Epidemiological insights into the prevalence of, and risk factors for, Eimeria species in Australian dairy goats Endris A. Ali, Abdul Ghafar, Sandra Baxendell, Charles Gauci, Ian Beveridge, Mark A. Stevenson, Abdul Jabbar Veterinary Journal, 2026 This cross-sectional study investigated the prevalence, species composition and risk factors for Eimeria infections in Australian dairy goats. A total of 1,188 goat faecal samples was collected from 71 herds between November 2023 and July 2024. Oocysts per gram (OPG) of faeces were quantified using the modified McMaster technique, and Eimeria species were identified morphologically. The animal-level prevalence of Eimeria was adjusted for the effect of herd, and risk factors were analysed using multivariable mixed-effects logistic regression models. The adjusted animal-level prevalence of Eimeria species was 71% (95% confidence intervals (CI) 63% to 77%), and a herd-level prevalence was 97% (95% CI 93% to 100%). The highest adjusted prevalence of Eimeria species (86%, 95% CI 80% to 91%) and median OPG (240; Q1:30, Q3:1,500) were identified in kids. Prevalence and oocyst shedding varied significantly by climatic zones, with the winter rainfall zone presenting the highest adjusted prevalence (75%, 95% CI 65% to 84%) and median OPG (60, Q1: 0, Q3: 360). Nine Eimeria species were identified, with E. arloingi (100%), E. ninakohlyakimovae (94%) and E. alijevi (91%) being most prevalent. Significant risk factors included age, sex, climatic zone, stocking rate, bedding type and bedding replacement frequency. These findings demonstrate that Eimeria infection is highly endemic and strongly clustered within Australian dairy goat herds, particularly in young animals, and highlight the importance of age-targeted and management-based control strategies. Improved husbandry practices may reduce environmental contamination and mitigate the production impact of caprine coccidiosis. • A total of 1,188 dairy goats from 71 herds across six Australian states was tested. • Adjusted animal-level prevalence of Eimeria spp. was 71% (95% CI: 63–77%). • Herd-level prevalence was 97% (95% CI: 93–100%). • Significant risk factors were age, sex, climatic zone, stocking rate, bedding type and replacement frequency. • The most abundant Eimeria species were E. arloingi , E. ninakohlyakimovae and E. alijevi .
Ten simple rules for implementing deep amplicon sequencing in parasitology Jan Šlapeta, Jürgen Krücken, Alicia Rojas, Alex Chambers, Lynsey A. Melville, María Martínez-Valladares, Candela Canton, Emily K. Francis, Osama Zahid, Ana Cláudia A. Albuquerque, Dave J. Bartley, Cesar C. Bassetto, Orla Byrne, Vito Colella, Livio M. Costa-Junior, Stephen R. Doyle, Mike Evans, Abdul Ghafar, Pablo Godoy, Naoki Hayashi, Mohamed A. Helal, Lucas G. Huggins, Abdul Jabbar, Rhys A. Jones, Benedict E. Karani, Juan Pedro Liron, Laura Maté, Amanda McEvoy, Khalid M. Mohammedsalih, Grace Mulcahy, Martin K. Nielsen, Barbora Pafčo, Laura E. Peachey, Joby Robleto-Quesada, Georg von Samson-Himmelstjerna, Lucas C. de Sousa-Paula, John S. Gilleard International Journal for Parasitology, 2026 Deep amplicon sequencing is transforming parasitology by enabling high-throughput profiling of parasite communities and detection of resistance-associated genetic variants. Despite its growing adoption, many researchers face challenges in implementation, and its full potential is often hindered by challenges in experimental design, including marker selection, data analysis and reproducibility. This article presents ten simple rules for applying deep amplicon sequencing in parasitology, developed through expert consensus at a deep amplicon sequencing symposium during the 2025 World Association for the Advancement of Veterinary Parasitology conference. These rules cover essential aspects from formulating research questions and choosing appropriate markers to managing data workflows and contributing to reference databases. We highlight the importance of integrating deep amplicon sequencing with traditional parasitological methods, ensuring transparent reporting and investing in capacity building. Whether you are new to deep amplicon sequencing or seeking to improve your current practices, these guidelines offer practical advice to enhance the robustness, reproducibility, and impact of your research. By adopting these principles, parasitologists can contribute to, and advance, a more reliable and collaborative scientific landscape.
