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Wilken L, Rimmelzwaan GF, Elbahesh H. The Raf kinase inhibitors Dabrafenib and Regorafenib impair Zika virus replication via distinct mechanisms. J Virol 2024:e0061824. [PMID: 39023323 DOI: 10.1128/jvi.00618-24] [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: 04/15/2024] [Accepted: 06/01/2024] [Indexed: 07/20/2024] Open
Abstract
Zika virus (ZIKV) is a re-emerging mosquito-borne flavivirus that has been associated with congenital neurological defects in fetuses born to infected mothers. At present, no vaccine or antiviral therapy is available to combat this devastating disease. Repurposing drugs that target essential host factors exploited by viruses is an attractive therapeutic approach. Here, we screened a panel of clinically approved small-molecule kinase inhibitors for their antiviral effects against a clinical isolate of ZIKV and thoroughly characterized their mechanisms of action. We found that the Raf kinase inhibitors Dabrafenib and Regorafenib potently impair the replication of ZIKV, but not that of its close relative dengue virus. Time-of-addition experiments showed that both inhibitors target ZIKV infection at post-entry steps. We found that Dabrafenib, but not Regorafenib, interfered with ZIKV genome replication by impairing both negative- and positive-strand RNA synthesis. Regorafenib, on the other hand, altered steady-state viral protein levels, viral egress, and blocked NS1 secretion. We also observed Regorafenib-induced ER fragmentation in ZIKV-infected cells, which might contribute to its antiviral effects. Because these inhibitors target different steps of the ZIKV infection cycle, their use in combination therapy may amplify their antiviral effects which could be further explored for future therapeutic strategies against ZIKV and possibly other flaviviruses. IMPORTANCE There is an urgent need to develop effective therapeutics against re-emerging arboviruses associated with neurological disorders like Zika virus (ZIKV). We identified two FDA-approved kinase inhibitors, Dabrafenib and Regorafenib, as potent inhibitors of contemporary ZIKV strains at distinct stages of infection despite overlapping host targets. Both inhibitors reduced viral titers by ~1 to 2 log10 (~10-fold to 100-fold) with minimal cytotoxicity. Furthermore, we show that Dabrafenib inhibits ZIKV RNA replication whereas Regorafenib inhibits ZIKV translation and egress. Regorafenib has the added benefit of limiting NS1 secretion, which contributes to the pathogenesis and disease progression of several flaviviruses. Because these inhibitors affect distinct post-entry steps of ZIKV infection, their therapeutic potential may be amplified by combination therapy and likely does not require prophylactic administration. This study provides further insight into ZIKV-host interactions and has implications for the development of novel antivirals against ZIKV and possibly other flaviviruses.
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Affiliation(s)
- Lucas Wilken
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine (TiHo), Hannover, Germany
| | - Guus F Rimmelzwaan
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine (TiHo), Hannover, Germany
| | - Husni Elbahesh
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine (TiHo), Hannover, Germany
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2
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James LP, Klaassen F, Sweeney S, Furin J, Franke MF, Yaesoubi R, Chesov D, Ciobanu N, Codreanu A, Crudu V, Cohen T, Menzies NA. Impact and cost-effectiveness of the 6-month BPaLM regimen for rifampicin-resistant tuberculosis in Moldova: A mathematical modeling analysis. PLoS Med 2024; 21:e1004401. [PMID: 38701084 PMCID: PMC11101189 DOI: 10.1371/journal.pmed.1004401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 05/17/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Emerging evidence suggests that shortened, simplified treatment regimens for rifampicin-resistant tuberculosis (RR-TB) can achieve comparable end-of-treatment (EOT) outcomes to longer regimens. We compared a 6-month regimen containing bedaquiline, pretomanid, linezolid, and moxifloxacin (BPaLM) to a standard of care strategy using a 9- or 18-month regimen depending on whether fluoroquinolone resistance (FQ-R) was detected on drug susceptibility testing (DST). METHODS AND FINDINGS The primary objective was to determine whether 6 months of BPaLM is a cost-effective treatment strategy for RR-TB. We used genomic and demographic data to parameterize a mathematical model estimating long-term health outcomes measured in quality-adjusted life years (QALYs) and lifetime costs in 2022 USD ($) for each treatment strategy for patients 15 years and older diagnosed with pulmonary RR-TB in Moldova, a country with a high burden of TB drug resistance. For each individual, we simulated the natural history of TB and associated treatment outcomes, as well as the process of acquiring resistance to each of 12 anti-TB drugs. Compared to the standard of care, 6 months of BPaLM was cost-effective. This strategy was estimated to reduce lifetime costs by $3,366 (95% UI: [1,465, 5,742] p < 0.001) per individual, with a nonsignificant change in QALYs (-0.06; 95% UI: [-0.49, 0.03] p = 0.790). For those stopping moxifloxacin under the BPaLM regimen, continuing with BPaL plus clofazimine (BPaLC) provided more QALYs at lower cost than continuing with BPaL alone. Strategies based on 6 months of BPaLM had at least a 93% chance of being cost-effective, so long as BPaLC was continued in the event of stopping moxifloxacin. BPaLM for 6 months also reduced the average time spent with TB resistant to amikacin, bedaquiline, clofazimine, cycloserine, moxifloxacin, and pyrazinamide, while it increased the average time spent with TB resistant to delamanid and pretomanid. Sensitivity analyses showed 6 months of BPaLM to be cost-effective across a broad range of values for the relative effectiveness of BPaLM, and the proportion of the cohort with FQ-R. Compared to the standard of care, 6 months of BPaLM would be expected to save Moldova's national TB program budget $7.1 million (95% UI: [1.3 million, 15.4 million] p = 0.002) over the 5-year period from implementation. Our analysis did not account for all possible interactions between specific drugs with regard to treatment outcomes, resistance acquisition, or the consequences of specific types of severe adverse events, nor did we model how the intervention may affect TB transmission dynamics. CONCLUSIONS Compared to standard of care, longer regimens, the implementation of the 6-month BPaLM regimen could improve the cost-effectiveness of care for individuals diagnosed with RR-TB, particularly in settings with a high burden of drug-resistant TB. Further research may be warranted to explore the impact and cost-effectiveness of shorter RR-TB regimens across settings with varied drug-resistant TB burdens and national income levels.
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Affiliation(s)
- Lyndon P. James
- PhD Program in Health Policy, Harvard University, Cambridge, Massachusetts, United States of America
- Center for Health Decision Science, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Fayette Klaassen
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sedona Sweeney
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jennifer Furin
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Molly F. Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Reza Yaesoubi
- Department of Health Policy and Management, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Dumitru Chesov
- Discipline of Pneumology and Allergology, Nicolae Testemitanu State University of Medicine and Pharmacy, Chişinǎu, Moldova
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
| | - Nelly Ciobanu
- Chiril Draganiuc Institute of Phthisiopneumology, Chișinǎu, Moldova
| | | | - Valeriu Crudu
- Chiril Draganiuc Institute of Phthisiopneumology, Chișinǎu, Moldova
| | - Ted Cohen
- Department of Epidemiology and Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Nicolas A. Menzies
- Center for Health Decision Science, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
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3
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He Q, Chaillet JK, Labbé F. Antigenic strain diversity predicts different biogeographic patterns of maintenance and decline of antimalarial drug resistance. eLife 2024; 12:RP90888. [PMID: 38363295 PMCID: PMC10942604 DOI: 10.7554/elife.90888] [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] [Indexed: 02/17/2024] Open
Abstract
The establishment and spread of antimalarial drug resistance vary drastically across different biogeographic regions. Though most infections occur in sub-Saharan Africa, resistant strains often emerge in low-transmission regions. Existing models on resistance evolution lack consensus on the relationship between transmission intensity and drug resistance, possibly due to overlooking the feedback between antigenic diversity, host immunity, and selection for resistance. To address this, we developed a novel compartmental model that tracks sensitive and resistant parasite strains, as well as the host dynamics of generalized and antigen-specific immunity. Our results show a negative correlation between parasite prevalence and resistance frequency, regardless of resistance cost or efficacy. Validation using chloroquine-resistant marker data supports this trend. Post discontinuation of drugs, resistance remains high in low-diversity, low-transmission regions, while it steadily decreases in high-diversity, high-transmission regions. Our study underscores the critical role of malaria strain diversity in the biogeographic patterns of resistance evolution.
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Affiliation(s)
- Qixin He
- Department of Biological Sciences, Purdue UniversityWest LafayetteUnited States
| | - John K Chaillet
- Department of Biological Sciences, Purdue UniversityWest LafayetteUnited States
| | - Frédéric Labbé
- Department of Ecology and Evolution, University of ChicagoChicagoUnited States
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4
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He Q, Chaillet JK, Labbé F. Antigenic strain diversity predicts different biogeographic patterns of maintenance and decline of anti-malarial drug resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531320. [PMID: 37987011 PMCID: PMC10659383 DOI: 10.1101/2023.03.06.531320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The establishment and spread of anti-malarial drug resistance vary drastically across different biogeographic regions. Though most infections occur in Sub-Saharan Africa, resistant strains often emerge in low-transmission regions. Existing models on resistance evolution lack consensus on the relationship between transmission intensity and drug resistance, possibly due to overlooking the feedback between antigenic diversity, host immunity, and selection for resistance. To address this, we developed a novel compartmental model that tracks sensitive and resistant parasite strains, as well as the host dynamics of generalized and antigen-specific immunity. Our results show a negative correlation between parasite prevalence and resistance frequency, regardless of resistance cost or efficacy. Validation using chloroquine-resistant marker data supports this trend. Post discontinuation of drugs, resistance remains high in low-diversity, low-transmission regions, while it steadily decreases in high-diversity, high-transmission regions. Our study underscores the critical role of malaria strain diversity in the biogeographic patterns of resistance evolution.
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Affiliation(s)
- Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - John K. Chaillet
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Frédéric Labbé
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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5
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Lässig M, Mustonen V, Nourmohammad A. Steering and controlling evolution - from bioengineering to fighting pathogens. Nat Rev Genet 2023; 24:851-867. [PMID: 37400577 PMCID: PMC11137064 DOI: 10.1038/s41576-023-00623-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Control interventions steer the evolution of molecules, viruses, microorganisms or other cells towards a desired outcome. Applications range from engineering biomolecules and synthetic organisms to drug, therapy and vaccine design against pathogens and cancer. In all these instances, a control system alters the eco-evolutionary trajectory of a target system, inducing new functions or suppressing escape evolution. Here, we synthesize the objectives, mechanisms and dynamics of eco-evolutionary control in different biological systems. We discuss how the control system learns and processes information about the target system by sensing or measuring, through adaptive evolution or computational prediction of future trajectories. This information flow distinguishes pre-emptive control strategies by humans from feedback control in biotic systems. We establish a cost-benefit calculus to gauge and optimize control protocols, highlighting the fundamental link between predictability of evolution and efficacy of pre-emptive control.
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Affiliation(s)
- Michael Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany.
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Armita Nourmohammad
- Department of Physics, University of Washington, Seattle, WA, USA.
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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6
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Dorigan AF, Moreira SI, da Silva Costa Guimarães S, Cruz-Magalhães V, Alves E. Target and non-target site mechanisms of fungicide resistance and their implications for the management of crop pathogens. PEST MANAGEMENT SCIENCE 2023; 79:4731-4753. [PMID: 37592727 DOI: 10.1002/ps.7726] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/14/2023] [Accepted: 08/18/2023] [Indexed: 08/19/2023]
Abstract
Fungicides are indispensable for high-quality crops, but the rapid emergence and evolution of fungicide resistance have become the most important issues in modern agriculture. Hence, the sustainability and profitability of agricultural production have been challenged due to the limited number of fungicide chemical classes. Resistance to site-specific fungicides has principally been linked to target and non-target site mechanisms. These mechanisms change the structure or expression level, affecting fungicide efficacy and resulting in different and varying resistance levels. This review provides background information about fungicide resistance mechanisms and their implications for developing anti-resistance strategies in plant pathogens. Here, our purpose was to review changes at the target and non-target sites of quinone outside inhibitor (QoI) fungicides, methyl-benzimidazole carbamate (MBC) fungicides, demethylation inhibitor (DMI) fungicides, and succinate dehydrogenase inhibitor (SDHI) fungicides and to evaluate if they may also be associated with a fitness cost on crop pathogen populations. The current knowledge suggests that understanding fungicide resistance mechanisms can facilitate resistance monitoring and assist in developing anti-resistance strategies and new fungicide molecules to help solve this issue. © 2023 Society of Chemical Industry.
