1
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Mansur MB, deSouza NM, Natrajan R, Abegglen LM, Schiffman JD, Greaves M. Evolutionary determinants of curability in cancer. Nat Ecol Evol 2023; 7:1761-1770. [PMID: 37620552 DOI: 10.1038/s41559-023-02159-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/05/2023] [Indexed: 08/26/2023]
Abstract
The emergence of drug-resistant cells, most of which have a mutated TP53 gene, prevents curative treatment in most advanced and common metastatic cancers of adults. Yet, a few, rarer malignancies, all of which are TP53 wild type, have high cure rates. In this Perspective, we discuss how common features of curable cancers offer insights into the evolutionary and developmental determinants of drug resistance. Acquired loss of TP53 protein function is the most common genetic change in cancer. This probably reflects positive selection in the context of strong ecosystem pressures including microenvironmental hypoxia. Loss of TP53's functions results in multiple fitness benefits and enhanced evolvability of cancer cells. TP53-null cells survive apoptosis, and tolerate potent oncogenic signalling, DNA damage and genetic instability. In addition, critically, they provide an expanded pool of self-renewing, or stem, cells, the primary units of evolutionary selection in cancer, making subsequent adaptation to therapeutic challenge by drug resistance highly probable. The exceptional malignancies that are curable, including the common genetic subtype of childhood acute lymphoblastic leukaemia and testicular seminoma, differ from the common adult cancers in originating prenatally from embryonic or fetal cells that are developmentally primed for TP53-dependent apoptosis. Plus, they have other genetic and phenotypic features that enable dissemination without exposure to selective pressures for TP53 loss, retaining their intrinsic drug hypersensitivity.
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Affiliation(s)
| | - Nandita M deSouza
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
- Department of Imaging, The Royal Marsden National Health Service (NHS) Foundation Trust, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
| | - Lisa M Abegglen
- Department of Pediatrics and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Joshua D Schiffman
- Department of Pediatrics and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Peel Therapeutics, Inc., Salt Lake City, UT, USA
| | - Mel Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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2
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Cavany S, Nanyonga S, Hauk C, Lim C, Tarning J, Sartorius B, Dolecek C, Caillet C, Newton PN, Cooper BS. The uncertain role of substandard and falsified medicines in the emergence and spread of antimicrobial resistance. Nat Commun 2023; 14:6153. [PMID: 37788991 PMCID: PMC10547756 DOI: 10.1038/s41467-023-41542-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023] Open
Abstract
Approximately 10% of antimicrobials used by humans in low- and middle-income countries are estimated to be substandard or falsified. In addition to their negative impact on morbidity and mortality, they may also be important drivers of antimicrobial resistance. Despite such concerns, our understanding of this relationship remains rudimentary. Substandard and falsified medicines have the potential to either increase or decrease levels of resistance, and here we discuss a range of mechanisms that could drive these changes. Understanding these effects and their relative importance will require an improved understanding of how different drug exposures affect the emergence and spread of resistance and of how the percentage of active pharmaceutical ingredients in substandard and falsified medicines is temporally and spatially distributed.
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Affiliation(s)
- Sean Cavany
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Stella Nanyonga
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Medicine Quality Research Group, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Cathrin Hauk
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Medicine Quality Research Group, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Cherry Lim
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Joel Tarning
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Benn Sartorius
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- School of Public Health, Faculty of Medicine, The University of Queensland, St Lucia, Australia
| | - Christiane Dolecek
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Céline Caillet
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Medicine Quality Research Group, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Paul N Newton
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Medicine Quality Research Group, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Infectious Diseases Data Observatory, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Ben S Cooper
- NDM Centre for Global Health Research, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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3
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Mansur MB, Greaves M. Convergent TP53 loss and evolvability in cancer. BMC Ecol Evol 2023; 23:54. [PMID: 37743495 PMCID: PMC10518978 DOI: 10.1186/s12862-023-02146-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/10/2023] [Indexed: 09/26/2023] Open
Abstract
Cancer cell populations evolve by a stepwise process involving natural selection of the fittest variants within a tissue ecosystem context and as modified by therapy. Genomic scrutiny of patient samples reveals an extraordinary diversity of mutational profiles both between patients with similar cancers and within the cancer cell population of individual patients. Does this signify highly divergent evolutionary trajectories or are there repetitive and predictable patterns?Major evolutionary innovations or adaptations in different species are frequently repeated, or convergent, reflecting both common selective pressures and constraints on optimal solutions. We argue this is true of evolving cancer cells, especially with respect to the TP53 gene. Functional loss variants in TP53 are the most common genetic change in cancer. We discuss the likely microenvironmental selective pressures involved and the profound impact this has on cell fitness, evolvability and probability of subsequent drug resistance.
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Affiliation(s)
- Marcela Braga Mansur
- Centre for Evolution and Cancer, The Institute of Cancer Research, ICR, London, UK
| | - Mel Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, ICR, London, UK.
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4
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Czuppon P, Day T, Débarre F, Blanquart F. A stochastic analysis of the interplay between antibiotic dose, mode of action, and bacterial competition in the evolution of antibiotic resistance. PLoS Comput Biol 2023; 19:e1011364. [PMID: 37578976 PMCID: PMC10449190 DOI: 10.1371/journal.pcbi.1011364] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/24/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
The use of an antibiotic may lead to the emergence and spread of bacterial strains resistant to this antibiotic. Experimental and theoretical studies have investigated the drug dose that minimizes the risk of resistance evolution over the course of treatment of an individual, showing that the optimal dose will either be the highest or the lowest drug concentration possible to administer; however, no analytical results exist that help decide between these two extremes. To address this gap, we develop a stochastic mathematical model of bacterial dynamics under antibiotic treatment. We explore various scenarios of density regulation (bacterial density affects cell birth or death rates), and antibiotic modes of action (biostatic or biocidal). We derive analytical results for the survival probability of the resistant subpopulation until the end of treatment, the size of the resistant subpopulation at the end of treatment, the carriage time of the resistant subpopulation until it is replaced by a sensitive one after treatment, and we verify these results with stochastic simulations. We find that the scenario of density regulation and the drug mode of action are important determinants of the survival of a resistant subpopulation. Resistant cells survive best when bacterial competition reduces cell birth and under biocidal antibiotics. Compared to an analogous deterministic model, the population size reached by the resistant type is larger and carriage time is slightly reduced by stochastic loss of resistant cells. Moreover, we obtain an analytical prediction of the antibiotic concentration that maximizes the survival of resistant cells, which may help to decide which drug dosage (not) to administer. Our results are amenable to experimental tests and help link the within and between host scales in epidemiological models.
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Affiliation(s)
- Peter Czuppon
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, UPEC, CNRS, IRD, INRA, Paris, France
- Center for Interdisciplinary Research in Biology, CNRS, Collège de France, PSL Research University, Paris, France
| | - Troy Day
- Department of Mathematics and Statistics, Department of Biology, Queen’s University, Kingston, Canada
| | - Florence Débarre
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, UPEC, CNRS, IRD, INRA, Paris, France
| | - François Blanquart
- Center for Interdisciplinary Research in Biology, CNRS, Collège de France, PSL Research University, Paris, France
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5
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Lin-Rahardja K, Weaver DT, Scarborough JA, Scott JG. Evolution-Informed Strategies for Combating Drug Resistance in Cancer. Int J Mol Sci 2023; 24:6738. [PMID: 37047714 PMCID: PMC10095117 DOI: 10.3390/ijms24076738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023] Open
Abstract
The ever-changing nature of cancer poses the most difficult challenge oncologists face today. Cancer's remarkable adaptability has inspired many to work toward understanding the evolutionary dynamics that underlie this disease in hopes of learning new ways to fight it. Eco-evolutionary dynamics of a tumor are not accounted for in most standard treatment regimens, but exploiting them would help us combat treatment-resistant effectively. Here, we outline several notable efforts to exploit these dynamics and circumvent drug resistance in cancer.
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Affiliation(s)
- Kristi Lin-Rahardja
- Systems Biology & Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Davis T. Weaver
- Systems Biology & Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jessica A. Scarborough
- Systems Biology & Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jacob G. Scott
- Systems Biology & Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Translational Hematology & Oncology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44106, USA
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6
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Natterson-Horowitz B, Aktipis A, Fox M, Gluckman PD, Low FM, Mace R, Read A, Turner PE, Blumstein DT. The future of evolutionary medicine: sparking innovation in biomedicine and public health. FRONTIERS IN SCIENCE 2023; 1:997136. [PMID: 37869257 PMCID: PMC10590274 DOI: 10.3389/fsci.2023.997136] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Evolutionary medicine - i.e. the application of insights from evolution and ecology to biomedicine - has tremendous untapped potential to spark transformational innovation in biomedical research, clinical care and public health. Fundamentally, a systematic mapping across the full diversity of life is required to identify animal model systems for disease vulnerability, resistance, and counter-resistance that could lead to novel clinical treatments. Evolutionary dynamics should guide novel therapeutic approaches that target the development of treatment resistance in cancers (e.g., via adaptive or extinction therapy) and antimicrobial resistance (e.g., via innovations in chemistry, antimicrobial usage, and phage therapy). With respect to public health, the insight that many modern human pathologies (e.g., obesity) result from mismatches between the ecologies in which we evolved and our modern environments has important implications for disease prevention. Life-history evolution can also shed important light on patterns of disease burden, for example in reproductive health. Experience during the COVID-19 (SARS-CoV-2) pandemic has underlined the critical role of evolutionary dynamics (e.g., with respect to virulence and transmissibility) in predicting and managing this and future pandemics, and in using evolutionary principles to understand and address aspects of human behavior that impede biomedical innovation and public health (e.g., unhealthy behaviors and vaccine hesitancy). In conclusion, greater interdisciplinary collaboration is vital to systematically leverage the insight-generating power of evolutionary medicine to better understand, prevent, and treat existing and emerging threats to human, animal, and planetary health.
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Affiliation(s)
- B. Natterson-Horowitz
- Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Athena Aktipis
- Department of Psychology, Arizona State University, Tempe, AZ, United States
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
| | - Molly Fox
- Department of Anthropology, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, United States
| | - Peter D. Gluckman
- Koi Tū: The Centre for Informed Futures, University of Auckland, Auckland, New Zealand
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Felicia M. Low
- Koi Tū: The Centre for Informed Futures, University of Auckland, Auckland, New Zealand
| | - Ruth Mace
- Department of Anthropology, University College London, London, United Kingdom
| | - Andrew Read
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, State College, PA, United States
- Department of Entomology, The Pennsylvania State University, State College, PA, United States
- Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA, United States
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
- Program in Microbiology, Yale School of Medicine, New Haven, CT, United States
| | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
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7
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Yusuf E, Zeitlinger M, Meylan S. A narrative review of the intermediate category of the antimicrobial susceptibility test: relation with dosing and possible impact on antimicrobial stewardship. J Antimicrob Chemother 2023; 78:338-345. [PMID: 36583270 DOI: 10.1093/jac/dkac413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The interpretation of 'susceptible (S)' or 'resistant (R)' results of antimicrobial susceptibility testing is easily understood, but the interpretation of the 'intermediate (I)' category can be confusing. This review critically discusses how this categorization (clinical breakpoints) comes into being with the emphasis on the use of pharmacokinetics and pharmacodynamic data. It discusses the differences between the 'I' according to the CLSI and the EUCAST. This review also discusses the recent EUCAST change of the 'I' definition, and the impact of this change from laboratory and clinical points of view.
