To date, antibiotics have been identified on the basis of their ability to kill bacteria or inhibit their growth rather than directly for their capacity to improve clinical outcomes of infected patients. Although historically successful, this approach has led to the development of an antibiotic armamentarium that suffers from a number of shortcomings, including the inevitable emergence of resistance and, in certain infections, suboptimal efficacy leading to long treatment durations, infection recurrence, or high mortality and morbidity rates despite apparent bacterial sterilization. Conventional antibiotics fail to address the complexities of in vivo bacterial physiology and virulence, as well as the role of the host underlying the complex, dynamic interactions that cause disease. New interventions are needed, aimed at host outcome rather than microbiological cure. Here we review the role of screening models for cellular and whole-organism infection, including worms, flies, zebrafish, and mice, to identify novel therapeutic strategies and discuss their future implications.
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Brown, E. D. & Wright, G. D. Antibacterial drug discovery in the resistance era. Nature 529, 336–343 (2016).
Fernandes, P. The global challenge of new classes of antibacterial agents: an industry perspective. Curr. Opin. Pharmacol. 24, 7–11 (2015).
Young, M. H., Aronoff, D. M. & Engleberg, N. C. Necrotizing fasciitis: pathogenesis and treatment. Expert Rev. Anti Infect. Ther. 3, 279–294 (2005).
Young, M. H., Engleberg, N. C., Mulla, Z. D. & Aronoff, D. M. Therapies for necrotising fasciitis. Expert Opin. Biol. Ther. 6, 155–165 (2006).
Vinh, D. C. & Embil, J. M. Device-related infections: a review. J. Long Term Eff. Med. Implants 15, 467–488 (2005).
Song, T., Duperthuy, M. & Wai, S. N. Sub-optimal treatment of bacterial biofilms. Antibiotics (Basel) 5, 23 (2016).
Horsburgh, C. R. Jr., Barry, C. E. III & Lange, C. Treatment of tuberculosis. N. Engl. J. Med. 373, 2149–2160 (2015).
Baddour, L. M. et al. Infective endocarditis in adults: diagnosis, antimicrobial therapy, and management of complications: a scientific statement for healthcare professionals from the american heart association. Circulation 132, 1435–1486 (2015).
Deutschman, C. S. & Tracey, K. J. Sepsis: current dogma and new perspectives. Immunity 40, 463–475 (2014).
Prina, E., Ranzani, O. T. & Torres, A. Community-acquired pneumonia. Lancet 386, 1097–1108 (2015).
Kaukonen, K. M., Bailey, M., Suzuki, S., Pilcher, D. & Bellomo, R. Mortality related to severe sepsis and septic shock among critically ill patients in Australia and New Zealand, 2000–2012. J. Am. Med. Assoc. 311, 1308–1316 (2014).
Giamarellos-Bourboulis, E. J. The failure of biologics in sepsis: where do we stand? Int. J. Antimicrob. Agents 42, S45–S47 (2013).
Marshall, J. C. Such stuff as dreams are made on: mediator-directed therapy in sepsis. Nat. Rev. Drug Discov. 2, 391–405 (2003).
Czaplewski, L. et al. Alternatives to antibiotics-a pipeline portfolio review. Lancet Infect. Dis. 16, 239–251 (2016).
Allen, R. C., Popat, R., Diggle, S. P. & Brown, S. P. Targeting virulence: can we make evolution-proof drugs? Nat. Rev. Microbiol. 12, 300–308 (2014).
Rasko, D. A. & Sperandio, V. Anti-virulence strategies to combat bacteria-mediated disease. Nat. Rev. Drug Discov. 9, 117–128 (2010).
Orth, P. et al. Mechanism of action and epitopes of Clostridium difficile toxin B-neutralizing antibody bezlotoxumab revealed by X-ray crystallography. J. Biol. Chem. 289, 18008–18021 (2014).
Ewald, H. et al. Adjunctive corticosteroids for Pneumocystis jiroveci pneumonia in patients with HIV infection. Cochrane Database Syst. Rev. 2015, CD006150 (2015).
Prasad, K., Singh, M. B. & Ryan, H. Corticosteroids for managing tuberculous meningitis. Cochrane Database Syst. Rev. 4, CD002244 (2016).
