TY - JOUR AU - Alizon, S. AU - Hurford, A. AU - Mideo, N. AU - Van Baalen, M. PY - 2009 DA - 2009// TI - Virulence evolution the trade-off hypothesis: History, current state of affairs and the future JO - J Evol Biol VL - 22 UR - https://doi.org/10.1111/j.1420-9101.2008.01658.x DO - 10.1111/j.1420-9101.2008.01658.x ID - Alizon2009 ER - TY - JOUR AU - Walther, B. A. AU - Ewald, P. W. PY - 2004 DA - 2004// TI - Pathogen survival in the external environment and the evolution of virulence JO - Biol Rev VL - 79 UR - https://doi.org/10.1017/S1464793104006475 DO - 10.1017/S1464793104006475 ID - Walther2004 ER - TY - JOUR AU - King, A. A. AU - Shrestha, S. AU - Harvill, E. T. AU - Bjørnstad, O. N. PY - 2009 DA - 2009// TI - Evolution of acute infections and the invasion-persistence trade-off JO - Am Nat VL - 173 UR - https://doi.org/10.1086/597217 DO - 10.1086/597217 ID - King2009 ER - TY - BOOK AU - Pepper, I. L. AU - Gerba, C. P. AU - Gentry, T. J. PY - 2015 DA - 2015// TI - Environmental Microbiology PB - Elsevier CY - Amsterdam UR - https://doi.org/10.1016/B978-0-12-394626-3.00001-6 DO - 10.1016/B978-0-12-394626-3.00001-6 ID - Pepper2015 ER - TY - JOUR AU - Adams, B. L. AU - Bates, T. C. AU - Oliver, J. D. PY - 2003 DA - 2003// TI - Survival of Helicobacter pylori in a natural freshwater environment JO - Appl Environ Microbiol VL - 69 UR - https://doi.org/10.1128/AEM.69.12.7462-7466.2003 DO - 10.1128/AEM.69.12.7462-7466.2003 ID - Adams2003 ER - TY - JOUR AU - Poole, K. PY - 2012 DA - 2012// TI - Bacterial stress responses as determinants of antimicrobial resistance JO - J Antimicrob Chemother VL - 67 UR - https://doi.org/10.1093/jac/dks196 DO - 10.1093/jac/dks196 ID - Poole2012 ER - TY - JOUR AU - Alizon, S. AU - Mėthot, P. O. PY - 2018 DA - 2018// TI - Reconciling Pasteur and Darwin to control infectious diseases JO - PLoS Biol VL - 16 UR - https://doi.org/10.1371/journal.pbio.2003815 DO - 10.1371/journal.pbio.2003815 ID - Alizon2018 ER - TY - JOUR AU - Lukjancenko, O. AU - Wassenaar, T. M. AU - Ussery, D. W. PY - 2010 DA - 2010// TI - Comparison of 61 sequenced Escherichia coli genomes JO - Microb Ecol VL - 60 UR - https://doi.org/10.1007/s00248-010-9717-3 DO - 10.1007/s00248-010-9717-3 ID - Lukjancenko2010 ER - TY - BOOK AU - Haas, C. N. AU - Rose, J. B. AU - Gerba, C. P. PY - 2014 DA - 2014// TI - Quantitative Microbial Risk Assessment PB - Wiley CY - Hoboken UR - https://doi.org/10.1002/9781118910030 DO - 10.1002/9781118910030 ID - Haas2014 ER - TY - JOUR AU - van Elsas, J. D. AU - Semenov, A. V. AU - Costa, R. AU - Trevors, J. T. PY - 2011 DA - 2011// TI - Survival of Escherichia coli in the environment: fundamental and public health aspects JO - ISME J VL - 580 UR - https://doi.org/10.1038/ismej.2010.80 DO - 10.1038/ismej.2010.80 ID - van Elsas2011 ER - TY - JOUR AU - Durso, L. M. AU - Smith, D. AU - Hutkins, R. W. PY - 2004 DA - 2004// TI - Measurements of fitness and competition in commensal Escherichia coli and E. coli O157:H7 strains JO - Appl Environ Microbiol VL - 70 UR - https://doi.org/10.1128/AEM.70.11.6466-6472.2004 DO - 10.1128/AEM.70.11.6466-6472.2004 ID - Durso2004 ER - TY - JOUR AU - King, C. H. AU - Shotts, E. B. AU - Wooley, R. E. AU - Porter, K. G. PY - 1988 DA - 1988// TI - Survival of coliforms and bacterial pathogens within protozoa during chlorination JO - Appl Environ Microbiol VL - 54 ID - King1988 ER - TY - JOUR AU - Lambrecht, E. AU - Barė, J. AU - Chavatte, N. AU - Bert, W. AU - Sabbe, K. AU - Houf, K. PY - 2015 DA - 2015// TI - Protozoan cysts act as a survival niche and protective shelter for foodborne pathogenic bacteria JO - Appl Environ Microbiol VL - 81 UR - https://doi.org/10.1128/AEM.01031-15 DO - 10.1128/AEM.01031-15 ID - Lambrecht2015 ER - TY - JOUR AU - Schmid-Hempel, P. AU - Frank, S. A. PY - 2007 DA - 2007// TI - Pathogenesis, virulence, and infective dose JO - PLoS Pathog VL - 3 UR - https://doi.org/10.1371/journal.ppat.0030147 DO - 10.1371/journal.ppat.0030147 ID - Schmid-Hempel2007 ER - TY - JOUR AU - Leggett, H. C. AU - Cornwallis, C. K. AU - West, S. A. PY - 2012 DA - 2012// TI - Mechanisms of pathogenesis, infective dose and virulence in human parasites JO - PLoS Pathog VL - 8 UR - https://doi.org/10.1371/journal.ppat.1002512 DO - 10.1371/journal.ppat.1002512 ID - Leggett2012 ER - TY - JOUR AU - Caraco, T. AU - Wang, I. N. PY - 2008 DA - 2008// TI - Free-living pathogens: Life-history constraints and strain competition JO - J Theor Biol VL - 250 UR - https://doi.org/10.1016/j.jtbi.2007.10.029 DO - 10.1016/j.jtbi.2007.10.029 ID - Caraco2008 ER - TY - JOUR AU - Alizon, S. AU - Michalakis, Y. PY - 2015 DA - 2015// TI - Adaptive virulence evolution: The good old fitness-based approach JO - Trends Ecol Evol VL - 30 UR - https://doi.org/10.1016/j.tree.2015.02.009 DO - 10.1016/j.tree.2015.02.009 ID - Alizon2015 ER - TY - JOUR AU - Brouwer, A. F. AU - Eisenberg, M. C. AU - Remais, J. V. AU - Collender, P. A. AU - Meza, R. AU - Eisenberg, J. N. S. PY - 2017 DA - 2017// TI - Modeling biphasic environmental decay of pathogens and implications for risk analysis JO - Environ Sci Technol VL - 51 UR - https://doi.org/10.1021/acs.est.6b04030 DO - 10.1021/acs.est.6b04030 ID - Brouwer2017 ER - TY - JOUR AU - Easton, J. H. AU - Gauthier, J. J. AU - Lalor, M. M. AU - Pitt, R. E. PY - 2005 DA - 2005// TI - Die-off of pathogenic E. coli O157:H7 in sewage contaminated waters JO - J Am Water Resour Assoc VL - 41 UR - https://doi.org/10.1111/j.1752-1688.2005.tb03793.x DO - 10.1111/j.1752-1688.2005.tb03793.x ID - Easton2005 ER - TY - JOUR AU - Hellweger, F. L. AU - Bucci, V. AU - Litman, M. R. AU - Gu, A. Z. AU - Onnis-Hayden, A. PY - 2009 DA - 2009// TI - Biphasic decay kinetics of fecal bacteria in surface water not a density effect JO - J Environ Eng VL - 135 UR - https://doi.org/10.1061/(ASCE)0733-9372(2009)135:5(372) DO - 10.1061/(ASCE)0733-9372(2009)135:5(372) ID - Hellweger2009 ER - TY - JOUR AU - Rogers, S. W. AU - Donnelly, M. AU - Peed, L. AU - Kelty, C. A. AU - Mondal, S. AU - Zhong, Z. PY - 2011 DA - 2011// TI - Decay of bacterial pathogens, fecal indicators, and real-time quantitative PCR genetic markers in manure-amended soils JO - Appl Environ Microbiol VL - 77 UR - https://doi.org/10.1128/AEM.02427-10 