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Baquero F, Pérez-Cobas AE, Aracil-Gisbert S, Coque TM, Zamora J. Selection versus transmission: Quantitative and organismic biology in antibiotic resistance. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 121:105606. [PMID: 38768878 DOI: 10.1016/j.meegid.2024.105606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/12/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
We aimed to determine the importance of selection (mostly dependent on the anthropogenic use of antimicrobials) and transmission (mostly dependent on hygiene and sanitation) as drivers of the spread of antibiotic-resistant bacterial populations. The first obstacle to estimating the relative weight of both independent variables is the lack of detailed quantitative data concerning the number of bacterial cells, potentially either pathogenic or harmless, and bacterial species exposed to antimicrobial action in the microbiotas of specific environments. The second obstacle is the difficulty of considering the relative importance of the transmission and selection exerting their combined effects on antibiotic resistance across eco-biological levels. As a consequence, advances are urgently required in quantitative biology and organismic biology of antimicrobial resistance. The absolute number of humans exposed to antibiotics and the absolute number of potentially pathogenic and commensal bacteria in their microbiomes should influence both the selection and transmission of resistant bacterial populations. The "whole Earth" microbiome, with astonishingly high numbers of bacterial cells and species, which are also exposed to anthropogenic antimicrobials in various biogeographical spaces, shapes the antibiotic resistance landscape. These biogeographical spaces influence various intensities of selection and transmission of potentially pathogenic bacteria. While waiting for more precise data, biostatistics analysis and mathematical or computational modeling can provide proxies to compare the influence of selection and transmission in resistant bacteria. In European countries with lower sanitation levels, antibiotic consumption plays a major role in increasing antibiotic resistance; however, this is not the case in countries with high sanitation levels. Although both independent variables are linked, their relative influence on the level of antibiotic resistance varies according to the particular location. Therefore, interventions directed to decrease antibiotic resistance should be designed "a la carte" for specific locations with particular ecological conditions, including sanitation facilities.
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Affiliation(s)
- F Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain; Center for Biomedical Research in Epidemiology and Public Health Network (CIBERESP-Group 33), Madrid, Spain.
| | - A E Pérez-Cobas
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain; Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Madrid, Spain
| | - S Aracil-Gisbert
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain; Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Madrid, Spain
| | - T M Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain; Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Madrid, Spain
| | - J Zamora
- Clinical Biostatistics Unit, Ramón y Cajal University Hospital, and Ramón y Cajal Institute for Health Research (IRYCIS) Madrid, Spain; Center for Biomedical Research in Epidemiology and Public Health Network (CIBERESP-Group 42), Madrid, Spain; Institute of Metabolism and Systems Research, Biostatistics in Maternal and Perinatal Health, University of Birmingham, UK
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Gandon S, Guillemet M, Gatchitch F, Nicot A, Renaud AC, Tremblay DM, Moineau S. Building pyramids against the evolutionary emergence of pathogens. Proc Biol Sci 2024; 291:20231529. [PMID: 38471546 DOI: 10.1098/rspb.2023.1529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/29/2024] [Indexed: 03/14/2024] Open
Abstract
Mutations allowing pathogens to escape host immunity promote the spread of infectious diseases in heterogeneous host populations and can lead to major epidemics. Understanding the conditions that slow down this evolution is key for the development of durable control strategies against pathogens. Here, we use theory and experiments to compare the efficacy of three strategies for the deployment of resistance: (i) a mixing strategy where the host population contains two single-resistant genotypes, (ii) a pyramiding strategy where the host carries a double-resistant genotype, (iii) a combining strategy where the host population is a mix of a single-resistant genotype and a double-resistant genotype. First, we use evolutionary epidemiology theory to clarify the interplay between demographic stochasticity and evolutionary dynamics to show that the pyramiding strategy always yields lower probability of evolutionary emergence. Second, we test experimentally these predictions with the introduction of bacteriophages into bacterial populations where we manipulated the diversity and the depth of immunity using a Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated (CRISPR-Cas) system. These biological assays confirm that pyramiding multiple defences into the same host genotype and avoiding combination with single-defence genotypes is a robust way to reduce pathogen evolutionary emergence. The experimental validation of these theoretical recommendations has practical implications in various areas, including for the optimal deployment of resistance varieties in agriculture and for the design of durable vaccination strategies.
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Affiliation(s)
- Sylvain Gandon
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | | | - Antoine Nicot
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Ariane C Renaud
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec city, Canada G1V0A6
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Canada G1V 0A6
| | - Denise M Tremblay
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Canada G1V 0A6
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec city, Canada G1V0A6
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Canada G1V 0A6
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Khatri BS, Burt A. A theory of resistance to multiplexed gene drive demonstrates the significant role of weakly deleterious natural genetic variation. Proc Natl Acad Sci U S A 2022; 119:e2200567119. [PMID: 35914131 PMCID: PMC9371675 DOI: 10.1073/pnas.2200567119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/28/2022] [Indexed: 11/18/2022] Open
Abstract
Evolution of resistance is a major barrier to successful deployment of gene-drive systems to suppress natural populations, which could greatly reduce the burden of many vector-borne diseases. Multiplexed guide RNAs (gRNAs) that require resistance mutations in all target cut sites are a promising antiresistance strategy since, in principle, resistance would only arise in unrealistically large populations. Using stochastic simulations that accurately model evolution at very large population sizes, we explore the probability of resistance due to three important mechanisms: 1) nonhomologous end-joining mutations, 2) single-nucleotide mutants arising de novo, or 3) single-nucleotide polymorphisms preexisting as standing variation. Our results explore the relative importance of these mechanisms and highlight a complexity of the mutation-selection-drift balance between haplotypes with complete resistance and those with an incomplete number of resistant alleles. We find that this leads to a phenomenon where weakly deleterious naturally occurring variants greatly amplify the probability of multisite resistance compared to de novo mutation. This key result provides design criterion for antiresistance multiplexed systems, which, in general, will need a larger number of gRNAs compared to de novo expectations. This theory may have wider application to the evolution of resistance or evolutionary rescue when multiple changes are required before selection can act.