A reproducible, host-free feeding system for adult Haemaphysalis longicornis Abdul Ghafar, Bahar E. Mustafa, Charles Gauci, Ian Beveridge, Robin B. Gasser, Ard M. Nijhof, Abdul Jabbar Veterinary Journal, 2026 Haemaphysalis longicornis is a parthenogenetic three-host tick that has expanded from East Asia into Australasia and the Americas, where it poses increasing veterinary and public-health concern. Yet, laboratory research has been constrained partly by the absence of a reliable artificial feeding system. Here, we establish and optimise an artificial, host-free in vitro feeding platform for adult H. longicornis, utilising a thin silicone membrane that overcomes the species' short hypostome and limited mouthpart mobility. Across six independent experiments using field-collected parthenogenetic adult females from Australia, 67 % (35/52) of ticks attached and 74.3 % (26/35) engorged, achieving a mean engorgement weight of 161 mg (range: 44.8-275 mg), a mean egg mass of 67 mg (11.4-137 mg) and mean bloodmeal-to-egg conversion efficiency of 40 % (range: 16.7-59.9 %). All engorged females oviposited and produced viable larvae, with egg hatchability exceeding 92 % (mean ∼98 %) and engorgement weight strongly associating with fecundity (r = 0.82). Feeding was completed within 2-7 days, comparable to, or shorter than, feeding on live hosts; hair extract treatment did not enhance feeding or reproductive performance. This host-free system essentially replicates natural feeding performance under controlled laboratory conditions and supports the complete reproductive cycle of adult H. longicornis without an animal host. It provides a reproducible and ethical platform for acaricide and vaccine discovery and studies of tick physiology and pathogen-vector interactions, establishing a foundation for standardised, scalable and welfare-compliant tick research within a One Health framework.
Theileria orientalis Abdul Ghafar, Ard M. Nijhof, Abdul Jabbar Trends in Parasitology, 2026 Theileria orientalis is a tick-borne apicomplexan parasite causing oriental theileriosis in cattle and water buffalo. Once considered as benign, the emergence of pathogenic Ikeda and Chitose genotypes has led to outbreaks with affected animals showing severe anaemia, jaundice, abortion, and production losses predominantly in the Asia–Pacific, with cases rising in other parts of the world. The parasite cycles through schizogony in leukocytes, merogony in erythrocytes, and sexual development in Haemaphysalis longicornis ticks.
Knowledge, attitudes and practices of Australian dairy goat farmers towards the control of gastrointestinal parasites Endris A. Ali, Ghazanfar Abbas, Ian Beveridge, Sandra Baxendell, Berwyn Squire, Mark A. Stevenson, Abdul Ghafar, Abdul Jabbar Parasites and Vectors, 2025 Background Gastrointestinal parasites such as nematodes and coccidia are responsible for significant economic losses in the goat industry globally. An indiscriminate use of antiparasitic drugs, primarily registered for use in sheep and cattle, in goats has resulted in drug-resistant gastrointestinal parasites. Very little is known about the gastrointestinal parasite control practices used by Australian dairy goat farmers that are pivotal for achieving sustainable control of economically important parasites. The study reported here provides insights into gastrointestinal parasite control practices of Australian dairy goat farmers based on responses to an online survey. Methods The questionnaire comprised 58 questions on farm demography, husbandry and grazing management, knowledge of gastrointestinal parasites and their importance in dairy goats, diagnosis of infections, antiparasitic drugs and alternate control options. After a pilot survey (n = 15 respondents), a link to the questionnaire was available to all (n = 456) registered members of the Dairy Goat Society of Australia Ltd from 17 April to 16 June 2023. Multiple correspondence analyses (MCA) were performed