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Affiliation(s)
- Erlangga Yusuf
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands.,Centre for Antimicrobial Treatment Optimization Rotterdam (CATOR), Rotterdam, The Netherlands
| | - Markus Zeitlinger
- Department of Clinical Pharmacology, Clinical Pharmacokinetics/Pharmacogenetics and Imaging, Medical University of Vienna, Vienna, Austria
| | - Sylvain Meylan
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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8
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Aspenberg M, Maad Sasane S, Nilsson F, Brown SP, Wollein Waldetoft K. Hygiene may attenuate selection for antibiotic resistance by changing microbial community structure. Evol Med Public Health 2023; 11:1-7. [PMID: 36687161 PMCID: PMC9847546 DOI: 10.1093/emph/eoac038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/30/2022] [Indexed: 01/19/2023] Open
Abstract
Good hygiene, in both health care and the community, is central to containing the rise of antibiotic resistance, as well as to infection control more generally. But despite the well-known importance, the ecological mechanisms by which hygiene (or other transmission control measures) affect the evolution of resistance remain to be elucidated. Using metacommunity ecology theory, we here propose that hygiene attenuates the effect of antibiotic selection pressure. Specifically, we predict that hygiene limits the scope for antibiotics to induce competitive release of resistant bacteria within treated hosts, and that this is due to an effect of hygiene on the distribution of resistant and sensitive strains in the host population. We show this in a mathematical model of bacterial metacommunity dynamics, and test the results against data on antibiotic resistance, antibiotic treatment, and the use of alcohol-based hand rub in long-term care facilities. The data are consistent with hand rub use attenuating the resistance promoting effect of antibiotic treatment. Our results underscore the importance of hygiene, and point to a concrete way to weaken the link between antibiotic use and increasing resistance.
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Affiliation(s)
| | | | - Fredrik Nilsson
- Department of Clinical Pharmacology, Lund University Hospital, Lund, Sweden
| | - Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA,Center for Microbial Dynamics and Infection, GeorgiaInstitute of Technology, Atlanta, GA, USA
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9
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Abstract
The emergence of drug resistance during antimicrobial therapy is a major global health problem, especially for chronic infections like human immunodeficiency virus, hepatitis B and C, and tuberculosis. Sub-optimal adherence to long-term treatment is an important contributor to resistance risk. New long-acting drugs are being developed for weekly, monthly or less frequent dosing to improve adherence, but may lead to long-term exposure to intermediate drug levels. In this study, we analyse the effect of dosing frequency on the risk of resistance evolving during time-varying drug levels. We find that long-acting therapies can increase, decrease or have little effect on resistance, depending on the source (pre-existing or de novo) and degree of resistance, and rates of drug absorption and clearance. Long-acting therapies with rapid drug absorption, slow clearance and strong wild-type inhibition tend to reduce resistance caused by partially resistant strains in the early stages of treatment even if they do not improve adherence. However, if subpopulations of microbes persist and can reactivate during sub-optimal treatment, longer-acting therapies may substantially increase the resistance risk. Our results show that drug kinetics affect selection for resistance in a complicated manner, and that pathogen-specific models are needed to evaluate the benefits of new long-acting therapies.
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Affiliation(s)
- Anjalika Nande
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alison L. Hill
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
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10
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Masserey T, Lee T, Golumbeanu M, Shattock AJ, Kelly SL, Hastings IM, Penny MA. The influence of biological, epidemiological, and treatment factors on the establishment and spread of drug-resistant Plasmodium falciparum. eLife 2022; 11:e77634. [PMID: 35796430 PMCID: PMC9262398 DOI: 10.7554/elife.77634] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
The effectiveness of artemisinin-based combination therapies (ACTs) to treat Plasmodium falciparum malaria is threatened by resistance. The complex interplay between sources of selective pressure-treatment properties, biological factors, transmission intensity, and access to treatment-obscures understanding how, when, and why resistance establishes and spreads across different locations. We developed a disease modelling approach with emulator-based global sensitivity analysis to systematically quantify which of these factors drive establishment and spread of drug resistance. Drug resistance was more likely to evolve in low transmission settings due to the lower levels of (i) immunity and (ii) within-host competition between genotypes. Spread of parasites resistant to artemisinin partner drugs depended on the period of low drug concentration (known as the selection window). Spread of partial artemisinin resistance was slowed with prolonged parasite exposure to artemisinin derivatives and accelerated when the parasite was also resistant to the partner drug. Thus, to slow the spread of partial artemisinin resistance, molecular surveillance should be supported to detect resistance to partner drugs and to change ACTs accordingly. Furthermore, implementing more sustainable artemisinin-based therapies will require extending parasite exposure to artemisinin derivatives, and mitigating the selection windows of partner drugs, which could be achieved by including an additional long-acting drug.
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Affiliation(s)
- Thiery Masserey
- Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Tamsin Lee
- Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Monica Golumbeanu
- Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Andrew J Shattock
- Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Sherrie L Kelly
- Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
| | - Ian M Hastings
- Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
| | - Melissa A Penny
- Swiss Tropical and Public Health InstituteAllschwilSwitzerland
- University of BaselBaselSwitzerland
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11
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Farrokhian N, Maltas J, Dinh M, Durmaz A, Ellsworth P, Hitomi M, McClure E, Marusyk A, Kaznatcheev A, Scott JG. Measuring competitive exclusion in non-small cell lung cancer. SCIENCE ADVANCES 2022; 8:eabm7212. [PMID: 35776787 PMCID: PMC10883359 DOI: 10.1126/sciadv.abm7212] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this study, we experimentally measure the frequency-dependent interactions between a gefitinib-resistant non-small cell lung cancer population and its sensitive ancestor via the evolutionary game assay. We show that cost of resistance is insufficient to accurately predict competitive exclusion and that frequency-dependent growth rate measurements are required. Using frequency-dependent growth rate data, we then show that gefitinib treatment results in competitive exclusion of the ancestor, while the absence of treatment results in a likely, but not guaranteed, exclusion of the resistant strain. Then, using simulations, we demonstrate that incorporating ecological growth effects can influence the predicted extinction time. In addition, we show that higher drug concentrations may not lead to the optimal reduction in tumor burden. Together, these results highlight the potential importance of frequency-dependent growth rate data for understanding competing populations, both in the laboratory and as we translate adaptive therapy regimens to the clinic.
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Affiliation(s)
| | - Jeff Maltas
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Mina Dinh
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | | | | | - Masahiro Hitomi
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Erin McClure
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Andriy Marusyk
- Department of Cancer Physiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Artem Kaznatcheev
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacob G Scott
- CWRU School of Medicine, Cleveland, OH, USA
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
- Department of Radiation Oncology, Cleveland Clinic, Cleveland, OH, USA
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12
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O'Brien S, Baumgartner M, Hall AR. Species interactions drive the spread of ampicillin resistance in human-associated gut microbiota. EVOLUTION MEDICINE AND PUBLIC HEALTH 2021; 9:256-266. [PMID: 34447576 PMCID: PMC8385247 DOI: 10.1093/emph/eoab020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/22/2021] [Indexed: 12/23/2022]
Abstract
Background and objectives Slowing the spread of antimicrobial resistance is urgent if we are to continue treating infectious diseases successfully. There is increasing evidence microbial interactions between and within species are significant drivers of resistance. On one hand, cross-protection by resistant genotypes can shelter susceptible microbes from the adverse effects of antibiotics, reducing the advantage of resistance. On the other hand, antibiotic-mediated killing of susceptible genotypes can alleviate competition and allow resistant strains to thrive (competitive release). Here, by observing interactions both within and between species in microbial communities sampled from humans, we investigate the potential role for cross-protection and competitive release in driving the spread of ampicillin resistance in the ubiquitous gut commensal and opportunistic pathogen Escherichia coli. Methodology Using anaerobic gut microcosms comprising E.coli embedded within gut microbiota sampled from humans, we tested for cross-protection and competitive release both within and between species in response to the clinically important beta-lactam antibiotic ampicillin. Results While cross-protection gave an advantage to antibiotic-susceptible E.coli in standard laboratory conditions (well-mixed LB medium), competitive release instead drove the spread of antibiotic-resistant E.coli in gut microcosms (ampicillin boosted growth of resistant bacteria in the presence of susceptible strains). Conclusions and implications Competition between resistant strains and other members of the gut microbiota can restrict the spread of ampicillin resistance. If antibiotic therapy alleviates competition with resident microbes by killing susceptible strains, as here, microbiota-based interventions that restore competition could be a key for slowing the spread of resistance. Lay Summary Slowing the spread of global antibiotic resistance is an urgent task. In this paper, we ask how interactions between microbial species drive the spread of resistance. We show that antibiotic killing of susceptible microbes can free up resources for resistant microbes and allow them to thrive. Therefore, we should consider microbes in light of their social interactions to understand the spread of resistance.
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Affiliation(s)
- Siobhán O'Brien
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK.,Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - Michael Baumgartner
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - Alex R Hall
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
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13
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SONG TIANQI, WANG CHUNCHENG, TIAN BOPING. MULTIPLE PERIODIC SOLUTIONS OF A WITHIN-HOST MALARIA INFECTION MODEL WITH TIME DELAY. J BIOL SYST 2021. [DOI: 10.1142/s0218339021500108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this paper, we study a within-host malaria infection model recently proposed by Schneider et al. in 2018. The stability and Hopf bifurcation analysis at the interior equilibrium are carried out, finding that the basic reproduction number plays a key role in the dynamics of the model, and incrementing the time delay will induce Hopf bifurcation at this equilibrium. The global extension of the local Hopf branch is further tracked numerically by the MatLab package DDE-BIFTOOL. Neimark-Sacker bifurcation of Poincaré map and period-doubling bifurcation of the bifurcated periodic solution are also detected, resulting in the existence of quasi-periodic and multiple periodic solutions, respectively. These results reveal that Hopf bifurcation will indeed bring about the rich dynamics of the model.
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Affiliation(s)
- TIANQI SONG
- School of Economics and Management, Shanghai Maritime University, Shanghai, P. R. China
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang, P. R. China
| | - CHUNCHENG WANG
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang, P. R. China
| | - BOPING TIAN
- School of Mathematics, Harbin Institute of Technology, Harbin, Heilongjiang, P. R. China
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14
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Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biol Lett 2021; 17:20200913. [PMID: 33975485 PMCID: PMC8113895 DOI: 10.1098/rsbl.2020.0913] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains.
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Affiliation(s)
- Mato Lagator
- IST Austria, Am Campus 1, 3400 Klosterneuburg, Austria.,School of Biological Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Hildegard Uecker
- IST Austria, Am Campus 1, 3400 Klosterneuburg, Austria.,Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland.,Research group Stochastic Evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Paul Neve
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.,Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård 9, Tåstrup 2630, Denmark
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15
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Gjini E, Paupério FFS, Ganusov VV. Treatment timing shifts the benefits of short and long antibiotic treatment over infection. Evol Med Public Health 2020; 2020:249-263. [PMID: 33376597 PMCID: PMC7750949 DOI: 10.1093/emph/eoaa033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Antibiotics are the major tool for treating bacterial infections. Rising antibiotic resistance, however, calls for a better use of antibiotics. While classical recommendations favor long and aggressive treatments, more recent clinical trials advocate for moderate regimens. In this debate, two axes of 'aggression' have typically been conflated: treatment intensity (dose) and treatment duration. The third dimension of treatment timing along each individual's infection course has rarely been addressed. By using a generic mathematical model of bacterial infection controlled by immune response, we examine how the relative effectiveness of antibiotic treatment varies with its timing, duration and antibiotic kill rate. We show that short or long treatments may both be beneficial depending on treatment onset, the target criterion for success and on antibiotic efficacy. This results from the dynamic trade-off between immune response build-up and resistance risk in acute, self-limiting infections, and uncertainty relating symptoms to infection variables. We show that in our model early optimal treatments tend to be 'short and strong', while late optimal treatments tend to be 'mild and long'. This suggests a shift in the aggression axis depending on the timing of treatment. We find that any specific optimal treatment schedule may perform more poorly if evaluated by other criteria, or under different host-specific conditions. Our results suggest that major advances in antibiotic stewardship must come from a deeper empirical understanding of bacterial infection processes in individual hosts. To guide rational therapy, mathematical models need to be constrained by data, including a better quantification of personal disease trajectory in humans. Lay summary: Bacterial infections are becoming more difficult to treat worldwide because bacteria are becoming resistant to the antibiotics used. Addressing this problem requires a better understanding of how treatment along with other host factors impact antibiotic resistance. Until recently, most theoretical research has focused on the importance of antibiotic dosing on antibiotic resistance, however, duration and timing of treatment remain less explored. Here, we use a mathematical model of a generic bacterial infection to study three aspects of treatment: treatment dose/efficacy (defined by the antibiotic kill rate), duration, and timing, and their impact on several infection endpoints. We show that short and long treatment success strongly depends on when treatment begins (defined by the symptom threshold), the target criterion to optimize, and on antibiotic efficacy. We find that if administered early in an infection, "strong and short" therapy performs better, while if treatment begins at higher bacterial densities, a "mild and long" course of antibiotics is favored. In the model host immune defenses are key in preventing relapses, controlling antibiotic resistant bacteria and increasing the effectiveness of moderate intervention. In order to improve rational treatments of human infections, we call for a better quantification of individual disease trajectories in bacteria-immunity space.
