A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES)

In this article, we introduce ARES (Antibiotic Resistance Evolution Simulator) a software device that simulates P-system model scenarios with five types of nested computing membranes oriented to emulate a hierarchy of eco-biological compartments, i.e. a) peripheral ecosystem; b) local environment; c) reservoir of supplies; d) animal host; and e) host's associated bacterial organisms (microbiome). Computational objects emulating molecular entities such as plasmids, antibiotic resistance genes, antimicrobials, and/or other substances can be introduced into this framework and may interact and evolve together with the membranes, according to a set of pre-established rules and specifications. ARES has been implemented as an online server and offers additional tools for storage and model editing and downstream analysis This work has also been supported by grants BFU2012-39816-C02-01 (co-financed by FEDER funds and the Ministry of Economy and Competitiveness, Spain) to AL and Prometeo/2009/092 (Ministry of Education, Government of Valencia, Spain) and Explora Ciencia y Explora Tecnologia/SAF2013-49788-EXP (Spanish Ministry of Economy and Competitiveness) to AM. IRF is recipient of a "Sara Borrell" postdoctoral fellowship (Ref. CD12/00492) from the Ministry of Economy and Competitiveness (Spain). We are also grateful to the Spanish Network for the Study of Plasmids and Extrachromosomal Elements (REDEEX) for encouraging and funding cooperation among Spanish microbiologists working on the biology of mobile genetic elements (Spanish Ministry of Science and Innovation, reference number BFU2011-14145-E). Campos Frances, M.; Llorens, C.; Sempere Luna, JM.; Futami, R.; Rodríguez, I.; Carrasco, P.; Capilla, R... (2015). A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES). Biology Direct. 10(41):1-13. https://doi.org/10.1186/s13062-015-0070-9 Baquero F, Coque TM, Canton R. Counteracting antibiotic resistance: breaking barriers among antibacterial strategies. Expert Opin Ther Targets. 2014;18:851–61. Baquero F, Lanza VF, Canton R, Coque TM. Public health evolutionary biology of antimicrobial resistance: priorities for intervention. Evol Appl. 2014;8:223–39. Baquero F, Coque TM, de la Cruz F. Ecology and evolution as targets: the need for novel eco-evo drugs and strategies to fight antibiotic resistance. Antimicrob Agents Chemother. 2011;55:3649–60. Carlet J, Jarlier V, Harbarth S, Voss A, Goo