DO - 10.1128/AEM.02427-10 ID - Rogers2011 ER - TY - JOUR AU - Hofsteenge, N. AU - van Nimwegen, E. AU - Silander, O. K. PY - 2013 DA - 2013// TI - Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli JO - BMC Microbiol VL - 13 UR - https://doi.org/10.1186/1471-2180-13-25 DO - 10.1186/1471-2180-13-25 ID - Hofsteenge2013 ER - TY - JOUR AU - Zhang, Q. AU - He, X. AU - Yan, T. PY - 2015 DA - 2015// TI - Differential decay of wastewater bacteria and change of microbial communities in beach sand and seawater microcosms JO - Environ Sci Technol VL - 49 UR - https://doi.org/10.1021/acs.est.5b01879 DO - 10.1021/acs.est.5b01879 ID - Zhang2015 ER - TY - JOUR AU - Oliver, J. D. PY - 2010 DA - 2010// TI - Recent findings on the viable but nonculturable state in pathogenic bacteria JO - FEMS Microbiol Rev VL - 34 UR - https://doi.org/10.1111/j.1574-6976.2009.00200.x DO - 10.1111/j.1574-6976.2009.00200.x ID - Oliver2010 ER - TY - JOUR AU - Ramamurthy, T. AU - Ghosh, A. AU - Pazhani, G. P. AU - Shinoda, S. PY - 2014 DA - 2014// TI - Current perspectives on viable but non-culturable (VBNC) pathogenic bacteria JO - Front Publc Health VL - 2 ID - Ramamurthy2014 ER - TY - JOUR AU - Li, L. AU - Mendis, N. AU - Trigui, H. AU - Oliver, J. D. AU - Faucher, S. P. PY - 2014 DA - 2014// TI - The importance of the viable but non-culturable state in human bacterial pathogens JO - Front Microbiol VL - 5 ID - Li2014 ER - TY - JOUR AU - Balaban, N. Q. AU - Merrin, J. AU - Chait, R. AU - Kowalik, L. AU - Leibler, S. PY - 2004 DA - 2004// TI - Bacterial persistence as a phenotypic switch JO - Science VL - 305 UR - https://doi.org/10.1126/science.1099390 DO - 10.1126/science.1099390 ID - Balaban2004 ER - TY - JOUR AU - Lewis, K. PY - 2007 DA - 2007// TI - Persister cells, dormancy and infectious disease JO - Nat Rev Microbiol VL - 5 UR - https://doi.org/10.1038/nrmicro1557 DO - 10.1038/nrmicro1557 ID - Lewis2007 ER - TY - JOUR AU - Maisonneuve, E. AU - Gerdes, K. PY - 2014 DA - 2014// TI - Molecular mechanisms underlying bacterial persisters JO - Cell VL - 157 UR - https://doi.org/10.1016/j.cell.2014.02.050 DO - 10.1016/j.cell.2014.02.050 ID - Maisonneuve2014 ER - TY - JOUR AU - Ryan, M. AU - Hamilton, K. AU - Hamilton, M. AU - Haas, C. N. PY - 2014 DA - 2014// TI - Evaluating the potential for a Helicobacter pylori drinking water guideline JO - Risk Anal VL - 34 UR - https://doi.org/10.1111/risa.12190 DO - 10.1111/risa.12190 ID - Ryan2014 ER - TY - JOUR AU - Boehnke, K. F. AU - Eaton, K. A. AU - Fontaine, C. AU - Brewster, R. AU - Wu, J. AU - Eisenberg, J. N. S. PY - 2017 DA - 2017// TI - Reduced infectivity of waterborne viable but nonculturable Helicobacter pylori strain SS1 in mice JO - Helicobacter VL - 22 UR - https://doi.org/10.1111/hel.12391 DO - 10.1111/hel.12391 ID - Boehnke2017 ER - TY - JOUR AU - Li, S. AU - Spicknall, I. H. AU - Koopman, J. S. AU - Eisenberg, J. N. S. PY - 2009 DA - 2009// TI - Dynamics and control of infections transmitted from person to person through the environment JO - Am J Epidemiol VL - 170 UR - https://doi.org/10.1093/aje/kwp116 DO - 10.1093/aje/kwp116 ID - Li2009 