Multidrug-resistant Enterobacteriaceae (MDR-E) have become a major public health threat in many European countries. While traditional infection control strategies primarily target the containment of intra-hospital transmission, there is growing evidence highlighting the importance of inter-hospital patient traffic for the spread of MDR-E within healthcare systems. Going substantially beyond previous research, the EMerGE-NeT consortium will unite expertise in theoretical modelling, numerical simulation studies, epidemiology, clinical medicine, and microbiology in order to develop a generic network modelling platform, which combines inter- and intra-hospital transmission of MDR-E in a single framework. This multi-level network model will reflect patient traffic in various European healthcare systems and will thus provide the framework to study systematically transmission dynamics of MDR-E and the effectiveness of infection control strategies to contain their spread within and across healthcare systems. Corresponding to the requirements of this modelling approach, we will conduct specific molecular studies assessing the transmissibility of different MDR-E species and strains. In these studies, we will apply a novel cutting-edge methodology of targeted sequencing, which makes the large studies planned in this project economically feasible. Based on a systematic literature review and a formal Delphi process for collating evidence, we will identify promising infection control strategies for containing MDR-E and assess their effectiveness in simulation studies in the multi-level network model using species and strain specific transmission parameters. The multidisciplinary character of this project will create a unique opportunity to evaluate results of computer simulations against practical knowledge and experience, thus allowing researchers to determine whether targeted, unified infection control strategies could stop or reduce the spread of MDR-E, and whether they are practically feasible.

Work Packages

The project is designed to be conducted in three highly interconnected work packages (WPs 1-3) which will be supplemented by a separate WP for the management of the project and the dissemination of the project results (WP 4).


Warsaw team is involved in WP 1, WP 3 and WP 4 while Bydgoszcz team in WP 2 (as a leader), WP3 and WP 4. In particular Warsaw team will develop computational models and numerical algorithms to model dispersion of the pathogens within inter-hospital networks taking into account transfer of patients. Next the derived algorithms will be used to broaden the current knowledge about that phenomenon. One of the main objectives would be to analyse and verify such models using the available data. Initial part of these analyses will be based on archival data, e.g. from Germany and from Israel, provided by the members of consortium and next on collected prospective data from Poland. On the other hand Bydgoszcz, team will collect the data on potential transmission events based on screening for MDR-E of patients together with the information on patients’ movement within the hospital. Moreover, transmission events will be confirmed with phenotypic and molecular methods. Collected data will be included into the intra-hospital network developed by Dutch member of the consortium. Next, both models will be combined to obtain multi-level network model reflecting patient traffic in various European healthcare systems and will thus provide the framework for the systematic study of the transmission dynamics of MDR-E and of the effectiveness of potential interventions to contain their spread within and across healthcare systems. Within the project, we will identify the promising infection control strategies for containing MDR-E and assess their effectiveness in simulation studies based on the multi-level network model using species and strain specific transmission information.

Developed code


EMerGE-NeT Package

Developed computer code is devoted to simulations of the pathogen spread in system of healthcare facilities. It consists of several modules for accomplishing the following tasks:
This code implements both deterministic models as well as stochastic agent-based variants. The main objective is to simulate hospital infections, which develop mostly during stays in healthcare facilities and do not transmit well in the environment. The typical usage of this software is supposed to be as follows. A healthcare admission data set should be provided and it should be loaded to the standardized database provided by this module. Then the given transfer model has to be chosen with a corresponding compatible intra-hospital model. The models must be initialized with an initial state, e.g. initial susceptible/infectious patient distribution, etc. After this step, the simulations can be performed. The inter-hospital module provides parallelization through MPI library. It is assumed that the number of healthcare facilities in systems under consideration is high, so that the distribution of the facilities between processors and then executing serial intra-hospital models is enough to provide adequate speedup. Finally, the simulation results may be processed with aid of the auxiliary utilities provided by this module. Please note that this code has a form of library, so there is no GUI or application provided for activities described above. Access to the functionalities provided by this code is through provided Python API.

For the description of the inter-hospital models provided by this library, please refer to submodule emergenet.inter. On the other hand, intra-hospital models are implemented in submodule emergenet.intra.

Requirements

Hardware requirements: any decent desktop computer; RAM usage may vary depending on input database size and number of healthcare facilities in simulations.
Software requirements:

EMerGE-NeT Package Code and Documentation

To download the code and documentation (release 0.5, 1.0 and 2.0) please fill out the details in the form. Then the link to the download page will be provided.

Preprints/publications




Popularization




More information on partners and realization of the project can be found at the official project web page.