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Affiliation(s)
| | | | | | | | - Eduardo Alves
- Department of Plant Pathology, Federal University of Lavras, Lavras, Brazil
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7
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Ogunlana L, Kaur D, Shaw LP, Jangir P, Walsh T, Uphoff S, MacLean RC. Regulatory fine-tuning of mcr-1 increases bacterial fitness and stabilises antibiotic resistance in agricultural settings. THE ISME JOURNAL 2023; 17:2058-2069. [PMID: 37723338 PMCID: PMC10579358 DOI: 10.1038/s41396-023-01509-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/20/2023]
Abstract
Antibiotic resistance tends to carry fitness costs, making it difficult to understand how resistance can be maintained in the absence of continual antibiotic exposure. Here we investigate this problem in the context of mcr-1, a globally disseminated gene that confers resistance to colistin, an agricultural antibiotic that is used as a last resort for the treatment of multi-drug resistant infections. Here we show that regulatory evolution has fine-tuned the expression of mcr-1, allowing E. coli to reduce the fitness cost of mcr-1 while simultaneously increasing colistin resistance. Conjugative plasmids have transferred low-cost/high-resistance mcr-1 alleles across an incredible diversity of E. coli strains, further stabilising mcr-1 at the species level. Regulatory mutations were associated with increased mcr-1 stability in pig farms following a ban on the use of colistin as a growth promoter that decreased colistin consumption by 90%. Our study shows how regulatory evolution and plasmid transfer can combine to stabilise resistance and limit the impact of reducing antibiotic consumption.
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Affiliation(s)
- Lois Ogunlana
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Divjot Kaur
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Liam P Shaw
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Pramod Jangir
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Timothy Walsh
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - R C MacLean
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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8
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Volz E. Fitness, growth and transmissibility of SARS-CoV-2 genetic variants. Nat Rev Genet 2023; 24:724-734. [PMID: 37328556 DOI: 10.1038/s41576-023-00610-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2023] [Indexed: 06/18/2023]
Abstract
The massive scale of the global SARS-CoV-2 sequencing effort created new opportunities and challenges for understanding SARS-CoV-2 evolution. Rapid detection and assessment of new variants has become one of the principal objectives of genomic surveillance of SARS-CoV-2. Because of the pace and scale of sequencing, new strategies have been developed for characterizing fitness and transmissibility of emerging variants. In this Review, I discuss a wide range of approaches that have been rapidly developed in response to the public health threat posed by emerging variants, ranging from new applications of classic population genetics models to contemporary synthesis of epidemiological models and phylodynamic analysis. Many of these approaches can be adapted to other pathogens and will have increasing relevance as large-scale pathogen sequencing becomes a regular feature of many public health systems.
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Affiliation(s)
- Erik Volz
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.
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9
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Alexander HK. Quantifying stochastic establishment of mutants in microbial adaptation. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001365. [PMID: 37561015 PMCID: PMC10482372 DOI: 10.1099/mic.0.001365] [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: 03/21/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023]
Abstract
Studies of microbial evolution, especially in applied contexts, have focused on the role of selection in shaping predictable, adaptive responses to the environment. However, chance events - the appearance of novel genetic variants and their establishment, i.e. outgrowth from a single cell to a sizeable population - also play critical initiating roles in adaptation. Stochasticity in establishment has received little attention in microbiology, potentially due to lack of awareness as well as practical challenges in quantification. However, methods for high-replicate culturing, mutant labelling and detection, and statistical inference now make it feasible to experimentally quantify the establishment probability of specific adaptive genotypes. I review methods that have emerged over the past decade, including experimental design and mathematical formulas to estimate establishment probability from data. Quantifying establishment in further biological settings and comparing empirical estimates to theoretical predictions represent exciting future directions. More broadly, recognition that adaptive genotypes may be stochastically lost while rare is significant both for interpreting common lab assays and for designing interventions to promote or inhibit microbial evolution.
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Affiliation(s)
- Helen K. Alexander
- Institute of Ecology & Evolution, University of Edinburgh, Edinburgh, UK
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10
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Woods RJ, Barbosa C, Koepping L, Raygoza JA, Mwangi M, Read AF. The evolution of antibiotic resistance in an incurable and ultimately fatal infection: A retrospective case study. Evol Med Public Health 2023; 11:163-173. [PMID: 37325804 PMCID: PMC10266578 DOI: 10.1093/emph/eoad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 04/06/2023] [Indexed: 06/17/2023] Open
Abstract
Background and objectives The processes by which pathogens evolve within a host dictate the efficacy of treatment strategies designed to slow antibiotic resistance evolution and influence population-wide resistance levels. The aim of this study is to describe the underlying genetic and phenotypic changes leading to antibiotic resistance within a patient who died as resistance evolved to available antibiotics. We assess whether robust patterns of collateral sensitivity and response to combinations existed that might have been leveraged to improve therapy. Methodology We used whole-genome sequencing of nine isolates taken from this patient over 279 days of a chronic infection with Enterobacter hormaechei, and systematically measured changes in resistance against five of the most relevant drugs considered for treatment. Results The entirety of the genetic change is consistent with de novo mutations and plasmid loss events, without acquisition of foreign genetic material via horizontal gene transfer. The nine isolates fall into three genetically distinct lineages, with early evolutionary trajectories being supplanted by previously unobserved multi-step evolutionary trajectories. Importantly, although the population evolved resistance to all the antibiotics used to treat the infection, no single isolate was resistant to all antibiotics. Evidence of collateral sensitivity and response to combinations therapy revealed inconsistent patterns across this diversifying population. Conclusions Translating antibiotic resistance management strategies from theoretical and laboratory data to clinical situations, such as this, will require managing diverse population with unpredictable resistance trajectories.
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Affiliation(s)
- Robert J Woods
- Corresponding author. 2215 Fuller Rd, Ann Arbor, MI 48105, USA. Tel: +734 845-3460; E-mail:
| | - Camilo Barbosa
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Laura Koepping
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Juan A Raygoza
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Michael Mwangi
- Machine Learning Modeling Working Group, Synopsys, Mountain View, CA, USA
| | - Andrew F Read
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
- Department of Entomology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
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11
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Naidoo A, Kajee A, Mvelase NR, Swe-Han KS. Antimicrobial susceptibility of bacterial uropathogens in a South African regional hospital. Afr J Lab Med 2023; 12:1920. [PMID: 37063604 PMCID: PMC10091058 DOI: 10.4102/ajlm.v12i1.1920] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/13/2022] [Indexed: 03/05/2023] Open
Abstract
Background Urinary tract infections are common bacterial infections affecting millions worldwide. Although treatment options for urinary tract infections are well established, with ciprofloxacin long considered one of the antibiotics of choice, increasing antibiotic resistance may delay the initiation of appropriate therapy. While this increase in antimicrobial resistance has been demonstrated in multiple studies around the world, there is a dearth of information from developing countries. Objective This study aimed to describe the antimicrobial susceptibility patterns of commonly isolated bacterial uropathogens in a South African hospital. Methods Antimicrobial susceptibility data of isolates obtained from urine specimens at the RK Khan Hospital, a regional hospital in KwaZulu-Natal, South Africa, between January 2018 and December 2020 were retrieved from the hospital's laboratory information system and analysed to determine the differences in resistance rates between the most frequently isolated bacterial uropathogens. Results Of the 3048 bacterial urinary pathogens isolated between 2018 and 2020, Escherichia coli (1603; 53%) was the most common, followed by Klebsiella spp. (437; 14%). Both E. coli and Klebsiella spp. showed high rates of resistance to amoxicillin/clavulanic acid (29.8% and 42.3%) and ciprofloxacin (37.7% and 30.4%). Nitrofurantoin resistance was low among E. coli (6.2%) but high among Klebsiella spp. (61.3%). Conclusion E. coli and Klebsiella spp. in this study were highly resistant to amoxicillin/clavulanic acid and ciprofloxacin, two of the frequently prescribed oral treatment options. What this study adds This study highlights the importance of regular local antimicrobial resistance surveillance to inform appropriate empiric therapy.
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Affiliation(s)
- Alicia Naidoo
- Department of Medical Microbiology, RK Khan Laboratory, National Health Laboratory Service, Durban, South Africa
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Afsana Kajee
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Medical Microbiology, Inkosi Albert Luthuli Central Hospital, National Health Laboratory Services, Durban, South Africa
| | - Nomonde R. Mvelase
- Department of Medical Microbiology, RK Khan Laboratory, National Health Laboratory Service, Durban, South Africa
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Khine Swe Swe-Han
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Medical Microbiology, Inkosi Albert Luthuli Central Hospital, National Health Laboratory Services, Durban, South Africa
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12
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Qasim M, Clarkson AN, Hinkley SFR. Green Synthesis of Carbon Nanoparticles (CNPs) from Biomass for Biomedical Applications. Int J Mol Sci 2023; 24:ijms24021023. [PMID: 36674532 PMCID: PMC9863453 DOI: 10.3390/ijms24021023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023] Open
Abstract
In this review, we summarize recent work on the "green synthesis" of carbon nanoparticles (CNPs) and their application with a focus on biomedical applications. Recent developments in the green synthesis of carbon nanoparticles, from renewable precursors and their application for environmental, energy-storage and medicinal applications are discussed. CNPs, especially carbon nanotubes (CNTs), carbon quantum dots (CQDs) and graphene, have demonstrated utility as high-density energy storage media, environmental remediation materials and in biomedical applications. Conventional fabrication of CNPs can entail the use of toxic catalysts; therefore, we discuss low-toxicity manufacturing as well as sustainable and environmentally friendly methodology with a focus on utilizing readily available biomass as the precursor for generating CNPs.
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Affiliation(s)
- Muhammad Qasim
- Department of Anatomy, Brain Health Research Centre and Brain Research New Zealand, University of Otago, Dunedin 9054, New Zealand
| | - Andrew N. Clarkson
- Department of Anatomy, Brain Health Research Centre and Brain Research New Zealand, University of Otago, Dunedin 9054, New Zealand
- Correspondence: (A.N.C.); (S.F.R.H.); Tel.: +64-3-279-7326 (A.N.C.); +64-4-463-0052 (S.F.R.H)
| | - Simon F. R. Hinkley
- Ferrier Research Institute, Victoria University of Wellington, Wellington 5012, New Zealand
- Correspondence: (A.N.C.); (S.F.R.H.); Tel.: +64-3-279-7326 (A.N.C.); +64-4-463-0052 (S.F.R.H)
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13
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Lyons N, Berman J. Protocols for Measuring Tolerant and Heteroresistant Drug Responses of Pathogenic Yeasts. Methods Mol Biol 2023; 2658:67-79. [PMID: 37024696 DOI: 10.1007/978-1-0716-3155-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
The classic definition of antimicrobial susceptibility to antifungal drugs ignores the persistence of subpopulations that survive in the presence of a drug. Even in entirely clonal populations, small subpopulations of yeast can grow in the presence of a drug, sometimes up to extremely high drug concentrations, such that they may be clinically relevant. Identifying and quantifying the incidence with which these subpopulations arise is an essential step in understanding how pathogenic yeast, such as Candida species (i.e., C. albicans, C. glabrata, C. auris, C. tropicalis, C. parapsilosis, and others) as well as Cryptococcus species, behave in response to antifungal therapeutics. Here we describe simple in vitro protocols for the quantification of drug responses with subpopulation resolution.
