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Levin BR, Berryhill BA, Gil-Gil T, Manuel JA, Smith AP, Choby JE, Andersson DI, Weiss DS, Baquero F. Theoretical considerations and empirical predictions of the pharmaco- and population dynamics of heteroresistance. Proc Natl Acad Sci U S A 2024; 121:e2318600121. [PMID: 38588431 PMCID: PMC11032463 DOI: 10.1073/pnas.2318600121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/28/2024] [Indexed: 04/10/2024] Open
Abstract
Antibiotics are considered one of the most important contributions to clinical medicine in the last century. Due to the use and overuse of these drugs, there have been increasing frequencies of infections with resistant pathogens. One form of resistance, heteroresistance, is particularly problematic; pathogens appear sensitive to a drug by common susceptibility tests. However, upon exposure to the antibiotic, resistance rapidly ascends, and treatment fails. To quantitatively explore the processes contributing to the emergence and ascent of resistance during treatment and the waning of resistance following cessation of treatment, we develop two distinct mathematical and computer-simulation models of heteroresistance. In our analysis of the properties of these models, we consider the factors that determine the response to antibiotic-mediated selection. In one model, heteroresistance is progressive, with each resistant state sequentially generating a higher resistance level. In the other model, heteroresistance is non-progressive, with a susceptible population directly generating populations with different resistance levels. The conditions where resistance will ascend in the progressive model are narrower than those of the non-progressive model. The rates of reversion from the resistant to the sensitive states are critically dependent on the transition rates and the fitness cost of resistance. Our results demonstrate that the standard test used to identify heteroresistance is insufficient. The predictions of our models are consistent with empirical results. Our results demand a reevaluation of the definition and criteria employed to identify heteroresistance. We recommend that the definition of heteroresistance should include a consideration of the rate of return to susceptibility.
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Affiliation(s)
- Bruce R. Levin
- Department of Biology, Emory University, Atlanta, GA30322
- Emory Antibiotic Resistance Center, Atlanta, GA30322
| | - Brandon A. Berryhill
- Department of Biology, Emory University, Atlanta, GA30322
- Program in Microbiology and Molecular Genetics, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA30322
| | - Teresa Gil-Gil
- Department of Biology, Emory University, Atlanta, GA30322
| | | | | | - Jacob E. Choby
- Emory Antibiotic Resistance Center, Atlanta, GA30322
- Emory Vaccine Center, Atlanta, GA30322
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, UppsalaSE-75123, Sweden
| | - David S. Weiss
- Emory Antibiotic Resistance Center, Atlanta, GA30322
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA30322
- Georgia Emerging Infections Program, Georgia Department of Public Health, Atlanta, GA30322
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, and Centro de Investigación Biomédica en Red Epidemiología y Salud Pública, Madrid28034, Spain
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2
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Nielsen KAG, Skårn MN, Talgø V, Pettersson M, Fløistad IS, Strømeng GM, Brurberg MB, Stensvand A. Fungicide-Resistant Botrytis in Forest Nurseries May Impact Disease Control in Norway Spruce. PLANT DISEASE 2024; 108:139-148. [PMID: 37578357 DOI: 10.1094/pdis-01-23-0037-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Gray mold, caused by Botrytis spp., is a serious problem in Norway spruce seedling production in forest nurseries. From 2013 to 2019, 125 isolates of Botrytis were obtained from eight forest nurseries in Norway: 53 from Norway spruce seedlings, 16 from indoor air, 52 from indoor surfaces, and four from weeds growing close to seedlings. The majority of isolates were identified as B. cinerea, and over 60% of these were characterized as Botrytis group S. B. pseudocinerea isolates were obtained along with isolates with DNA sequence similarities to B. prunorum. Fungicide resistance was assessed with a mycelial growth assay, and resistance was found for the following: boscalid (8.8%), fenhexamid (33.6%), fludioxonil (17.6%), pyraclostrobin (36.0%), pyrimethanil (13.6%), and thiophanate-methyl (50.4%). Many isolates (38.4%) were resistant to two to six different fungicides. A selection of isolates was analyzed for the presence of known resistance-conferring mutations in the cytb, erg27, mrr1, sdhB, and tubA genes, and mutations leading to G143A, F412S, ΔL497, H272R, and E198A/F200Y were detected, respectively. Detection of fungicide resistance in Botrytis from Norway spruce and forest nursery facilities reinforces the necessity of employing resistance management strategies to improve control and delay development of fungicide resistance in the gray mold pathogens.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Katherine Ann Gredvig Nielsen
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
- Department of Plant Sciences (IPV), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
| | - Magne Nordang Skårn
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
| | - Venche Talgø
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
| | - Martin Pettersson
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
| | - Inger Sundheim Fløistad
- Division of Forest and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
| | - Gunn Mari Strømeng
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
