Steering Phages to Combat Bacterial Pathogens
Tài liệu tham khảo
Read, 2011, The evolution of drug resistance and the curious orthodoxy of aggressive chemotherapy, Proc. Natl Acad. Sci. U. S. A., 108, 10871, 10.1073/pnas.1100299108
Smith, 2015, Antibiotic resistance: a primer and call to action, Health Commun., 30, 309, 10.1080/10410236.2014.943634
Samore, 2005, Mechanisms by which antibiotics promote dissemination of resistant pneumococci in human populations, Am. J. Epidemiol., 163, 160, 10.1093/aje/kwj021
Schaberle, 2013, Overcoming the current deadlock in antibiotic research, Trends Microbiol., 22, 165, 10.1016/j.tim.2013.12.007
Silver, 2011, Challenges of antibacterial discovery, Clin. Microbiol. Rev., 24, 71, 10.1128/CMR.00030-10
Fair, 2014, Antibiotics and bacterial resistance in the 21st century, Perspect. Medicin. Chem., 6, 25, 10.4137/PMC.S14459
Tanwar, 2014, Multidrug resistance: an emerging crisis, Interdiscip. Perspect. Infect. Dis., 2014, 541340, 10.1155/2014/541340
Ventola, 2015, The antibiotic resistance crisis: part 1: causes and threats, P&T, 40, 277
Allen, 2014, Targeting virulence: can we make evolution-proof drugs?, Nat. Rev. Microbiol., 12, 300, 10.1038/nrmicro3232
Jansen, 2018, The role of vaccines in fighting antimicrobial resistance (AMR), Hum. Vaccines Immunother., 14, 2142, 10.1080/21645515.2018.1476814
Wright, 2016, Antibiotic adjuvants: rescuing antibiotics from resistance, Trends Microbiol., 24, 862, 10.1016/j.tim.2016.06.009
McAdams, 2019, Resistance diagnostics as a public health tool to combat antibiotic resistance: A model-based evaluation, PLoS Biol., 17, e3000250, 10.1371/journal.pbio.3000250
Kortright, 2019, Phage therapy: a renewed approach to combat antibiotic-resistant bacteria, Cell Host Microbe, 25, 219, 10.1016/j.chom.2019.01.014
Lin, 2017, Phage therapy: an alternative to antibiotics in the age of multi-drug resistance, World J. Gastrointest. Pharmacol. Ther., 8, 162, 10.4292/wjgpt.v8.i3.162
Torres-Barcelo, 2016, Evolutionary rationale for phages as complements of antibiotics, Trends Microbiol., 24, 249, 10.1016/j.tim.2015.12.011
Chan, 2013, Phage cocktails and the future of phage therapy, Future Microbiol., 8, 769, 10.2217/fmb.13.47
Betts, 2013, Back to the future: evolving bacteriophages to increase their effectiveness against the pathogen Pseudomonas aeruginosa PAO1, Evol. Appl., 6, 1054, 10.1111/eva.12085
Friman, 2016, Pre-adapting parasitic phages to a pathogen leads to increased pathogen clearance and lowered resistance evolution with Pseudomonas aeruginosa cystic fibrosis bacterial isolates, J. Evol. Biol., 29, 188, 10.1111/jeb.12774
Chen, 2019, Genetic engineering of bacteriophages against infectious diseases, Front. Microbiol., 10, 954, 10.3389/fmicb.2019.00954
Chaudhry, 2017, Synergy and order effects of antibiotics and phages in killing Pseudomonas aeruginosa biofilms, PLoS One, 12, e0168615, 10.1371/journal.pone.0168615
Vale, 2014, Limiting damage during infection: lessons from infection tolerance for novel therapeutics, PLoS Biol., 12, e1001769, 10.1371/journal.pbio.1001769
Vale, 2016, Beyond killing: can we find new ways to manage infection?, Evol. Med. Pub. Health, 2016, 148, 10.1093/emph/eow012
León, 2015, Virulence reduction in bacteriophage resistant bacteria, Front. Microbiol., 6, 343, 10.3389/fmicb.2015.00343
Smith, 2016, Fitness landscapes reveal simple strategies for steering evolution to minimize antibiotic resistance, bioRxiv
Allen, 2019, Modified antibiotic adjuvant ratios can slow and steer the evolution of resistance: co-amoxiclav as a case study, mBio, 10, 10.1128/mBio.01831-19
Gallaher, 2018, Spatial heterogeneity and evolutionary dynamics modulate time to recurrence in continuous and adaptive cancer therapies, Cancer Res, 78, 2127, 10.1158/0008-5472.CAN-17-2649
Petrova, 2012, Sticky situations: key components that control bacterial surface attachment, J. Bacteriol., 194, 2413, 10.1128/JB.00003-12