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Affiliation(s)
- Naomi Lyons
- Shmunis School of Biomedical and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
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14
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DelaFuente J, Toribio-Celestino L, Santos-Lopez A, León-Sampedro R, Alonso-Del Valle A, Costas C, Hernández-García M, Cui L, Rodríguez-Beltrán J, Bikard D, Cantón R, San Millan A. Within-patient evolution of plasmid-mediated antimicrobial resistance. Nat Ecol Evol 2022; 6:1980-1991. [PMID: 36303001 PMCID: PMC7613874 DOI: 10.1038/s41559-022-01908-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/12/2022] [Indexed: 12/15/2022]
Abstract
Antimicrobial resistance (AMR) in bacteria is a major threat to public health; one of the key elements in the spread and evolution of AMR in clinical pathogens is the transfer of conjugative plasmids. The drivers of AMR evolution have been studied extensively in vitro but the evolution of plasmid-mediated AMR in vivo remains poorly explored. Here, we tracked the evolution of the clinically relevant plasmid pOXA-48, which confers resistance to the last-resort antibiotics carbapenems, in a large collection of enterobacterial clones isolated from the gut of hospitalized patients. Combining genomic and experimental approaches, we first characterized plasmid diversity and the genotypic and phenotypic effects of multiple plasmid mutations on a common genetic background. Second, using cutting-edge genomic editing in wild-type multidrug-resistant enterobacteria, we dissected three cases of within-patient plasmid-mediated AMR evolution. Our results revealed compensatory evolution of plasmid-associated fitness cost and the evolution of enhanced plasmid-mediated AMR in bacteria evolving in the gut of hospitalized patients. Crucially, we observed that the evolution of pOXA-48-mediated AMR in vivo involves a pivotal trade-off between resistance levels and bacterial fitness. This study highlights the need to develop new evolution-informed approaches to tackle plasmid-mediated AMR dissemination.
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Affiliation(s)
- Javier DelaFuente
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain.
| | - Laura Toribio-Celestino
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Alfonso Santos-Lopez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Ricardo León-Sampedro
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
- Institute of Integrative Biology, Department of Environmental Systems Science, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Aida Alonso-Del Valle
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Coloma Costas
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Marta Hernández-García
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Lun Cui
- Institut Pasteur, Universite de Paris Cité, Centre National de la Recherche Scientifique Unité Mixte de Recherche 6047, Synthetic Biology, Paris, France
| | - Jerónimo Rodríguez-Beltrán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - David Bikard
- Institut Pasteur, Universite de Paris Cité, Centre National de la Recherche Scientifique Unité Mixte de Recherche 6047, Synthetic Biology, Paris, France
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alvaro San Millan
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain.
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain.
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15
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Dorigan AF, Moreira SI, Ceresini PC, Pozza EA, Belan LL, da Silveira PR, Alves E. Higher fitness and competitive advantage of Pyricularia oryzae Triticum lineage resistant to QoI fungicides. PEST MANAGEMENT SCIENCE 2022; 78:5251-5258. [PMID: 36054071 DOI: 10.1002/ps.7144] [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: 05/27/2022] [Revised: 08/12/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Quinone outside inhibitor (QoI) fungicides have not been effective in controlling the wheat blast disease [Pyricularia oryzae Triticum lineage (PoTl)] in Brazil. The first report of resistance of PoTl to QoIs in this country occurred in 2015. This study aimed to test hypotheses about the changes in fitness parameters and competitive advantage of the QoI-resistant (R) PoTl isolate group compared to the sensitive (S) isolate group. Mycelial growth on PDA medium and in vivo conidial production, incubation period and disease severity were analyzed as fitness parameters. The competitive ability was measured on wheat leaves and heads inoculated with mixtures of R:S isolates at the following proportions: 0S:100R, 20S:80R, 50S:50R, 80S:20R, 100S:0R, and 0S:0R. RESULTS The QoI-R isolate group had significantly higher fitness than the sensitive isolate group, considering both in vitro and in vivo parameters. The highest in vivo conidial production on wheat leaves and the highest leaf and head disease severity were detected when resistant strains were predominant in the isolate's mixtures (20S:80R or 0S:100R proportions), in the absence of fungicide pressure. Conidia harvested from wheat blast lesions on leaves inoculated with 20S:80R and 0S:100R mixtures were resistant to QoIs in vitro assays based on discriminatory doses of the fungicide. CONCLUSION Therefore, QoI resistance facilitated a higher fitness and a competitive advantage in PoTl, which contrasts with the evolutionary theory that associates a fitness cost to fungicide resistance. We discuss the evolutionary and ecological implications of the higher fitness as found in the fungicide-resistant adapted populations of the wheat blast pathogen. © 2022 Society of Chemical Industry.
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Affiliation(s)
| | | | - Paulo Cezar Ceresini
- Department of Crop Protection, Agricultural Engineering and Soils São Paulo State University, São Paulo, Brazil
| | | | - Leônidas Leoni Belan
- Center for Agricultural Sciences Campus Imperatriz, State University of Tocantina Region of Maranhão, São Luís, Brazil
| | | | - Eduardo Alves
- Department of Plant Pathology, Federal University of Lavras, Lavras, Brazil
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16
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Kamiya T, Paton DG, Catteruccia F, Reece SE. Targeting malaria parasites inside mosquitoes: ecoevolutionary consequences. Trends Parasitol 2022; 38:1031-1040. [PMID: 36209032 PMCID: PMC9815470 DOI: 10.1016/j.pt.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 11/05/2022]
Abstract
Proof-of-concept studies demonstrate that antimalarial drugs designed for human treatment can also be applied to mosquitoes to interrupt malaria transmission. Deploying a new control tool is ideally undertaken within a stewardship programme that maximises a drug's lifespan by minimising the risk of resistance evolution and slowing its spread once emerged. We ask: what are the epidemiological and evolutionary consequences of targeting parasites within mosquitoes? Our synthesis argues that targeting parasites inside mosquitoes (i) can be modelled by readily expanding existing epidemiological frameworks; (ii) provides a functionally novel control method that has potential to be more robust to resistance evolution than targeting parasites in humans; and (iii) could extend the lifespan and clinical benefit of antimalarials used exclusively to treat humans.
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Affiliation(s)
- Tsukushi Kamiya
- Centre for Interdisciplinary Research in Biology, Collège de France, Paris, France; HRB Clinical Research Facility, National University of Ireland, Galway, Ireland; Institute of Ecology and Evolution, and Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| | - Douglas G Paton
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Flaminia Catteruccia
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA
| | - Sarah E Reece
- Institute of Ecology and Evolution, and Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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17
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Stennett HL, Back CR, Race PR. Derivation of a Precise and Consistent Timeline for Antibiotic Development. Antibiotics (Basel) 2022; 11:1237. [PMID: 36140015 PMCID: PMC9495031 DOI: 10.3390/antibiotics11091237] [Citation(s) in RCA: 4] [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: 08/26/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
Antibiotic resistance is a global health crisis. New classes of antibiotics that can treat drug-resistant infections are urgently needed. To communicate this message, researchers have used antibiotic development timelines, but these are often contradictory or imprecise. We conducted a systematic literature review to produce an antibiotic timeline that incorporates the dates of discovery, first use, and initial reports of the emergence of resistance for the 38 classes of clinically used antibiotics. From our timeline, we derive lessons for identifying new antibiotics that are less prone to resistance. These include a required focus on molecules that exhibit multiple modes of action, possess unusually long 'resistance windows', or those that engage cellular targets whose molecular architectures are at least in part decoupled from evolutionary pressures. Our analysis also further highlights the importance of safeguarding antibiotics as a mechanism for mitigating the development of resistance. We have made our data and sources freely available so that the research community can adapt them to their own needs.
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Affiliation(s)
- Henry L. Stennett
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
- BrisSynBio Synthetic Biology Research Centre, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Catherine R. Back
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Paul R. Race
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
- BrisSynBio Synthetic Biology Research Centre, Tyndall Avenue, Bristol BS8 1TQ, UK
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18
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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; 11:77634. [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] [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 Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Tamsin Lee
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Monica Golumbeanu
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Andrew J Shattock
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Sherrie L Kelly
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Ian M Hastings
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Melissa A Penny
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
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19
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Kapel N, Caballero JD, MacLean RC. Localized pmrB hypermutation drives the evolution of colistin heteroresistance. Cell Rep 2022; 39:110929. [PMID: 35675785 PMCID: PMC9189680 DOI: 10.1016/j.celrep.2022.110929] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/02/2021] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
Colistin has emerged as an important last line of defense for the treatment of infections caused by antibiotic-resistant gram-negative pathogens, but colistin resistance remains poorly understood. Here, we investigate the responses of ≈1,000 populations of a multi-drug-resistant (MDR) strain of P. aeruginosa to a high dose of colistin. Colistin exposure causes rapid cell death, but some populations eventually recover due to the growth of sub-populations of heteroresistant cells. Heteroresistance is unstable, and resistance is rapidly lost under culture in colistin-free medium. The evolution of heteroresistance is primarily driven by selection for heteroresistance at two hotspot sites in the PmrAB regulatory system. Localized hypermutation of pmrB generates colistin resistance at 103–104 times the background resistance mutation rate (≈2 × 10-5 per cell division). PmrAB provides resistance to antimicrobial peptides that are involved in host immunity, suggesting that this pathogen may have evolved a highly mutable pmrB as an adaptation to host immunity. Pseudomonas populations recover from colistin due to the growth of heteroresistant cells Heteroresistance is driven by pre-existing mutations in the PmrAB regulatory system pmrB mutations arise at 103–104 times the background mutation rate Heteroresistance is unstable and is rapidly lost in the absence of colistin
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Affiliation(s)
- Natalia Kapel
- University of Oxford, Department of Zoology, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Julio Diaz Caballero
- University of Oxford, Department of Zoology, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - R Craig MacLean
- University of Oxford, Department of Zoology, 11a Mansfield Road, Oxford OX1 3SZ, UK.
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20
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Hu X, Fu Y, Shi H, Xu W, Shen C, Hu B, Ma L, Lou L. Neglected resistance risks: Cooperative resistance of antibiotic resistant bacteria influenced by primary soil components. JOURNAL OF HAZARDOUS MATERIALS 2022; 429:128229. [PMID: 35074748 DOI: 10.1016/j.jhazmat.2022.128229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Various antibiotic resistant bacteria (ARB) can thrive in soil and resist such environmental pressures as antibiotics through cooperative resistance, thereby promoting ARB retention and antibiotic resistance genes transmission. However, there has been finite knowledge in regard to the mechanisms and potential ecological risks of cooperative resistance in soil microbiome. In this study, soil minerals and organic matters were designed to treat a mixture of two Escherichia coli strains with different antibiotic resistance (E. coli DH5α/pUC19 and E. coli XL2-Blue) to determine how soil components affected cooperative resistance, and Luria-Bertani plates containing two antibiotics were used to observe dual-drug resistant bacteria (DRB) developed via cooperative resistance. Results showed quartz, humic acid, and biochar promoted E. coli XL2-Blue with high fitness costs, whereas kaolin, montmorillonite, and soot inhibited both strains. Using fluorescence microscope and PCR, it was speculated DRB could resist the antibiotic pressure via E. coli XL2-Blue coating E. coli DH5α/pUC19. E. coli DH5α/pUC19 dominated cooperative resistance. Correlation analysis and scanning electron microscope images indicated soil components influenced cooperative resistance. Biochar promoted cooperative resistance by increasing intracellular reactive oxygen species, thereby reducing the dominant strain concentration required for DRB development. Kaolin inhibited cooperative resistance the most, followed by soot and montmorillonite.
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Affiliation(s)
- Xinyi Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Yulong Fu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Hongyu Shi
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Weijian Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China
| | - Chaofeng Shen
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310020, People's Republic of China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310020, People's Republic of China
| | - Liping Ma
- School of Ecological and Environmental Sciences, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, East China Normal University, Shanghai 200062, People's Republic of China.
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, People's Republic of China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310020, People's Republic of China.