| | - May Bente Brurberg
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
- Department of Plant Sciences (IPV), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
| | - Arne Stensvand
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
- Department of Plant Sciences (IPV), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
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3
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Levin BR, Berryhill BA, Gil-Gil T, Manuel JA, Smith AP, Choby JE, Andersson DI, Weiss DS, Baquero F. Theoretical Considerations and Empirical Predictions of the Pharmaco- and Population Dynamics of Heteroresistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558832. [PMID: 37790545 PMCID: PMC10542493 DOI: 10.1101/2023.09.21.558832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Antibiotics are considered one of the most important contributions to clinical medicine in the last 100 years. Due to the use and overuse of these drugs, there have been increasing frequencies of infections with resistant pathogens. One form of resistance, heteroresistance, is particularly problematic; pathogens appear sensitive to a drug by common susceptibility tests. However, upon exposure to the antibiotic, resistance rapidly ascends, and treatment fails. To quantitatively explore the processes contributing to the emergence and ascent of resistance during treatment and the waning of resistance following cessation of treatment, we develop two distinct mathematical and computer-simulations models of heteroresistance. In our analysis of the properties of these models, we consider the factors that determine the response to antibiotic-mediated selection. In one model, heteroresistance is progressive, with each resistant state sequentially generating a higher resistance level. In the other model, heteroresistance is non-progressive, with a susceptible population directly generating populations with different resistance levels. The conditions where resistance will ascend in the progressive model are narrower than those of the non-progressive model. The rates of reversion from the resistant to the sensitive states are critically dependent on the transition rates and the fitness cost of resistance. Our results demonstrate that the standard test used to identify heteroresistance is insufficient. The predictions of our models are consistent with empirical results. Our results demand a reevaluation of the definition and criteria employed to identify heteroresistance. We recommend the definition of heteroresistance should include a consideration of the rate of return to susceptibility.
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Affiliation(s)
- Bruce R. Levin
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
- Emory Antibiotic Resistance Center; Atlanta, Georgia, 30322, USA
| | - Brandon A. Berryhill
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
- Program in Microbiology and Molecular Genetics, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University; Atlanta, GA, 30322, USA
| | - Teresa Gil-Gil
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Joshua A. Manuel
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Andrew P. Smith
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Jacob E. Choby
- Emory Antibiotic Resistance Center; Atlanta, Georgia, 30322, USA
- Emory Vaccine Center; Atlanta, Georgia, 30322, USA
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-75123, Sweden
| | - David S. Weiss
- Emory Antibiotic Resistance Center; Atlanta, Georgia, 30322, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, GA, 30322, USA
- Georgia Emerging Infections Program, Georgia Department of Public Health; Atlanta, GA, 30322, USA
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, and Centro de Investigación Médica en Red, Epidemiología y Salud Pública (CIBERESP) Madrid, Spain
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4
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Arunkumar R, Zhou SO, Day JP, Bakare S, Pitton S, Zhang Y, Hsing CY, O’Boyle S, Pascual-Gil J, Clark B, Chandler RJ, Leitão AB, Jiggins FM. Natural selection has driven the recurrent loss of an immunity gene that protects Drosophila against a major natural parasite. Proc Natl Acad Sci U S A 2023; 120:e2211019120. [PMID: 37552757 PMCID: PMC10438844 DOI: 10.1073/pnas.2211019120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 06/26/2023] [Indexed: 08/10/2023] Open
Abstract
Polymorphisms in immunity genes can have large effects on susceptibility to infection. To understand the origins of this variation, we have investigated the genetic basis of resistance to the parasitoid wasp Leptopilina boulardi in Drosophila melanogaster. We found that increased expression of the gene lectin-24A after infection by parasitic wasps was associated with a faster cellular immune response and greatly increased rates of killing the parasite. lectin-24A encodes a protein that is strongly up-regulated in the fat body after infection and localizes to the surface of the parasite egg. In certain susceptible lines, a deletion upstream of the lectin-24A has largely abolished expression. Other mutations predicted to abolish the function of this gene have arisen recurrently in this gene, with multiple loss-of-expression alleles and premature stop codons segregating in natural populations. The frequency of these alleles varies greatly geographically, and in some southern African populations, natural selection has driven them near to fixation. We conclude that natural selection has favored the repeated loss of an important component of the immune system, suggesting that in some populations, a pleiotropic cost to lectin-24A expression outweighs the benefits of resistance.