to explore the association between selected parasite control practices. Results A total of 66 (14%) respondents completed the questionnaire. Of these, 74% (49/66) observed parasite-related illnesses in their goats; two-thirds of them assessed worms burden using faecal egg counts (FECs), with 26% (39/149) deworming their goats based on the results of the FECs. Most respondents (97%; 183/188) perceived that gastrointestinal parasites caused production losses and ranked Haemonchus contortus as the most important parasite. Anitparasitic drugs were used by 94% (62/66) of respondents, with the most frequently used anthelmintics being a commercial combination of four anthelmintics (levamisole, closantel, albendazole and abamectin), benzimidazoles and macrocyclic lactones. Most respondents (77%; 51/66) were unaware of anthelmintic resistance on their property. MCA results delineated two clusters of gastrointestinal parasites management. Conclusions This study provides insights into the demography of Australian dairy goat farms, the husbandry and grazing practices used by dairy goat farmers, their knowledge regarding gastrointestinal parasites and their practices for internal parasite control, thereby paving the way for tackling drug resistance in gastrointestinal parasites in dairy goats. Graphical Abstract
Recent advances in intestinal helminth parasites of horses in the Asia-Pacific region: Current trends, challenges and future directions Ghazanfar Abbas, Martin K. Nielsen, Charles E-Hage, Abdul Ghafar, Ian Beveridge, Jenni Bauquier, Anne Beasley, Edwina J.A. Wilkes, Peter Carrigan, Lucy Cudmore, Caroline Jacobson, Kristopher J. Hughes, Abdul Jabbar International Journal for Parasitology Drugs and Drug Resistance, 2025 Over the past 25 years, significant progress has been made in understanding and managing equine gastrointestinal parasites in the Asia-Pacific region, particularly in Australia and New Zealand. This review synthesises current knowledge of the epidemiology, diagnostic methods, anthelmintic resistance (AR), and control strategies for major equine intestinal parasites, including cyathostomins, Parascaris spp., Anoplocephala perfoliata, and Strongyloides westeri. Recent studies highlight substantial regional variation in parasite prevalence, egg shedding and cyathostomin population composition, shaped by diverse climatic conditions. Of increasing concern is the emergence of resistance to commonly used anthelmintics which is now evident in both Parascaris and cyathostomins, although data for S. westeri and A. perfoliata remain limited. High-throughput molecular diagnostics, such as next-generation sequencing, have advanced species-level characterisation in Australia and Thailand. ELISA-based tests for A. perfoliata and encysted cyathostomins are promising but remain unvalidated and underutilised regionally. The routine use of combination anthelmintics, including benzimidazoles, praziquantel, pyrimidines, and macrocyclic lactones, may accelerate resistance across nematode and cestode populations, emphasising the need for regular efficacy monitoring and improved antiparasitic stewardship. Findings from recent research on horse parasites in Australia have informed the development of country's first national equine parasite control guidelines which recommend targeted or selective treatment strategies. However, the effectiveness of these strategies requires ongoing evaluation, particularly in year-round grazing systems in tropical and subtropical regions. Sustainable parasite control will depend on the integration of non-chemical strategies along with the use of anthelmintics and the establishment of a national parasite surveillance database. This review highlights the need for climate-specific treatment protocols, strengthened collaborative research infrastructure, and continued investment in innovative diagnostic and control methods to preserve equine health and anthelmintic efficacy across the region.
