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Babineau M, Collis E, Ruffell A, Bunch R, McNally J, Lyons RE, Kotze AC, Hunt PW. Selection of genome-wide SNPs for pooled allelotyping assays useful for population monitoring. Genome Biol Evol 2022; 14:6531970. [PMID: 35179579 PMCID: PMC8911822 DOI: 10.1093/gbe/evac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2022] [Indexed: 11/13/2022] Open
Abstract
Parasitic worms are serious pests of humans, livestock and crops worldwide. Multiple management strategies are employed in order to reduce their impact, and some of these may affect their genome and population allelic frequency distribution. The evolution of chemical resistance, ecological changes, and pest dispersal have allowed an increasing number of pests to become difficult to control with current management methods. Their lifestyle limits the use of ecological and individual-based management of populations. There is a need to develop rapid, affordable, and simple diagnostics to assess the efficacy of management strategies and delay the evolution of resistance to these strategies. This study presents a multi-locus, equal-representation, whole genome pooled SNPs selection approach as a monitoring tool for the ovine nematode parasite Haemonchus contortus. The SNP selection method used two reference genomes of different quality, then validated these SNPs against a high-quality recent genome assembly. From over 11 million high-quality SNPs identified, 334 SNPs were selected, of which 262 were species-specific, yielded similar allele frequencies when assessed as multiple individuals or as pools of individuals, and suitable to distinguish mixed nematode isolate pools from single isolate pools. As a proof-of-concept, 21 Australian H. contortus populations with various phenotypes and genotypes were screened. This analysis confirmed the overall low-level of genetic differentiation between populations collected from the field, but clearly identifying highly inbred populations, and populations showing genetic signatures associated with chemical resistance. The analysis showed that 66% of the SNPs were necessary for stability in assessing population genetic patterns, and SNP pairs did not show linkage according to allelic frequencies across the 21 populations. This method demonstrates that ongoing monitoring of parasite allelic frequencies and genetic changes can be achieved as a management assessment tool to identify drug-treatment failure, population incursions, and inbreeding signatures due to selection. The SNP selection method could also be applied to other parasite species.
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Affiliation(s)
- M Babineau
- CSIRO Agriculture and Food, Armidale, Australia
| | - E Collis
- School of Veterinary Science, The University of Queensland, Gatton, Qld, 4343, Australia
| | - A Ruffell
- CSIRO Agriculture and Food, St-Lucia, Australia
| | - R Bunch
- CSIRO Agriculture and Food, Armidale, Australia
| | - J McNally
- CSIRO Agriculture and Food, Armidale, Australia
| | - R E Lyons
- School of Veterinary Science, The University of Queensland, Gatton, Qld, 4343, Australia
| | - A C Kotze
- CSIRO Agriculture and Food, St-Lucia, Australia
| | - P W Hunt
- CSIRO Agriculture and Food, Armidale, Australia
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Whittaker JH, Carlson SA, Jones DE, Brewer MT. Molecular mechanisms for anthelmintic resistance in strongyle nematode parasites of veterinary importance. J Vet Pharmacol Ther 2016; 40:105-115. [PMID: 27302747 DOI: 10.1111/jvp.12330] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 05/02/2016] [Indexed: 11/26/2022]
Abstract
Veterinarians rely on a relatively limited spectrum of anthelmintic agents to control nematode parasites in domestic animals. Unfortunately, anthelmintic resistance has been an emerging problem in veterinary medicine. In particular, resistance has emerged among the strongyles, a group of gastrointestinal nematodes that infect a variety of hosts that range from large herbivores to small companion animals. Over the last several decades, a great deal of research effort has been directed toward developing an understanding of the mechanisms conferring resistance against the three major groups of anthelmintics: macrocyclic lactones, benzimidazoles, and nicotinic agonists. Our understanding of anthelmintic resistance has been largely formed by determining the mechanism of action for each drug class and then evaluating drug-resistant nematode isolates for mutations or differences in expression of target genes. More recently, drug efflux pumps have been recognized for their potential contribution to anthelmintic resistance. In this mini-review, we summarize the evidence for mechanisms of resistance in strongyle nematodes.