Feldman, C. & Anderson, R. Corticosteroids in the adjunctive therapy of community-acquired pneumonia: an appraisal of recent meta-analyses of clinical trials. J. Thorac. Dis. 8, E162–E171 (2016).
Yadav, H. & Cartin-Ceba, R. Balance between hyperinflammation and immunosuppression in sepsis. Semin. Respir. Crit. Care Med. 37, 42–50 (2016).
Louie, A., Song, K. H., Hotson, A., Thomas Tate, A. & Schneider, D. S. How many parameters does it take to describe disease tolerance? PLoS Biol. 14, e1002435 (2016). This study describes disease-tolerance curves in L. monocytogenes infected D. melanogaster as sigmoidal and governed by the parameters of vigor, slope, EC50, and the severity of disease.
MacRae, C. A. & Peterson, R. T. Zebrafish as tools for drug discovery. Nat. Rev. Drug Discov. 14, 721–731 (2015).
Swinney, D. C. & Anthony, J. How were new medicines discovered? Nat. Rev. Drug Discov. 10, 507–519 (2011).
Mattiazzi Usaj, M. et al. High-content screening for quantitative cell biology. Trends Cell Biol. 26, 598–611 (2016).
Raby, A. C. et al. Targeting the TLR co-receptor CD14 with TLR2-derived peptides modulates immune responses to pathogens. Sci. Transl. Med. 5, 185ra64 (2013).
Hancock, R. E., Nijnik, A. & Philpott, D. J. Modulating immunity as a therapy for bacterial infections. Nat. Rev. Microbiol. 10, 243–254 (2012).
Dowling, J. K. & Mansell, A. Toll-like receptors: the swiss army knife of immunity and vaccine development. Clin. Transl. Immunology 5, e85 (2016).
Stanley, S. A. et al. Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth. PLoS Pathog. 10, e1003946 (2014).
Napier, R. J. et al. Imatinib-sensitive tyrosine kinases regulate mycobacterial pathogenesis and represent therapeutic targets against tuberculosis. Cell Host Microbe 10, 475–485 (2011).
Kuijl, C. et al. Intracellular bacterial growth is controlled by a kinase network around PKB/AKT1. Nature 450, 725–730 (2007).
Schiebler, M. et al. Functional drug screening reveals anticonvulsants as enhancers of mTOR-independent autophagic killing of Mycobacterium tuberculosis through inositol depletion. EMBO Mol. Med. 7, 127–139 (2015).
Fatehullah, A., Tan, S. H. & Barker, N. Organoids as an in vitro model of human development and disease. Nat. Cell Biol. 18, 246–254 (2016).
Ranga, A., Gjorevski, N. & Lutolf, M. P. Drug discovery through stem cell-based organoid models. Adv. Drug Deliv. Rev. 69-70, 19–28 (2014).
Bartfeld, S. et al. In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection. Gastroenterology 148, 126–136.e6 (2015).
Ng, S. et al. Human iPSC-derived hepatocyte-like cells support Plasmodium liver-stage infection in vitro. Stem Cell Rep. 4, 348–359 (2015).
Kaufmann, S. H. Paul Ehrlich: founder of chemotherapy. Nat. Rev. Drug Discov. 7, 373 (2008).
Raju, T. N. The Nobel chronicles. 1939: Gerhard Domagk (1895–1964). Lancet 353, 681 (1999).
Campbell, W. C. Ivermectin: a reflection on simplicity (Nobel Lecture). Angew. Chem. Int. Edn. Engl. 55, 10184–10189 (2016).
Omura, S. & Crump, A. The life and times of ivermectin - a success story. Nat. Rev. Microbiol. 2, 984–989 (2004).
Yarnell, A. in Chemical and Engineering News, Vol. 83 (ed. Baum, R.M.) p. 63 (American Chemical Society, Washington DC, 2005).
Powell, J. R. & Ausubel, F. M. Models of Caenorhabditis elegans infection by bacterial and fungal pathogens. Methods Mol. Biol. 415, 403–427 (2008).
Ewbank, J. J. & Zugasti, O. C. elegans: model host and tool for antimicrobial drug discovery. Dis. Model. Mech. 4, 300–304 (2011).