Integrative use of conventional and DNA metabarcoding methods reveals high diversity, prevalence and intensity of gastrointestinal parasites in pigs from Victoria, Australia Ghazanfar Abbas, Yuet On Lee, Hannah Mitchell, Abdul Ghafar, Mark A. Stevenson, Charles G. Gauci, Leah G. Starick, Regina M. Fogarty, Bernie Gleeson, Dianne E. Phillips, Tao Wang, Robin B. Gasser, Abdul Jabbar Research in Veterinary Science, 2025 This cross-sectional study provides the first integrated parasitological and molecular survey of gastrointestinal parasites in pigs from 69 commercial and backyard farms across Victoria, Australia. In total, 1222 faecal samples were tested using the modified McMaster technique to determine faecal egg and oocyst counts. Samples test-positive for strongylid nematode stages were characterised further using next-generation sequencing (NGS) targeting the second internal transcribed spacer (ITS-2) of ribosomal DNA as a species-specific genetic marker. Based on faecal egg/oocyst count, 39.1 % of farms tested positive for at least one parasite taxon. Coccidia were most prevalent (9.5 %) in samples, followed by Ascaris suum (5.2 %), Trichuris suis (4.5 %) and strongylid nematodes (1.8 %). Infection intensity was highest for coccidia, with notable burdens also for Ascaris suum and strongylid in individual samples. Eggs of Metastrongylus spp. were detected for the first time in Australian domestic pigs on an outdoor farm. Prevalence patterns varied substantially according to the production system and pig age group: coccidia dominated in mature breeders (17.8 %) and piglets (15.4 %) in backyard settings (33.7 %), whereas Ascaris peaked in mature breeders (9.1 %) and growers/finishers (up to 5 %) in semi-intensive systems (21.7 %). Strongylid eggs were most frequently detected in gilts and mature breeders from backyard and extensive systems. Notably, NGS revealed a diverse community of strongylid nematodes, including Oesophagostomum dentatum, O. quadrispinulatum and Trichostrongylus axei and Metastrongylus apri and M. salmi . This is the first molecular detection of Metastrongylus species in domestic pigs in Australia. These findings uncover a considerable and underappreciated parasitic burden in pig populations across multiple production systems in Victoria. • Survey of 69 Australian pig farms revealed varying levels of helminth and coccidian infections. • Parasite prevalence differed according to pig age and farming system. • Coccidia were the most prevalent parasites, followed by Ascaris, Trichuris, and strongyles. • Metastrongylus spp. were detected for the first time in domestic pigs in Australia. • DNA metabarcoding identified Oesophagostomum dentatum and Metastrongylus apri as relatively abundant species.
Bayesian latent class analyses show that serological testing outperforms conventional diagnostic methods for the detection of Ascaris in (individual) pigs Ghazanfar Abbas, Hannah Mitchell, Mark Stevenson, Yuet On Lee, Abdul Ghafar, Charles Gauci, Hagan Brodziak, Leah G. Starick, Regina M. Fogarty, Bernie Gleeson, Dianne Phillips, Tao Wang, Robin B. Gasser, Abdul Jabbar Veterinary Journal, 2025 This study employed Bayesian latent class analyses to estimate the diagnostic accuracy of faecal egg count (FEC), milk spot detection and the ELISA for detection of Ascaris suum using matched samples from individual pigs in Australia. A total of 251 blood, faecal and liver samples were collected from finisher pigs from four Victorian pig farms. Matched samples (n = 189) were used to compare the three diagnostic tests. The ELISA detected a higher proportion of positive samples (56 %; 95 % CI 48-62 %) compared to milk spot detection (42 %; 95 % CI 35-49 %) and FEC (17 %; 95 % CI 12-23 %). Only the ELISA detected A. suum infections on two of the four farms, with 14 % and 41 % within-farm prevalence estimates. Agreement between diagnostic tests was moderate for FEC and milk spot detection (Cohen's kappa 0.42; 95 % CI 0.30-0.53) and ELISA and milk spot detection (0.52; 0.41-0.64), while fair agreement was observed between FEC and ELISA (0.28; 0.19-0.37). Our latent class analyses identified a higher diagnostic sensitivity for the ELISA (0.92; 95 % CrI [credible interval] 0.86-0.96) than FEC (0.43; 0.34-0.53) and milk spot detection (0.86; 0.79-0.92). A strong association was observed between ELISA outcomes (optical density [OD] and OD ratio [ODr]) and milk spot grades (low, medium, high), with higher OD and ODr values corresponding to an increased number of milk spots on the liver. This study highlights the limitations of conventional A. suum detection methods. Quantitative estimates of the diagnostic sensitivity of the ELISA facilitate its use as a tool for assessing A. suum exposure in pig herds.