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Affiliation(s)
- Ramesh Arunkumar
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Shuyu Olivia Zhou
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Jonathan P. Day
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Sherifat Bakare
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Department of Biochemical Sciences, School of Biosciences, University of Surrey, 388 Stag Hill, Guildford,GU2 7XH, United Kingdom
| | - Simone Pitton
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Biosciences Department, Università degli Studi di Milano, Via Celoria 26, Milano, MI20133, Italy
| | - Yexin Zhang
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Chi-Yun Hsing
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Sinead O’Boyle
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- School of Biomolecular and Biomedical Science, University College Dublin, DublinD04 V1W8, Ireland
| | - Juan Pascual-Gil
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Facultad de Ciencias, Universidad Autónoma de Madrid, C. Francisco Tomás y Valiente 7, 28049Madrid, Spain
| | - Belinda Clark
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Rachael J. Chandler
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Department of Biochemical Sciences, School of Biosciences, University of Surrey, 388 Stag Hill, Guildford,GU2 7XH, United Kingdom
| | - Alexandre B. Leitão
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Francis M. Jiggins
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
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5
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Montero MM, Domene-Ochoa S, López-Causapé C, Luque S, Sorlí L, Campillo N, Padilla E, Prim N, Ferrer-Alapont L, Angulo-Brunet A, Grau S, Oliver A, Horcajada JP. Impact of ceftolozane/tazobactam concentrations in continuous infusion against extensively drug-resistant Pseudomonas aeruginosa isolates in a hollow-fiber infection model. Sci Rep 2021; 11:22178. [PMID: 34773066 PMCID: PMC8589991 DOI: 10.1038/s41598-021-01784-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/03/2021] [Indexed: 11/20/2022] Open
Abstract
Ceftolozane/tazobactam (C/T) has emerged as a potential agent for the treatment of extensively drug-resistant (XDR) Pseudomonas aeruginosa infections. As it is a time-dependent antimicrobial, prolonged infusion may help achieve pharmacokinetic/pharmacodynamic (PK/PD) targets. To compare alternative steady-state concentrations (Css) of C/T in continuous infusion (CI) against three XDR P. aeruginosa ST175 isolates with C/T minimum inhibitory concentration (MIC) values of 2 to 16 mg/L in a hollow-fiber infection model (HFIM). Duplicate 10-day HFIM assays were performed to evaluate Css of C/T in CI: one compared 20 and 45 mg/L against the C/T-susceptible isolate while the other compared 45 and 80 mg/L against the two C/T-non-susceptible isolates. C/T resistance emerged when C/T-susceptible isolate was treated with C/T in CI at a Css of 20 mg/L; which showed a deletion in the gene encoding AmpC β-lactamase. The higher dosing regimen (80 mg/L) showed a slight advantage in effectiveness. The higher dosing regimen has the greatest bactericidal effect, regardless of C/T MIC. Exposure to the suboptimal Css of 20 mg/L led to the emergence of C/T resistance in the susceptible isolate. Antimicrobial regimens should be optimized through C/T levels monitoring and dose adjustments to improve clinical management.