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21
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Feng S, Wu Z, Liang W, Zhang X, Cai X, Li J, Liang L, Lin D, Stoesser N, Doi Y, Zhong LL, Liu Y, Xia Y, Dai M, Zhang L, Chen X, Yang JR, Tian GB. Prediction of Antibiotic Resistance Evolution by Growth Measurement of All Proximal Mutants of Beta-Lactamase. Mol Biol Evol 2022; 39:msac086. [PMID: 35485492 PMCID: PMC9087888 DOI: 10.1093/molbev/msac086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The antibiotic resistance crisis continues to threaten human health. Better predictions of the evolution of antibiotic resistance genes could contribute to the design of more sustainable treatment strategies. However, comprehensive prediction of antibiotic resistance gene evolution via laboratory approaches remains challenging. By combining site-specific integration and high-throughput sequencing, we quantified relative growth under the respective selection of cefotaxime or ceftazidime selection in ∼23,000 Escherichia coli MG1655 strains that each carried a unique, single-copy variant of the extended-spectrum β-lactamase gene blaCTX-M-14 at the chromosomal att HK022 site. Significant synergistic pleiotropy was observed within four subgenic regions, suggesting key regions for the evolution of resistance to both antibiotics. Moreover, we propose PEARP and PEARR, two deep-learning models with strong clinical correlations, for the prospective and retrospective prediction of blaCTX-M-14 evolution, respectively. Single to quintuple mutations of blaCTX-M-14 predicted to confer resistance by PEARP were significantly enriched among the clinical isolates harboring blaCTX-M-14 variants, and the PEARR scores matched the minimal inhibitory concentrations obtained for the 31 intermediates in all hypothetical trajectories. Altogether, we conclude that the measurement of local fitness landscape enables prediction of the evolutionary trajectories of antibiotic resistance genes, which could be useful for a broad range of clinical applications, from resistance prediction to designing novel treatment strategies.
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Affiliation(s)
- Siyuan Feng
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Zhuoxing Wu
- Department of Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Wanfei Liang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Xin Zhang
- Department of Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiujuan Cai
- Department of Genetics and Cellular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiachen Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Lujie Liang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Daixi Lin
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Nicole Stoesser
- Modernising Medical Microbiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh 15261, PA, USA
- Department of Microbiology, Fujita Health University School of Medicine, Aichi 470-1192, Japan
- Department of Infectious Diseases, Fujita Health University School of Medicine, Aichi 470-1192, Japan
| | - Lan-lan Zhong
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Yan Liu
- Clinical Laboratory, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Yong Xia
- Department of Clinical Laboratory Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Min Dai
- School of Laboratory Medicine, Chengdu Medical College, Chengdu 610500, China
| | - Liyan Zhang
- Department of Clinical Laboratory, Guangdong Provincial People’s Hospital/Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Xiaoshu Chen
- Department of Genetics and Cellular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jian-Rong Yang
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
- Department of Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Guo-bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
- School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
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22
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Liu Z, Zhang T, Wu K, Li Z, Chen X, Jiang S, Du L, Lu S, Lin C, Wu J, Wang X. Metagenomic Analysis Reveals A Possible Association Between Respiratory Infection and Periodontitis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:260-273. [PMID: 34252627 PMCID: PMC9684085 DOI: 10.1016/j.gpb.2021.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 04/30/2021] [Accepted: 07/01/2021] [Indexed: 01/05/2023]
Abstract
Periodontitis is an inflammatory disease that is characterized by progressive destruction of the periodontium and causes tooth loss in adults. Periodontitis is known to be associated with dysbiosis of the oral microflora, which is often linked to various diseases. However, the complexity of plaque microbial communities of periodontitis, antibiotic resistance, and enhanced virulence make this disease difficult to treat. In this study, using metagenomic shotgun sequencing, we investigated the etiology, antibiotic resistance genes (ARGs), and virulence genes (VirGs) of periodontitis. We revealed a significant shift in the composition of oral microbiota as well as several functional pathways that were represented significantly more abundantly in periodontitis patients than in controls. In addition, we observed several positively selected ARGs and VirGs with the Ka/Ks ratio > 1 by analyzing our data and a previous periodontitis dataset, indicating that ARGs and VirGs in oral microbiota may be subjected to positive selection. Moreover, 5 of 12 positively selected ARGs and VirGs in periodontitis patients were found in the genomes of respiratory tract pathogens. Of note, 91.8% of the background VirGs with at least one non-synonymous single-nucleotide polymorphism for natural selection were also from respiratory tract pathogens. These observations suggest a potential association between periodontitis and respiratory infection at the gene level. Our study enriches the knowledge of pathogens and functional pathways as well as the positive selection of antibiotic resistance and pathogen virulence in periodontitis patients, and provides evidence at the gene level for an association between periodontitis and respiratory infection.
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Affiliation(s)
- Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Tao Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Keke Wu
- Wenzhou Center for Disease Control and Prevention, Wenzhou 325000, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Xiaomin Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Shan Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Lifeng Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Saisai Lu
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 352000, China
| | - Chongxiang Lin
- Department of Stomatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China,Corresponding authors.
| | - Xiaobing Wang
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 352000, China,Corresponding authors.
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23
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Deka A, Bhattacharyya S. The effect of human vaccination behaviour on strain competition in an infectious disease: An imitation dynamic approach. Theor Popul Biol 2021; 143:62-76. [PMID: 34942233 DOI: 10.1016/j.tpb.2021.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 10/19/2022]
Abstract
Strain competition plays an important role in shaping the dynamics of multiple pathogen outbreaks in a population. Competition may lead to exclusion of some pathogens, while it may influence the invasion of an emerging mutant in the population. However, little emphasis has been given to understand the influence of human vaccination choice on pathogen competition or strain invasion for vaccine-preventable infectious diseases. Coupling game dynamic framework of vaccination choice and compartmental disease transmission model of two strains, we explore invasion and persistence of a mutant in the population despite having a lower reproduction rate than the resident one. We illustrate that higher perceived strain severity and lower perceived vaccine efficacy are necessary conditions for the persistence of a mutant strain. The numerical simulation also extends these invasion and persistence analyses under asymmetric cross-protective immunity of these strains. We show that the dynamics of this cross-immunity model under human vaccination choices is determined by the interplay of parameters defining the cross-immune response function, perceived risk of infection, and vaccine efficacy, and it can exhibit invasion and persistence of mutant strain, even complete exclusion of resident strain in the regime of sufficiently high perceived risk. We conclude by discussing public health implications of the results, that proper risk communication in public about the severity of the disease is an important task to reduce the chance of mutant invasion. Thus, understanding pathogen competitions under social interactions and choices may be an important component for policymakers for strategic decision-making.
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Affiliation(s)
- Aniruddha Deka
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, State College, 16802, PA, USA; Disease Modelling Laboratory, Department of Mathematics, Shiv Nadar University, Gautam Buddha Nagar, 201314, UP, India.
| | - Samit Bhattacharyya
- Disease Modelling Laboratory, Department of Mathematics, Shiv Nadar University, Gautam Buddha Nagar, 201314, UP, India.
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24
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Steketee PC, Giordani F, Vincent IM, Crouch K, Achcar F, Dickens NJ, Morrison LJ, MacLeod A, Barrett MP. Transcriptional differentiation of Trypanosoma brucei during in vitro acquisition of resistance to acoziborole. PLoS Negl Trop Dis 2021; 15:e0009939. [PMID: 34752454 PMCID: PMC8648117 DOI: 10.1371/journal.pntd.0009939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 12/06/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022] Open
Abstract
Subspecies of the protozoan parasite Trypanosoma brucei are the causative agents of Human African Trypanosomiasis (HAT), a debilitating neglected tropical disease prevalent across sub-Saharan Africa. HAT case numbers have steadily decreased since the start of the century, and sustainable elimination of one form of the disease is in sight. However, key to this is the development of novel drugs to combat the disease. Acoziborole is a recently developed benzoxaborole, currently in advanced clinical trials, for treatment of stage 1 and stage 2 HAT. Importantly, acoziborole is orally bioavailable, and curative with one dose. Recent studies have made significant progress in determining the molecular mode of action of acoziborole. However, less is known about the potential mechanisms leading to acoziborole resistance in trypanosomes. In this study, an in vitro-derived acoziborole-resistant cell line was generated and characterised. The AcoR line exhibited significant cross-resistance with the methyltransferase inhibitor sinefungin as well as hypersensitisation to known trypanocides. Interestingly, transcriptomics analysis of AcoR cells indicated the parasites had obtained a procyclic- or stumpy-like transcriptome profile, with upregulation of procyclin surface proteins as well as differential regulation of key metabolic genes known to be expressed in a life cycle-specific manner, even in the absence of major morphological changes. However, no changes were observed in transcripts encoding CPSF3, the recently identified protein target of acoziborole. The results suggest that generation of resistance to this novel compound in vitro can be accompanied by transcriptomic switches resembling a procyclic- or stumpy-type phenotype.
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Affiliation(s)
- Pieter C. Steketee
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Federica Giordani
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Isabel M. Vincent
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Kathryn Crouch
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Fiona Achcar
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Nicholas J. Dickens
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Liam J. Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Annette MacLeod
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Michael P. Barrett
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
- Glasgow Polyomics, University of Glasgow, United Kingdom
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25
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Riou J, Dupont C, Bertagnolio S, Gupta RK, Kouyos RD, Egger M, L Althaus C. Drivers of HIV-1 drug resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTIs) in nine southern African countries: a modelling study. BMC Infect Dis 2021; 21:1042. [PMID: 34620119 PMCID: PMC8499543 DOI: 10.1186/s12879-021-06757-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022] Open
Abstract
INTRODUCTION The rise of HIV-1 drug resistance to non-nucleoside reverse-transcriptase inhibitors (NNRTI) threatens antiretroviral therapy's long-term success (ART). NNRTIs will remain an essential drug for the management of HIV-1 due to safety concerns associated with integrase inhibitors. We fitted a dynamic transmission model to historical data from 2000 to 2018 in nine countries of southern Africa to understand the mechanisms that have shaped the HIV-1 epidemic and the rise of pretreatment NNRTI resistance. METHODS We included data on HIV-1 prevalence, ART coverage, HIV-related mortality, and survey data on pretreatment NNRTI resistance from nine southern Africa countries from a systematic review, UNAIDS and World Bank. Using a Bayesian hierarchical framework, we developed a dynamic transmission model linking data on the HIV-1 epidemic to survey data on NNRTI drug resistance in each country. We estimated the proportion of resistance attributable to unregulated, off-programme use of ART. We examined each national ART programme's vulnerability to NNRTI resistance by defining a fragility index: the ratio of the rate of NNRTI resistance emergence during first-line ART over the rate of switching to second-line ART. We explored associations between fragility and characteristics of the health system of each country. RESULTS The model reliably described the dynamics of the HIV-1 epidemic and NNRTI resistance in each country. Predicted levels of resistance in 2018 ranged between 3.3% (95% credible interval 1.9-7.1) in Mozambique and 25.3% (17.9-33.8) in Eswatini. The proportion of pretreatment NNRTI resistance attributable to unregulated antiretroviral use ranged from 6% (2-14) in Eswatini to 64% (26-85) in Mozambique. The fragility index was low in Botswana (0.01; 0.0-0.11) but high in Namibia (0.48; 0.16-10.17), Eswatini (0.64; 0.23-11.8) and South Africa (1.21; 0.83-9.84). The combination of high fragility of ART programmes and high ART coverage levels was associated with a sharp increase in pretreatment NNRTI resistance. CONCLUSIONS This comparison of nine countries shows that pretreatment NNRTI resistance can be controlled despite high ART coverage levels. This was the case in Botswana, Mozambique, and Zambia, most likely because of better HIV care delivery, including rapid switching to second-line ART of patients failing first-line ART.
