Next-generation sequencing amplicon analysis of the genetic diversity of Eimeria populations in livestock and wildlife samples from Australia

Alireza Zahedi; Dandan Liu; Rongchang Yang; Jill M Austen; Abbey Potter; Una Ryan

doi:10.1007/s00436-022-07764-5

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Next-generation sequencing amplicon analysis of the genetic diversity of Eimeria populations in livestock and wildlife samples from Australia

Journal article

Peer reviewed

Next-generation sequencing amplicon analysis of the genetic diversity of Eimeria populations in livestock and wildlife samples from Australia

Alireza Zahedi, Dandan Liu, Rongchang Yang, Jill M Austen, Abbey Potter and Una Ryan

Parasitology research (1987), Vol.122(2), pp.615-624

2023

DOI: https://doi.org/10.1007/s00436-022-07764-5

PMID: 36544013

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Abstract

18S ribosomal RNA

Eimeria

Next-generation sequencing (NGS)

Eimeria is an important coccidian enteric parasite that infects a wide range of hosts and can cause substantial economic losses in the poultry and livestock industries. It is common for multiple Eimeria species to infect individual hosts, and this can make species identification difficult due to morphological similarities between species and mixed chromatograms when using Sanger sequencing. Relatively few studies have applied next-generation amplicon sequencing (NGS) to determining the genetic diversity of Eimeria species in different hosts. The present study screened 408 faecal samples from a range of hosts including livestock and wildlife using a previously developed quantitative polymerase chain reaction (qPCR) at the 18S locus and conducted amplicon NGS on the positives using a ~ 455-bp fragment of the 18S locus. A total of 41 positives (10.1%) were identified by qPCR from various hosts and NGS was successful for 38 of these positives. Fifteen Eimeria species and three genotypes were detected by NGS: E. ferrisi, E. kanyana, E. potoroi, E. quokka, E. setonicis, E. trichosuri, E. reichenowi, E. angustus, E. ahsata, E. auburnensis, E. bovis, E. brasiliensis, E. christenseni, E. crandallis, E. ovinoidalis, Eimeria sp. (JF419345), Eimeria sp. (JF419349) and Eimeria sp. (JF419351). Mixed infections were detected in 55.3% (21/38) of positive samples. The most striking finding was the identification of the same species in different hosts. This could be due to contamination and/or mechanical transmission or may provide support for previous studies suggesting that Eimeria species can infect not just closely related hosts but different genera and further research is required. This is also the first study to audit Eimeria populations in livestock (sheep and cattle) by NGS and could be applied in the future to determine the extent of pathogenic species and outcomes of Eimeria control strategies

Details

Title: Next-generation sequencing amplicon analysis of the genetic diversity of Eimeria populations in livestock and wildlife samples from Australia
Authors/Creators: Alireza Zahedi - Murdoch University
Dandan Liu - Yangzhou University
Rongchang Yang - Murdoch University
Jill M Austen - Murdoch University
Abbey Potter - Government of Western Australia Department of Health
Una Ryan - Murdoch University
Publication Details: Parasitology research (1987), Vol.122(2), pp.615-624
Identifiers: 991005578663307891
Murdoch Affiliation: Centre for Biosecurity and One Health
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.217 Parasitology - Malaria, Toxoplasmosis & Coccidiosis; 1.217.1890 Coccidiosis
Web Of Science research areas: Parasitology
ESI research areas: Microbiology