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Affiliation(s)
- María M Montero
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain.
| | - Sandra Domene-Ochoa
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Carla López-Causapé
- Servicio de Microbiología y Unidad de Investigación, Hospital Son Espases, IdISBa, Palma de Mallorca, Spain
| | - Sonia Luque
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain.,Pharmacy Service, Hospital del Mar, Barcelona, Spain
| | - Luisa Sorlí
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | | | | | - Núria Prim
- Laboratori de Referència de Catalunya, Barcelona, Spain
| | - Lorena Ferrer-Alapont
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Ariadna Angulo-Brunet
- Psychology and Education Science Studies, Universitat Oberta de Catalunya, Barcelona, Spain
| | - Santiago Grau
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain.,Pharmacy Service, Hospital del Mar, Barcelona, Spain
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Son Espases, IdISBa, Palma de Mallorca, Spain
| | - Juan P Horcajada
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-29, 08003, Barcelona, Spain
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6
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Hawkins NJ, Fraaije BA. Contrasting levels of genetic predictability in the evolution of resistance to major classes of fungicides. Mol Ecol 2021; 30:5318-5327. [PMID: 33706414 DOI: 10.1111/mec.15877] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/05/2021] [Indexed: 12/14/2022]
Abstract
The evolution of resistance has been seen across all major classes of xenobiotics, including antimicrobial drugs and agricultural pesticides. This repeated emergence of resistance is a case of phenotypic parallel evolution, but often the parallelism extends to the molecular level too, with multiple species gaining the same mutation in response to the same chemical treatment. We review the degree of repeatability in target-site resistance mutations affecting different classes of site-specific agricultural fungicides used in crop protection, comparing the extent to which resistance in different pathogen species has evolved via the same or different mutations. For all major fungicide target sites, substantial levels of molecular parallel evolution can be seen, with at least one mutation recurring in over 50% of species. Target-site mutations appear to be most repeatable in cytochrome b, target site of quinone-outside inhibitor fungicides, and least predictable for CYP51, target site of the azoles. Intermediate levels of repeatability are seen for the MBC target site β-tubulin, and the SDHI target site succinate dehydrogenase. Repeatability may be lower where there are selective trade-offs between resistance and pleiotropic fitness penalties, or differing levels of cross-resistance across members of a fungicide class; or where single mutations confer only partial resistance, and epistatic interactions between multiple mutations result in a rugged fitness landscape. This affects the predictive power of in vitro mutation studies, and has practical implications for resistance monitoring strategies and diagnostic methods.
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Affiliation(s)
- Nichola J Hawkins
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire, UK.,NIAB, Cambridge, UK
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7
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Affiliation(s)
- Christopher Witzany
- Freie Universität Berlin, Institut für Biologie, Evolutionary Biology, Berlin, Germany
| | | | - Jens Rolff
- Freie Universität Berlin, Institut für Biologie, Evolutionary Biology, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
- * E-mail:
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8
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Huijben S, Macete E, Mombo-Ngoma G, Ramharter M, Kariuki S, Desai M, Shi YP, Mwangoka G, Massougbodji A, Cot M, Ndam NT, Uberegui E, Gupta H, Cisteró P, Aponte JJ, González R, Menéndez C, Mayor A. Counter-Selection of Antimalarial Resistance Polymorphisms by Intermittent Preventive Treatment in Pregnancy. J Infect Dis 2020; 221:293-303. [PMID: 31677349 DOI: 10.1093/infdis/jiz451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/19/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Innovative approaches are needed to limit antimalarial resistance evolution. Understanding the role of intermittent preventive treatment in pregnancy (IPTp) on the selection for resistance and the impact such selection has on pregnancy outcomes can guide future interventions. METHODS Plasmodium falciparum isolates (n = 914) from 2 randomized clinical trials were screened for pfmdr1 copy number variation and pfcrt, pfmdr1, pfdhfr, and pfdhps resistance markers. The trials were conducted between 2010 and 2013 in Benin, Gabon, Kenya, and Mozambique to establish the efficacy of IPTp-mefloquine (MQ) compared with IPTp-sulphadoxine-pyrimethamine (SP) in human immunodeficiency virus (HIV)-uninfected and to IPTp-placebo in HIV-infected women. RESULTS In HIV-uninfected women, the prevalence of pfcrt mutants, pfdhfr/pfdhps quintuple mutants, and pfmdr1 copy number was similar between women receiving IPT-SP and IPTp-MQ. However, prevalence of pfmdr1 polymorphism 86Y was lower in the IPTp-MQ group than in the IPTp-SP group, and within the IPTp-MQ group it was lower at delivery compared with recruitment. No effect of IPTp-MQ on resistance markers was observed among HIV-infected women. The carriage of resistance markers was not associated with pregnancy outcomes. CONCLUSIONS Selection of wild-type pfmdr1 polymorphism N86 by IPTp-MQ highlights the strong selective pressure IPTp can exert and the opportunity for using negative cross-resistance in drug choice for clinical treatment and IPTp.
