This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A c c e p t e d M a n u s c r i p t 2 AbstractA total of 477 fecal samples from pre-weaned sheep from 5 different farms in the south west of Western Australia were screened for the presence of Cryptosporidium and Giardia using PCR. There were substantial differences in prevalence between the farms and overall prevalence was 24.5% and 11.1% respectively for Cryptosporidium and Giardia. At the 18S locus, 66 Cryptosporidium positives were identified, the majority of which were C. bovis (n = 52), followed by the cervid genotype (n= 10) and C. parvum (n = 2). At a second diagnostic locus, using C. parvum and C. hominis specific qPCR primers, 63 C. parvum positives were identified, some of which were co-infections with C. bovis. The C. parvum/C. hominis qPCR was more sensitive than the nested 18S PCR at detecting C. parvum. This may be due to the low numbers of oocysts present, as quantitation data indicated that all the C. parvum detected was present in low numbers (1-10 oocysts). It may also be that using C. parvum-specific primers is necessary to determine the true prevalence of C. parvum. Amongst Giardia positive isolates, G. duodenalis genotype E (livestock) was the most prevalent (36/53), with G.duodenalis genotype A detected in 5 positive isolates. There were also 11 mixed A and E infections detected. The findings of the present study indicate that pre-weaned lambs are not an important source of zoonotic Giardia genotypes in Australia but may be an important source of zoonotic Cryptosporidium.

This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.Page 1 of 28A c c e p t e d M a n u s c r i p t The prevalence of Cryptosporidium in sheep in the eastern states of Australia has not been 21 well described, therefore a study of the prevalence, oocyst concentration, species and subtypes of 22Cryptosporidium were assessed from lamb faecal samples at three sampling periods (weaning, post-23 weaning and pre-slaughter) from eight farms across South Australia, New South Wales, Victoria 24 and Western Australia. A total of 3,412 faecal samples were collected from approximately 1,182 25 lambs across the 4 states and screened for the presence of Cryptosporidium using a quantitative 26 PCR (qPCR) at the actin locus. Positives were typed at the 18S locus and at a second locus using C. 27 parvum and C. hominis specific qPCR primers. The overall prevalence was 16.9% (95% CI: 15.6-28 18.1%) and of the 576 positives, 500 were successfully genotyped. In general, the prevalence of 29Cryptosporidium was higher in WA than the eastern states. Cryptosporidium prevalence peaked at 30 43.9% and 37.1% at Pingelly (WA2) and Arthur River (WA1) respectively during weaning and at 31

This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.Page 1 As it has been 30 years since a new anthelmintic class was released, it is appropriate 22 to review management practices aimed at slowing the development of anthelmintic 23 resistance to all drug classes. Recommendations to delay anthelmintic resistance and 24 provide "refugia" are reviewed and a simulation model used to find optimum 25 treatment strategies that maintain nematode control. Simulated Australian conditions 26 indicated that a common successful low-risk treatment program was a rapid rotation 27 between a "triple-combination" product (benzimidazole + levamisole + abamectin) 28 and a new high-efficacy drug (monepantel). Where Haemonchus contortus was a 29 threat, moxidectin was required at critical times because of its persistent activity 30 against this parasite. Leaving up to 4% of adult sheep untreated provided sufficient 31 "refugia" for non-selected worms to reduce the risk of selecting for anthelmintic 32 resistance without compromising nematode control. 33For a new anthelmintic, efficacy estimated by faecal egg count reduction (FECR) is 34 likely to be at or close to 100%, however using current methods the 95% confidence 35 limits (CL) for 100% are incorrectly determined as 100%. The fewer eggs counted 36 pre-treatment, the more likely an estimate of 100% will occur, particularly if the true 37 efficacy is >90%. A novel way to determine the lower-CL (LCL) for 100% efficacy is 38 to reframe FECR as a binomial proportion, i.e. define: n and x as the total number of 39 eggs counted (rather than eggs per gram of faeces) for all pre-treatment and post-40 treatment animals, respectively; p the proportion of resistant eggs is p=x/n and 41 percent efficacy is 100*(1-p) (assuming equal treatment group sizes and detection 42 levels, pre-and post-treatment). The LCL is approximated from the cumulative 43 inverse beta distribution by: 95%LCL=100*(1-(BETAINV(0.975,x+1,n-x+1))). This 44 method is simpler than the current method, independent of the number of animals 45Page 3 of 47 A c c e p t e d M a n u s c r i p t 3 tested, and demonstrates that for 100% efficacy at least 37 eggs (not eggs per gram) 46 need to be counted pre-treatment before the LCL can exceed 90%. When nematode 47 aggregation is high, this method can be usefully applied to efficacy estimates lower 48 than 100%, and in this case the 95% upper-CL (UCL) can be estimated by: 49 95%UCL=100*(1-(BETAINV(0.025,x+1,n-x+1))), with the LCL approximated as 50 described above. A simulation study to estimate the precision and accuracy of this 51 method found that the more conservative 99%CL...