Green, 2016, Bacterial secretion systems: an overview, Microbiol. Spectr., 4, 10.1128/microbiolspec.VMBF-0012-2015
Skaar, 2010, The battle for iron between bacterial pathogens and their vertebrate hosts, PLoS Pathog., 6, e1000949, 10.1371/journal.ppat.1000949
Yu, 2010, PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes, Bioinformatics, 26, 1608, 10.1093/bioinformatics/btq249
Chan, 2016, Phage selection restores antibiotic sensitivity in MDR Pseudomonas aeruginosa, Sci. Rep., 6, 26717, 10.1038/srep26717
Chan, 2018, Phage treatment of an aortic graft infected with Pseudomonas aeruginosa, Evol. Med. Pub. Health, 2018, 60, 10.1093/emph/eoy005
Hochberg, 2018, An ecosystem framework for understanding and treating disease, Evol. Med. Pub. Health, 2018, 270
d'Herelle, 1931, Bacteriophage as a treatment in acute medical and surgical infections, Bull. New York Acad. Med., 7, 329
Smith, 1982, Successful treatment of experimental Escherichia coli infections in mice using phage: its general superiority over antibiotics, J. Gen. Microbiol., 128, 307
Hosseinidoust, 2013, Evolution of Pseudomonas aeruginosa virulence as a result of phage predation, Appl. Environ. Microbiol., 79, 6110, 10.1128/AEM.01421-13
Álvarez, 2017, Bacteriophage-based bacterial wilt biocontrol for an environmentally sustainable agriculture, Front. Plant Sci., 8, 1218, 10.3389/fpls.2017.01218
Askora, 2015, Two different evolutionary lines of filamentous phages in Ralstonia solanacearum: their effects on bacterial virulence, Front. Genetics, 6, 217, 10.3389/fgene.2015.00217
Ricci, 2006, Ciprofloxacin-resistant Salmonella enterica serovar Typhimurium strains are difficult to select in the absence of AcrB and TolC, Antimicrob. Agents Chemother., 50, 38, 10.1128/AAC.50.1.38-42.2006
Ricci, 2010, Exploiting the role of TolC in pathogenicity: identification of a bacteriophage for eradication of Salmonella serovars from poultry, Appl. Environ. Microbiol., 76, 1704, 10.1128/AEM.02681-09
Turner, 2015, Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum, Proc. Natl Acad. Sci. U. S. A., 112, 4110, 10.1073/pnas.1419677112
Lipsitch, 2002, Antibiotics in agriculture: when is it time to close the barn door?, Proc. Natl Acad. Sci. U. S. A., 99, 5752, 10.1073/pnas.092142499
Lipsitch, 2002, Antimicrobial use and antimicrobial resistance: a population perspective, Emerg. Infect. Dis., 8, 347, 10.3201/eid0804.010312
King, 2009, Review: Lipopolysaccharide biosynthesis in Pseudomonas aeruginosa, Innate Immun., 15, 261, 10.1177/1753425909106436
Ernst, 2007, Unique lipid a modifications in Pseudomonas aeruginosa isolated from the airways of patients with cystic fibrosis, J. Infect. Dis., 196, 1088, 10.1086/521367
Maura, 2012, Intestinal colonization by enteroaggregative Escherichia coli supports long-term bacteriophage replication in mice, Environ. Microbiol., 14, 1844, 10.1111/j.1462-2920.2011.02644.x
Torres-Barceló, 2018, Phage therapy faces evolutionary challenges, Viruses, 10, 323, 10.3390/v10060323
Betts, 2014, Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages, Proc. Natl Acad. Sci. U. S. A., 111, 11109, 10.1073/pnas.1406763111
Gurney, 2019, Why put up with immunity when there is resistance: an excursion into the population and evolutionary dynamics of restriction-modification and CRISPR-Cas, Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci., 374, 20180096, 10.1098/rstb.2018.0096
Darch, 2017, Phage inhibit pathogen dissemination by targeting bacterial migrants in a chronic infection model, mBio, 8, 2, 10.1128/mBio.00240-17
Liu, 2002, Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage, Science, 295, 2091, 10.1126/science.1067467
Wright, 2018, Cross-resistance is modular in bacteria–phage interactions, PLoS Biol., 16, e2006057, 10.1371/journal.pbio.2006057