ER - TY - JOUR AU - Tien, J. H. AU - Earn, D. J. D. PY - 2010 DA - 2010// TI - Multiple transmission pathways and disease dynamics in a waterborne pathogen model JO - Bull Math Biol VL - 72 UR - https://doi.org/10.1007/s11538-010-9507-6 DO - 10.1007/s11538-010-9507-6 ID - Tien2010 ER - TY - JOUR AU - Rinaldo, A. AU - Bertuzzo, E. AU - Mari, L. AU - Righetto, L. AU - Blokesch, M. AU - Gatto, M. PY - 2012 DA - 2012// TI - Reassessment of the 2010-2011 Haiti cholera outbreak and rainfall-driven multiseason projections JO - Proc Natl Acad Sci VL - 109 UR - https://doi.org/10.1073/pnas.1203333109 DO - 10.1073/pnas.1203333109 ID - Rinaldo2012 ER - TY - STD TI - Kraay ANm, Hayashi MAl, Hernandez-ceron N, Spicknall IH, Eisenberg MC, Meza R, et al.Fomite-mediated transmission as a sufficient pathway: a comparative analysis across three viral pathogens. BMC Infect Dis. 2018; 18:540. https://doi.org/10.1186/s12879-018-3425-x. ID - ref35 ER - TY - JOUR AU - Brouwer, A. F. AU - Masters, N. B. AU - Eisenberg, J. N. S. PY - 2018 DA - 2018// TI - Quantitative microbial risk assessment and infectious disease transmission modeling of waterborne enteric pathogens JO - Curr Environ Health Rep VL - 5 UR - https://doi.org/10.1007/s40572-018-0196-x DO - 10.1007/s40572-018-0196-x ID - Brouwer2018 ER - TY - JOUR AU - Brouwer, A. F. AU - Weir, M. H. AU - Eisenberg, M. C. AU - Meza, R. AU - Eisenberg, J. N. S. PY - 2017 DA - 2017// TI - Dose-response relationships for environmentally mediated infectious disease transmission models JO - PLOS Comput Biol VL - 13 UR - https://doi.org/10.1371/journal.pcbi.1005481 DO - 10.1371/journal.pcbi.1005481 ID - Brouwer2017 ER - TY - JOUR AU - Bellman, R. AU - Åstrȯm, K. J. PY - 1970 DA - 1970// TI - On structural identifiability JO - Math Biosci VL - 7 UR - https://doi.org/10.1016/0025-5564(70)90132-X DO - 10.1016/0025-5564(70)90132-X ID - Bellman1970 ER - TY - JOUR AU - Rothenberg, T. J. PY - 1971 DA - 1971// TI - Identification in Parametric Models JO - Econometrica VL - 39 UR - https://doi.org/10.2307/1913267 DO - 10.2307/1913267 ID - Rothenberg1971 ER - TY - JOUR AU - Cobelli, C. AU - DiStefano, J. J. PY - 1980 DA - 1980// TI - Parameter and structural identifiability concepts and ambiguities: a critical review and analysis JO - Am J Physiol VL - 239 ID - Cobelli1980 ER - TY - JOUR AU - Miao, H. AU - Xia, X. AU - Perelson, A. S. AU - Wu, H. PY - 2011 DA - 2011// TI - On identifiability of nonlinear ODE models and applications in viral dynamics JO - SIAM Rev VL - 53 UR - https://doi.org/10.1137/090757009 DO - 10.1137/090757009 ID - Miao2011 ER - TY - JOUR AU - Saccomani, M. P. AU - Audoly, S. AU - Bellu, G. AU - D’Angio, L. PY - 2001 DA - 2001// TI - A new differential algebra algorithm to test identifiability of nonlinear systems with given initial conditions JO - Proc 40th IEEE Conf Dec Control VL - 4 UR - https://doi.org/10.1109/CDC.2001.980295 DO - 10.1109/CDC.2001.980295 ID - Saccomani2001 ER - TY - JOUR AU - Audoly, S. AU - Bellu, G. AU - D’Angiȯ, L. AU - Saccomani, M. P. AU - Cobelli, C. PY - 2001 DA - 2001// TI - Global identifiability of nonlinear