Irazoqui, J. E., Urbach, J. M. & Ausubel, F. M. Evolution of host innate defence: insights from Caenorhabditis elegans and primitive invertebrates. Nat. Rev. Immunol. 10, 47–58 (2010).
Richardson, C. E., Kooistra, T. & Kim, D. H. An essential role for XBP-1 in host protection against immune activation in C. elegans. Nature 463, 1092–1095 (2010).
Moy, T. I. et al. Identification of novel antimicrobials using a live-animal infection model. Proc. Natl Acad. Sci. USA 103, 10414–10419 (2006).
Conery, A. L., Larkins-Ford, J., Ausubel, F. M. & Kirienko, N. V. High-throughput screening for novel anti-infectives using a C. elegans pathogenesis model. Curr. Protoc. Chem. Biol. 6, 25–37 (2014).
Moy, T. I. et al. High-throughput screen for novel antimicrobials using a whole animal infection model. ACS Chem. Biol. 4, 527–533 (2009).
Pukkila-Worley, R. et al. Stimulation of host immune defenses by a small molecule protects C. elegans from bacterial infection. PLoS Genet. 8, e1002733 (2012). This study describes the use of whole-organism transcriptional profiling, classical epistasis analysis, and RNAi screens in C. elegans to define pathways perturbed by the small molecule RPW-24, identified through whole-organism screening in C. elegans.
Buchon, N., Silverman, N. & Cherry, S. Immunity in Drosophila melanogaster—from microbial recognition to whole-organism physiology. Nat. Rev. Immunol. 14, 796–810 (2014).
Apidianakis, Y. & Rahme, L. G. Drosophila melanogaster as a model host for studying Pseudomonas aeruginosa infection. Nat. Protoc. 4, 1285–1294 (2009).
Tzelepis, I., Kapsetaki, S. E., Panayidou, S. & Apidianakis, Y. Drosophila melanogaster: a first step and a stepping-stone to anti-infectives. Curr. Opin. Pharmacol. 13, 763–768 (2013).
Ayres, J. S., Freitag, N. & Schneider, D. S. Identification of Drosophila mutants altering defense of and endurance to Listeria monocytogenes infection. Genetics 178, 1807–1815 (2008). This study identified D. melanogaster mutants that were more susceptible to L. monocytogenes infection, though their ability to control bacterial burden was unchanged compared to wild type.
Corby-Harris, V., Habel, K. E., Ali, F. G. & Promislow, D. E. Alternative measures of response to Pseudomonas aeruginosa infection in Drosophila melanogaster. J. Evol. Biol. 20, 526–533 (2007).
Chang, S. et al. Identification of small molecules rescuing fragile X syndrome phenotypes in Drosophila. Nat. Chem. Biol. 4, 256–263 (2008).
Qurashi, A. et al. Chemical screen reveals small molecules suppressing fragile X premutation rCGG repeat-mediated neurodegeneration in Drosophila. Hum. Mol. Genet. 21, 2068–2075 (2012).
Gladstone, M. et al. A translation inhibitor identified in a Drosophila screen enhances the effect of ionizing radiation and taxol in mammalian models of cancer. Dis. Model. Mech. 5, 342–350 (2012).
Willoughby, L. F. et al. An in vivo large-scale chemical screening platform using Drosophila for anti-cancer drug discovery. Dis. Model. Mech. 6, 521–529 (2013).
Markstein, M. et al. Systematic screen of chemotherapeutics in Drosophila stem cell tumors. Proc. Natl Acad. Sci. USA 111, 4530–4535 (2014).
Fernández-Hernández, I., Scheenaard, E., Pollarolo, G. & Gonzalez, C. The translational relevance of Drosophila in drug discovery. EMBO Rep. 17, 471–472 (2016).
Kesarwani, M. et al. A quorum sensing regulated small volatile molecule reduces acute virulence and promotes chronic infection phenotypes. PLoS Pathog. 7, e1002192 (2011).