Turner, 2014, Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection, PLoS Genet., 10, e1004518, 10.1371/journal.pgen.1004518
Brown, 2012, Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control, Trends Microbiol, 20, 336, 10.1016/j.tim.2012.04.005
Abedon, 2009, Phage evolution and ecology, Adv. Appl. Microbiol., 67, 1, 10.1016/S0065-2164(08)01001-0
Clokie, 2011, Phages in nature, Bacteriophage, 1, 31, 10.4161/bact.1.1.14942
Conrad, 2013, Cystic fibrosis therapy: a community ecology perspective, Am. J. Resp. Cell Mol. Biol., 48, 150, 10.1165/rcmb.2012-0059PS
Pedersen, 2007, Emphasizing the ecology in parasite community ecology, Trends Ecol. Evol., 22, 133, 10.1016/j.tree.2006.11.005
Popat, 2017, Environmental modification via a quorum sensing molecule influences the social landscape of siderophore production, Proc. Biol. Sci., 284, 1852
Wollein Waldetoft, 2014, To harm or not to harm? On the evolution and expression of virulence in group A streptococci, Trends Microbiol., 22, 7, 10.1016/j.tim.2013.10.006
Martens, 2017, The antibiotic resistance crisis, with a focus on the United States, J. Antibiotics, 70, 520, 10.1038/ja.2017.30
Gill, 2010, Phage choice, isolation, and preparation for phage therapy, Curr. Pharmaceut. Biotechnol., 11, 2, 10.2174/138920110790725311
Rohde, 2018, Expert opinion on three phage therapy related topics: bacterial phage resistance, phage training and prophages in bacterial production strains, Viruses, 10, 178, 10.3390/v10040178
Waldor, 1996, Lysogenic conversion by a filamentous phage encoding cholera toxin, Science, 272, 1910, 10.1126/science.272.5270.1910
Moulton-Brown, 2018, Rapid evolution of generalized resistance mechanisms can constrain the efficacy of phage–antibiotic treatments, Evol. Appl., 11, 1630, 10.1111/eva.12653
Blasdel, 2018, Comparative transcriptomics reveals a conserved bacterial adaptive phage response (BAPR) to viral predation, bioRxiv
Pal, 2007, Coevolution with viruses drives the evolution of bacterial mutation rates, Nature, 450, 1079, 10.1038/nature06350
Oliver, 2000, High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection, Science, 288, 1251, 10.1126/science.288.5469.1251
Maciá, 2005, Hypermutation is a key factor in development of multiple-antimicrobial resistance in Pseudomonas aeruginosa strains causing chronic lung infections, Antimicrob. Agents Chemother., 49, 3382, 10.1128/AAC.49.8.3382-3386.2005
MacLean, 2015, Limits to compensatory adaptation and the persistence of antibiotic resistance in pathogenic bacteria, Evol. Med. Public Health, 2015, 4, 10.1093/emph/eou032
Labrie, 2010, Bacteriophage resistance mechanisms, Nat. Rev. Microbiol., 8, 317, 10.1038/nrmicro2315
Cong, 2013, Multiplex genome engineering using CRISPR/Cas systems, Science, 339, 819, 10.1126/science.1231143
Jackson, 1972, Biochemical method for inserting new genetic information into DNA of Simian virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of Escherichia coli, Proc. Natl Acad. Sci. U. S. A., 69, 2904, 10.1073/pnas.69.10.2904
Hall, 2011, Host–parasite coevolutionary arms races give way to fluctuating selection, Ecol. Lett., 14, 635, 10.1111/j.1461-0248.2011.01624.x
Gurney, 2017, Network structure and local adaptation in co-evolving bacteria–phage interactions, Mol. Ecol., 26, 1764, 10.1111/mec.14008
Alseth, 2019, Bacterial biodiversity drives the evolution of CRISPR-based phage resistance, Nature, 574, 549, 10.1038/s41586-019-1662-9
Diavatopoulos, 2006, Adaptive evolution of the Bordetella autotransporter pertactin, J. Evol. Biol., 19, 1931, 10.1111/j.1420-9101.2006.01154.x
Moon, 2017, The BvgAS regulon of Bordetella pertussis, mBio, 8, 10.1128/mBio.01526-17
Yuk, 1998, The BvgAS virulence control system regulates type III secretion in Bordetella bronchiseptica, Mol. Microbiol., 28, 945, 10.1046/j.1365-2958.1998.00850.x
Wang, 2017, Parasites and competitors suppress bacterial pathogen synergistically due to evolutionary trade-offs, Evolution, 71, 733, 10.1111/evo.13143