Fetal loss and lamb mortality between mid‐pregnancy and weaning are important economic and welfare issues for the Australian sheep industry. The aim of this study was to determine common causes of ovine abortion and stillbirths based on submissions to veterinary laboratories and identify factors that impact the determination of an aetiological diagnosis. Data for 529 investigations on abortion or stillbirth between 2000 and 2018 were retrieved from four state veterinary laboratories in Western Australia, South Australia, Victoria and Tasmania. An aetiological diagnosis was made for 57% of investigations. Investigations that included placental tissue samples were more than twice as likely to have an aetiological diagnosis compared to investigations without placenta (P = 0.017, 95% confidence interval 1.1, 4.5). Of the investigations where an aetiological diagnosis was made, 81% involved infectious abortion, with Campylobacter spp. (32%), Listeria spp. (25%) and Toxoplasma gondii (9%) being the three most common abortigenic pathogens implicated. The remaining 19% of investigations with an aetiological diagnosis included a wide range of infectious and non‐infectious diseases. Diagnoses made varied year to year and between states. No evidence of exotic abortigenic pathogens were reported. Veterinary practitioners can improve the probability of an aetiological diagnosis by emphasising to farmers the importance of collecting any aborted material, especially placenta, and appropriate storage of the tissues until they can be submitted to the laboratory. Some diseases that cause abortion in Australian sheep have zoonotic potential, and veterinary practitioners play an important role in educating clients about appropriate hygiene when handling pregnant and lambing ewes or any aborted material.

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14In this study, 96 faecal samples were collected from pregnant Merino ewes, at two broad-15 acre, commercial sheep farms in southern Western Australia, on two separate occasions 16 (16 and 2 weeks prior to lambing). Following lambing, 111 (Farm A) and 124 (Farm B) 17 female crossbred lambs (2 -6 weeks old), were individually identified using ear tags (a 18 numbered tag and a radio-frequency tag). A total of 1,155 faecal samples were collected 19 only from these individually identified lambs on five separate sampling occasions. All 20 samples were screened using PCR to detect Cryptosporidium (18S rRNA and actin loci) 21and Giardia duodenalis (glutamate dehydrogenase and triosephosphate isomerise loci). 22The overall prevalences (lambs positive for a parasite on at least one of the five 23 samplings) at Farm A and B were 81.3% and 71.4%, respectively for Cryptosporidium and 24 similarly 67.3% and 60.5% for Giardia, respectively. Cryptosporidium and Giardia 25 prevalences at individual samplings ranged between 18.5 -42.6% in lambs and were 26 <10% in the ewes. Cryptosporidium xiaoi was the most prevalent species detected at all 27 five samplings and was also isolated from lamb dam water on Farm B. Cryptosporidium 28 ubiquitum was most commonly detected in younger lambs and C. parvum was detected in 29 lambs at all five samplings, typically in older lambs and as part of a mixed species infection 30 with C. xiaoi. A novel, possibly new genotype (sheep genotype I), was identified in six 31Cryptosporidium isolates from Farm B. Giardia duodenalis assemblage E was the most 32 common genotype detected at all five samplings, with greater proportions of assemblage A 33 and mixed assemblage A and E infections identified in older lambs. This longitudinal study 34 identified high overall prevalences of Cryptosporidium and Giardia in lambs grazed 35 extensively on pastures, whilst reinforcing that sampling a random selection of animals 36 from a flock/herd on one occasion (point prevalence), underestimates the overall 37 prevalence of these parasites in the flock/herd across an extended time period. Based on 38 these findings, grazing lambs were identified as a low risk source of zoonotic 39Page 3 of 36 Cryptosporidium and Giardia species/genotypes, with these protozoa detected at all five 40 samplings in some lambs, indicating that these individuals were either unable to clear the 41 naturally acquired protozoan infections or were repeatedly re-infected from their 42 environment or other flock members. 43

Background Equine gastrointestinal nematodes (GINs) have been the subject of intermittent studies in Australia over the past few decades. However, comprehensive information on the epidemiology of equine GINs, the efficacy of available anthelmintic drugs and the prevalence of anthelmintic resistance (AR) in Australasia is lacking. Herein, we have systematically reviewed existing knowledge on the horse GINs recorded in Australia, and main aspects of their pathogeneses, epidemiology, diagnoses, treatment and control. Methods Six electronic databases were searched for publications on GINs of Australian horses that met our inclusion criteria for the systematic review. Subsets of publications were subjected to review epidemiology, diagnoses, pathogeneses, treatment and control of GINs of horses from Australia. Results A total of 51 articles published between 1950 to 2018 were included. The main GINs reported in Australian horses were cyathostomins (at least 28 species), Draschia megastoma , Habronema muscae , H. majus , Oxyuris equi , Parascaris equorum , Strongyloides westeri and Trichostrongylus axei across different climatic regions of Queensland, New South Wales, Victoria, and Western Australia. Nematodes are diagnosed based on the traditional McMaster egg counting technique, though molecular markers to characterise common GINs of equines were characterised in 1990s. The use of anthelmintic drugs remains the most widely-used strategy for controlling equine GIN parasites in Australia; however, the threshold of faecal egg count that should trigger treatment in horses, remains controversial. Furthermore, anthelmintic resistance within GIN population of horses is becoming a common problem in Australia. Conclusions Although GINs infecting Australian horses have been the subject of occasional studies over the past few decades, the effective control of GIN infections is hampered by a generalised lack of knowledge in various disciplines of equine parasitology. Therefore, coordinated and focused research is required to fill our knowledge gaps in these areas to maximise equine health and minimise economic losses associated with the parasitic infections in Australia. Electronic supplementary material The online version of this article (10.1186/s13071-019-3445-4) contains supplementary material, which is available to authorized users.

Live weight, growth rate and BCS were inconsistently associated with protozoa detection 37 across different samplings and farms. Adjusted WEC was correlated positively with FCS 38 and negatively with faecal DM%, differing between sampling occasions and farms. 39Campylobacter jejuni prevalence was very low (<1%). Adjusted WEC were not correlated 40 with carcase attributes, growth rates or live weights. This study is the first to quantify 41 productivity consequences of naturally acquired protozoa infections in lambs managed 42 under extensive farming conditions. 43