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Affiliation(s)
- Silvie Huijben
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Eusebio Macete
- Centro de Investigação em Saúde da Manhiça, Manhiça, Mozambique
| | - Ghyslain Mombo-Ngoma
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Institut für Tropenmedizin, Universität Tübingen, und Deutsches Zentrum für Infektionsforschung, Tübingen, Germany.,Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine and Department of Medicine I, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Ramharter
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine and Department of Medicine I, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon Kariuki
- Kenya Medical Research Institute/Centre for Global Health Research, Kisumu, Kenya
| | - Meghna Desai
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ya Ping Shi
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Achille Massougbodji
- Unité d'Enseignement et de Recherche de Parasitologie Mycologie, Faculté des Sciences de la Santé, Cotonou, Bénin
| | - Michel Cot
- Université de Paris, MERIT, IRD, Paris, France
| | | | | | - Himanshu Gupta
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Pau Cisteró
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - John J Aponte
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Centro de Investigação em Saúde da Manhiça, Manhiça, Mozambique
| | - Raquel González
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Centro de Investigação em Saúde da Manhiça, Manhiça, Mozambique
| | - Clara Menéndez
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Centro de Investigação em Saúde da Manhiça, Manhiça, Mozambique
| | - Alfredo Mayor
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Centro de Investigação em Saúde da Manhiça, Manhiça, Mozambique
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9
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Gent DH, Block M, Claassen BJ. High Levels of Insensitivity to Phosphonate Fungicides in Pseudoperonospora humuli. PLANT DISEASE 2020; 104:1400-1406. [PMID: 32196418 DOI: 10.1094/pdis-10-19-2067-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phosphonate (phosphite; HPO3-2) is fungicidal against oomycetes and certain other organisms. The Fungicide Resistance Action Committee has deemed phosphonate to be at low risk of resistance development, and reduced sensitivity to phosphonate has been reported only occasionally in plant pathogens. Reduced sensitivity to the fungicide fosetyl-Al was documented in the hop downy mildew pathogen, Pseudoperonospora humuli, in the early 2000s, but disease caused by insensitive isolates could still be managed commercially if the fungicide rate was doubled from 2.24 to 4.48 kg/ha. In this research, we document the occurrence of isolates of P. humuli in Oregon that possess even higher levels of insensitivity to fosetyl-Al and other phosphonate fungicides. The median estimated effective concentration required to reduce infection by 50% (EC50) for isolates collected from two farms reporting disease control failures was 2.7% (vol/vol) phosphonate (range = 1.6 to 164.2), which was 1.6 times (range = 0.9 to 96.0) the maximum labeled rate of the phosphonate fungicide utilized. In contrast, the median EC50 for isolates obtained from experimental plots that have received only a single application of a phosphonate fungicide was 0.6% (vol/vol) phosphonate (range = 0.11 to 2.3) or 0.3 times the maximum allowable rate. Sensitivity of isolates to a phosphorous acid fungicide, fosetyl-Al, and a plant nutrient product containing an unspecified level of phosphorous acid were linearly related. Insensitivity to the maximum allowable rate of a phosphorous acid fungicide was widespread within and among hop farms in Oregon. Among 54 isolates assayed for phosphonate insensitivity, 96% had EC50 values that exceeded the maximum allow rate of the fungicide used in the assays. Field studies conducted in 2 years further demonstrated that a phosphorous fungicide, a nutrient product containing phosphorous acid, and fosetyl-Al failed to provide commercially acceptable suppression of downy mildew when applied at the maximum allowable rates and even double these rates, whereas fungicides with different modes of action provided 91% or greater disease control. The whole of this research indicates that P. humuli has been selected to tolerate fosetyl-Al and other phosphonate fungicides at rates four times greater than those used earlier to obtain satisfactory suppression of downy mildew. This finding has implications for management of the disease not only in Oregon but also, in other production regions should insensitive isolates be introduced on infected planting material.