Filkins, 2015, Cystic fibrosis lung infections: polymicrobial, complex, and hard to treat, PLoS Pathog., 11, e1005258, 10.1371/journal.ppat.1005258
Estrela, 2018, Community interactions and spatial structure shape selection on antibiotic resistant lineages, PLoS Comput. Biol., 14, e1006179, 10.1371/journal.pcbi.1006179
Seed, 2014, Evolutionary consequences of intra-patient phage predation on microbial populations, eLife, 3, e03497, 10.7554/eLife.03497
Wibbenmeyer, 2002, Vibrio cholerae OmpU and OmpT porins are differentially affected by bile, Infect. Immun., 70, 121, 10.1128/IAI.70.1.121-126.2002
Fu, 2013, Tn-Seq analysis of Vibrio cholerae intestinal colonization reveals a role for T6SS-mediated antibacterial activity in the host, Cell Host Microbe, 14, 652, 10.1016/j.chom.2013.11.001
Kamp, 2013, Gene fitness landscapes of Vibrio cholerae at important stages of its life cycle, PLoS Pathog., 9, e1003800, 10.1371/journal.ppat.1003800
Li, 2018, Crystal structure of the outer membrane protein OmpU from Vibrio cholerae at 2.2 A resolution, Acta Crystallogr. D Struct. Biol., 74, 21, 10.1107/S2059798317017697
Craig, 2004, Type IV pilus structure and bacterial pathogenicity, Nat. Rev. Microbiol., 2, 363, 10.1038/nrmicro885
Giltner, 2012, Type IV pilin proteins: versatile molecular modules, Microbiol. Mol. Biol. Rev., 76, 740, 10.1128/MMBR.00035-12
Brockhurst, 2005, The effect of a bacteriophage on diversification of the opportunistic bacterial pathogen, Pseudomonas aeruginosa, Proc. Biol. Sci., 272, 1385
Betts, 2016, Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria–phage system, Evolution, 70, 969, 10.1111/evo.12909
Ishiguro, 1983, A lipopolysaccharide-specific bacteriophage for Aeromonas salmonicida, Can. J. Microbiol., 29, 1458, 10.1139/m83-223
Michel, 2010, Bacteriophage PhiX174 ecological niche and the flexibility of Escherichia coli lipopolysaccharide receptor, Appl. Environ. Microbiol., 76, 7310, 10.1128/AEM.02721-09
Kiljunen, 2011, Identification of the lipopolysaccharide core of Yersinia pestis and Yersinia pseudotuberculosis as the receptor for bacteriophage φA1122, J. Bacteriol., 193, 4963, 10.1128/JB.00339-11
Rebeil, 2004, Variation in lipid A structure in the pathogenic yersiniae, Mol. Microbiol., 52, 1363, 10.1111/j.1365-2958.2004.04059.x
Hoare, 2006, The outer core lipopolysaccharide of Salmonella enterica serovar Typhi is required for bacterial entry into epithelial cells, Infect. Immun., 74, 1555, 10.1128/IAI.74.3.1555-1564.2006
Pier, 2007, Pseudomonas aeruginosa lipopolysaccharide: a major virulence factor, initiator of inflammation and target for effective immunity, Int. J. Med. Microbiol., 297, 277, 10.1016/j.ijmm.2007.03.012
Pålsson-McDermott, 2004, Signal transduction by the lipopolysaccharide receptor, Toll-like receptor-4, Immunology, 113, 153, 10.1111/j.1365-2567.2004.01976.x
Chart, 1989, Conversion of Salmonella enteritidis phage type 4 to phage type 7 involves loss of lipopolysaccharide with concomitant loss of virulence, FEMS Microbiol. Lett., 51, 37, 10.1111/j.1574-6968.1989.tb03415.x
Javier, 2007, Phage-resistance of Salmonella enterica serovar Enteritidis and pathogenesis in Caenorhabditis elegans is mediated by the lipopolysaccharide, Electron. J. Biotechnol., 10, 2007
Gunn, 2001, Bacterial modification of LPS and resistance to antimicrobial peptides, J. Endotoxin Res., 7, 57, 10.1177/09680519010070011001
Moskowitz, 2010, The role of Pseudomonas lipopolysaccharide in cystic fibrosis airway infection, Sub-cell. Biochem., 53, 241, 10.1007/978-90-481-9078-2_11
Rabsch, 2007, FepA- and TonB-dependent bacteriophage H8: receptor binding and genomic sequence, J. Bacteriol., 189, 5658, 10.1128/JB.00437-07
Tyrrell, 2016, Iron acquisition in the cystic fibrosis lung and potential for novel therapeutic strategies, Microbiology, 162, 191, 10.1099/mic.0.000220