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Affiliation(s)
- Erida Gjini
- Mathematical Modeling of Biological Processes Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, Oeiras, 2780-156, Portugal
| | - Francisco F S Paupério
- Mathematical Modeling of Biological Processes Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, Oeiras, 2780-156, Portugal
- Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, 1749-016, Portugal
| | - Vitaly V Ganusov
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
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16
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Acosta MM, Bram JT, Sim D, Read AF. Effect of drug dose and timing of treatment on the emergence of drug resistance in vivo in a malaria model. Evol Med Public Health 2020; 2020:196-210. [PMID: 33209305 PMCID: PMC7652304 DOI: 10.1093/emph/eoaa016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/15/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND OBJECTIVES There is a significant interest in identifying clinically effective drug treatment regimens that minimize the de novo evolution of antimicrobial resistance in pathogen populations. However, in vivo studies that vary treatment regimens and directly measure drug resistance evolution are rare. Here, we experimentally investigate the role of drug dose and treatment timing on resistance evolution in an animal model. METHODOLOGY In a series of experiments, we measured the emergence of atovaquone-resistant mutants of Plasmodium chabaudi in laboratory mice, as a function of dose or timing of treatment (day post-infection) with the antimalarial drug atovaquone. RESULTS The likelihood of high-level resistance emergence increased with atovaquone dose. When varying the timing of treatment, treating either very early or late in infection reduced the risk of resistance. When we varied starting inoculum, resistance was more likely at intermediate inoculum sizes, which correlated with the largest population sizes at time of treatment. CONCLUSIONS AND IMPLICATIONS (i) Higher doses do not always minimize resistance emergence and can promote the emergence of high-level resistance. (ii) Altering treatment timing affects the risk of resistance emergence, likely due to the size of the population at the time of treatment, although we did not test the effect of immunity whose influence may have been important in the case of late treatment. (iii) Finding the 'right' dose and 'right' time to maximize clinical gains and limit resistance emergence can vary depending on biological context and was non-trivial even in our simplified experiments. LAY SUMMARY In a mouse model of malaria, higher drug doses led to increases in drug resistance. The timing of drug treatment also impacted resistance emergence, likely due to the size of the population at the time of treatment.
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Affiliation(s)
- Mónica M Acosta
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA
| | - Joshua T Bram
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA
| | - Derek Sim
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew F Read
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
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17
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Hansen E, Karslake J, Woods RJ, Read AF, Wood KB. Antibiotics can be used to contain drug-resistant bacteria by maintaining sufficiently large sensitive populations. PLoS Biol 2020; 18:e3000713. [PMID: 32413038 PMCID: PMC7266357 DOI: 10.1371/journal.pbio.3000713] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 06/02/2020] [Accepted: 04/23/2020] [Indexed: 12/15/2022] Open
Abstract
Standard infectious disease practice calls for aggressive drug treatment that rapidly eliminates the pathogen population before resistance can emerge. When resistance is absent, this elimination strategy can lead to complete cure. However, when resistance is already present, removing drug-sensitive cells as quickly as possible removes competitive barriers that may slow the growth of resistant cells. In contrast to the elimination strategy, a containment strategy aims to maintain the maximum tolerable number of pathogens, exploiting competitive suppression to achieve chronic control. Here, we combine in vitro experiments in computer-controlled bioreactors with mathematical modeling to investigate whether containment strategies can delay failure of antibiotic treatment regimens. To do so, we measured the "escape time" required for drug-resistant Escherichia coli populations to eclipse a threshold density maintained by adaptive antibiotic dosing. Populations containing only resistant cells rapidly escape the threshold density, but we found that matched resistant populations that also contain the maximum possible number of sensitive cells could be contained for significantly longer. The increase in escape time occurs only when the threshold density-the acceptable bacterial burden-is sufficiently high, an effect that mathematical models attribute to increased competition. The findings provide decisive experimental confirmation that maintaining the maximum number of sensitive cells can be used to contain resistance when the size of the population is sufficiently large.
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Affiliation(s)
- Elsa Hansen
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jason Karslake
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert J. Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrew F. Read
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences and Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kevin B. Wood
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Physics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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18
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Scire J, Hozé N, Uecker H. Aggressive or moderate drug therapy for infectious diseases? Trade-offs between different treatment goals at the individual and population levels. PLoS Comput Biol 2019; 15:e1007223. [PMID: 31404059 PMCID: PMC6742410 DOI: 10.1371/journal.pcbi.1007223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/12/2019] [Accepted: 06/25/2019] [Indexed: 01/28/2023] Open
Abstract
Antimicrobial resistance is one of the major public health threats of the 21st century. There is a pressing need to adopt more efficient treatment strategies in order to prevent the emergence and spread of resistant strains. The common approach is to treat patients with high drug doses, both to clear the infection quickly and to reduce the risk of de novo resistance. Recently, several studies have argued that, at least in some cases, low-dose treatments could be more suitable to reduce the within-host emergence of antimicrobial resistance. However, the choice of a drug dose may have consequences at the population level, which has received little attention so far. Here, we study the influence of the drug dose on resistance and disease management at the host and population levels. We develop a nested two-strain model and unravel trade-offs in treatment benefits between an individual and the community. We use several measures to evaluate the benefits of any dose choice. Two measures focus on the emergence of resistance, at the host level and at the population level. The other two focus on the overall treatment success: the outbreak probability and the disease burden. We find that different measures can suggest different dosing strategies. In particular, we identify situations where low doses minimize the risk of emergence of resistance at the individual level, while high or intermediate doses prove most beneficial to improve the treatment efficiency or even to reduce the risk of resistance in the population.
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Affiliation(s)
- Jérémie Scire
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nathanaël Hozé
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France
- * E-mail: (NH); (HU)
| | - Hildegard Uecker
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Research group Stochastic Evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
- * E-mail: (NH); (HU)
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19
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Blanquart F. Evolutionary epidemiology models to predict the dynamics of antibiotic resistance. Evol Appl 2019; 12:365-383. [PMID: 30828361 PMCID: PMC6383707 DOI: 10.1111/eva.12753] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/22/2018] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
The evolution of resistance to antibiotics is a major public health problem and an example of rapid adaptation under natural selection by antibiotics. The dynamics of antibiotic resistance within and between hosts can be understood in the light of mathematical models that describe the epidemiology and evolution of the bacterial population. "Between-host" models describe the spread of resistance in the host community, and in more specific settings such as hospitalized hosts (treated by antibiotics at a high rate), or farm animals. These models make predictions on the best strategies to limit the spread of resistance, such as reducing transmission or adapting the prescription of several antibiotics. Models can be fitted to epidemiological data in the context of intensive care units or hospitals to predict the impact of interventions on resistance. It has proven harder to explain the dynamics of resistance in the community at large, in particular because models often do not reproduce the observed coexistence of drug-sensitive and drug-resistant strains. "Within-host" models describe the evolution of resistance within the treated host. They show that the risk of resistance emergence is maximal at an intermediate antibiotic dose, and some models successfully explain experimental data. New models that include the complex host population structure, the interaction between resistance-determining loci and other loci, or integrating the within- and between-host levels will allow better interpretation of epidemiological and genomic data from common pathogens and better prediction of the evolution of resistance.
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Affiliation(s)
- François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERMPSL Research UniversityParisFrance
- IAME, UMR 1137, INSERMUniversité Paris DiderotParisFrance
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20
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Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building. Epidemics 2019; 26:116-127. [PMID: 30446431 PMCID: PMC7105018 DOI: 10.1016/j.epidem.2018.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/06/2018] [Accepted: 10/17/2018] [Indexed: 12/24/2022] Open
Abstract
Due to a combination of ecological, political, and demographic factors, the emergence of novel pathogens has been increasingly observed in animals and humans in recent decades. Enhancing global capacity to study and interpret infectious disease surveillance data, and to develop data-driven computational models to guide policy, represents one of the most cost-effective, and yet overlooked, ways to prepare for the next pandemic. Epidemiological and behavioral data from recent pandemics and historic scourges have provided rich opportunities for validation of computational models, while new sequencing technologies and the 'big data' revolution present new tools for studying the epidemiology of outbreaks in real time. For the past two decades, the Division of International Epidemiology and Population Studies (DIEPS) of the NIH Fogarty International Center has spearheaded two synergistic programs to better understand and devise control strategies for global infectious disease threats. The Multinational Influenza Seasonal Mortality Study (MISMS) has strengthened global capacity to study the epidemiology and evolutionary dynamics of influenza viruses in 80 countries by organizing international research activities and training workshops. The Research and Policy in Infectious Disease Dynamics (RAPIDD) program and its precursor activities has established a network of global experts in infectious disease modeling operating at the research-policy interface, with collaborators in 78 countries. These activities have provided evidence-based recommendations for disease control, including during large-scale outbreaks of pandemic influenza, Ebola and Zika virus. Together, these programs have coordinated international collaborative networks to advance the study of emerging disease threats and the field of computational epidemic modeling. A global community of researchers and policy-makers have used the tools and trainings developed by these programs to interpret infectious disease patterns in their countries, understand modeling concepts, and inform control policies. Here we reflect on the scientific achievements and lessons learnt from these programs (h-index = 106 for RAPIDD and 79 for MISMS), including the identification of outstanding researchers and fellows; funding flexibility for timely research workshops and working groups (particularly relative to more traditional investigator-based grant programs); emphasis on group activities such as large-scale modeling reviews, model comparisons, forecasting challenges and special journal issues; strong quality control with a light touch on outputs; and prominence of training, data-sharing, and joint publications.
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21
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Campos M, Capilla R, Naya F, Futami R, Coque T, Moya A, Fernandez-Lanza V, Cantón R, Sempere JM, Llorens C, Baquero F. Simulating Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model. mBio 2019; 10:mBio.02460-18. [PMID: 30696743 PMCID: PMC6355984 DOI: 10.1128/mbio.02460-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Membrane computing is a bio-inspired computing paradigm whose devices are the so-called membrane systems or P systems. The P system designed in this work reproduces complex biological landscapes in the computer world. It uses nested "membrane-surrounded entities" able to divide, propagate, and die; to be transferred into other membranes; to exchange informative material according to flexible rules; and to mutate and be selected by external agents. This allows the exploration of hierarchical interactive dynamics resulting from the probabilistic interaction of genes (phenotypes), clones, species, hosts, environments, and antibiotic challenges. Our model facilitates analysis of several aspects of the rules that govern the multilevel evolutionary biology of antibiotic resistance. We examined a number of selected landscapes where we predict the effects of different rates of patient flow from hospital to the community and vice versa, the cross-transmission rates between patients with bacterial propagules of different sizes, the proportion of patients treated with antibiotics, and the antibiotics and dosing found in the opening spaces in the microbiota where resistant phenotypes multiply. We also evaluated the selective strengths of some drugs and the influence of the time 0 resistance composition of the species and bacterial clones in the evolution of resistance phenotypes. In summary, we provide case studies analyzing the hierarchical dynamics of antibiotic resistance using a novel computing model with reciprocity within and between levels of biological organization, a type of approach that may be expanded in the multilevel analysis of complex microbial landscapes.IMPORTANCE The work that we present here represents the culmination of many years of investigation in looking for a suitable methodology to simulate the multihierarchical processes involved in antibiotic resistance. Everything started with our early appreciation of the different independent but embedded biological units that shape the biology, ecology, and evolution of antibiotic-resistant microorganisms. Genes, plasmids carrying these genes, cells hosting plasmids, populations of cells, microbial communities, and host's populations constitute a complex system where changes in one component might influence the other ones. How would it be possible to simulate such a complexity of antibiotic resistance as it occurs in the real world? Can the process be predicted, at least at the local level? A few years ago, and because of their structural resemblance to biological systems, we realized that membrane computing procedures could provide a suitable frame to approach these questions. Our manuscript describes the first application of this modeling methodology to the field of antibiotic resistance and offers a bunch of examples-just a limited number of them in comparison with the possible ones to illustrate its unprecedented explanatory power.