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Affiliation(s)
- Julien Riou
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland.
| | - Carole Dupont
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
| | - Silvia Bertagnolio
- HIV/Hepatitis/STI Department, World Health Organization, Geneva, Switzerland
| | - Ravindra K Gupta
- Department of Infection, University College London, London, UK
- Africa Health Research Institute, Durban, South Africa
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
- Centre for Infectious Disease Epidemiology and Research (CIDER), University of Cape Town, Cap Town, South Africa
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christian L Althaus
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
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26
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Smith DR, Temime L, Opatowski L. Microbiome-pathogen interactions drive epidemiological dynamics of antibiotic resistance: A modeling study applied to nosocomial pathogen control. eLife 2021; 10:68764. [PMID: 34517942 PMCID: PMC8560094 DOI: 10.7554/elife.68764] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/31/2021] [Indexed: 12/16/2022] Open
Abstract
The human microbiome can protect against colonization with pathogenic antibiotic-resistant bacteria (ARB), but its impacts on the spread of antibiotic resistance are poorly understood. We propose a mathematical modeling framework for ARB epidemiology formalizing within-host ARB-microbiome competition, and impacts of antibiotic consumption on microbiome function. Applied to the healthcare setting, we demonstrate a trade-off whereby antibiotics simultaneously clear bacterial pathogens and increase host susceptibility to their colonization, and compare this framework with a traditional strain-based approach. At the population level, microbiome interactions drive ARB incidence, but not resistance rates, reflecting distinct epidemiological relevance of different forces of competition. Simulating a range of public health interventions (contact precautions, antibiotic stewardship, microbiome recovery therapy) and pathogens (Clostridioides difficile, methicillin-resistant Staphylococcus aureus, multidrug-resistant Enterobacteriaceae) highlights how species-specific within-host ecological interactions drive intervention efficacy. We find limited impact of contact precautions for Enterobacteriaceae prevention, and a promising role for microbiome-targeted interventions to limit ARB spread.
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Affiliation(s)
- David Rm Smith
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France.,Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, Montigny-Le-Bretonneux, France.,Modélisation, épidémiologie et surveillance des risques sanitaires (MESuRS), Conservatoire national des arts et métiers, Paris, France
| | - Laura Temime
- Modélisation, épidémiologie et surveillance des risques sanitaires (MESuRS), Conservatoire national des arts et métiers, Paris, France.,PACRI unit, Institut Pasteur, Conservatoire national des arts et métiers, Paris, France
| | - Lulla Opatowski
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France.,Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, Montigny-Le-Bretonneux, France
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27
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Castro RAD, Borrell S, Gagneux S. The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiol Rev 2021; 45:fuaa071. [PMID: 33320947 PMCID: PMC8371278 DOI: 10.1093/femsre/fuaa071] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) has been responsible for the greatest number of human deaths due to an infectious disease in general, and due to antimicrobial resistance (AMR) in particular. The etiological agents of human TB are a closely-related group of human-adapted bacteria that belong to the Mycobacterium tuberculosis complex (MTBC). Understanding how MTBC populations evolve within-host may allow for improved TB treatment and control strategies. In this review, we highlight recent works that have shed light on how AMR evolves in MTBC populations within individual patients. We discuss the role of heteroresistance in AMR evolution, and review the bacterial, patient and environmental factors that likely modulate the magnitude of heteroresistance within-host. We further highlight recent works on the dynamics of MTBC genetic diversity within-host, and discuss how spatial substructures in patients' lungs, spatiotemporal heterogeneity in antimicrobial concentrations and phenotypic drug tolerance likely modulates the dynamics of MTBC genetic diversity in patients during treatment. We note the general characteristics that are shared between how the MTBC and other bacterial pathogens evolve in humans, and highlight the characteristics unique to the MTBC.
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Affiliation(s)
- Rhastin A D Castro
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
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28
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Wheatley R, Diaz Caballero J, Kapel N, de Winter FHR, Jangir P, Quinn A, Del Barrio-Tofiño E, López-Causapé C, Hedge J, Torrens G, Van der Schalk T, Xavier BB, Fernández-Cuenca F, Arenzana A, Recanatini C, Timbermont L, Sifakis F, Ruzin A, Ali O, Lammens C, Goossens H, Kluytmans J, Kumar-Singh S, Oliver A, Malhotra-Kumar S, MacLean C. Rapid evolution and host immunity drive the rise and fall of carbapenem resistance during an acute Pseudomonas aeruginosa infection. Nat Commun 2021; 12:2460. [PMID: 33911082 PMCID: PMC8080559 DOI: 10.1038/s41467-021-22814-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/31/2021] [Indexed: 02/08/2023] Open
Abstract
It is well established that antibiotic treatment selects for resistance, but the dynamics of this process during infections are poorly understood. Here we map the responses of Pseudomonas aeruginosa to treatment in high definition during a lung infection of a single ICU patient. Host immunity and antibiotic therapy with meropenem suppressed P. aeruginosa, but a second wave of infection emerged due to the growth of oprD and wbpM meropenem resistant mutants that evolved in situ. Selection then led to a loss of resistance by decreasing the prevalence of low fitness oprD mutants, increasing the frequency of high fitness mutants lacking the MexAB-OprM efflux pump, and decreasing the copy number of a multidrug resistance plasmid. Ultimately, host immunity suppressed wbpM mutants with high meropenem resistance and fitness. Our study highlights how natural selection and host immunity interact to drive both the rapid rise, and fall, of resistance during infection.
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Affiliation(s)
| | | | - Natalia Kapel
- University of Oxford, Department of Zoology, Oxford, UK
| | - Fien H R de Winter
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Pramod Jangir
- University of Oxford, Department of Zoology, Oxford, UK
| | - Angus Quinn
- University of Oxford, Department of Zoology, Oxford, UK
| | | | | | - Jessica Hedge
- University of Oxford, Department of Zoology, Oxford, UK
| | - Gabriel Torrens
- Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Thomas Van der Schalk
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | | | - Angel Arenzana
- Departamento de Medicina, Universidad de Sevilla, Seville, Spain
| | - Claudia Recanatini
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | | | - Alexey Ruzin
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Omar Ali
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
- Viela Bio, Gaithersburg, MD, USA
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Jan Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Microvida Laboratory for Medical Microbiology and Department of Infection Control, Amphia Hospital, Breda, The Netherlands
| | - Samir Kumar-Singh
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
- Molecular Pathology Group, Faculty of Medicine-Laboratory of Cell Biology and Histology, University of Antwerp, Wilrijk, Belgium
| | - Antonio Oliver
- Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Craig MacLean
- University of Oxford, Department of Zoology, Oxford, UK.
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29
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Intracellular Redox-Modulated Pathways as Targets for Effective Approaches in the Treatment of Viral Infection. Int J Mol Sci 2021; 22:ijms22073603. [PMID: 33808471 PMCID: PMC8036776 DOI: 10.3390/ijms22073603] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Host-directed therapy using drugs that target cellular pathways required for virus lifecycle or its clearance might represent an effective approach for treating infectious diseases. Changes in redox homeostasis, including intracellular glutathione (GSH) depletion, are one of the key events that favor virus replication and contribute to the pathogenesis of virus-induced disease. Redox homeostasis has an important role in maintaining an appropriate Th1/Th2 balance, which is necessary to mount an effective immune response against viral infection and to avoid excessive inflammatory responses. It is known that excessive production of reactive oxygen species (ROS) induced by viral infection activates nuclear factor (NF)-kB, which orchestrates the expression of viral and host genes involved in the viral replication and inflammatory response. Moreover, redox-regulated protein disulfide isomerase (PDI) chaperones have an essential role in catalyzing formation of disulfide bonds in viral proteins. This review aims at describing the role of GSH in modulating redox sensitive pathways, in particular that mediated by NF-kB, and PDI activity. The second part of the review discusses the effectiveness of GSH-boosting molecules as broad-spectrum antivirals acting in a multifaceted way that includes the modulation of immune and inflammatory responses.
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30
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Garnault M, Duplaix C, Leroux P, Couleaud G, David O, Walker AS, Carpentier F. Large-scale study validates that regional fungicide applications are major determinants of resistance evolution in the wheat pathogen Zymoseptoria tritici in France. THE NEW PHYTOLOGIST 2021; 229:3508-3521. [PMID: 33226662 DOI: 10.1111/nph.17107] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/16/2020] [Indexed: 06/11/2023]
Abstract
In modern cropping systems, the near-universal use of plant protection products selects for resistance in pest populations. The emergence and evolution of this adaptive trait threaten treatment efficacy. We identified determinants of fungicide resistance evolution and quantified their effects at a large spatiotemporal scale. We focused on Zymoseptoria tritici, which causes leaf blotch in wheat. Phenotypes of qualitative or quantitative resistance to various fungicides were monitored annually, from 2004 to 2017, at about 70 sites throughout 22 regions of France (territorial units of 25 000 km2 on average). We modelled changes in resistance frequency with regional anti-Septoria fungicide use, yield losses due to the disease and the regional area under organic wheat. The major driver of resistance dynamics was fungicide use at the regional scale. We estimated its effect on the increase in resistance and relative apparent fitness of each resistance phenotype. The predictions of the model replicated the spatiotemporal patterns of resistance observed in field populations (R2 from 0.56 to 0.82). The evolution of fungicide resistance is mainly determined at the regional scale. This study therefore showed that collective management at the regional scale could effectively complete local actions.
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Affiliation(s)
- Maxime Garnault
- AgroParisTech, UMR BIOGER, INRAE, Université Paris-Saclay, Thiverval-Grignon, 78850, France
- MaIAGE, INRAE, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Clémentine Duplaix
- AgroParisTech, UMR BIOGER, INRAE, Université Paris-Saclay, Thiverval-Grignon, 78850, France
| | - Pierre Leroux
- AgroParisTech, UMR BIOGER, INRAE, Université Paris-Saclay, Thiverval-Grignon, 78850, France
| | | | - Olivier David
- MaIAGE, INRAE, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Anne-Sophie Walker
- AgroParisTech, UMR BIOGER, INRAE, Université Paris-Saclay, Thiverval-Grignon, 78850, France
| | - Florence Carpentier
- AgroParisTech, UMR BIOGER, INRAE, Université Paris-Saclay, Thiverval-Grignon, 78850, France
- MaIAGE, INRAE, Université Paris-Saclay, Jouy-en-Josas, 78350, France
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31
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Schuts EC, Boyd A, Muller AE, Mouton JW, Prins JM. The Effect of Antibiotic Restriction Programs on Prevalence of Antimicrobial Resistance: A Systematic Review and Meta-Analysis. Open Forum Infect Dis 2021; 8:ofab070. [PMID: 33880388 PMCID: PMC8043261 DOI: 10.1093/ofid/ofab070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/09/2021] [Indexed: 11/17/2022] Open
Abstract
Background In hospital settings, restriction of selected classes of antibiotics is usually believed to contribute to containment of resistance development. We performed a systematic review and meta-analysis to assess the effect of restricting the use of specific antibiotic classes on the prevalence of resistant bacterial pathogens. Methods We conducted a systematic literature search in Embase and PubMed/OVID MEDLINE. We included studies until June 4, 2020 in which a restrictive antibiotic policy was applied and prevalence of resistance and use of antibiotics were reported. We calculated the overall effect of antimicrobial resistance between postintervention versus preintervention periods using pooled odds ratios (ORs) from a mixed-effects model. We stratified meta-analysis by antibiotic-pathogen combinations. We assessed heterogeneity between studies using the I2 statistic and sources of heterogeneity using meta-regression. Results We included 15 individual studies with an overall low quality of evidence. In meta-analysis, significant reductions in resistance were only observed with nonfermenters after restricting fluoroquinolones (OR = 0.77, 95% confidence interval [CI] = 0.62–0.97) and piperacillin-tazobactam (OR = 0.81, 95% CI = 0.72–0.92). High degrees of heterogeneity were observed with studies restricting carbapenem (Enterobacterales, I2 = 70.8%; nonfermenters, I2 = 81.9%), third-generation cephalosporins (nonfermenters, I2 = 63.3%), and fluoroquiolones (nonfermenters, I2 = 64.0%). Results were comparable when excluding studies with fewer than 50 bacteria. There was no evidence of publication bias for any of the antibiotic-pathogen combinations. Conclusions We could not confirm that restricting carbapenems or third-generation cephalosporins leads to decrease in prevalence of antibiotic resistance among Enterobacterales, nonfermenters, or Gram-positive bacteria in hospitalized patients. Nevertheless, reducing fluoroquinolone and piperacilline-tazobactam use may decrease resistance in nonfermenters.