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Affiliation(s)
- Bhavin S. Khatri
- Department of Life Sciences, Imperial College London, Ascot SL5 7PY, United Kingdom
- Chromosome Segregation Laboratory, and Mechanobiology and Biophysics Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, Ascot SL5 7PY, United Kingdom
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McLeod DV, Gandon S. Effects of epistasis and recombination between vaccine-escape and virulence alleles on the dynamics of pathogen adaptation. Nat Ecol Evol 2022; 6:786-793. [PMID: 35437006 DOI: 10.1038/s41559-022-01709-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022]
Abstract
Pathogen adaptation to public health interventions such as vaccination may take tortuous routes and involve multiple mutations at different locations in the pathogen genome, acting on distinct phenotypic traits. Yet how these multi-locus adaptations jointly evolve is poorly understood. Here we consider the joint evolution of two adaptations: pathogen escape from the vaccine-induced immune response and adjustments to pathogen virulence affecting transmission or clearance. We elucidate the role played by epistasis and recombination, with an emphasis on the different protective effects of vaccination. We show that vaccines blocking infection, reducing transmission and/or increasing clearance generate positive epistasis between the vaccine-escape and virulence alleles, favouring strains that carry both mutations, whereas vaccines reducing virulence mortality generate negative epistasis, favouring strains that carry either mutation but not both. High rates of recombination can affect these predictions. If epistasis is positive, frequent recombination can prevent the transient build-up of more virulent escape strains. If epistasis is negative, frequent recombination between loci can create an evolutionary bistability, favouring whichever adaptation is more accessible. Our work provides a timely alternative to the variant-centred perspective on pathogen adaptation and captures the effect of different types of vaccine on the interference between multiple adaptive mutations.
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Affiliation(s)
- David V McLeod
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France. .,Institute of Ecology and Evolution, Universität Bern, Bern, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Sylvain Gandon
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France.
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Jamieson-Lane A, Friedrich A, Blasius B. Comparing optimization criteria in antibiotic allocation protocols. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220181. [PMID: 35345436 PMCID: PMC8941386 DOI: 10.1098/rsos.220181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/02/2022] [Indexed: 05/03/2023]
Abstract
Clinicians prescribing antibiotics in a hospital context follow one of several possible 'treatment protocols'-heuristic rules designed to balance the immediate needs of patients against the long-term threat posed by the evolution of antibiotic resistance and multi-resistant bacteria. Several criteria have been proposed for assessing these protocols; unfortunately, these criteria frequently conflict with one another, each providing a different recommendation as to which treatment protocol is best. Here, we review and compare these optimization criteria. We are able to demonstrate that criteria focused primarily on slowing evolution of resistance are directly antagonistic to patient health both in the short and long term. We provide a new optimization criteria of our own, intended to more meaningfully balance the needs of the future and present. Asymptotic methods allow us to evaluate this criteria and provide insights not readily available through the numerical methods used previously in the literature. When cycling antibiotics, we find an antibiotic switching time which proves close to optimal across a wide range of modelling assumptions.
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Affiliation(s)
- Alastair Jamieson-Lane
- University of Auckland, Mathematics, Auckland 1142, New Zealand
- Carl von Ossietzky, Universität Oldenburg, Oldenburg, Germany
| | | | - Bernd Blasius
- Carl von Ossietzky, Universität Oldenburg, Oldenburg, Germany
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Gandon S, Lion S. Targeted vaccination and the speed of SARS-CoV-2 adaptation. Proc Natl Acad Sci U S A 2022; 119:e2110666119. [PMID: 35031567 PMCID: PMC8784131 DOI: 10.1073/pnas.2110666119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/18/2021] [Indexed: 12/16/2022] Open
Abstract
The limited supply of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) raises the question of targeted vaccination. Many countries have opted to vaccinate older and more sensitive hosts first to minimize the disease burden. However, what are the evolutionary consequences of targeted vaccination? We clarify the consequences of different vaccination strategies through the analysis of the speed of viral adaptation measured as the rate of change of the frequency of a vaccine-adapted variant. We show that such a variant is expected to spread faster if vaccination targets individuals who are likely to be involved in a higher number of contacts. We also discuss the pros and cons of dose-sparing strategies. Because delaying the second dose increases the proportion of the population vaccinated with a single dose, this strategy can both speed up the spread of the vaccine-adapted variant and reduce the cumulative number of deaths. Hence, strategies that are most effective at slowing viral adaptation may not always be epidemiologically optimal. A careful assessment of both the epidemiological and evolutionary consequences of alternative vaccination strategies is required to determine which individuals should be vaccinated first.
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Affiliation(s)
- Sylvain Gandon
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
| | - Sébastien Lion
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
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Abstract
In recognition that evolutionary theory is critical for understanding modern human health, eLife is publishing a special issue on evolutionary medicine to showcase recent research in this growing and increasingly interdisciplinary field.
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Affiliation(s)
- George H Perry
- Departments of Anthropology and Biology, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, United States
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