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Affiliation(s)
- J H Whittaker
- Department of Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, USA
| | - S A Carlson
- Department of Biomedical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, USA
| | - D E Jones
- Department of Veterinary Pathology, Iowa State University College of Veterinary Medicine, Ames, IA, USA
| | - M T Brewer
- Department of Veterinary Pathology, Iowa State University College of Veterinary Medicine, Ames, IA, USA
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Kotze AC, Hunt PW, Skuce P, von Samson-Himmelstjerna G, Martin RJ, Sager H, Krücken J, Hodgkinson J, Lespine A, Jex AR, Gilleard JS, Beech RN, Wolstenholme AJ, Demeler J, Robertson AP, Charvet CL, Neveu C, Kaminsky R, Rufener L, Alberich M, Menez C, Prichard RK. Recent advances in candidate-gene and whole-genome approaches to the discovery of anthelmintic resistance markers and the description of drug/receptor interactions. Int J Parasitol Drugs Drug Resist 2014; 4:164-84. [PMID: 25516826 PMCID: PMC4266812 DOI: 10.1016/j.ijpddr.2014.07.007] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/25/2014] [Accepted: 07/29/2014] [Indexed: 12/30/2022]
Abstract
Anthelmintic resistance has a great impact on livestock production systems worldwide, is an emerging concern in companion animal medicine, and represents a threat to our ongoing ability to control human soil-transmitted helminths. The Consortium for Anthelmintic Resistance and Susceptibility (CARS) provides a forum for scientists to meet and discuss the latest developments in the search for molecular markers of anthelmintic resistance. Such markers are important for detecting drug resistant worm populations, and indicating the likely impact of the resistance on drug efficacy. The molecular basis of resistance is also important for understanding how anthelmintics work, and how drug resistant populations arise. Changes to target receptors, drug efflux and other biological processes can be involved. This paper reports on the CARS group meeting held in August 2013 in Perth, Australia. The latest knowledge on the development of molecular markers for resistance to each of the principal classes of anthelmintics is reviewed. The molecular basis of resistance is best understood for the benzimidazole group of compounds, and we examine recent work to translate this knowledge into useful diagnostics for field use. We examine recent candidate-gene and whole-genome approaches to understanding anthelmintic resistance and identify markers. We also look at drug transporters in terms of providing both useful markers for resistance, as well as opportunities to overcome resistance through the targeting of the transporters themselves with inhibitors. Finally, we describe the tools available for the application of the newest high-throughput sequencing technologies to the study of anthelmintic resistance.
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Affiliation(s)
- Andrew C. Kotze
- CSIRO Animal, Food and Health Sciences, Brisbane, QLD, Australia
| | - Peter W. Hunt
- CSIRO Animal, Food and Health Sciences, Armidale, NSW, Australia
| | - Philip Skuce
- Parasitology Division, Moredun Research Institute, Penicuik, Midlothian, UK
| | | | - Richard J. Martin
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Heinz Sager
- Novartis Centre de Recherche Sante Animale, St. Aubin, Switzerland
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universitat Berlin, Berlin, Germany
| | - Jane Hodgkinson
- Veterinary Parasitology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Anne Lespine
- INRA, Toxalim, Research Centre in Food Toxicology, Toulouse, France
| | - Aaron R. Jex
- Faculty of Veterinary Science, University of Melbourne, Parkville, VIC, Australia
| | - John S. Gilleard
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Robin N. Beech
- Institute of Parasitology, McGill University, QC, Canada
| | - Adrian J. Wolstenholme
- Department of Infectious Diseases & Center for Tropical and Emerging Global Disease, University of Georgia, Athens, GA, USA
| | - Janina Demeler
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universitat Berlin, Berlin, Germany
| | - Alan P. Robertson
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Claude L. Charvet
- INRA, Infectiologie et Santé Publique, Nouzilly, France
- Université François Rabelais de Tours, Infectiologie et Santé Publique, Tours, France
| | - Cedric Neveu
- INRA, Infectiologie et Santé Publique, Nouzilly, France
- Université François Rabelais de Tours, Infectiologie et Santé Publique, Tours, France
| | - Ronald Kaminsky
- Novartis Centre de Recherche Sante Animale, St. Aubin, Switzerland
| | - Lucien Rufener
- Novartis Centre de Recherche Sante Animale, St. Aubin, Switzerland
| | - Melanie Alberich
- INRA, Toxalim, Research Centre in Food Toxicology, Toulouse, France
| | - Cecile Menez
- INRA, Toxalim, Research Centre in Food Toxicology, Toulouse, France
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