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Affiliation(s)
- David H Gent
- Forage Seed and Cereal Research Unit, U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Mary Block
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Briana J Claassen
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
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10
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Saralegui C, Ponce-Alonso M, Pérez-Viso B, Moles Alegre L, Escribano E, Lázaro-Perona F, Lanza VF, de Pipaón MS, Rodríguez JM, Baquero F, Del Campo R. Genomics of Serratia marcescens Isolates Causing Outbreaks in the Same Pediatric Unit 47 Years Apart: Position in an Updated Phylogeny of the Species. Front Microbiol 2020; 11:451. [PMID: 32296400 PMCID: PMC7136904 DOI: 10.3389/fmicb.2020.00451] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/02/2020] [Indexed: 12/16/2022] Open
Abstract
The first documented nosocomial outbreak caused by Serratia marcescens in Spain occurred in 1969 at the neonatal intensive care unit (NICU) of the tertiary La Paz Children's Hospital in Madrid, Spain, and based on the available phenotyping techniques at this time, it was considered as a monoclonal outbreak. Only 47 years later, another S. marcescens outbreak of an equivalent dimension occurred at the same NICU. The aim of the present study was to study isolates from these historical and contemporary outbreaks by phenotypic analysis and whole-genome sequencing techniques and to position these strains along with 444 publicly available S. marcescens genomes, separately comparing core genome and accessory genome contents. Clades inferred by both approaches showed high correlation, indicating that core and accessory genomes seem to evolve in the same manner for S. marcescens. Nine S. marcescens clusters were identified, and isolates were grouped in two of them according to sampling year. One exception was isolate 13F-69, the most genetically distant strain, located in a different cluster. Categorical functions in the annotated accessory genes of both collections were preserved among all isolates. No significant differences in frequency of insertion sequences in historical (0.18-0.20)-excluding the outlier strain-versus contemporary isolates (0.11-0.19) were found despite the expected resting effect. The most dissimilar isolate, 13F-69, contains a highly preserved plasmid previously described in Bordetella bronchiseptica. This strain exhibited a few antibiotic resistance genes not resulting in a resistant phenotype, suggesting the value of gene down expression in adaptation to long-term starvation.
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Affiliation(s)
- Claudia Saralegui
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,Red Española de Investigación en Patología Infecciosa, Madrid, Spain
| | - Manuel Ponce-Alonso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,Red Española de Investigación en Patología Infecciosa, Madrid, Spain
| | - Blanca Pérez-Viso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Laura Moles Alegre
- Unidad de Esclerosis Múltiple, Instituto de Investigación Sanitaria Biodonostia, Donostia-San Sebastián, Spain
| | - Esperanza Escribano
- Servicio de Neonatología, Hospital Universitario La Paz, and Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Val F Lanza
- Unidad de Bioinformática del IRYCIS, Madrid, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain
| | - Miguel Sáenz de Pipaón
- Servicio de Neonatología, Hospital Universitario La Paz, and Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan Miguel Rodríguez
- Departamento de Nutrición y Ciencia de los Alimentos, Universidad Complutense de Madrid, Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain
| | - Rosa Del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,Red Española de Investigación en Patología Infecciosa, Madrid, Spain
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11
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Tepekule B, Abel Zur Wiesch P, Kouyos RD, Bonhoeffer S. Quantifying the impact of treatment history on plasmid-mediated resistance evolution in human gut microbiota. Proc Natl Acad Sci U S A 2019; 116:23106-23116. [PMID: 31666328 PMCID: PMC6859334 DOI: 10.1073/pnas.1912188116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
To understand how antibiotic use affects the risk of a resistant infection, we present a computational model of the population dynamics of gut microbiota including antibiotic resistance-conferring plasmids. We then describe how this model is parameterized based on published microbiota data. Finally, we investigate how treatment history affects the prevalence of resistance among opportunistic enterobacterial pathogens. We simulate treatment histories and identify which properties of prior antibiotic exposure are most influential in determining the prevalence of resistance. We find that resistance prevalence can be predicted by 3 properties, namely the total days of drug exposure, the duration of the drug-free period after last treatment, and the center of mass of the treatment pattern. Overall this work provides a framework for capturing the role of the microbiome in the selection of antibiotic resistance and highlights the role of treatment history for the prevalence of resistance.
