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Hinz A, Amado A, Kassen R, Bank C, Wong A. Unpredictability of the Fitness Effects of Antimicrobial Resistance Mutations Across Environments in Escherichia coli. Mol Biol Evol 2024; 41:msae086. [PMID: 38709811 PMCID: PMC11110942 DOI: 10.1093/molbev/msae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/11/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
The evolution of antimicrobial resistance (AMR) in bacteria is a major public health concern, and antibiotic restriction is often implemented to reduce the spread of resistance. These measures rely on the existence of deleterious fitness effects (i.e. costs) imposed by AMR mutations during growth in the absence of antibiotics. According to this assumption, resistant strains will be outcompeted by susceptible strains that do not pay the cost during the period of restriction. The fitness effects of AMR mutations are generally studied in laboratory reference strains grown in standard growth environments; however, the genetic and environmental context can influence the magnitude and direction of a mutation's fitness effects. In this study, we measure how three sources of variation impact the fitness effects of Escherichia coli AMR mutations: the type of resistance mutation, the genetic background of the host, and the growth environment. We demonstrate that while AMR mutations are generally costly in antibiotic-free environments, their fitness effects vary widely and depend on complex interactions between the mutation, genetic background, and environment. We test the ability of the Rough Mount Fuji fitness landscape model to reproduce the empirical data in simulation. We identify model parameters that reasonably capture the variation in fitness effects due to genetic variation. However, the model fails to accommodate the observed variation when considering multiple growth environments. Overall, this study reveals a wealth of variation in the fitness effects of resistance mutations owing to genetic background and environmental conditions, which will ultimately impact their persistence in natural populations.
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Affiliation(s)
- Aaron Hinz
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - André Amado
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Division of Theoretical Ecology and Evolution, Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Evolutionary Dynamics Group, Gulbenkian Science Institute, Oeiras, Portugal
| | - Rees Kassen
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Claudia Bank
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Division of Theoretical Ecology and Evolution, Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Evolutionary Dynamics Group, Gulbenkian Science Institute, Oeiras, Portugal
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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2
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Diaz-Colunga J, Sanchez A, Ogbunugafor CB. Environmental modulation of global epistasis in a drug resistance fitness landscape. Nat Commun 2023; 14:8055. [PMID: 38052815 DOI: 10.1038/s41467-023-43806-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 11/21/2023] [Indexed: 12/07/2023] Open
Abstract
Interactions between mutations (epistasis) can add substantial complexity to genotype-phenotype maps, hampering our ability to predict evolution. Yet, recent studies have shown that the fitness effect of a mutation can often be predicted from the fitness of its genetic background using simple, linear relationships. This phenomenon, termed global epistasis, has been leveraged to reconstruct fitness landscapes and infer adaptive trajectories in a wide variety of contexts. However, little attention has been paid to how patterns of global epistasis may be affected by environmental variation, despite this variation frequently being a major driver of evolution. This is particularly relevant for the evolution of drug resistance, where antimicrobial drugs may change the environment faced by pathogens and shape their adaptive trajectories in ways that can be difficult to predict. By analyzing a fitness landscape of four mutations in a gene encoding an essential enzyme of P. falciparum (a parasite cause of malaria), here we show that patterns of global epistasis can be strongly modulated by the concentration of a drug in the environment. Expanding on previous theoretical results, we demonstrate that this modulation can be quantitatively explained by how specific gene-by-gene interactions are modified by drug dose. Importantly, our results highlight the need to incorporate potential environmental variation into the global epistasis framework in order to predict adaptation in dynamic environments.
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Affiliation(s)
- Juan Diaz-Colunga
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06511, USA.
- Department of Microbial Biotechnology, Spanish National Center for Biotechnology CNB-CSIC, 28049, Madrid, Spain.
- Institute of Functional Biology and Genomics IBFG-CSIC, University of Salamanca, 37007, Salamanca, Spain.
| | - Alvaro Sanchez
- Department of Microbial Biotechnology, Spanish National Center for Biotechnology CNB-CSIC, 28049, Madrid, Spain.
- Institute of Functional Biology and Genomics IBFG-CSIC, University of Salamanca, 37007, Salamanca, Spain.
| | - C Brandon Ogbunugafor
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06511, USA.
- Santa Fe Institute, Santa Fe, NM, 87501, USA.