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Affiliation(s)
- Emelie C Schuts
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Anders Boyd
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands.,Stichting HIV Monitoring, Amsterdam, Netherlands
| | - Anouk E Muller
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands.,Department of Medical Microbiology, Haaglanden Medical Centre, The Hague, the Netherlands
| | - Johan W Mouton
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | - Jan M Prins
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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32
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Within-host bacterial growth dynamics with both mutation and horizontal gene transfer. J Math Biol 2021; 82:16. [PMID: 33544239 DOI: 10.1007/s00285-021-01571-9] [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: 12/07/2019] [Revised: 01/08/2021] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
The evolution and emergence of antibiotic resistance is a major public health concern. The understanding of the within-host microbial dynamics combining mutational processes, horizontal gene transfer and resource consumption, is one of the keys to solving this problem. We analyze a generic model to rigorously describe interactions dynamics of four bacterial strains: one fully sensitive to the drug, one with mutational resistance only, one with plasmidic resistance only, and one with both resistances. By defining thresholds numbers (i.e. each strain's effective reproduction and each strain's transition threshold numbers), we first express conditions for the existence of non-trivial stationary states. We find that these thresholds mainly depend on bacteria quantitative traits such as nutrient consumption ability, growth conversion factor, death rate, mutation (forward or reverse), and segregational loss of plasmid probabilities (for plasmid-bearing strains). Next, concerning the order in the set of strain's effective reproduction thresholds numbers, we show that the qualitative dynamics of the model range from the extinction of all strains, coexistence of sensitive and mutational resistance strains, to the coexistence of all strains at equilibrium. Finally, we go through some applications of our general analysis depending on whether bacteria strains interact without or with drug action (either cytostatic or cytotoxic).
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33
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Houy N, Flaig J. Optimal dynamic empirical therapy in a health care facility: A Monte-Carlo look-ahead method. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2021; 198:105767. [PMID: 33086150 DOI: 10.1016/j.cmpb.2020.105767] [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: 07/24/2019] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND OBJECTIVES Empirical antimicrobial prescription strategies have been proposed to counteract the selection of resistant pathogenic strains. The respective merits of such strategies have been debated. Rather than comparing a finite number of policies, we take an optimization approach and propose a solution to the problem of finding an empirical therapy policy in a health care facility that minimizes the cumulative infected patient-days over a given time horizon. METHODS We assume that the parameters of the model are known and that when the policy is implemented, all patients receive the same treatment at a given time. We model the emergence and spread of antimicrobial resistance at the population level with the stochastic version of a compartmental model. The model features two drugs and the possibility of double resistance. Our solution method is a rollout algorithm. RESULTS In our example, the optimal policy computed with this method allows to reduce the average cumulative infected patient-days over two years by 22% compared to the best standard therapy. Considering regularity constraints, we could derive a policy with a fixed period and a performance close to that of the optimal policy. The average cumulative infected patient-days over two years obtained with the optimal policy is 6% lower (significantly at the 95% threshold) than that obtained with the fixed period policy. CONCLUSION Our results illustrate the performance of a highly flexible solution method that will contribute to the development of implementable empirical therapy policies.
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Affiliation(s)
- Nicolas Houy
- University of Lyon, Lyon, F-69007, France; CNRS, GATE Lyon Saint-Etienne, F-69130, France.
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Alizon S. Treating symptomatic infections and the co-evolution of virulence and drug resistance. PEER COMMUNITY JOURNAL 2021; 1:e47. [PMID: 38707518 PMCID: PMC7615929 DOI: 10.24072/pcjournal.38] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Antimicrobial therapeutic treatments are by definition applied after the onset of symptoms, which tend to correlate with infection severity. Using mathematical epidemiology models, I explore how this link affects the coevolutionary dynamics between the virulence of an infection, measured via host mortality rate, and its susceptibility to chemotherapy. I show that unless resistance pre-exists in the population, drug-resistant infections are initially more virulent than drug-sensitive ones. As the epidemic unfolds, virulence is more counter-selected in drug-sensitive than in drug-resistant infections. This difference decreases over time and, eventually, the exact shape of genetic trade-offs govern long-term evolutionary dynamics. Using adaptive dynamics, I show that two types of evolutionary stable strategies (ESS) may be reached in the context of this simple model and that, depending on the parameter values, an ESS may only be locally stable. In general, the more the treatment rate increases with virulence, the lower the ESS value. Overall, both on the short-term and long-term, having treatment rate depend on infection virulence tend to favour less virulent strains in drug-sensitive infections. These results highlight the importance of the feedbacks between epidemiology, public health policies and parasite evolution, and have implications for the monitoring of virulence evolution.
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Affiliation(s)
- Samuel Alizon
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
- MIVEGEC, CNRS, IRD, Université de Montpellier, France
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Jhawat V, Gulia M, Gupta S, Maddiboyina B, Dutt R. Integration of pharmacogenomics and theranostics with nanotechnology as quality by design (QbD) approach for formulation development of novel dosage forms for effective drug therapy. J Control Release 2020; 327:500-511. [PMID: 32858073 DOI: 10.1016/j.jconrel.2020.08.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022]
Abstract
To cater to medication needs in the future healthcare system, we need to shift from the conventional system of drug delivery to modern molecular signature-based drug delivery systems. The current drug therapies are either less effective, ineffective, or produce numerous adverse reactions. One scientific principle or discipline cannot adequately address all the problems, so we need an innovative application of the current scientific principles. Here we are proposing a novel concept of nanoformulation based on pharmacogenomics and theranostics for personalized error-free and targeted therapeutic agent delivery. The addition of more knowledge about the human genome opens the new way to study disease-gene, gene-drug, and drug-effect interactions, which is the basis of future medicines. Pharmacogenomics provides information about the disease etiology, role in genes in disease pathophysiology, disease biomarkers, drug targets, drug effects, and the fate of drugs inside the body. Theranostics approach utilizes the above information in diagnosis, treatment, and monitoring of the disease on a real-time basis. Personalized dosage forms can be formulated into a nanoformulation that provides a better therapeutic effect and minimizes adverse drug reactions. The therapeutic system needs to be shifted from the principle of one drug fits all to one drug unique population. In the present manuscript, we tried to conceptualize a modern therapeutic system by combining the three approaches viz. pharmacogenomics, theranostics, and nanotechnology applied in the area of formulation development to produce a multifunctional single tiny entity.
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Affiliation(s)
- Vikas Jhawat
- Department of Pharmaceutical Sciences, School of Medical and Allied Sciences, GD Goenka University, Gurugram, Haryana, India.
| | - Monika Gulia
- Department of Pharmaceutical Sciences, School of Medical and Allied Sciences, GD Goenka University, Gurugram, Haryana, India
| | - Sumeet Gupta
- Department of Pharmaceutical Sciences, Maharishi Markandeshwar (Deemed to be) University, Mullana, Ambala, Haryana, India
| | - Balaji Maddiboyina
- Department of Pharmaceutical Sciences, Vishwa Bharathi College of Pharmaceutical Sciences, Guntur, A.P, India
| | - Rohit Dutt
- Department of Pharmaceutical Sciences, School of Medical and Allied Sciences, GD Goenka University, Gurugram, Haryana, India
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Alexander HK, MacLean RC. Stochastic bacterial population dynamics restrict the establishment of antibiotic resistance from single cells. Proc Natl Acad Sci U S A 2020; 117:19455-19464. [PMID: 32703812 PMCID: PMC7431077 DOI: 10.1073/pnas.1919672117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A better understanding of how antibiotic exposure impacts the evolution of resistance in bacterial populations is crucial for designing more sustainable treatment strategies. The conventional approach to this question is to measure the range of concentrations over which resistant strain(s) are selectively favored over a sensitive strain. Here, we instead investigate how antibiotic concentration impacts the initial establishment of resistance from single cells, mimicking the clonal expansion of a resistant lineage following mutation or horizontal gene transfer. Using two Pseudomonas aeruginosa strains carrying resistance plasmids, we show that single resistant cells have <5% probability of detectable outgrowth at antibiotic concentrations as low as one-eighth of the resistant strain's minimum inhibitory concentration (MIC). This low probability of establishment is due to detrimental effects of antibiotics on resistant cells, coupled with the inherently stochastic nature of cell division and death on the single-cell level, which leads to loss of many nascent resistant lineages. Our findings suggest that moderate doses of antibiotics, well below the MIC of resistant strains, may effectively restrict de novo emergence of resistance even though they cannot clear already-large resistant populations.
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Affiliation(s)
- Helen K Alexander
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom;
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - R Craig MacLean
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
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Biset S, Moges F, Endalamaw D, Eshetie S. Multi-drug resistant and extended-spectrum β-lactamases producing bacterial uropathogens among pregnant women in Northwest Ethiopia. Ann Clin Microbiol Antimicrob 2020; 19:25. [PMID: 32493343 PMCID: PMC7268622 DOI: 10.1186/s12941-020-00365-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 05/25/2020] [Indexed: 01/22/2023] Open
Abstract
INTRODUCTION Above 80% of urinary tract infections are caused by enteric bacteria, which are known for years by their drug-resistant ability. Though the prevalence of drug-resistant strains is increasing in the world, it is not well known in low-income countries. The aim of this study was to assess the prevalence of Multi-drug resistance, Extended-spectrum β-lactamases production, and associated risk factors among pregnant women in Northwest Ethiopia. METHODS A hospital-based cross-sectional study was conducted among pregnant women from March to May 2017. A total of 384 clean-catch midstream urine sample was collected from study participants. Bacterial identification and drug susceptibility testing were done following standard microbiological techniques; Extended-spectrum β-lactamase production was screened using a disc diffusion test and confirmed by a combination disc test. The data were entered and analyzed by using SPSS version 20, and a p-value of less than 0.05 was considered as statistically significant. RESULT The overall prevalence of urinary tract infection was 15.9% (95% CI 12.8-20.1%). E. coli (49.2%), CoNS (27.9%), and S. aureus (18%) were the main uropathogens. The prevalence of MDR uropathogens was 60.65%. The prevalence of ESBLs production among cases caused by Enterobacteriaceae was 18.2%. The drug resistance rate of Gram-negative isolates was higher for ampicillin (90.9%), cephalothin (84.8%), and augmentin (57.6%). The drug nitrofurantoin showed the highest activity (100%) against Gram-negative isolates. Gram-positive isolates were showed low susceptibility to penicillin (89.3%) and cotrimoxazole (75%); however highest susceptibility rate for gentamicin (100%), amikacin (100%), and nitrofurantoin (98.36%) was recorded. Prior antibiotic therapy (AOR = 5.46, 95% CI 1.38-21.65) was a risk factor for the presence of multi-drug resistant bacteria. CONCLUSION AND RECOMMENDATION The multi-drug resistance prevalence was high among uropathogen, thus treatment of urinary tract infection during pregnancy; should be based on the antibacterial susceptibility testing result. The isolation of drug-resistant strains like Extended-spectrum β-lactamases in this study calls for the need of periodic and continuous follow-up of antibiotic usage among pregnant women. Nitrofurantoin, gentamicin, amikacin, and ciprofloxacin/norfloxacin showed higher activity against bacterial uropathogen.