Bandyopadhaya, A. et al. The quorum sensing volatile molecule 2-amino acetophenon modulates host immune responses in a manner that promotes life with unwanted guests. PLoS Pathog. 8, e1003024 (2012). This study demonstrated that pretreatment with 2-AA prior to lethal infection with P. aeruginosa resulted in downregulation of pro-inflammatory cytokines, upregulation of anti-inflammatory cytokines, higher bacterial burden, and a significant survival benefit in treated animals, suggesting that 2-AA is an immunomodulatory molecule that ‘tolerizes’ the host to the presence of the pathogen.
Bandyopadhaya, A., Tsurumi, A., Maura, D., Jeffrey, K. L. & Rahme, L. G. A quorum-sensing signal promotes host tolerance training through HDAC1-mediated epigenetic reprogramming. Nat. Microbiol. 1, 16174 (2016). This study demonstrated that the effect of 2-AA on downregulation of pro-inflammatory cytokine induction is mediated through HDAC-1, and the survival benefit provided by 2-AA in infected animals could be inhibited with HDAC inhibitors.
Davis, J. M. et al. Real-time visualization of mycobacterium-macrophage interactions leading to initiation of granuloma formation in zebrafish embryos. Immunity 17, 693–702 (2002).
Prajsnar, T. K., Cunliffe, V. T., Foster, S. J. & Renshaw, S. A. A novel vertebrate model of Staphylococcus aureus infection reveals phagocyte-dependent resistance of zebrafish to non-host specialized pathogens. Cell. Microbiol. 10, 2312–2325 (2008).
van der Sar, A. M. et al. Zebrafish embryos as a model host for the real time analysis of Salmonella typhimurium infections. Cell. Microbiol. 5, 601–611 (2003).
Brannon, M. K. et al. Pseudomonas aeruginosa Type III secretion system interacts with phagocytes to modulate systemic infection of zebrafish embryos. Cell. Microbiol. 11, 755–768 (2009).
Clatworthy, A. E. et al. Pseudomonas aeruginosa infection of zebrafish involves both host and pathogen determinants. Infect. Immun. 77, 1293–1303 (2009).
Renshaw, S. A. & Trede, N. S. A model 450 million years in the making: zebrafish and vertebrate immunity. Dis. Model. Mech. 5, 38–47 (2012).
Dalton, J. P. et al. Screening of anti-mycobacterial compounds in a naturally infected zebrafish larvae model. J. Antimicrob. Chemother. 72, 421–427 (2017).
Takaki, K., Cosma, C. L., Troll, M. A. & Ramakrishnan, L. An in vivo platform for rapid high-throughput antitubercular drug discovery. Cell Rep. 2, 175–184 (2012).
Deans, R. M. et al. Parallel shRNA and CRISPR-Cas9 screens enable antiviral drug target identification. Nat. Chem. Biol. 12, 361–366 (2016).
Neggers, J. E. et al. Identifying drug-target selectivity of small-molecule CRM1/XPO1 inhibitors by CRISPR/Cas9 genome editing. Chem. Biol. 22, 107–116 (2015).
Nijman, S. M. Functional genomics to uncover drug mechanism of action. Nat. Chem. Biol. 11, 942–948 (2015).
Ziegler, S., Pries, V., Hedberg, C. & Waldmann, H. Target identification for small bioactive molecules: finding the needle in the haystack. Angew. Chem. Int. Edn. Engl. 52, 2744–2792 (2013).
North, T. E. et al. Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis. Nature 447, 1007–1011 (2007).
Owens, K. N. et al. Identification of genetic and chemical modulators of zebrafish mechanosensory hair cell death. PLoS Genet. 4, e1000020 (2008).
Yu, P. B. et al. Dorsomorphin inhibits BMP signals required for embryogenesis and iron metabolism. Nat. Chem. Biol. 4, 33–41 (2008).
Adams, K. N. et al. Drug tolerance in replicating mycobacteria mediated by a macrophage-induced efflux mechanism. Cell 145, 39–53 (2011).
Carvalho, R. et al. A high-throughput screen for tuberculosis progression. PLoS One 6, e16779 (2011).
Veneman, W. J. et al. Establishment and optimization of a high throughput setup to study Staphylococcus epidermidis and Mycobacterium marinum infection as a model for drug discovery. J. Vis. Exp. 2014, e51649 (2014).