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Affiliation(s)
- Marcelino Campos
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Department of Information Systems and Computation (DSIC), Universitat Politècnica de València, Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | | | | | | | - Teresa Coque
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Antibiotic Resistance and Bacterial Virulence Unit (HRYC-CSIC), Superior Council of Scientific Research (CSIC), Madrid, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Andrés Moya
- Integrative Systems Biology Institute, University of Valencia and Spanish Research Council (CSIC), Paterna, Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research in the Valencian Community (FISABIO), Valencia, Spain
| | - Val Fernandez-Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Bioinformatics Support Unit, IRYCIS, Madrid, Spain
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Antibiotic Resistance and Bacterial Virulence Unit (HRYC-CSIC), Superior Council of Scientific Research (CSIC), Madrid, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - José M Sempere
- Department of Information Systems and Computation (DSIC), Universitat Politècnica de València, Valencia, Spain
| | | | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Antibiotic Resistance and Bacterial Virulence Unit (HRYC-CSIC), Superior Council of Scientific Research (CSIC), Madrid, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
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22
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Adaptive plasticity in the gametocyte conversion rate of malaria parasites. PLoS Pathog 2018; 14:e1007371. [PMID: 30427935 PMCID: PMC6261640 DOI: 10.1371/journal.ppat.1007371] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 11/28/2018] [Accepted: 10/02/2018] [Indexed: 11/30/2022] Open
Abstract
Sexually reproducing parasites, such as malaria parasites, experience a trade-off between the allocation of resources to asexual replication and the production of sexual forms. Allocation by malaria parasites to sexual forms (the conversion rate) is variable but the evolutionary drivers of this plasticity are poorly understood. We use evolutionary theory for life histories to combine a mathematical model and experiments to reveal that parasites adjust conversion rate according to the dynamics of asexual densities in the blood of the host. Our model predicts the direction of change in conversion rates that returns the greatest fitness after perturbation of asexual densities by different doses of antimalarial drugs. The loss of a high proportion of asexuals is predicted to elicit increased conversion (terminal investment), while smaller losses are managed by reducing conversion (reproductive restraint) to facilitate within-host survival and future transmission. This non-linear pattern of allocation is consistent with adaptive reproductive strategies observed in multicellular organisms. We then empirically estimate conversion rates of the rodent malaria parasite Plasmodium chabaudi in response to the killing of asexual stages by different doses of antimalarial drugs and forecast the short-term fitness consequences of these responses. Our data reveal the predicted non-linear pattern, and this is further supported by analyses of previous experiments that perturb asexual stage densities using drugs or within-host competition, across multiple parasite genotypes. Whilst conversion rates, across all datasets, are most strongly influenced by changes in asexual density, parasites also modulate conversion according to the availability of red blood cell resources. In summary, increasing conversion maximises short-term transmission and reducing conversion facilitates in-host survival and thus, future transmission. Understanding patterns of parasite allocation to reproduction matters because within-host replication is responsible for disease symptoms and between-host transmission determines disease spread. Malaria parasites in the host replicate asexually and, during each replication cycle, some asexuals transform into sexual stages that enable between-host transmission. It is not understood why the rate of conversion to sexual stages varies during infections despite its importance for the severity and spread of the disease. We combined a mathematical model and experiments to show that parasites adjust conversion rates depending on changes in their in-host population size. When population sizes plummet, between-host transmission is prioritised. However, smaller losses in number elicit reproductive restraint, which facilitates in-host survival and future transmission. We show that increased and decreased conversion in response to a range of in-host environments are actually part of one continuum: a sophisticated reproductive strategy similar to that of multicellular organisms.
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23
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Hochberg ME. An ecosystem framework for understanding and treating disease. EVOLUTION MEDICINE AND PUBLIC HEALTH 2018; 2018:270-286. [PMID: 30487969 PMCID: PMC6252061 DOI: 10.1093/emph/eoy032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/02/2018] [Indexed: 12/28/2022]
Abstract
Pathogens and cancers are pervasive health risks in the human population. I argue that if we are to better understand disease and its treatment, then we need to take an ecological perspective of disease itself. I generalize and extend an emerging framework that views disease as an ecosystem and many of its components as interacting in a community. I develop the framework for biological etiological agents (BEAs) that multiply within humans—focusing on bacterial pathogens and cancers—but the framework could be extended to include other host and parasite species. I begin by describing why we need an ecosystem framework to understand disease, and the main components and interactions in bacterial and cancer disease ecosystems. Focus is then given to the BEA and how it may proceed through characteristic states, including emergence, growth, spread and regression. The framework is then applied to therapeutic interventions. Central to success is preventing BEA evasion, the best known being antibiotic resistance and chemotherapeutic resistance in cancers. With risks of evasion in mind, I propose six measures that either introduce new components into the disease ecosystem or manipulate existing ones. An ecosystem framework promises to enhance our understanding of disease, BEA and host (co)evolution, and how we can improve therapeutic outcomes.
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Affiliation(s)
- Michael E Hochberg
- Institut des Sciences de l'Evolution, Université de Montpellier, 34095 Montpellier, France.,Santa Fe Institute, Santa Fe, NM 87501, USA.,Institute for Advanced Study in Toulouse, 31015 Toulouse, France
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24
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Huijben S, Chan BHK, Nelson WA, Read AF. The impact of within-host ecology on the fitness of a drug-resistant parasite. EVOLUTION MEDICINE AND PUBLIC HEALTH 2018; 2018:127-137. [PMID: 30087774 PMCID: PMC6061792 DOI: 10.1093/emph/eoy016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/18/2018] [Indexed: 02/05/2023]
Abstract
Background and objectives The rate of evolution of drug resistance depends on the fitness of resistant pathogens. The fitness of resistant pathogens is reduced by competition with sensitive pathogens in untreated hosts and so enhanced by competitive release in drug-treated hosts. We set out to estimate the magnitude of those effects on a variety of fitness measures, hypothesizing that competitive suppression and competitive release would have larger impacts when resistance was rarer to begin with. Methodology We infected mice with varying densities of drug-resistant Plasmodium chabaudi malaria parasites in a fixed density of drug-sensitive parasites and followed infection dynamics using strain-specific quantitative PCR. Results Competition with susceptible parasites reduced the absolute fitness of resistant parasites by 50–100%. Drug treatment increased the absolute fitness from 2- to >10 000-fold. The ecological context and choice of fitness measure was responsible for the wide variation in those estimates. Initial population growth rates poorly predicted parasite abundance and transmission probabilities. Conclusions and implications (i) The sensitivity of estimates of pathogen fitness to ecological context and choice of fitness measure make it difficult to derive field-relevant estimates of the fitness costs and benefits of resistance from experimental settings. (ii) Competitive suppression can be a key force preventing resistance from emerging when it is rare, as it is when it first arises. (iii) Drug treatment profoundly affects the fitness of resistance. Resistance evolution could be slowed by developing drug use policies that consider in-host competition.
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Affiliation(s)
- Silvie Huijben
- Departments of Biology and Entomology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Brian H K Chan
- Departments of Biology and Entomology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - William A Nelson
- Department of Biology, Queen's University, Kingston, ON K7L3N6, Canada
| | - Andrew F Read
- Departments of Biology and Entomology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA.,Department of Fogarty, National Institutes of Health, Fogarty International Center, Bethesda, MD, USA
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Estrela S, Brown SP. Community interactions and spatial structure shape selection on antibiotic resistant lineages. PLoS Comput Biol 2018; 14:e1006179. [PMID: 29927925 PMCID: PMC6013025 DOI: 10.1371/journal.pcbi.1006179] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 05/06/2018] [Indexed: 01/21/2023] Open
Abstract
Polymicrobial interactions play an important role in shaping the outcome of antibiotic treatment, yet how multispecies communities respond to antibiotic assault is still little understood. Here we use an individual-based simulation model of microbial biofilms to investigate how competitive and mutualistic interactions between an antibiotic-resistant and a susceptible strain (or species) influence the two-lineage community response to antibiotic exposure. Our model predicts that while increasing competition and antibiotics leads to increasing competitive release of the antibiotic-resistant strain, hitting a mutualistic community of cross-feeding species with antibiotics leads to a mutualistic suppression effect where both susceptible and resistant species are harmed. We next show that the impact of antibiotics is further governed by emergent spatial feedbacks within communities. Mutualistic cross-feeding communities can rescue susceptible members by subsidizing their growth inside the biofilm despite lack of access to the nutrient-rich and high-antibiotic growing front. Moreover, we show that antibiotic detoxification by resistant cells can protect nearby susceptible cells, but such cross-protection is more effective in mutualistic communities because mutualism drives mixing of resistant and susceptible cells. In contrast, competition leads to segregation, which ultimately prevents susceptible cells to profit from detoxification. Understanding how the interplay between microbial metabolic interactions and community spatial structuring shapes the outcome of antibiotic treatment can be key to effectively leverage the power of antibiotics and promote microbiome health. Pathogens -microorganisms that make us sick- often live within dynamic and complex multispecies communities, where they may not only compete for limiting resources but also exchange beneficial resources or services with other resident species. While antibiotics are commonly used to get rid of such harmful microbes, the community-wide effects of antibiotic treatment and its consequences for antibiotic resistance are still not well understood. How do competitive or mutually beneficial interactions between antibiotic resistant and susceptible species influence community resistance to antibiotics? Here we investigate this question using a computational model. We find that antibiotic exposure favours the resistant lineage when resistant and susceptible strains are competitors but harms both types when they are mutualists. With antibiotic-detoxifying resistant cells, cross-protection of susceptible cells is more effective in mutualistic communities because mutualism drives mixing of susceptible and resistant cells. In contrast, competition leads to their segregation, precluding susceptible cells to profit from their competitor’s local detoxification. Our findings highlight that knowing not only what species are present but also how they interact with each other and arrange themselves in space is central to understanding antibiotic resistance and to informing the development of strategies that promote microbiome health.
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Affiliation(s)
- Sylvie Estrela
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- * E-mail:
| | - Sam P. Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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26
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Antibiotic combination efficacy (ACE) networks for a Pseudomonas aeruginosa model. PLoS Biol 2018; 16:e2004356. [PMID: 29708964 PMCID: PMC5945231 DOI: 10.1371/journal.pbio.2004356] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 05/10/2018] [Accepted: 03/28/2018] [Indexed: 11/19/2022] Open
Abstract
The spread of antibiotic resistance is always a consequence of evolutionary processes. The consideration of evolution is thus key to the development of sustainable therapy. Two main factors were recently proposed to enhance long-term effectiveness of drug combinations: evolved collateral sensitivities between the drugs in a pair and antagonistic drug interactions. We systematically assessed these factors by performing over 1,600 evolution experiments with the opportunistic nosocomial pathogen Pseudomonas aeruginosa in single- and multidrug environments. Based on the growth dynamics during these experiments, we reconstructed antibiotic combination efficacy (ACE) networks as a new tool for characterizing the ability of the tested drug combinations to constrain bacterial survival as well as drug resistance evolution across time. Subsequent statistical analysis of the influence of the factors on ACE network characteristics revealed that (i) synergistic drug interactions increased the likelihood of bacterial population extinction-irrespective of whether combinations were compared at the same level of inhibition or not-while (ii) the potential for evolved collateral sensitivities between 2 drugs accounted for a reduction in bacterial adaptation rates. In sum, our systematic experimental analysis allowed us to pinpoint 2 complementary determinants of combination efficacy and to identify specific drug pairs with high ACE scores. Our findings can guide attempts to further improve the sustainability of antibiotic therapy by simultaneously reducing pathogen load and resistance evolution.