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Affiliation(s)
- Burcu Tepekule
- Department of Environmental Systems Science, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland;
| | - Pia Abel Zur Wiesch
- Department of Pharmacy, Faculty of Health Sciences, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
- Centre for Molecular Medicine Norway, 0318 Oslo, Norway
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Sebastian Bonhoeffer
- Department of Environmental Systems Science, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
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12
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Allen RC, Angst DC, Hall AR. Resistance Gene Carriage Predicts Growth of Natural and Clinical Escherichia coli Isolates in the Absence of Antibiotics. Appl Environ Microbiol 2019; 85:e02111-18. [PMID: 30530714 PMCID: PMC6365833 DOI: 10.1128/aem.02111-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/29/2018] [Indexed: 11/20/2022] Open
Abstract
Bacterial pathogens that carry antibiotic resistance alleles sometimes pay a cost in the form of impaired growth in antibiotic-free conditions. This cost of resistance is expected to be a key parameter for understanding how resistance spreads and persists in pathogen populations. Analysis of individual resistance alleles from laboratory evolution and natural isolates has shown they are typically costly, but these costs are highly variable and influenced by genetic variation at other loci. It therefore remains unclear how strongly resistance is linked to impaired antibiotic-free growth in bacteria from natural and clinical scenarios, where resistance alleles are likely to coincide with other types of genetic variation. To investigate this, we measured the growth of 92 natural and clinical Escherichia coli isolates across three antibiotic-free environments. We then tested whether variation of antibiotic-free growth among isolates was predicted by their resistance to 10 antibiotics, while accounting for the phylogenetic structure of the data. We found that isolates with similar resistance profiles had similar antibiotic-free growth profiles, but it was not simply that higher average resistance was associated with impaired growth. Next, we used whole-genome sequences to identify antibiotic resistance genes and found that isolates carrying a greater number of resistance gene types grew relatively poorly in antibiotic-free conditions, even when the resistance genes they carried were different. This suggests that the resistance of bacterial pathogens is linked to growth costs in nature, but it is the total genetic burden and multivariate resistance phenotype that predict these costs, rather than individual alleles or mean resistance across antibiotics.IMPORTANCE Managing the spread of antibiotic resistance in bacterial pathogens is a major challenge for global public health. Central to this challenge is understanding whether resistance is linked to impaired bacterial growth in the absence of antibiotics, because this determines whether resistance declines when bacteria are no longer exposed to antibiotics. We studied 92 isolates of the key bacterial pathogen Escherichia coli; these isolates varied in both their antibiotic resistance genes and other parts of the genome. Taking this approach, rather than focusing on individual genetic changes associated with resistance as in much previous work, revealed that growth without antibiotics was linked to the number of specialized resistance genes carried and the combination of antibiotics to which isolates were resistant but was not linked to average antibiotic resistance. This approach provides new insights into the genetic factors driving the long-term persistence of antibiotic-resistant bacteria, which is important for future efforts to predict and manage resistance.