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3
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Cellier MFM. Slc11 Synapomorphy: A Conserved 3D Framework Articulating Carrier Conformation Switch. Int J Mol Sci 2023; 24:15076. [PMID: 37894758 PMCID: PMC10606218 DOI: 10.3390/ijms242015076] [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: 08/15/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Transmembrane carriers of the Slc11 family catalyze proton (H+)-dependent uptake of divalent metal ions (Me2+) such as manganese and iron-vital elements coveted during infection. The Slc11 mechanism of high-affinity Me2+ cell import is selective and conserved between prokaryotic (MntH) and eukaryotic (Nramp) homologs, though processes coupling the use of the proton motive force to Me2+ uptake evolved repeatedly. Adding bacterial piracy of Nramp genes spread in distinct environmental niches suggests selective gain of function that may benefit opportunistic pathogens. To better understand Slc11 evolution, Alphafold (AF2)/Colabfold (CF) 3D predictions for bacterial sequences from sister clades of eukaryotic descent (MCb and MCg) were compared using both native and mutant templates. AF2/CF model an array of native MCb intermediates spanning the transition from outwardly open (OO) to inwardly open (IO) carriers. In silico mutagenesis targeting (i) a set of (evolutionarily coupled) sites that may define Slc11 function (putative synapomorphy) and (ii) residues from networked communities evolving during MCb transition indicates that Slc11 synapomorphy primarily instructs a Me2+-selective conformation switch which unlocks carrier inner gate and contributes to Me2+ binding site occlusion and outer gate locking. Inner gate opening apparently proceeds from interaction between transmembrane helix (h) h5, h8 and h1a. MCg1 xenologs revealed marked differences in carrier shape and plasticity, owing partly to an altered intramolecular H+ network. Yet, targeting Slc11 synapomorphy also converted MCg1 IO models to an OO state, apparently mobilizing the same residues to control gates. But MCg1 response to mutagenesis differed, with extensive divergence within this clade correlating with MCb-like modeling properties. Notably, MCg1 divergent epistasis marks the emergence of the genus Bordetella-Achromobacter. Slc11 synapomorphy localizes to the 3D areas that deviate least among MCb and MCg1 models (either IO or OO) implying that it constitutes a 3D network of residues articulating a Me2+-selective carrier conformation switch which is maintained in fast-evolving clades at the cost of divergent epistatic interactions impacting carrier shape and dynamics.
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Affiliation(s)
- Mathieu F M Cellier
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, QC H7V 1B7, Canada
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Coluzzi C, Guillemet M, Mazzamurro F, Touchon M, Godfroid M, Achaz G, Glaser P, Rocha EPC. Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes. Mol Biol Evol 2023; 40:msad217. [PMID: 37788575 PMCID: PMC10575684 DOI: 10.1093/molbev/msad217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
Bacterial lineages acquire novel traits at diverse rates in part because the genetic background impacts the successful acquisition of novel genes by horizontal transfer. Yet, how horizontal transfer affects the subsequent evolution of core genes remains poorly understood. Here, we studied the evolution of resistance to quinolones in Escherichia coli accounting for population structure. We found 60 groups of genes whose gain or loss induced an increase in the probability of subsequently becoming resistant to quinolones by point mutations in the gyrase and topoisomerase genes. These groups include functions known to be associated with direct mitigation of the effect of quinolones, with metal uptake, cell growth inhibition, biofilm formation, and sugar metabolism. Many of them are encoded in phages or plasmids. Although some of the chronologies may reflect epidemiological trends, many of these groups encoded functions providing latent phenotypes of antibiotic low-level resistance, tolerance, or persistence under quinolone treatment. The mutations providing resistance were frequent and accumulated very quickly. Their emergence was found to increase the rate of acquisition of other antibiotic resistances setting the path for multidrug resistance. Hence, our findings show that horizontal gene transfer shapes the subsequent emergence of adaptive mutations in core genes. In turn, these mutations further affect the subsequent evolution of resistance by horizontal gene transfer. Given the substantial gene flow within bacterial genomes, interactions between horizontal transfer and point mutations in core genes may be a key to the success of adaptation processes.