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27
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Beyond dose: Pulsed antibiotic treatment schedules can maintain individual benefit while reducing resistance. Sci Rep 2018; 8:5866. [PMID: 29650999 PMCID: PMC5897575 DOI: 10.1038/s41598-018-24006-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 03/19/2018] [Indexed: 12/13/2022] Open
Abstract
The emergence of treatment-resistant microbes is a key challenge for disease treatment and a leading threat to human health and wellbeing. New drugs are always in development, but microbes regularly and rapidly acquire resistance. We must consider if altering how we administer drugs at the individual level could slow development of resistance. Here we use mathematical models to show that exposing microbes to drug pulses could greatly reduce resistance without increasing individual pathogen load. Our results stem from two key factors: the presence of antibiotics creates a selection pressure for antibiotic resistant microbes, and large populations of bacteria are more likely to harbor drug resistance than small populations. Drug pulsing targets these factors simultaneously. Short duration pulses minimize the time during which there is selection for resistance, and high drug concentrations minimize pathogen abundance. Our work provides a theoretical basis for the design of in vitro and in vivo experiments to test how drug pulsing might reduce the impact of drug resistant infections.
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28
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Huijben S, Paaijmans KP. Putting evolution in elimination: Winning our ongoing battle with evolving malaria mosquitoes and parasites. Evol Appl 2018; 11:415-430. [PMID: 29636796 PMCID: PMC5891050 DOI: 10.1111/eva.12530] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/01/2017] [Indexed: 12/17/2022] Open
Abstract
Since 2000, the world has made significant progress in reducing malaria morbidity and mortality, and several countries in Africa, South America and South-East Asia are working hard to eliminate the disease. These elimination efforts continue to rely heavily on antimalarial drugs and insecticide-based interventions, which remain the cornerstones of malaria treatment and prevention. However, resistance has emerged against nearly every antimalarial drug and insecticide that is available. In this review we discuss the evolutionary consequences of the way we currently implement antimalarial interventions, which is leading to resistance and may ultimately lead to control failure, but also how evolutionary principles can be applied to extend the lifespan of current and novel interventions. A greater understanding of the general evolutionary principles that are at the core of emerging resistance is urgently needed if we are to develop improved resistance management strategies with the ultimate goal to achieve a malaria-free world.
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Affiliation(s)
- Silvie Huijben
- ISGlobalBarcelona Ctr. Int. Health Res. (CRESIB)Hospital Clínic ‐ Universitat de BarcelonaBarcelonaSpain
| | - Krijn P. Paaijmans
- ISGlobalBarcelona Ctr. Int. Health Res. (CRESIB)Hospital Clínic ‐ Universitat de BarcelonaBarcelonaSpain
- Centro de Investigação em Saúde de ManhiçaMaputoMozambique
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29
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Birget PLG, Greischar MA, Reece SE, Mideo N. Altered life history strategies protect malaria parasites against drugs. Evol Appl 2018; 11:442-455. [PMID: 29636798 PMCID: PMC5891063 DOI: 10.1111/eva.12516] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/30/2017] [Indexed: 11/26/2022] Open
Abstract
Drug resistance has been reported against all antimalarial drugs, and while parasites can evolve classical resistance mechanisms (e.g., efflux pumps), it is also possible that changes in life history traits could help parasites evade the effects of treatment. The life history of malaria parasites is governed by an intrinsic resource allocation problem: specialized stages are required for transmission, but producing these stages comes at the cost of producing fewer of the forms required for within-host survival. Drug treatment, by design, alters the probability of within-host survival, and so should alter the costs and benefits of investing in transmission. Here, we use a within-host model of malaria infection to predict optimal patterns of investment in transmission in the face of different drug treatment regimes and determine the extent to which alternative patterns of investment can buffer the fitness loss due to drugs. We show that over a range of drug doses, parasites are predicted to adopt "reproductive restraint" (investing more in asexual replication and less in transmission) to maximize fitness. By doing so, parasites recoup some of the fitness loss imposed by drugs, though as may be expected, increasing dose reduces the extent to which altered patterns of transmission investment can benefit parasites. We show that adaptation to drug-treated infections could result in more virulent infections in untreated hosts. This work emphasizes that in addition to classical resistance mechanisms, drug treatment generates selection for altered parasite life history. Understanding how any shifts in life history will alter the efficacy of drugs, as well as any limitations on such shifts, is important for evaluating and predicting the consequences of drug treatment.
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Affiliation(s)
- Philip L. G. Birget
- Institutes of Evolutionary Biology, Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
| | - Megan A. Greischar
- Department of Ecology & Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Sarah E. Reece
- Institutes of Evolutionary Biology, Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
| | - Nicole Mideo
- Department of Ecology & Evolutionary BiologyUniversity of TorontoTorontoONCanada
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30
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The role of antimalarial quality in the emergence and transmission of resistance. Med Hypotheses 2017; 111:49-54. [PMID: 29406996 DOI: 10.1016/j.mehy.2017.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/14/2017] [Accepted: 12/13/2017] [Indexed: 11/23/2022]
Abstract
The emergence and transmission of antimalarial resistance is hampering malaria eradication efforts and is shortening the useful therapeutic life of currently available antimalarials. Drug selection pressure has been identified as a contributing factor to the emergence and transmission of resistance, especially population treatment coverage and sub-therapeutic concentrations of active pharmaceutical ingredient (API) in the bloodstream. Medicine quality can be defined as good quality or poor quality. Poor quality antimalarials can be falsified, substandard or degraded and are estimated to make up between 10 and 50% of the antimalarial market in developing countries, and can be a source of sub-therapeutic doses of antimalarial API(s). The availability and use of poor quality antimalarials and the non-recommended use of quality assured monotherapies have historically been linked to treatment failure and in some cases, have coincided with the emergence and transmission of resistance in regions. We propose and outline the hypotheses that the use of poor quality antimalarial treatments and non-recommended quality assured monotherapies promote the (i) emergence and/or (ii) transmission of antimalarial resistance.
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31
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Graves CJ, Weinreich DM. Variability in fitness effects can preclude selection of the fittest. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2017; 48:399-417. [PMID: 31572069 DOI: 10.1146/annurev-ecolsys-110316-022722] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Evolutionary biologists often predict the outcome of natural selection on an allele by measuring its effects on lifetime survival and reproduction of individual carriers. However, alleles affecting traits like sex, evolvability, and cooperation can cause fitness effects that depend heavily on differences in the environmental, social, and genetic context of individuals carrying the allele. This variability makes it difficult to summarize the evolutionary fate of an allele based solely on its effects on any one individual. Attempts to average over this variability can sometimes salvage the concept of fitness. In other cases evolutionary outcomes can only be predicted by considering the entire genealogy of an allele, thus limiting the utility of individual fitness altogether. We describe a number of intriguing new evolutionary phenomena that have emerged in studies that explicitly model long-term lineage dynamics and discuss implications for the evolution of infectious diseases.
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Affiliation(s)
- Christopher J Graves
- Brown University, Department of Ecology and Evolutionary Biology and Center for Computational and Molecular Biology. Providence, RI, USA
| | - Daniel M Weinreich
- Brown University, Department of Ecology and Evolutionary Biology and Center for Computational and Molecular Biology. Providence, RI, USA
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32
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Levin BR, Baquero F, Ankomah PP, McCall IC. Phagocytes, Antibiotics, and Self-Limiting Bacterial Infections. Trends Microbiol 2017; 25:878-892. [PMID: 28843668 DOI: 10.1016/j.tim.2017.07.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/21/2017] [Accepted: 07/21/2017] [Indexed: 12/16/2022]
Abstract
Most antibiotic use in humans is to reduce the magnitude and term of morbidity of acute, community-acquired infections in immune competent patients, rather than to save lives. Thanks to phagocytic leucocytes and other host defenses, the vast majority of these infections are self-limiting. Nevertheless, there has been a negligible amount of consideration of the contribution of phagocytosis and other host defenses in the research for, and the design of, antibiotic treatment regimens, which hyper-emphasizes antibiotics as if they were the sole mechanism responsible for the clearance of infections. Here, we critically review this approach and its limitations. With the aid of a heuristic mathematical model, we postulate that if the rate of phagocytosis is great enough, for acute, normally self-limiting infections, then (i) antibiotics with different pharmacodynamic properties would be similarly effective, (ii) low doses of antibiotics can be as effective as high doses, and (iii) neither phenotypic nor inherited antibiotic resistance generated during therapy are likely to lead to treatment failure.
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Affiliation(s)
- Bruce R Levin
- Department of Biology, Emory University, Atlanta, GA, USA; Co-first authors.
| | - Fernando Baquero
- Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, CIBERESP, Madrid, Spain; Co-first authors
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33
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Mikaberidze A, Paveley N, Bonhoeffer S, van den Bosch F. Emergence of Resistance to Fungicides: The Role of Fungicide Dose. PHYTOPATHOLOGY 2017; 107:545-560. [PMID: 28079455 DOI: 10.1094/phyto-08-16-0297-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Resistance to antimicrobial drugs allows pathogens to survive drug treatment. The time taken for a new resistant mutant to reach a population size that is unlikely to die out by chance is called "emergence time." Prolonging emergence time would delay loss of control. We investigate the effect of fungicide dose on the emergence time in fungal plant pathogens. A population dynamical model is combined with dose-response data for Zymoseptoria tritici, an important wheat pathogen. Fungicides suppress sensitive pathogen population. This has two effects. First, the rate of appearance of resistant mutants is reduced, hence the emergence takes longer. Second, more healthy host tissue becomes available for resistant mutants, increasing their chances to invade and accelerates emergence. In theory, the two competing effects may lead to a non-monotonic dependence of the emergence time on fungicide dose that exhibits a minimum. But according to field data, fungicides are unable to reduce the fungicide-sensitive population strongly enough even at high doses. Hence, for full resistance over realistic ranges of pathogen's life history and fungicide dose-response parameters, emergence time decreases monotonically with increasing dose. For partial resistance, there can be cases within a limited parameter range, when emergence decelerates at higher doses.
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Affiliation(s)
- Alexey Mikaberidze
- First author: Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, LFW, Zurich, CH-8092, Switzerland; second author: ADAS, Duggleby YO17 8BP, United Kingdom; third author: Theoretical Biology, Institute of Integrative Biology, ETH Zurich, CHN, Zurich, CH-8092; and fourth author: Rothamsted Research, Harpenden, AL5 2JQ, United Kingdom
| | - Neil Paveley
- First author: Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, LFW, Zurich, CH-8092, Switzerland; second author: ADAS, Duggleby YO17 8BP, United Kingdom; third author: Theoretical Biology, Institute of Integrative Biology, ETH Zurich, CHN, Zurich, CH-8092; and fourth author: Rothamsted Research, Harpenden, AL5 2JQ, United Kingdom
| | - Sebastian Bonhoeffer
- First author: Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, LFW, Zurich, CH-8092, Switzerland; second author: ADAS, Duggleby YO17 8BP, United Kingdom; third author: Theoretical Biology, Institute of Integrative Biology, ETH Zurich, CHN, Zurich, CH-8092; and fourth author: Rothamsted Research, Harpenden, AL5 2JQ, United Kingdom
| | - Frank van den Bosch
- First author: Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, LFW, Zurich, CH-8092, Switzerland; second author: ADAS, Duggleby YO17 8BP, United Kingdom; third author: Theoretical Biology, Institute of Integrative Biology, ETH Zurich, CHN, Zurich, CH-8092; and fourth author: Rothamsted Research, Harpenden, AL5 2JQ, United Kingdom
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34
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Brock AR, Ross JV, Greenhalgh S, Durham DP, Galvani A, Parikh S, Esterman A. Modelling the impact of antimalarial quality on the transmission of sulfadoxine-pyrimethamine resistance in Plasmodium falciparum. Infect Dis Model 2017; 2:161-187. [PMID: 29928735 PMCID: PMC6001968 DOI: 10.1016/j.idm.2017.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 12/26/2022] Open
Abstract
Background The use of poor quality antimalarial medicines, including the use of non-recommended medicines for treatment such as sulfadoxine-pyrimethamine (SP) monotherapy, undermines malaria control and elimination efforts. Furthermore, the use of subtherapeutic doses of the active ingredient(s) can theoretically promote the emergence and transmission of drug resistant parasites. Methods We developed a deterministic compartmental model to quantify the impact of antimalarial medicine quality on the transmission of SP resistance, and validated it using sensitivity analysis and a comparison with data from Kenya collected in 2006. We modelled human and mosquito population dynamics, incorporating two Plasmodium falciparum subtypes (SP-sensitive and SP-resistant) and both poor quality and good quality (artemether-lumefantrine) antimalarial use. Findings The model predicted that an increase in human malaria cases, and among these, an increase in the proportion of SP-resistant infections, resulted from an increase in poor quality SP antimalarial use, whether it was full- or half-dose SP monotherapy. Interpretation Our findings suggest that an increase in poor quality antimalarial use predicts an increase in the transmission of resistance. This highlights the need for stricter control and regulation on the availability and use of poor quality antimalarial medicines, in order to offer safe and effective treatments, and work towards the eradication of malaria.