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Affiliation(s)
- Sirak Biset
- Department of Medical Microbiology, College of Medicine and Health Sciences, University of Gondar, P.O. Box: 196 Gondar, Ethiopia
| | - Feleke Moges
- Department of Medical Microbiology, College of Medicine and Health Sciences, University of Gondar, P.O. Box: 196 Gondar, Ethiopia
| | - Demeke Endalamaw
- Department of Medical Microbiology, College of Medicine and Health Sciences, University of Gondar, P.O. Box: 196 Gondar, Ethiopia
| | - Setegn Eshetie
- Department of Medical Microbiology, College of Medicine and Health Sciences, University of Gondar, P.O. Box: 196 Gondar, Ethiopia
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Marrec L, Bitbol AF. Resist or perish: Fate of a microbial population subjected to a periodic presence of antimicrobial. PLoS Comput Biol 2020; 16:e1007798. [PMID: 32275712 PMCID: PMC7176291 DOI: 10.1371/journal.pcbi.1007798] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/22/2020] [Accepted: 03/19/2020] [Indexed: 12/22/2022] Open
Abstract
The evolution of antimicrobial resistance can be strongly affected by variations of antimicrobial concentration. Here, we study the impact of periodic alternations of absence and presence of antimicrobial on resistance evolution in a microbial population, using a stochastic model that includes variations of both population composition and size, and fully incorporates stochastic population extinctions. We show that fast alternations of presence and absence of antimicrobial are inefficient to eradicate the microbial population and strongly favor the establishment of resistance, unless the antimicrobial increases enough the death rate. We further demonstrate that if the period of alternations is longer than a threshold value, the microbial population goes extinct upon the first addition of antimicrobial, if it is not rescued by resistance. We express the probability that the population is eradicated upon the first addition of antimicrobial, assuming rare mutations. Rescue by resistance can happen either if resistant mutants preexist, or if they appear after antimicrobial is added to the environment. Importantly, the latter case is fully prevented by perfect biostatic antimicrobials that completely stop division of sensitive microorganisms. By contrast, we show that the parameter regime where treatment is efficient is larger for biocidal drugs than for biostatic drugs. This sheds light on the respective merits of different antimicrobial modes of action.
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Affiliation(s)
- Loïc Marrec
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin (UMR 8237), F-75005 Paris, France
| | - Anne-Florence Bitbol
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin (UMR 8237), F-75005 Paris, France
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Taguwa S, Yeh MT, Rainbolt TK, Nayak A, Shao H, Gestwicki JE, Andino R, Frydman J. Zika Virus Dependence on Host Hsp70 Provides a Protective Strategy against Infection and Disease. Cell Rep 2020; 26:906-920.e3. [PMID: 30673613 DOI: 10.1016/j.celrep.2018.12.095] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/28/2018] [Accepted: 12/21/2018] [Indexed: 01/23/2023] Open
Abstract
The spread of mosquito-borne Zika virus (ZIKV), which causes neurological disorders and microcephaly, highlights the need for countermeasures against sudden viral epidemics. Here, we tested the concept that drugs targeting host proteostasis provide effective antivirals. We show that different cytosolic Hsp70 isoforms are recruited to ZIKV-induced compartments and are required for virus replication at pre- and post-entry steps. Drugs targeting Hsp70 significantly reduce replication of different ZIKV strains in human and mosquito cells, including human neural stem cells and a placental trophoblast cell line, at doses without appreciable toxicity to the host cell. By targeting several ZIKV functions, including entry, establishment of active replication complexes, and capsid assembly, Hsp70 inhibitors are refractory to the emergence of drug-resistant virus. Importantly, these drugs protected mouse models from ZIKV infection, reducing viremia, mortality, and disease symptoms. Hsp70 inhibitors are thus attractive candidates for ZIKV therapeutics with the added benefit of a broad spectrum of action.
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Affiliation(s)
- Shuhei Taguwa
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ming-Te Yeh
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - T Kelly Rainbolt
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Arabinda Nayak
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hao Shao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA.
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Morley VJ, Firgens EPC, Vanderbilt RR, Zhou Y, Zook M, Read AF, MacGeorge EL. Factors associated with antibiotic prescribing for acute bronchitis at a university health center. BMC Infect Dis 2020; 20:177. [PMID: 32102652 PMCID: PMC7045376 DOI: 10.1186/s12879-020-4825-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/24/2020] [Indexed: 11/10/2022] Open
Abstract
Background Antibiotics are not indicated for treating acute bronchitis cases, yet up to 70% of adult acute bronchitis medical visits in the USA result in an antibiotic prescription. Reducing unnecessary antibiotic prescribing for acute bronchitis is a key antibiotic stewardship goal set forth by the Centers for Disease Control and Prevention. Understanding what factors influence prescribing for bronchitis cases can inform antimicrobial stewardship initiatives. The goal of this study was to identify factors associated with antibiotic prescribing at a high-volume student health center at a large US university. The Pennsylvania State University Health Services offers on-campus medical care to a population of over 40,000 students and receives over 50,000 visits every year. Methods We conducted a retrospective chart review of acute bronchitis visits for the 2015–2016 academic year and used a multivariate logistic regression analysis to identify variables associated with antibiotic prescribing. Results Findings during lung exams increased the likelihood of an antibiotic prescription (rales OR 13.95, 95% CI 3.31–80.73; rhonchi OR 5.50, 95% CI 3.08–10.00; percussion abnormality OR 13.02, 95% CI 4.00–50.09). Individual clinicians had dramatically different rates of prescribing (OR range 0.03–12.3). Male patients were more likely than female patients to be prescribed antibiotics (OR 1.68, 95% CI 1.17–2.41). Patients who reported longer duration since the onset of symptoms were slightly more likely to receive prescriptions (OR 1.04 per day, 95% CI 1.03–1.06), as were patients who reported worsening symptoms (OR 1.78, 95% CI 1.03–3.10). Visits with diagnoses or symptoms associated with viral infections or allergies were less likely to result in prescriptions (upper respiratory tract infection (URI) diagnosis OR 0.33, 95% CI 0.18–0.58; sneezing OR 0.39, 95% CI 0.17–0.86; vomiting OR 0.31, 95% CI 0.10–0.83). An exam finding of anterior cervical lymphadenopathy was associated with antibiotic prescribing (tender OR 3.85, 95% CI 1.70–8.83; general OR 2.63, 95% CI 1.25–5.54). Conclusions Suspicious findings during lung examinations (rales, rhonchi, percussion abnormality) and individual healthcare providers were important factors influencing antibiotic prescribing rates for acute bronchitis visits. Patient gender, worsening symptoms, duration of illness, symptoms associated with viral infections or allergies, and anterior cervical lymphadenopathy also influenced prescribing rates.
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Affiliation(s)
- Valerie J Morley
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, State College, PA, USA
| | - Emily P C Firgens
- Department of Communication Arts & Sciences, The Pennsylvania State University, University Park, State College, PA, USA
| | - Rachel R Vanderbilt
- Department of Communication Arts & Sciences, The Pennsylvania State University, University Park, State College, PA, USA
| | - Yanmengqian Zhou
- Department of Communication Arts & Sciences, The Pennsylvania State University, University Park, State College, PA, USA
| | - Michelle Zook
- University Health Services, The Pennsylvania State University, University Park, State College, PA, USA
| | - Andrew F Read
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, State College, PA, USA.,Huck Institutes for the Life Sciences, The Pennsylvania State University, University Park, State College, PA, USA.,Department of Entomology, The Pennsylvania State University, University Park, State College, PA, USA
| | - Erina L MacGeorge
- Department of Communication Arts & Sciences, The Pennsylvania State University, University Park, State College, PA, USA.
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Castro RAD, Ross A, Kamwela L, Reinhard M, Loiseau C, Feldmann J, Borrell S, Trauner A, Gagneux S. The Genetic Background Modulates the Evolution of Fluoroquinolone-Resistance in Mycobacterium tuberculosis. Mol Biol Evol 2020; 37:195-207. [PMID: 31532481 PMCID: PMC6984360 DOI: 10.1093/molbev/msz214] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Fluoroquinolones (FQ) form the backbone in experimental treatment regimens against drug-susceptible tuberculosis. However, little is known on whether the genetic variation present in natural populations of Mycobacterium tuberculosis (Mtb) affects the evolution of FQ-resistance (FQ-R). To investigate this question, we used nine genetically distinct drug-susceptible clinical isolates of Mtb and measured their frequency of resistance to the FQ ofloxacin (OFX) in vitro. We found that the Mtb genetic background led to differences in the frequency of OFX-resistance (OFX-R) that spanned two orders of magnitude and substantially modulated the observed mutational profiles for OFX-R. Further, in vitro assays showed that the genetic background also influenced the minimum inhibitory concentration and the fitness effect conferred by a given OFX-R mutation. To test the clinical relevance of our in vitro work, we surveyed the mutational profile for FQ-R in publicly available genomic sequences from clinical Mtb isolates, and found substantial Mtb lineage-dependent variability. Comparison of the clinical and the in vitro mutational profiles for FQ-R showed that 51% and 39% of the variability in the clinical frequency of FQ-R gyrA mutation events in Lineage 2 and Lineage 4 strains, respectively, can be attributed to how Mtb evolves FQ-R in vitro. As the Mtb genetic background strongly influenced the evolution of FQ-R in vitro, we conclude that the genetic background of Mtb also impacts the evolution of FQ-R in the clinic.
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Affiliation(s)
- Rhastin A D Castro
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Amanda Ross
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Lujeko Kamwela
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Miriam Reinhard
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Chloé Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Julia Feldmann
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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Georgieva M, Buckee CO, Lipsitch M. Models of immune selection for multi-locus antigenic diversity of pathogens. Nat Rev Immunol 2019; 19:55-62. [PMID: 30479379 DOI: 10.1038/s41577-018-0092-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
It is well accepted that pathogens can evade recognition and elimination by the host immune system by varying their antigenic targets. Thus, it has become a truism that host immunity is a major driver and determinant of the antigenic diversity of pathogens. However, it remains puzzling how host immunity selects for antigenic diversity at the level of the pathogen population, given that hosts have acquired immune responses to multiple antigens of most pathogens - sometimes through multiple effectors of both humoral and cellular immunity. In this Opinion article, we address this puzzle and the related question of why pathogens often have diversity at multiple antigenic loci. Here, we describe five hypotheses to explain the polymorphism of multiple antigens in a single pathogen species and highlight research relevant to our current models of thinking about multi-locus antigenic diversity.
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Affiliation(s)
- Maria Georgieva
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Department of Physiology, University of Lausanne, Lausanne, Switzerland.
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa. Proc Natl Acad Sci U S A 2019; 116:23284-23291. [PMID: 31659018 PMCID: PMC6859317 DOI: 10.1073/pnas.1906636116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antimicrobial-resistant (AMR) infections pose a major threat to global public health. Similar to other AMR pathogens, both historical and ongoing drug-resistant tuberculosis (TB) epidemics are characterized by transmission of a limited number of predominant Mycobacterium tuberculosis (Mtb) strains. Understanding how these predominant strains achieve sustained transmission, particularly during the critical period before they are detected via clinical or public health surveillance, can inform strategies for prevention and containment. In this study, we employ whole-genome sequence (WGS) data from TB clinical isolates collected in KwaZulu-Natal, South Africa to examine the pre-detection history of a successful strain of extensively drug-resistant (XDR) TB known as LAM4/KZN, first identified in a widely reported cluster of cases in 2005. We identify marked expansion of this strain concurrent with the onset of the generalized HIV epidemic 12 y prior to 2005, localize its geographic origin to a location in northeastern KwaZulu-Natal ∼400 km away from the site of the 2005 outbreak, and use protein structural modeling to propose a mechanism for how strain-specific rpoB mutations offset fitness costs associated with rifampin resistance in LAM4/KZN. Our findings highlight the importance of HIV coinfection, high preexisting rates of drug-resistant TB, human migration, and pathoadaptive evolution in the emergence and dispersal of this critical public health threat. We propose that integrating whole-genome sequencing into routine public health surveillance can enable the early detection and local containment of AMR pathogens before they achieve widespread dispersal.