models of biological systems JO - IEEE Trans Biomed Eng VL - 48 UR - https://doi.org/10.1109/10.900248 DO - 10.1109/10.900248 ID - Audoly2001 ER - TY - JOUR AU - Meshkat, N. AU - Eisenberg, M. AU - Distefano, J. J. PY - 2009 DA - 2009// TI - An algorithm for finding globally identifiable parameter combinations of nonlinear ODE models using Gröbner Bases JO - Math Biosci VL - 222 UR - https://doi.org/10.1016/j.mbs.2009.08.010 DO - 10.1016/j.mbs.2009.08.010 ID - Meshkat2009 ER - TY - JOUR AU - Diekmann, O. AU - Heesterbeek, J. A. P. AU - Metz, J. A. J. PY - 1990 DA - 1990// TI - On the definition and the computation of the basic reproduction ratio R0 in models for infectious diseases in heterogeneous populations JO - J Math Biol VL - 28 UR - https://doi.org/10.1007/BF00178324 DO - 10.1007/BF00178324 ID - Diekmann1990 ER - TY - JOUR AU - van den Driessche, P. AU - Watmough, J. PY - 2002 DA - 2002// TI - Reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission JO - Math Biosci VL - 180 UR - https://doi.org/10.1016/S0025-5564(02)00108-6 DO - 10.1016/S0025-5564(02)00108-6 ID - van den Driessche2002 ER - TY - STD TI - Soetaert K, Petzoldt T, Setzer W. Package ’deSolve’; 2018. https://cran.r-project.org/web/packages/deSolve/deSolve.pdf, Accessed 5 Nov 2018. UR - https://cran.r-project.org/web/packages/deSolve/deSolve.pdf ID - ref47 ER - TY - STD TI - Luebeck G, Meza R. Package ’Bhat’; 2013. https://cran.r-project.org/web/packages/Bhat/Bhat.pdf, Accessed 5 Nov 2018. UR - https://cran.r-project.org/web/packages/Bhat/Bhat.pdf ID - ref48 ER - TY - JOUR AU - Eisenberg, M. C. AU - Robertson, S. L. AU - Tien, J. H. PY - 2013 DA - 2013// TI - Identifiability and estimation of multiple transmission pathways in cholera and waterborne disease JO - J Theor Biol VL - 324 UR - https://doi.org/10.1016/j.jtbi.2012.12.021 DO - 10.1016/j.jtbi.2012.12.021 ID - Eisenberg2013 ER - TY - JOUR AU - Gluck-Thaler, E. AU - Slot, J. C. PY - 2015 DA - 2015// TI - Dimensions of horizontal gene transfer in eukaryotic microbial pathogens JO - PLOS Pathog VL - 11 UR - https://doi.org/10.1371/journal.ppat.1005156 DO - 10.1371/journal.ppat.1005156 ID - Gluck-Thaler2015 ER - TY - JOUR AU - Ayrapetyan, M. AU - Williams, T. C. AU - Baxter, R. AU - Oliver, J. D. PY - 2015 DA - 2015// TI - Viable but nonculturable and persister cells coexist stochastically and are induced by human serum JO - Infect Immun VL - 83 UR - https://doi.org/10.1128/IAI.00404-15 DO - 10.1128/IAI.00404-15 ID - Ayrapetyan2015 ER - TY - JOUR AU - Ayrapetyan, M. AU - Williams, T. C. AU - Oliver, J. D. PY - 2015 DA - 2015// TI - Bridging the gap between viable but non-culturable and antibiotic persistent bacteria JO - Trends Microbiol VL - 23 UR - https://doi.org/10.1016/j.tim.2014.09.004 DO - 10.1016/j.tim.2014.09.004 ID - Ayrapetyan2015 ER - TY - JOUR AU - Winfield, M. D. AU - Groisman, E. A. PY - 2003 DA - 2003// TI - Role of nonhost environments in the lifestyles of Salmonella and Escherichia coli JO - Appl Environ Microbiol VL - 69 UR - https://doi.org/10.1128/AEM.69.7.3687-3694.2003 DO - 10.1128/AEM.69.7.3687-3694.2003 ID - Winfield2003 ER -