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Affiliation(s)
- Aleisha R Brock
- School of Nursing & Midwifery, University of South Australia, Adelaide, SA, Australia
| | - Joshua V Ross
- School of Mathematical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Scott Greenhalgh
- Department of Mathematics and Statistics, Queen's University, Kingston, ON, Canada
| | - David P Durham
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT, USA
| | - Alison Galvani
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT, USA
| | - Sunil Parikh
- Yale School of Public Health, New Haven, CT, USA
| | - Adrian Esterman
- Sansom Institute for Research Health, University of South Australia, Adelaide, SA, Australia.,Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
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35
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Hansen E, Woods RJ, Read AF. How to Use a Chemotherapeutic Agent When Resistance to It Threatens the Patient. PLoS Biol 2017; 15:e2001110. [PMID: 28182734 PMCID: PMC5300106 DOI: 10.1371/journal.pbio.2001110] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/06/2017] [Indexed: 12/21/2022] Open
Abstract
When resistance to anticancer or antimicrobial drugs evolves in a patient, highly effective chemotherapy can fail, threatening patient health and lifespan. Standard practice is to treat aggressively, effectively eliminating drug-sensitive target cells as quickly as possible. This prevents sensitive cells from acquiring resistance de novo but also eliminates populations that can competitively suppress resistant populations. Here we analyse that evolutionary trade-off and consider recent suggestions that treatment regimens aimed at containing rather than eliminating tumours or infections might more effectively delay the emergence of resistance. Our general mathematical analysis shows that there are situations in which regimens aimed at containment will outperform standard practice even if there is no fitness cost of resistance, and, in those cases, the time to treatment failure can be more than doubled. But, there are also situations in which containment will make a bad prognosis worse. Our analysis identifies thresholds that define these situations and thus can guide treatment decisions. The analysis also suggests a variety of interventions that could be used in conjunction with cytotoxic drugs to inhibit the emergence of resistance. Fundamental principles determine, across a wide range of disease settings, the circumstances under which standard practice best delays resistance emergence-and when it can be bettered.
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Affiliation(s)
- Elsa Hansen
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, Pennsylvania, United States of America
- * E-mail:
| | - Robert J. Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrew F. Read
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, Pennsylvania, United States of America
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36
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Knipl D, Röst G, Moghadas SM. Population dynamics of epidemic and endemic states of drug-resistance emergence in infectious diseases. PeerJ 2017; 5:e2817. [PMID: 28097052 PMCID: PMC5228518 DOI: 10.7717/peerj.2817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022] Open
Abstract
The emergence and spread of drug-resistance during treatment of many infectious diseases continue to degrade our ability to control and mitigate infection outcomes using therapeutic measures. While the coverage and efficacy of treatment remain key factors in the population dynamics of resistance, the timing for the start of the treatment in infectious individuals can significantly influence such dynamics. We developed a between-host disease transmission model to investigate the short-term (epidemic) and long-term (endemic) states of infections caused by two competing pathogen subtypes, namely the wild-type and resistant-type, when the probability of developing resistance is a function of delay in start of the treatment. We characterize the behaviour of disease equilibria and obtain a condition to minimize the fraction of population infectious at the endemic state in terms of probability of developing resistance and its transmission fitness. For the short-term epidemic dynamics, we illustrate that depending on the likelihood of resistance development at the time of treatment initiation, the same epidemic size may be achieved with different delays in start of the treatment, which may correspond to significantly different treatment coverages. Our results demonstrate that early initiation of treatment may not necessarily be the optimal strategy for curtailing the incidence of resistance or the overall disease burden. The risk of developing drug-resistance in-host remains an important factor in the management of resistance in the population.
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Affiliation(s)
- Diána Knipl
- Department of Mathematics, University College London, London, United Kingdom; MTA-SZTE Analysis and Stochastic Research Group, University of Szeged, Szeged, Hungary
| | - Gergely Röst
- Bolyai Institute, University of Szeged , Szeged , Hungary
| | - Seyed M Moghadas
- Agent-Based Modelling Laboratory, York University , Toronto , Canada
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37
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Beams AB, Toth DJA, Khader K, Adler FR. Harnessing Intra-Host Strain Competition to Limit Antibiotic Resistance: Mathematical Model Results. Bull Math Biol 2016; 78:1828-1846. [PMID: 27670431 DOI: 10.1007/s11538-016-0201-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 08/25/2016] [Indexed: 11/24/2022]
Abstract
Antibiotic overuse has promoted the spread of antibiotic resistance. To compound the issue, treating individuals dually infected with antibiotic-resistant and antibiotic-vulnerable strains can make their infections completely resistant through competitive release. We formulate mathematical models of transmission dynamics accounting for dual infections and extensions accounting for lag times between infection and treatment or between cure and ending treatment. Analysis using the Next-Generation Matrix reveals how competition within hosts and the costs of resistance determine whether vulnerable and resistant strains persist, coexist, or drive each other to extinction. Invasion analysis predicts that treatment of dually infected cases will promote resistance. By varying antibiotic strength, the models suggest that physicians have two ways to achieve a particular resistance target: prescribe relatively weak antibiotics to everyone infected with an antibiotic-vulnerable strain or give more potent prescriptions to only those patients singly infected with the vulnerable strain after ruling out the possibility of them being dually infected with resistance. Through selectivity and moderation in antibiotic prescription, resistance might be limited.
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Affiliation(s)
- Alexander B Beams
- Department of Mathematics, University of Utah, Salt Lake City, UT, USA.
| | - Damon J A Toth
- Informatics, Decision Enhancement, and Analytical Sciences (IDEAS) 2.0 Center, VA Salt Lake City Health Care System, Salt Lake City, UT, USA.,Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Karim Khader
- Informatics, Decision Enhancement, and Analytical Sciences (IDEAS) 2.0 Center, VA Salt Lake City Health Care System, Salt Lake City, UT, USA.,Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Frederick R Adler
- Department of Mathematics, University of Utah, Salt Lake City, UT, USA.,Department of Biology, University of Utah, Salt Lake City, UT, USA
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38
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Fingerhuth SM, Bonhoeffer S, Low N, Althaus CL. Antibiotic-Resistant Neisseria gonorrhoeae Spread Faster with More Treatment, Not More Sexual Partners. PLoS Pathog 2016; 12:e1005611. [PMID: 27196299 PMCID: PMC4872991 DOI: 10.1371/journal.ppat.1005611] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 04/12/2016] [Indexed: 11/18/2022] Open
Abstract
The sexually transmitted bacterium Neisseria gonorrhoeae has developed resistance to all antibiotic classes that have been used for treatment and strains resistant to multiple antibiotic classes have evolved. In many countries, there is only one antibiotic remaining for empirical N. gonorrhoeae treatment, and antibiotic management to counteract resistance spread is urgently needed. Understanding dynamics and drivers of resistance spread can provide an improved rationale for antibiotic management. In our study, we first used antibiotic resistance surveillance data to estimate the rates at which antibiotic-resistant N. gonorrhoeae spread in two host populations, heterosexual men (HetM) and men who have sex with men (MSM). We found higher rates of spread for MSM (0.86 to 2.38 y−1, mean doubling time: 6 months) compared to HetM (0.24 to 0.86 y−1, mean doubling time: 16 months). We then developed a dynamic transmission model to reproduce the observed dynamics of N. gonorrhoeae transmission in populations of heterosexual men and women (HMW) and MSM. We parameterized the model using sexual behavior data and calibrated it to N. gonorrhoeae prevalence and incidence data. In the model, antibiotic-resistant N. gonorrhoeae spread with a median rate of 0.88 y−1 in HMW and 3.12 y−1 in MSM. These rates correspond to median doubling times of 9 (HMW) and 3 (MSM) months. Assuming no fitness costs, the model shows the difference in the host population’s treatment rate rather than the difference in the number of sexual partners explains the differential spread of resistance. As higher treatment rates result in faster spread of antibiotic resistance, treatment recommendations for N. gonorrhoeae should carefully balance prevention of infection and avoidance of resistance spread. More and more infectious disease treatments fail because the causative pathogens are resistant to the drugs used for treatment. For the treatment of Neisseria gonorrhoeae, a sexually transmitted bacterium, drug resistance is a particularly big problem: there is only a single antibiotic left that is recommended for treatment. We aimed to understand how antibiotic-resistant N. gonorrhoeae spread in a sexually active host population and how the spread of resistance can be slowed. From antibiotic resistance surveillance data, we first estimated the rate at which antibiotic-resistant N. gonorrhoeae spread. Second, we reproduced the observed dynamics in a mathematical model describing the transmission between hosts. We found that antibiotic-resistant N. gonorrhoeae spread faster in host populations of men who have sex with men than in host populations of heterosexuals. We could attribute the faster spread of resistant pathogens to higher treatment rates. This finding implies that promoting screening to control antibiotic-resistant N. gonorrhoeae could in fact accelerate their spread.
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Affiliation(s)
- Stephanie M. Fingerhuth
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
- * E-mail:
| | | | - Nicola Low
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
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39
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Gjini E, Brito PH. Integrating Antimicrobial Therapy with Host Immunity to Fight Drug-Resistant Infections: Classical vs. Adaptive Treatment. PLoS Comput Biol 2016; 12:e1004857. [PMID: 27078624 PMCID: PMC4831758 DOI: 10.1371/journal.pcbi.1004857] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/09/2016] [Indexed: 12/18/2022] Open
Abstract
Antimicrobial resistance of infectious agents is a growing problem worldwide. To prevent the continuing selection and spread of drug resistance, rational design of antibiotic treatment is needed, and the question of aggressive vs. moderate therapies is currently heatedly debated. Host immunity is an important, but often-overlooked factor in the clearance of drug-resistant infections. In this work, we compare aggressive and moderate antibiotic treatment, accounting for host immunity effects. We use mathematical modelling of within-host infection dynamics to study the interplay between pathogen-dependent host immune responses and antibiotic treatment. We compare classical (fixed dose and duration) and adaptive (coupled to pathogen load) treatment regimes, exploring systematically infection outcomes such as time to clearance, immunopathology, host immunization, and selection of resistant bacteria. Our analysis and simulations uncover effective treatment strategies that promote synergy between the host immune system and the antimicrobial drug in clearing infection. Both in classical and adaptive treatment, we quantify how treatment timing and the strength of the immune response determine the success of moderate therapies. We explain key parameters and dimensions, where an adaptive regime differs from classical treatment, bringing new insight into the ongoing debate of resistance management. Emphasizing the sensitivity of treatment outcomes to the balance between external antibiotic intervention and endogenous natural defenses, our study calls for more empirical attention to host immunity processes.