High Prevalence and Genetic Heterogeneity of Anaplasma marginale in Smallholder Bovine Populations of Pakistan, and Its Implications Abdul Ghafar, Waseem Shaukat, Muhammad Waqas, Charles G. Gauci, Robin B. Gasser, Abdul Jabbar Pathogens, 2025 Bovine anaplasmosis, caused by Anaplasma marginale, is a major tick-borne disease in tropical and subtropical regions of the world, leading to significant production losses. Prolonged convalescence periods are common and surviving animals often become subclinical carriers. This study aimed to detect and characterise A. marginale in bovines in smallholder dairy farms across diverse climatic zones of Pakistan using molecular methods. In total, 321 blood DNA samples from apparently healthy cattle (n = 174) and buffaloes (n = 147) from six districts in Pakistan were tested for A. marginale using a nested PCR assay, targeting part of the major surface protein B gene (msp1β) as a genetic marker, followed by agarose gel electrophoresis and selective sequencing of amplicons from test-positive samples. Of the 321 DNA samples tested, 135 (42.1%) were test-positive for A. marginale. Prevalence was significantly higher in cattle (64.4%; 112/174) than in buffaloes (15.6%; 23/147), and female bovines (43.5%; 108/248) were more frequently infected than males (37%; 27/73). Phylogenetic analysis of the msp1β sequence data (n = 42) revealed that A. marginale from Pakistan clustered with those from Brazil, Thailand, South Africa, and the USA. This study represents the first comprehensive investigation of A. marginale from bovines from diverse agroecological zones of Pakistan and will further stimulate population genetic studies of A. marginale and investigations into the economic impact of subclinical infections in bovines in smallholder farming systems.
A national survey of anthelmintic resistance in ascarid and strongylid nematodes in Australian Thoroughbred horses Ghazanfar Abbas, Abdul Ghafar, Emma McConnell, Anne Beasley, Jenni Bauquier, Edwina J.A. Wilkes, Charles El-Hage, Peter Carrigan, Lucy Cudmore, John Hurley, Charles G. Gauci, Ian Beveridge, Elysia Ling, Caroline Jacobson, Mark A. Stevenson, Martin K. Nielsen, Kristopher J. Hughes, Abdul Jabbar International Journal for Parasitology Drugs and Drug Resistance, 2024
Egg reappearance periods of anthelmintics against equine cyathostomins: The state of play revisited Stephanie L. Macdonald, Ghazanfar Abbas, Abdul Ghafar, Charles G. Gauci, Jenni Bauquier, Charles El-Hage, Brett Tennent-Brown, Edwina J.A. Wilkes, Anne Beasley, Caroline Jacobson, Lucy Cudmore, Peter Carrigan, John Hurley, Ian Beveridge, Kristopher J. Hughes, Martin K. Nielsen, Abdul Jabbar International Journal for Parasitology Drugs and Drug Resistance, 2023
Unravelling the Diversity of Microorganisms in Ticks from Australian Wildlife Abdul Ghafar, Nick Davies, Mythili Tadepalli, Amanda Breidahl, Clare Death, Philip Haros, Yuting Li, Peter Dann, Alejandro Cabezas-Cruz, Sara Moutailler, Angélique Foucault-Simonin, Charles G. Gauci, John Stenos, Jasmin Hufschmid, Abdul Jabbar Pathogens, 2023
Molecular diagnostics for gastrointestinal helminths in equids: Past, present and future Abdul Ghafar, Ghazanfar Abbas, Anne Beasley, Jenni Bauquier, Edwina J.A. Wilkes, Caroline Jacobson, Emma McConnell, Charles El-Hage, Peter Carrigan, Lucy Cudmore, Brett Tennent-Brown, John Hurley, Martin K. Nielsen, Charles G. Gauci, Ian Beveridge, Kristopher J. Hughes, Abdul Jabbar Veterinary Parasitology, 2023
Cyathostomin resistance to moxidectin and combinations of anthelmintics in Australian horses Ghazanfar Abbas, Abdul Ghafar, John Hurley, Jenni Bauquier, Anne Beasley, Edwina J. A. Wilkes, Caroline Jacobson, Charles El-Hage, Lucy Cudmore, Peter Carrigan, Brett Tennent-Brown, Charles G. Gauci, Martin K. Nielsen, Kristopher J. Hughes, Ian Beveridge, Abdul Jabbar Parasites and Vectors, 2021
Molecular detection of Strongyloides sp. in Australian Thoroughbred foals Ghazanfar Abbas, Abdul Ghafar, Anson V. Koehler, Jenni Bauquier, Edwina J. A. Wilkes, Caroline Jacobson, Anne Beasley, John Hurley, Lucy Cudmore, Peter Carrigan, Brett Tennent-Brown, Charles El-Hage, Martin K. Nielsen, Charles G. Gauci, Kristopher J. Hughes, Ian Beveridge, Abdul Jabbar Parasites and Vectors, 2021
