PT  - JOURNAL ARTICLE
AU  - OE Glushchenko
AU  - NA Prianichnikov
AU  - EI Olekhnovich
AU  - AI Manolov
AU  - VE Odinzova
AU  - AB Tyaht
AU  - ES Kostrukova
AU  - EN Ilina
TI  - VERA: agent-based modeling transmission of antibiotic resistance between human pathogens and gut microbiota
AID  - 10.1101/356824
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 356824
4099  - http://biorxiv.org/content/early/2018/06/28/356824.short
4100  - http://biorxiv.org/content/early/2018/06/28/356824.full
AB  - The resistance of bacterial pathogens to antibiotics is one of the most important issues of the modern health care. The human microbiota can accumulate resistance determinants and transfer them to pathogenic microflora by means of horizontal gene transfer (HGT). Thus, at the moment it is important to develop methods of prediction and monitoring of antibiotics resistance in human population. We represent the agent-based VERA model, which allows to simulate the spread of pathogen with account of possible horizontal transfer of resistance determinants from commensal microbiota community. The model considers the opportunity of residents to stay in the town or in medical institution, have wrong self-treatment, reception of several antibiotics types, transfer and accumulation of resistance determinants from a microbiota to a pathogen. In this model we have also created assessment of optimum intensity of observation of infection spread among the population. Investigating model behavior we show a number of nonlinear dependencies, including the exponential nature of dependence of total of the diseased on average resistance of a pathogen. As the model infection we considered infection with Shigella spp, though it could be applied to a wide range of other pathogens.Availability and implementation Source code and binaries VERA and VERA.viewer are freely available for download at github.com/lpenguin/microbiota-resistome. The code is written in Java, JavaScript and R for Linux platform.