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Djebala S, Moula N, Bayrou C, Sartelet A, Bossaert P. Prophylactic antibiotic usage by Belgian veterinarians during elective caesarean section in Belgian blue cattle. Prev Vet Med 2019; 172:104785. [PMID: 31614283 DOI: 10.1016/j.prevetmed.2019.104785] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/26/2019] [Accepted: 09/30/2019] [Indexed: 10/25/2022]
Abstract
The use of prophylactic antibiotics in veterinary surgery reduces the occurrence of postoperative complications. In order to limit the development of antimicrobial resistance in bacteria and to maximize therapy efficacy, antibiotics should be used prudently and efficiently. A survey was sent to Wallonian rural veterinarians in order to assess the use of antibiotics before, during and after bovine elective caesarean section, the most common surgical procedure in Belgian rural practice. Results were analysed in the light of the current guidelines formulated by the Belgian Centre of Expertise on Antimicrobial Consumption and Resistance in Animals. Among 380 contacted veterinarians, 113 answered the survey. All veterinarians use antibiotics during caesarean section. Veterinarians predominantly use penicillin as the first drug of choice, whereas a minority use drugs considered as second or third choice, such as amoxicillin, oxytetracyclin or lincomycin-spectinomycin. Also, 31/113 veterinarians simultaneously use molecules from different antibiotic classes. The majority (100/113) of veterinarians inject antibiotics during or after surgery, while a minority (13/113) administer antibiotics preoperatively. Most veterinarians (67/113) limit the duration of their antibiotic treatment to 1 day. Considering the administration route, most veterinarians (88/113) systematically use the intraperitoneal injection route, which is not registered. Intramuscular injection and injection between muscle layers during surgery are carried out by 82/113 and 43/113 respondents, respectively. Twenty-two respondents apply intra-uterine antibiotics. Most veterinarians (87/113) combine several administration routes. The dosage of antibiotics varies enormously and excessive injection volumes are common, especially when multiple injection routes are combined. Our results show a striking lack of consistency in the antibiotic therapy during elective CS by rural veterinarians. Whereas the drug of choice and the treatment duration were largely in line with the current guidelines, this is certainly not the case for the dosage and the administration route. The intraperitoneal injection of antibiotics cannot be justified. Incorrect dosage of antibiotics should be avoided at all cost. The use of second and third line molecules and the simultaneous use of different antibiotic classes should be discouraged. A major challenge lies in the education of veterinary students and the sensitization of practitioners to avoid or unlearn unnecessary habits concerning antibiotic use. Finally, more clinical trials are needed in order to refine the current guidelines for antibiotic use and to determine the optimal drug of choice, treatment moment and application route in elective caesarean section in cattle.
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Affiliation(s)
- Salem Djebala
- Clinical department of ruminant, University of liege, Quartier Vallée 2, Avenue de Cureghem 7A-7D, Liège 4000, Belgium.
| | - Nassim Moula
- Department of animal production, University of liege, Quartier Vallée 2, Avenue de Cureghem 6, Liège 4000, Belgium
| | - Calixte Bayrou
- Clinical department of ruminant, University of liege, Quartier Vallée 2, Avenue de Cureghem 7A-7D, Liège 4000, Belgium
| | - Arnaud Sartelet
- Clinical department of ruminant, University of liege, Quartier Vallée 2, Avenue de Cureghem 7A-7D, Liège 4000, Belgium
| | - Philippe Bossaert
- Clinical department of ruminant, University of liege, Quartier Vallée 2, Avenue de Cureghem 7A-7D, Liège 4000, Belgium
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Demars A, Lison A, Machelart A, Van Vyve M, Potemberg G, Vanderwinden JM, De Bolle X, Letesson JJ, Muraille E. Route of Infection Strongly Impacts the Host-Pathogen Relationship. Front Immunol 2019; 10:1589. [PMID: 31354728 PMCID: PMC6637429 DOI: 10.3389/fimmu.2019.01589] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/25/2019] [Indexed: 12/24/2022] Open
Abstract
Live attenuated vaccines play a key role in the control of many human and animal pathogens. Their rational development is usually helped by identification of the reservoir of infection, the lymphoid subpopulations associated with protective immunity as well as the virulence genes involved in pathogen persistence. Here, we compared the course of Brucella melitensis infection in C57BL/6 mice infected via intraperitoneal (i.p.), intranasal (i.n.) and intradermal (i.d.) route and demonstrated that the route of infection strongly impacts all of these parameters. Following i.p. and i.n. infection, most infected cells observed in the spleen or lung were F4/80+ myeloid cells. In striking contrast, infected Ly6G+ neutrophils and CD140a+ fibroblasts were also observed in the skin after i.d. infection. The virB operon encoding for the type IV secretion system is considered essential to deflecting vacuolar trafficking in phagocytic cells and allows Brucella to multiply and persist. Unexpectedly, the ΔvirB Brucella strain, which does not persist in the lung after i.n. infection, persists longer in skin tissues than the wild strain after i.d. infection. While the CD4+ T cell-mediated Th1 response is indispensable to controlling the Brucella challenge in the i.p. model, it is dispensable for the control of Brucella in the i.d. and i.n. models. Similarly, B cells are indispensable in the i.p. and i.d. models but dispensable in the i.n. model. γδ+ T cells appear able to compensate for the absence of αβ+ T cells in the i.d. model but not in the other models. Taken together, our results demonstrate the crucial importance of the route of infection for the host pathogen relationship.
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Affiliation(s)
- Aurore Demars
- Unité de Recherche en Biologie des Microorganismes, Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur, Namur, Belgium
| | - Aurore Lison
- Unité de Recherche en Biologie des Microorganismes, Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur, Namur, Belgium
| | - Arnaud Machelart
- Unité de Recherche en Biologie des Microorganismes, Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur, Namur, Belgium
| | - Margaux Van Vyve
- Unité de Recherche en Biologie des Microorganismes, Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur, Namur, Belgium
| | - Georges Potemberg
- Unité de Recherche en Biologie des Microorganismes, Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur, Namur, Belgium
| | | | - Xavier De Bolle
- Unité de Recherche en Biologie des Microorganismes, Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur, Namur, Belgium
| | - Jean-Jacques Letesson
- Unité de Recherche en Biologie des Microorganismes, Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur, Namur, Belgium
| | - Eric Muraille
- Unité de Recherche en Biologie des Microorganismes, Laboratoire d'Immunologie et de Microbiologie, NARILIS, Université de Namur, Namur, Belgium
- Laboratoire de Parasitologie, Faculté de Médecine, Université Libre de Bruxelles, Bruxelles, Belgium
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Orwa TO, Mbogo RW, Luboobi LS. Multiple-Strain Malaria Infection and Its Impacts on Plasmodium falciparum Resistance to Antimalarial Therapy: A Mathematical Modelling Perspective. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2019; 2019:9783986. [PMID: 31341510 PMCID: PMC6594251 DOI: 10.1155/2019/9783986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/15/2019] [Indexed: 11/18/2022]
Abstract
The emergence of parasite resistance to antimalarial drugs has contributed significantly to global human mortality and morbidity due to malaria infection. The impacts of multiple-strain malarial parasite infection have further generated a lot of scientific interest. In this paper, we demonstrate, using the epidemiological model, the effects of parasite resistance and competition between the strains on the dynamics and control of Plasmodium falciparum malaria. The analysed model has a trivial equilibrium point which is locally asymptotically stable when the parasite's effective reproduction number is less than unity. Using contour plots, we observed that the efficacy of antimalarial drugs used, the rate of development of resistance, and the rate of infection by merozoites are the most important parameters in the multiple-strain P. falciparum infection and control model. Although the drug-resistant strain is shown to be less fit, the presence of both strains in the human host has a huge impact on the cost and success of antimalarial treatment. To reduce the emergence of resistant strains, it is vital that only effective antimalarial drugs are administered to patients in hospitals, especially in malaria-endemic regions. Our results emphasize the call for regular and strict surveillance on the use and distribution of antimalarial drugs in health facilities in malaria-endemic countries.
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Affiliation(s)
- Titus Okello Orwa
- Institute of Mathematical Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Rachel Waema Mbogo
- Institute of Mathematical Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
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Bansept F, Marrec L, Bitbol AF, Loverdo C. Antibody-mediated crosslinking of gut bacteria hinders the spread of antibiotic resistance. Evolution 2019; 73:1077-1088. [PMID: 30957218 DOI: 10.1111/evo.13730] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/24/2019] [Indexed: 12/23/2022]
Abstract
The body is home to a diverse microbiota, mainly in the gut. Resistant bacteria are selected by antibiotic treatments, and once resistance becomes widespread in a population of hosts, antibiotics become useless. Here, we develop a multiscale model of the interaction between antibiotic use and resistance spread in a host population, focusing on an important aspect of within-host immunity. Antibodies secreted in the gut enchain bacteria upon division, yielding clonal clusters of bacteria. We demonstrate that immunity-driven bacteria clustering can hinder the spread of a novel resistant bacterial strain in a host population. We quantify this effect both in the case where resistance preexists and in the case where acquiring a new resistance mutation is necessary for the bacteria to spread. We further show that the reduction of spread by clustering can be countered when immune hosts are silent carriers, and are less likely to get treated, and/or have more contacts. We demonstrate the robustness of our findings to including stochastic within-host bacterial growth, a fitness cost of resistance, and its compensation. Our results highlight the importance of interactions between immunity and the spread of antibiotic resistance, and argue in the favor of vaccine-based strategies to combat antibiotic resistance.
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Affiliation(s)
- Florence Bansept
- Sorbonne Université, CNRS, Laboratoire Jean Perrin (UMR 8237),, F-75005 Paris, France
| | - Loïc Marrec
- Sorbonne Université, CNRS, Laboratoire Jean Perrin (UMR 8237),, F-75005 Paris, France
| | - Anne-Florence Bitbol
- Sorbonne Université, CNRS, Laboratoire Jean Perrin (UMR 8237),, F-75005 Paris, France
| | - Claude Loverdo
- Sorbonne Université, CNRS, Laboratoire Jean Perrin (UMR 8237),, F-75005 Paris, France
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48
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Nichol D, Bonomo RA, Scott JG. It's too soon to pull the plug on antibiotic cycling. THE LANCET. INFECTIOUS DISEASES 2019; 18:493. [PMID: 29695354 DOI: 10.1016/s1473-3099(18)30214-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 03/12/2018] [Indexed: 10/17/2022]
Affiliation(s)
- Daniel Nichol
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Robert A Bonomo
- Research Service, Louis Stokes Department of Veterans Affairs Hospital, Cleveland, OH, USA; Department of Medicine and Departments of Biochemistry, Molecular Biology and Microbiology, and Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jacob G Scott
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Departments of Translational Hematology and Oncology Research and Radiation Oncology, Cleveland Clinic, Cleveland, OH 44040, USA.
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49
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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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50
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Kottara A, Hall JPJ, Harrison E, Brockhurst MA. Variable plasmid fitness effects and mobile genetic element dynamics across Pseudomonas species. FEMS Microbiol Ecol 2019; 94:4689093. [PMID: 29228229 PMCID: PMC5812508 DOI: 10.1093/femsec/fix172] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/30/2017] [Indexed: 11/28/2022] Open
Abstract
Mobile genetic elements (MGE) such as plasmids and transposons mobilise genes within and between species, playing a crucial role in bacterial evolution via horizontal gene transfer (HGT). Currently, we lack data on variation in MGE dynamics across bacterial host species. We tracked the dynamics of a large conjugative plasmid, pQBR103, and its Tn5042 mercury resistance transposon, in five diverse Pseudomonas species in environments with and without mercury selection. Plasmid fitness effects and stability varied extensively between host species and environments, as did the propensity for chromosomal capture of the Tn5042 mercury resistance transposon associated with loss of the plasmid. Whereas Pseudomonas fluorescens and Pseudomonas savastanoi stably maintained the plasmid in both environments, the plasmid was highly unstable in Pseudomonas aeruginosa and Pseudomonas putida, where plasmid-free genotypes with Tn5042 captured to the chromosome invaded to higher frequency under mercury selection. These data confirm that plasmid stability is dependent upon the specific genetic interaction of the plasmid and host chromosome rather than being a property of plasmids alone, and moreover imply that MGE dynamics in diverse natural communities are likely to be complex and driven by a subset of species capable of stably maintaining plasmids that would then act as hubs of HGT.
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Affiliation(s)
- Anastasia Kottara
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - James P J Hall
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Corresponding author: Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK. Tel: +44 (0)1142220051; E-mail:
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