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Affiliation(s)
| | - Daniel C Angst
- Institute for Integrative Biology, ETH Zürich, Switzerland
| | - Alex R Hall
- Institute for Integrative Biology, ETH Zürich, Switzerland
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13
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The high prevalence of antibiotic heteroresistance in pathogenic bacteria is mainly caused by gene amplification. Nat Microbiol 2019; 4:504-514. [PMID: 30742072 DOI: 10.1038/s41564-018-0342-0] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/06/2018] [Indexed: 12/22/2022]
Abstract
When choosing antibiotics to treat bacterial infections, it is assumed that the susceptibility of the target bacteria to an antibiotic is reflected by laboratory estimates of the minimum inhibitory concentration (MIC) needed to prevent bacterial growth. A caveat of using MIC data for this purpose is heteroresistance, the presence of a resistant subpopulation in a main population of susceptible cells. We investigated the prevalence and mechanisms of heteroresistance in 41 clinical isolates of the pathogens Escherichia coli, Salmonella enterica, Klebsiella pneumoniae and Acinetobacter baumannii against 28 different antibiotics. For the 766 bacteria-antibiotic combinations tested, as much as 27.4% of the total was heteroresistant. Genetic analysis demonstrated that a majority of heteroresistance cases were unstable, with an increased resistance of the subpopulations resulting from spontaneous tandem amplifications, typically including known resistance genes. Using mathematical modelling, we show how heteroresistance in the parameter range estimated in this study can result in the failure of antibiotic treatment of infections with bacteria that are classified as antibiotic susceptible. The high prevalence of heteroresistance with the potential for treatment failure highlights the limitations of MIC as the sole criterion for susceptibility determinations. These results call for the development of facile and rapid protocols to identify heteroresistance in pathogens.
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14
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Hawkins NJ, Fraaije BA. Fitness Penalties in the Evolution of Fungicide Resistance. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:339-360. [PMID: 29958074 DOI: 10.1146/annurev-phyto-080417-050012] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The evolution of resistance poses an ongoing threat to crop protection. Fungicide resistance provides a selective advantage under fungicide selection, but resistance-conferring mutations may also result in fitness penalties, resulting in an evolutionary trade-off. These penalties may result from the functional constraints of an evolving target site or from the resource allocation costs of overexpression or active transport. The extent to which such fitness penalties are present has important implications for resistance management strategies, determining whether resistance persists or declines between treatments, and for resistance risk assessments for new modes of action. Experimental results have proven variable, depending on factors such as temperature, nutrient status, osmotic or oxidative stress, and pathogen life-cycle stage. Functional genetics tools allow pathogen genetic background to be controlled, but this in turn raises the question of epistatic interactions. Combining fitness penalties under various conditions into a field-realistic scenario poses an important future challenge.
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Affiliation(s)
- N J Hawkins
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom;
| | - B A Fraaije
- Biointeractions and Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom;
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15
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Durão P, Balbontín R, Gordo I. Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance. Trends Microbiol 2018; 26:677-691. [DOI: 10.1016/j.tim.2018.01.005] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/05/2018] [Accepted: 01/24/2018] [Indexed: 01/10/2023]
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16
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Ross LS, Lafuente-Monasterio MJ, Sakata-Kato T, Mandt REK, Gamo FJ, Wirth DF, Lukens AK. Identification of Collateral Sensitivity to Dihydroorotate Dehydrogenase Inhibitors in Plasmodium falciparum. ACS Infect Dis 2018; 4:508-515. [PMID: 29336544 PMCID: PMC5899019 DOI: 10.1021/acsinfecdis.7b00217] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
Drug
resistance has been reported for every antimalarial in use highlighting
the need for new strategies to protect the efficacy of therapeutics
in development. We have previously shown that resistance can be suppressed
with a population biology trap: by identifying situations where resistance
to one compound confers hypersensitivity to another (collateral sensitivity),
we can design combination therapies that not only kill the parasite
but also guide its evolution away from resistance. We applied this
concept to the Plasmodium falciparum dihydroorotate
dehydrogenase (PfDHODH) enzyme, a well validated
antimalarial target with inhibitors in the development pipeline. Here,
we report a high-throughput screen to identify compounds specifically
active against PfDHODH resistant mutants. We additionally
perform extensive cross-resistance profiling allowing us to identify
compound pairs demonstrating the potential for mutually incompatible
resistance. These combinations represent promising starting points
for exploiting collateral sensitivity to extend the useful lifespan
of new antimalarial therapeutics.
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Affiliation(s)
- Leila Saxby Ross
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Maria José Lafuente-Monasterio
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Tomoyo Sakata-Kato
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Rebecca E. K. Mandt
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Francisco Javier Gamo
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Dyann F. Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
- Infectious Disease and Microbiome Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Amanda K. Lukens
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, United States
- Infectious Disease and Microbiome Program, The Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
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