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Eccleston RC, Manko E, Campino S, Clark TG, Furnham N. A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations. eLife 2023; 12:e84756. [PMID: 38132182 PMCID: PMC10807863 DOI: 10.7554/elife.84756] [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: 11/07/2022] [Accepted: 12/21/2023] [Indexed: 12/23/2023] Open
Abstract
Pathogen evolution of drug resistance often occurs in a stepwise manner via the accumulation of multiple mutations that in combination have a non-additive impact on fitness, a phenomenon known as epistasis. The evolution of resistance via the accumulation of point mutations in the DHFR genes of Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) has been studied extensively and multiple studies have shown epistatic interactions between these mutations determine the accessible evolutionary trajectories to highly resistant multiple mutations. Here, we simulated these evolutionary trajectories using a model of molecular evolution, parameterised using Rosetta Flex ddG predictions, where selection acts to reduce the target-drug binding affinity. We observe strong agreement with pathways determined using experimentally measured IC50 values of pyrimethamine binding, which suggests binding affinity is strongly predictive of resistance and epistasis in binding affinity strongly influences the order of fixation of resistance mutations. We also infer pathways directly from the frequency of mutations found in isolate data, and observe remarkable agreement with the most likely pathways predicted by our mechanistic model, as well as those determined experimentally. This suggests mutation frequency data can be used to intuitively infer evolutionary pathways, provided sufficient sampling of the population.
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Affiliation(s)
- Ruth Charlotte Eccleston
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Emilia Manko
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Susana Campino
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Taane G Clark
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
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Ali Q, Zahid O, Mhadhbi M, Jones B, Darghouth MA, Raynes G, Afshan K, Birtles R, Sargison ND, Betson M, Chaudhry U. Genetic characterisation of the Theileria annulata cytochrome b locus and its impact on buparvaquone resistance in bovine. Int J Parasitol Drugs Drug Resist 2022; 20:65-75. [PMID: 36183440 PMCID: PMC9529669 DOI: 10.1016/j.ijpddr.2022.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/11/2022] [Accepted: 08/21/2022] [Indexed: 12/14/2022]
Abstract
Control of tropical theileriosis, caused by the apicomplexan Theileria annulata, depends on the use of a single drug, buparvaquone, the efficacy of which is compromised by the emergence of resistance. The present study was undertaken to improve understanding of the role of mutations conferring buparvaquone resistance in T. annulata, and the effects of selection pressures on their emergence and spread. First, we investigated genetic characteristics of the cytochrome b locus associated with buparvaquone resistance in 10 susceptible and 7 resistant T. annulata isolates. The 129G (GGC) mutation was found in the Q01 binding pocket and 253S (TCT) and 262S (TCA) mutations were identified within the Q02 binding pocket. Next, we examined field isolates and identified cytochrome b mutations 129G (GGC), 253S (TCT) and 262S (TCA) in 21/75 buffalo-derived and 19/119 cattle-derived T. annulata isolates, providing evidence of positive selection pressure. Both hard and soft selective sweeps were identified, with striking differences between isolates. For example, 19 buffalo-derived and 7 cattle-derived isolates contained 129G (GGC) and 253S (TCT) resistance haplotypes at a high frequency, implying the emergence of resistance by a single mutation. Two buffalo-derived and 12 cattle-derived isolates contained equally high frequencies of 129G (GGC), 253S (TCT), 129G (GGC)/253S (TCT) and 262S (TCA) resistance haplotypes, implying the emergence of resistance by pre-existing or recurrent mutations. Phylogenetic analysis further revealed that 9 and 21 unique haplotypes in buffalo and cattle-derived isolates were present in a single lineage, suggesting a single origin. We propose that animal migration between farms is an important factor in the spread of buparvaquone resistance in endemic regions of Pakistan. The overall outcomes will be useful in understanding how drug resistance emerges and spreads, and this information will help design strategies to optimise the use and lifespan of the single most drug use to control tropical theileriosis.
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Affiliation(s)
- Qasim Ali
- Faculty of Veterinary and Animal Sciences, University of Agriculture, Dera Ismail Khan, Pakistan
| | - Osama Zahid
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, UK
| | - Moez Mhadhbi
- Laboratoire de Parasitologie, École Nationale de Médecine Vétérinaire, Université de La Manouba, Sidi Thabet, Tunisia
| | - Ben Jones
- School of Veterinary Medicine, University of Surrey, UK
| | - Mohamed Aziz Darghouth
- Laboratoire de Parasitologie, École Nationale de Médecine Vétérinaire, Université de La Manouba, Sidi Thabet, Tunisia
| | - George Raynes
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, UK
| | - Kiran Afshan
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Richard Birtles
- School of Science, Engineering and Environment, University of Salford, UK
| | - Neil D. Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, UK
| | - Martha Betson
- School of Veterinary Medicine, University of Surrey, UK
| | - Umer Chaudhry
- School of Veterinary Medicine, University of Surrey, UK,Corresponding author. School of Veterinary Medicine, University of Surrey, GU2 7AL, UK.
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