Veneman, W. J. et al. A zebrafish high throughput screening system used for Staphylococcus epidermidis infection marker discovery. BMC Genomics 14, 255 (2013).
Spaink, H. P. et al. Robotic injection of zebrafish embryos for high-throughput screening in disease models. Methods 62, 246–254 (2013).
Tobin, D. M. et al. The lta4h locus modulates susceptibility to mycobacterial infection in zebrafish and humans. Cell 140, 717–730 (2010). This study identified the requirement of the lta4h gene for defense against M. marinum infection in zebrafish and SNPs in the human homolog of lta4H that were associated with and provided heterozygous advantage for pulmonary and meningeal tuberculosis.
Tobin, D. M. et al. Host genotype-specific therapies can optimize the inflammatory response to mycobacterial infections. Cell 148, 434–446 (2012). This study demonstrated that host-directed therapies can be used to fine tune the inflammatory response—which may be either excessive or deficient dependening on host genotype—and improve host outcome during mycobacterial infection in both zebrafish and human tuberculous meningitis patients.
Figueiredo, N. et al. Anthracyclines induce DNA damage response-mediated protection against severe sepsis. Immunity 39, 874–884 (2013). This study demonstrated that anthracyclines provide a profound protective effect on host survival yet have no effect on bacterial burden in a severe sepsis model and that the survival effect is mediated through ATM and the autophagy pathway in the lung.
Moayeri, M., Leppla, S. H., Vrentas, C., Pomerantsev, A. P. & Liu, S. Anthrax Pathogenesis. Annu. Rev. Microbiol. 69, 185–208 (2015).
Liu, S. et al. Key tissue targets responsible for anthrax-toxin-induced lethality. Nature 501, 63–68 (2013). This study demonstrated that anthrax-toxin-induced mortality in mice is dependent on LT targeting of cardiomyocytes and vascular smooth muscle cells and ET targeting of hepatocytes.
Fink, M. P. Animal models of sepsis. Virulence 5, 143–153 (2014).
Munford, R. S. Murine responses to endotoxin: another dirty little secret? J. Infect. Dis. 201, 175–177 (2010).
Seok, J. et al. Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc. Natl Acad. Sci. USA 110, 3507–3512 (2013).
Takao, K. & Miyakawa, T. Genomic responses in mouse models greatly mimic human inflammatory diseases. Proc. Natl Acad. Sci. USA 112, 1167–1172 (2015).
Shay, T., Lederer, J. A. & Benoist, C. Genomic responses to inflammation in mouse models mimic humans: we concur, apples to oranges comparisons won’t do. Proc. Natl Acad. Sci. USA 112, E346 (2015).
Hackam, D. G. & Redelmeier, D. A. Translation of research evidence from animals to humans. J. Am. Med. Assoc. 296, 1731–1732 (2006).
van der Worp, H. B. et al. Can animal models of disease reliably inform human studies? PLoS Med. 7, e1000245 (2010).
Mak, I. W., Evaniew, N. & Ghert, M. Lost in translation: animal models and clinical trials in cancer treatment. Am. J. Transl. Res. 6, 114–118 (2014).
Rex, J. H. et al. A comprehensive regulatory framework to address the unmet need for new antibacterial treatments. Lancet Infect. Dis. 13, 269–275 (2013).
Lloyd, N. C., Morgan, H. W., Nicholson, B. K. & Ronimus, R. S. The composition of Ehrlich’s salvarsan: resolution of a century-old debate. Angew. Chem. Int. Ed. Engl. 44, 941–944 (2005).
Ayres, J. S. & Schneider, D. S. Tolerance of infections. Annu. Rev. Immunol. 30, 271–294 (2012).
Dillman, A. R. & Schneider, D. S. Defining resistance and tolerance to Cancer. Cell Rep. 13, 884–887 (2015).
We would like to acknowledge E. Office and S. Son for assistance with preparing the graphical abstract.
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Clatworthy, A.E., Romano, K.P. & Hung, D.T. Whole-organism phenotypic screening for anti-infectives promoting host health. Nat Chem Biol 14, 331–341 (2018). https://doi.org/10.1038/s41589-018-0018-3
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