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Affiliation(s)
- Erida Gjini
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail:
| | - Patricia H. Brito
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Nova Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
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40
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Bushman M, Morton L, Duah N, Quashie N, Abuaku B, Koram KA, Dimbu PR, Plucinski M, Gutman J, Lyaruu P, Kachur SP, de Roode JC, Udhayakumar V. Within-host competition and drug resistance in the human malaria parasite Plasmodium falciparum. Proc Biol Sci 2016; 283:20153038. [PMID: 26984625 PMCID: PMC4810865 DOI: 10.1098/rspb.2015.3038] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/16/2016] [Indexed: 11/12/2022] Open
Abstract
Infections with the malaria parasite Plasmodium falciparum typically comprise multiple strains, especially in high-transmission areas where infectious mosquito bites occur frequently. However, little is known about the dynamics of mixed-strain infections, particularly whether strains sharing a host compete or grow independently. Competition between drug-sensitive and drug-resistant strains, if it occurs, could be a crucial determinant of the spread of resistance. We analysed 1341 P. falciparum infections in children from Angola, Ghana and Tanzania and found compelling evidence for competition in mixed-strain infections: overall parasite density did not increase with additional strains, and densities of individual chloroquine-sensitive (CQS) and chloroquine-resistant (CQR) strains were reduced in the presence of competitors. We also found that CQR strains exhibited low densities compared with CQS strains (in the absence of chloroquine), which may underlie observed declines of chloroquine resistance in many countries following retirement of chloroquine as a first-line therapy. Our observations support a key role for within-host competition in the evolution of drug-resistant malaria. Malaria control and resistance-management efforts in high-transmission regions may be significantly aided or hindered by the effects of competition in mixed-strain infections. Consideration of within-host dynamics may spur development of novel strategies to minimize resistance while maximizing the benefits of control measures.
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Affiliation(s)
- Mary Bushman
- Department of Biology, Emory University, Atlanta, GA 30322, USA Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Lindsay Morton
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Nancy Duah
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Neils Quashie
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana Centre for Tropical Clinical Pharmacology and Therapeutics, University of Ghana Medical School, Accra, Ghana
| | - Benjamin Abuaku
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Kwadwo A Koram
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Mateusz Plucinski
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Julie Gutman
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Peter Lyaruu
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - S Patrick Kachur
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | | | - Venkatachalam Udhayakumar
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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41
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Day T, Read AF. Does High-Dose Antimicrobial Chemotherapy Prevent the Evolution of Resistance? PLoS Comput Biol 2016; 12:e1004689. [PMID: 26820986 PMCID: PMC4731197 DOI: 10.1371/journal.pcbi.1004689] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/30/2015] [Indexed: 12/25/2022] Open
Abstract
High-dose chemotherapy has long been advocated as a means of controlling drug resistance in infectious diseases but recent empirical studies have begun to challenge this view. We develop a very general framework for modeling and understanding resistance emergence based on principles from evolutionary biology. We use this framework to show how high-dose chemotherapy engenders opposing evolutionary processes involving the mutational input of resistant strains and their release from ecological competition. Whether such therapy provides the best approach for controlling resistance therefore depends on the relative strengths of these processes. These opposing processes typically lead to a unimodal relationship between drug pressure and resistance emergence. As a result, the optimal drug dose lies at either end of the therapeutic window of clinically acceptable concentrations. We illustrate our findings with a simple model that shows how a seemingly minor change in parameter values can alter the outcome from one where high-dose chemotherapy is optimal to one where using the smallest clinically effective dose is best. A review of the available empirical evidence provides broad support for these general conclusions. Our analysis opens up treatment options not currently considered as resistance management strategies, and it also simplifies the experiments required to determine the drug doses which best retard resistance emergence in patients. The evolution of antimicrobial resistant pathogens threatens much of modern medicine. For over one hundred years, the advice has been to ‘hit hard’, in the belief that high doses of antimicrobials best contain resistance evolution. We argue that nothing in evolutionary theory supports this as a good rule of thumb in the situations that challenge medicine. We show instead that the only generality is to either use the highest tolerable drug dose or the lowest clinically effective dose; that is, one of the two edges of the therapeutic window. This approach suggests treatment options not currently considered, and simplifies the experiments required to identify the dose that best retards resistance evolution.
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Affiliation(s)
- Troy Day
- Department of Mathematics and Statistics, Jeffery Hall, Queen’s University, Kingston, Ontario, Canada
- Department of Biology, Queen’s University, Kingston, Ontario, Canada
- The Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Andrew F. Read
- The Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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Ogbunugafor CB, Wylie CS, Diakite I, Weinreich DM, Hartl DL. Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance. PLoS Comput Biol 2016; 12:e1004710. [PMID: 26808374 PMCID: PMC4726534 DOI: 10.1371/journal.pcbi.1004710] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/16/2015] [Indexed: 12/12/2022] Open
Abstract
The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to applications of these concepts is a lack of detail concerning how the environment affects adaptive landscape topography, and consequently, the outcome of drug treatment. Here we combine empirical data, evolutionary theory, and computer simulations towards dissecting adaptive landscape by environment interactions for the evolution of drug resistance in two dimensions-drug concentration and drug type. We do so by studying the resistance mediated by Plasmodium falciparum dihydrofolate reductase (DHFR) to two related inhibitors-pyrimethamine and cycloguanil-across a breadth of drug concentrations. We first examine whether the adaptive landscapes for the two drugs are consistent with common definitions of cross-resistance. We then reconstruct all accessible pathways across the landscape, observing how their structure changes with drug environment. We offer a mechanism for non-linearity in the topography of accessible pathways by calculating of the interaction between mutation effects and drug environment, which reveals rampant patterns of epistasis. We then simulate evolution in several different drug environments to observe how these individual mutation effects (and patterns of epistasis) influence paths taken at evolutionary "forks in the road" that dictate adaptive dynamics in silico. In doing so, we reveal how classic metrics like the IC50 and minimal inhibitory concentration (MIC) are dubious proxies for understanding how evolution will occur across drug environments. We also consider how the findings reveal ambiguities in the cross-resistance concept, as subtle differences in adaptive landscape topography between otherwise equivalent drugs can drive drastically different evolutionary outcomes. Summarizing, we discuss the results with regards to their basic contribution to the study of empirical adaptive landscapes, and in terms of how they inform new models for the evolution of drug resistance.
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Affiliation(s)
- C. Brandon Ogbunugafor
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
| | - C. Scott Wylie
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Ibrahim Diakite
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniel M. Weinreich
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Daniel L. Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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43
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Ogbunugafor CB, Hartl D. A pivot mutation impedes reverse evolution across an adaptive landscape for drug resistance in Plasmodium vivax. Malar J 2016; 15:40. [PMID: 26809718 PMCID: PMC4727274 DOI: 10.1186/s12936-016-1090-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 01/10/2016] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The study of reverse evolution from resistant to susceptible phenotypes can reveal constraints on biological evolution, a topic for which evolutionary theory has relatively few general principles. The public health catastrophe of antimicrobial resistance in malaria has brought these constraints on evolution into a practical realm, with one proposed solution: withdrawing anti-malarial medication use in high resistance settings, built on the assumption that reverse evolution occurs readily enough that populations of pathogens may revert to their susceptible states. While past studies have suggested limits to reverse evolution, there have been few attempts to properly dissect its mechanistic constraints. METHODS Growth rates were determined from empirical data on the growth and resistance from a set of combinatorially complete set of mutants of a resistance protein (dihydrofolate reductase) in Plasmodium vivax, to construct reverse evolution trajectories. The fitness effects of individual mutations were calculated as a function of drug environment, revealing the magnitude of epistatic interactions between mutations and genetic backgrounds. Evolution across the landscape was simulated in two settings: starting from the population fixed for the quadruple mutant, and from a polymorphic population evenly distributed between double mutants. RESULTS A single mutation of large effect (S117N) serves as a pivot point for evolution to high resistance regions of the landscape. Through epistatic interactions with other mutations, this pivot creates an epistatic ratchet against reverse evolution towards the wild type ancestor, even in environments where the wild type is the most fit of all genotypes. This pivot mutation underlies the directional bias in evolution across the landscape, where evolution towards the ancestor is precluded across all examined drug concentrations from various starting points in the landscape. CONCLUSIONS The presence of pivot mutations can dictate dynamics of evolution across adaptive landscape through epistatic interactions within a protein, leaving a population trapped on local fitness peaks in an adaptive landscape, unable to locate ancestral genotypes. This irreversibility suggests that the structure of an adaptive landscape for a resistance protein should be understood before considering resistance management strategies. This proposed mechanism for constraints on reverse evolution corroborates evidence from the field indicating that phenotypic reversal often occurs via compensatory mutation at sites independent of those associated with the forward evolution of resistance. Because of this, molecular methods that identify resistance patterns via single SNPs in resistance-associated markers might be missing signals for resistance and compensatory mutation throughout the genome. In these settings, whole genome sequencing efforts should be used to identify resistance patterns, and will likely reveal a more complicated genomic signature for resistance and susceptibility, especially in settings where anti-malarial medications have been used intermittently. Lastly, the findings suggest that, given their role in dictating the dynamics of evolution across the landscape, pivot mutations might serve as future targets for therapy.
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Affiliation(s)
- C Brandon Ogbunugafor
- Department of Biology, University of Vermont, Burlington, VT, USA.
- Vermont Complex Systems Center, The University of Vermont, Burlington, VT, USA.
| | - Daniel Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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Naskar A, Bera S, Bhattacharya R, Saha P, Roy SS, Sen T, Jana S. Synthesis, characterization and antibacterial activity of Ag incorporated ZnO–graphene nanocomposites. RSC Adv 2016. [DOI: 10.1039/c6ra14808e] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
One pot low temperature synthesis of silver incorporated ZnO–chemically converted graphene nanocomposites is reported. An optimum of 10% Ag incorporated sample at 6.25 μg ml−1 dose shows an excellent antibacterial activity on E. coli and S. aureus.
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Affiliation(s)
- Atanu Naskar
- Sol-Gel Division
- CSIR-Central Glass and Ceramic Research Institute
- Kolkata 700032
- India
| | - Susanta Bera
- Sol-Gel Division
- CSIR-Central Glass and Ceramic Research Institute
- Kolkata 700032
- India
| | - Rahul Bhattacharya
- Cell Biology & Physiology Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Pritam Saha
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata 700032
- India
| | - Sib Sankar Roy
- Cell Biology & Physiology Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Tuhinadri Sen
- Department of Pharmaceutical Technology
- Jadavpur University
- Kolkata 700032
- India
| | - Sunirmal Jana
- Sol-Gel Division
- CSIR-Central Glass and Ceramic Research Institute
- Kolkata 700032
- India
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45
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Abstract
Mathematical modelling provides an effective way to challenge conventional wisdom about
parasite evolution and investigate why parasites ‘do what they do’ within the host. Models
can reveal when intuition cannot explain observed patterns, when more complicated biology
must be considered, and when experimental and statistical methods are likely to mislead.
We describe how models of within-host infection dynamics can refine experimental design,
and focus on the case study of malaria to highlight how integration between models and
data can guide understanding of parasite fitness in three areas: (1) the adaptive
significance of chronic infections; (2) the potential for tradeoffs between virulence and
transmission; and (3) the implications of within-vector dynamics. We emphasize that models
are often useful when they highlight unexpected patterns in parasite evolution, revealing
instead why intuition yields the wrong answer and what combination of theory and data are
needed to advance understanding.