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Affiliation(s)
- Charles Coluzzi
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Martin Guillemet
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Fanny Mazzamurro
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Marie Touchon
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Maxime Godfroid
- SMILE Group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Guillaume Achaz
- SMILE Group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Philippe Glaser
- Institut Pasteur, Université de Paris Cité, CNRS, UMR6047, Unité EERA, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
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Díaz-Palafox G, Tamayo-Ordoñez YDJ, Bello-López JM, Ayil-Gutiérrez BA, RodrÍguez-Garza MM, Antonio Rodríguez-de la Garza J, Sosa-Santillán GDJ, Acosta-Cruz E, Ruiz-Marín A, Córdova-Quiroz AV, Pérez-Reda LJ, Tamayo-Ordoñez FA, Tamayo-Ordoñez MC. Regulation Transcriptional of Antibiotic Resistance Genes (ARGs) in Bacteria Isolated from WWTP. Curr Microbiol 2023; 80:338. [PMID: 37672120 PMCID: PMC10482803 DOI: 10.1007/s00284-023-03449-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/15/2023] [Indexed: 09/07/2023]
Abstract
The incidence of antibiotics and transcriptional regulation of ARGs in isolated bacteria from wastewater needs to be explored. By HPLC, in samples of untreated wastewater, ampicillin (49.74 ± 5.70 µg/mL), chloramphenicol (0.60 ± 0.03 µg/mL), tylosin (72.95 ± 2.03 µg/mL), and oxytetracycline (0.22 ± 0.01 µg/mL) was determined. Through metagenomic analysis identified 58 bacterial species belonging to 9 phyla and at least 14 species have shown resistance to a variety of antibiotics. Twenty-two bacterial isolates were proved to be resistant to fifteen antibiotics of new generation and used in medical research to combat infectious diseases. Fourteen strains were shown to harbor plasmids in size ranges of 2-5 Kb, 6-10 Kb and plasmids with size greater than 10 Kb. By quantitative PCR it was possible to identify genes sul, qnr, cat1, aadA1, and sat-1 gene were shown to be present in gDNA samples from treated and untreated samples of wastewater and by relative expression analysis, differential expression of cat1, ermB, act, and tetA genes was demonstrated in strains that showed identity with Escherichia coli, Bacteroides fragilis, and Salmonella thyphi, and that were stressed with different concentrations of antibiotics. The presence of ARGs in untreated water samples, as well as in bacterial isolates, was indicative that in these habitats there are microorganisms that can resist β-lactams, aminoglycosides, tetracyclines, sulfonamides, and quinolones.
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Affiliation(s)
- Grethel Díaz-Palafox
- Laboratorio de Ingeniería Genética, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Ing J. Cárdenas Valdez s/n, República, 25280, Saltillo, Coah, Mexico
| | - Yahaira de Jesús Tamayo-Ordoñez
- Laboratorio de Biotecnología Ambiental del Centro de Biotecnología Genómica del Instituto Politécnico Nacional, CP 88710, Reynosa, TAMPS, México
| | | | - Benjamin Abraham Ayil-Gutiérrez
- CONACYT- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Biotecnologia Vegetal, Blvd. del Maestro, s/n, Esq. Elías Piña, 88710, Reynosa, Mexico
| | - Mónica Margarita RodrÍguez-Garza
- Laboratorio de Biotecnología Ambiental, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Ing J. Cárdenas Valdez s/n, República, 25280, Saltillo, Coah, Mexico
| | - José Antonio Rodríguez-de la Garza
- Laboratorio de Biotecnología Ambiental, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Ing J. Cárdenas Valdez s/n, República, 25280, Saltillo, Coah, Mexico
| | - Gerardo de Jesús Sosa-Santillán
- Laboratorio de Biosíntesis Enzimática, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Ing J. Cárdenas Valdez s/n, República, 25280, Saltillo, Coah, Mexico
| | - Erika Acosta-Cruz
- Laboratorio de Microbiología Molecular, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Ing J. Cárdenas Valdez s/n, República, 25280, Saltillo, Coah, Mexico
| | - Alejandro Ruiz-Marín
- Facultad de Química, Universidad Autónoma del Carmen, Campus "General José Ortiz Ávila, Calle 56 No. 4, 24180, Carmen, Campeche, Mexico
| | - Atl Victor Córdova-Quiroz
- Facultad de Química, Universidad Autónoma del Carmen, Campus "General José Ortiz Ávila, Calle 56 No. 4, 24180, Carmen, Campeche, Mexico
| | - Luis Jorge Pérez-Reda
- Facultad de Química, Universidad Autónoma del Carmen, Campus "General José Ortiz Ávila, Calle 56 No. 4, 24180, Carmen, Campeche, Mexico
| | - Francisco Alberto Tamayo-Ordoñez
- Facultad de Química, Universidad Autónoma del Carmen, Campus "General José Ortiz Ávila, Calle 56 No. 4, 24180, Carmen, Campeche, Mexico
| | - Maria Concepción Tamayo-Ordoñez
- Laboratorio de Ingeniería Genética, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Ing J. Cárdenas Valdez s/n, República, 25280, Saltillo, Coah, Mexico.
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6
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Crocker J, Payne JL, Walczak AM, Wittkopp PJ. Interdisciplinary approaches to predicting evolutionary biology. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220042. [PMID: 37004718 PMCID: PMC10067262 DOI: 10.1098/rstb.2022.0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Affiliation(s)
- Justin Crocker
- European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Joshua L Payne
- Computational Biology Group, Institute of Integrative Biology, Building CHN H 75.1, Universitätstrasse 16, CH-8092 Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Aleksandra M Walczak
- Laboratoire de Physique de l'École Normale Supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, 75005 Paris, France
| | - Patricia J Wittkopp
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1382, USA
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