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46
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Colijn C, Cohen T. How competition governs whether moderate or aggressive treatment minimizes antibiotic resistance. eLife 2015; 4. [PMID: 26393685 PMCID: PMC4641510 DOI: 10.7554/elife.10559] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 09/18/2015] [Indexed: 11/16/2022] Open
Abstract
Understanding how our use of antimicrobial drugs shapes future levels of drug resistance is crucial. Recently, there has been debate over whether an aggressive (i.e., high dose) or more moderate (i.e., lower dose) treatment of individuals will most limit the emergence and spread of resistant bacteria. In this study, we demonstrate how one can understand and resolve these apparently contradictory conclusions. We show that a key determinant of which treatment strategy will perform best at the individual level is the extent of effective competition between resistant and sensitive pathogens within a host. We extend our analysis to the community level, exploring the spectrum between strict inter-strain competition and strain independence. From this perspective as well, we find that the magnitude of effective competition between resistant and sensitive strains determines whether an aggressive approach or moderate approach minimizes the burden of resistance in the population. DOI:http://dx.doi.org/10.7554/eLife.10559.001 Antibiotics are chemical compounds used to treat bacterial infections. The discovery of antibiotics, starting with penicillin in 1929, revolutionized medicine, making it possible to cure or prevent life-threatening infections such as tetanus and pneumonia. However, many bacteria have become resistant to one or more antibiotics and so can no longer be killed by these drugs. The emergence of antibiotic resistance reflects an evolutionary process that occurs during antibiotic treatment. While the antibiotic will kill most bacteria, some bacteria may naturally have a feature or genetic mutation that allows them to survive in the presence of the antibiotic. These bacteria then reproduce and pass on their resistant traits, eventually leading to the emergence of a new antibiotic-resistant strain of bacteria. Once a resistant strain exists it may be able to spread from one person to another. There is conflicting evidence about how best to prevent antibiotic-resistant bacteria from evolving and spreading. The results of some experiments suggest that treating bacteria with large doses of antibiotics early in an infection is the most effective way to optimize treatment and minimize the risk of an antibiotic-resistant strain developing. However, other studies suggest that exposing bacteria to high levels of antibiotics more efficiently selects for resistance; in this case a more moderate approach should be used when treating bacterial infections. Here, Colijn and Cohen present a mathematical model that suggests that the natural competition between the antibiotic-resistant and antibiotic-sensitive strains of bacteria influence which treatment strategy should be taken. Strains were modeled both within individual hosts and spreading in a community of individuals. In the models, aggressive antibiotic treatment is most effective (in that it minimizes antibiotic resistance) when the antibiotic-resistant strain either does not experience strong competition from the non-resistant strains of bacteria or is not fit enough to be a good competitor. However, a more moderate treatment is appropriate when the two strains are competing and the antibiotic-resistant strain is a fit competitor. Competition may mean that moderate treatment is best to avoid resistance at the community level, even in situations when aggressive treatment is likely best for individuals. Two important future challenges are to better understand the diversity of strains in bacterial infections, and to develop tools to measure to what extent strains are effectively competing with each other. DOI:http://dx.doi.org/10.7554/eLife.10559.002
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Affiliation(s)
- Caroline Colijn
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Ted Cohen
- School of Public Health, Yale University, New Haven, United States
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47
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Akhmetzhanov AR, Hochberg ME. Dynamics of preventive vs post-diagnostic cancer control using low-impact measures. eLife 2015; 4:e06266. [PMID: 26111339 PMCID: PMC4524440 DOI: 10.7554/elife.06266] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 06/24/2015] [Indexed: 01/23/2023] Open
Abstract
Cancer poses danger because of its unregulated growth, development of resistance, and metastatic spread to vital organs. We currently lack quantitative theory for how preventive measures and post-diagnostic interventions are predicted to affect risks of a life threatening cancer. Here we evaluate how continuous measures, such as life style changes and traditional treatments, affect both neoplastic growth and the frequency of resistant clones. We then compare and contrast preventive and post-diagnostic interventions assuming that only a single lesion progresses to invasive carcinoma during the life of an individual, and resection either leaves residual cells or metastases are undetected. Whereas prevention generally results in more positive therapeutic outcomes than post-diagnostic interventions, this advantage is substantially lowered should prevention initially fail to arrest tumour growth. We discuss these results and other important mitigating factors that should be taken into consideration in a comparative understanding of preventive and post-diagnostic interventions. DOI:http://dx.doi.org/10.7554/eLife.06266.001 About one person in every two will get cancer during their lives. Surgery and chemotherapy have long been mainstays of cancer treatment. Both, however, have substantial downsides. Surgery may leave behind undetected cancer cells that can grow into new tumours. Furthermore, in response to chemotherapy drugs, some cancer cells may emerge that resist further treatment. There is therefore interest in whether preventive strategies—including lifestyle changes and medications—could reduce the likelihood of confronting a life-threatening cancer. Now, Akhmetzhanov and Hochberg have developed a mathematical model to help compare the effectiveness of preventive strategies and traditional cancer treatments. The model—which assumes that a person can only develop a single cancer from a single region of pre-cancerous cells—suggests that long-term cancer prevention strategies reduce the risk of a life-threatening cancer by more than traditional treatment that begins after a tumour is discovered. The preventive measures may be less effective in some cases compared to traditional treatments if they initially fail to stop a tumour growing, although on average they still work better than treating the cancer after detection. According to Akhmetzhanov and Hochberg's model, surgical removal followed by chemotherapy is less likely to be successful than prevention, and when successful, requires larger impacts on the cancer (and therefore creates more side-effects for the patient) to achieve the same level of control as prevention. The model also suggests that even at very low levels of impact on residual cancer cells, chemotherapies are likely to be counterproductive by boosting the subsequent emergence of treatment-resistant tumours. Akhmetzhanov and Hochberg's model predicts how effective preventive measures need to be in terms of slowing the growth of cancer cells to result in given reductions in the future risk of a life-threatening cancer. Future work should test this model by measuring the effects on tumour growth of prevention and of traditional therapies. DOI:http://dx.doi.org/10.7554/eLife.06266.002
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Affiliation(s)
- Andrei R Akhmetzhanov
- Institut des Sciences de l'Evolution de Montpellier, University of Montpellier, Montpellier, France
| | - Michael E Hochberg
- Institut des Sciences de l'Evolution de Montpellier, University of Montpellier, Montpellier, France
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48
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Kouyos RD, Metcalf CJE, Birger R, Klein EY, Abel zur Wiesch P, Ankomah P, Arinaminpathy N, Bogich TL, Bonhoeffer S, Brower C, Chi-Johnston G, Cohen T, Day T, Greenhouse B, Huijben S, Metlay J, Mideo N, Pollitt LC, Read AF, Smith DL, Standley C, Wale N, Grenfell B. The path of least resistance: aggressive or moderate treatment? Proc Biol Sci 2015; 281:20140566. [PMID: 25253451 DOI: 10.1098/rspb.2014.0566] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The evolution of resistance to antimicrobial chemotherapy is a major and growing cause of human mortality and morbidity. Comparatively little attention has been paid to how different patient treatment strategies shape the evolution of resistance. In particular, it is not clear whether treating individual patients aggressively with high drug dosages and long treatment durations, or moderately with low dosages and short durations can better prevent the evolution and spread of drug resistance. Here, we summarize the very limited available empirical evidence across different pathogens and provide a conceptual framework describing the information required to effectively manage drug pressure to minimize resistance evolution.
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Affiliation(s)
- Roger D Kouyos
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Department of Zoology, Oxford University, Oxford, UK
| | - Ruthie Birger
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Eili Y Klein
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Center for Advanced Modeling, Department of Emergency Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Pia Abel zur Wiesch
- Division of Global Health Equity, Brigham and Women's Hospital and Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Peter Ankomah
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Nimalan Arinaminpathy
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Tiffany L Bogich
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Charles Brower
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Center for Disease Dynamics, Economics & Policy, Washington, DC, USA
| | - Geoffrey Chi-Johnston
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ted Cohen
- Division of Global Health Equity, Brigham and Women's Hospital and Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Troy Day
- Departments of Mathematics and Biology, Queen's University, Kingston, Ontario, Canada
| | - Bryan Greenhouse
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, VA, USA
| | - Silvie Huijben
- Barcelona Centre for International Health Research, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Joshua Metlay
- General Medicine Division, Massachusetts General Hospital, Boston, MA, USA
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Laura C Pollitt
- Centre for Infectious Disease Dynamics, The Pennsylvania State University, University Park, State College, PA, USA Departments of Biology and Entomology, The Pennsylvania State University, University Park, State College, PA, USA Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Andrew F Read
- Centre for Infectious Disease Dynamics, The Pennsylvania State University, University Park, State College, PA, USA Departments of Biology and Entomology, The Pennsylvania State University, University Park, State College, PA, USA Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - David L Smith
- Department of Zoology, Oxford University, Oxford, UK
| | - Claire Standley
- Department of Health Policy, George Washington University, Washington, DC, USA
| | - Nina Wale
- Centre for Infectious Disease Dynamics, The Pennsylvania State University, University Park, State College, PA, USA Departments of Biology and Entomology, The Pennsylvania State University, University Park, State College, PA, USA
| | - Bryan Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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49
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Birger RB, Kouyos RD, Cohen T, Griffiths EC, Huijben S, Mina MJ, Volkova V, Grenfell B, Metcalf CJE. The potential impact of coinfection on antimicrobial chemotherapy and drug resistance. Trends Microbiol 2015; 23:537-544. [PMID: 26028590 DOI: 10.1016/j.tim.2015.05.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/20/2015] [Accepted: 05/05/2015] [Indexed: 01/06/2023]
Abstract
Across a range of pathogens, resistance to chemotherapy is a growing problem in both public health and animal health. Despite the ubiquity of coinfection, and its potential effects on within-host biology, the role played by coinfecting pathogens on the evolution of resistance and efficacy of antimicrobial chemotherapy is rarely considered. In this review, we provide an overview of the mechanisms of interaction of coinfecting pathogens, ranging from immune modulation and resource modulation, to drug interactions. We discuss their potential implications for the evolution of resistance, providing evidence in the rare cases where it is available. Overall, our review indicates that the impact of coinfection has the potential to be considerable, suggesting that this should be taken into account when designing antimicrobial drug treatments.
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Affiliation(s)
- Ruthie B Birger
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zürich, Zürich, Switzerland.,Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Emily C Griffiths
- Department of Entomology, Gardner Hall, Derieux Place, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Silvie Huijben
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic -Universitat de Barcelona, Barcelona, Spain
| | - Michael J Mina
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Medical Scientist Training Program, Emory University School of Medicine, Atlanta, GA, USA
| | - Victoriya Volkova
- Department of Diagnostic Medicine/Pathobiology, Institute of Computational Comparative Medicine, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Bryan Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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Huijben S, Chan BHK, Read AF. Relevance of undetectably rare resistant malaria parasites in treatment failure: experimental evidence from Plasmodium chabaudi. Am J Trop Med Hyg 2015; 92:1214-21. [PMID: 25940195 DOI: 10.4269/ajtmh.15-0036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/25/2015] [Indexed: 01/24/2023] Open
Abstract
Resistant malaria parasites are frequently found in mixed infections with drug-sensitive parasites. Particularly early in the evolutionary process, the frequency of these resistant mutants can be extremely low and below the level of molecular detection. We tested whether the rarity of resistance in infections impacted the health outcomes of treatment failure and the potential for onward transmission of resistance. Mixed infections of different ratios of resistant and susceptible Plasmodium chabaudi parasites were inoculated in laboratory mice and dynamics tracked during the course of infection using highly sensitive genotype-specific quantitative polymerase chain reaction (qPCR). Frequencies of resistant parasites ranged from 10% to 0.003% at the onset of treatment. We found that the rarer the resistant parasites were, the lower the likelihood of their onward transmission, but the worse the treatment failure was in terms of parasite numbers and disease severity. Strikingly, drug resistant parasites had the biggest impact on health outcomes when they were too rare to be detected by any molecular methods currently available for field samples. Indeed, in the field, these treatment failures would not even have been attributed to resistance.
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Affiliation(s)
- Silvie Huijben
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania; ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic Universitat de Barcelona, Barcelona, Spain; Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom; Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Brian H K Chan
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania; ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic Universitat de Barcelona, Barcelona, Spain; Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom; Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Andrew F Read
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania; ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic Universitat de Barcelona, Barcelona, Spain; Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom; Fogarty International Center, National Institutes of Health, Bethesda, Maryland
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