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This review is aimed to (i) appraise the literature on the use of molecular techniques for the detection, quantification and differentiation of gastrointestinal helminths (GIH) of equids, (ii) identify the knowledge gaps and, (iii) discuss diagnostic prospects in equine parasitology. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for systematic reviews, we retrieved 54 studies (horses: 50/54; donkeys and zebras: 4/54) from four databases. Polymerase chain reaction (PCR) was employed in all of the studies whereas PCR amplicons were sequenced in only 18 of them. Other techniques used (including modifications of PCR) were reverse line blot, quantitative (q)PCR, restriction fragment length polymorphism, nested-PCR, PCR-directed next-generation sequencing, Southern blotting, single strand conformation polymorphism, PCR-enzyme linked immunosorbent assay, matrix-assisted laser desorption/ionisation-time of flight and random amplification of polymorphic DNA. Most of the studies (53/54) used nuclear ribosomal RNA (including the internal transcribed spacers, intergenic spacer, 5.8 S, 18 S, 28 S and 12 S) as target loci while cytochrome c oxidase subunit 1 and random genomic regions were targeted in only three and one studies, respectively. Overall, to date, the majority of molecular studies have focused on the diagnosis and identification of GIHs of equids (i.e. species of Anoplocephala, Craterostomum, cyathostomins, Oesophagodontus, Parascaris, Strongylus, Strongyloides and Triodontophorus), with a recent shift towards investigations on anthelmintic resistance and the use of high-throughput nemabiome metabarcoding. With the increasing reports of anthelmintic resistance in equid GIHs, it is crucial to develop and apply techniques such as advanced metabarcoding for surveillance of parasite populations in order to gain detailed insights into their diversity and sustainable control. To the best of our knowledge, this is the first systematic review that evaluates molecular investigations published on the diagnosis and quantification of equid GIHs and provides useful insights into important knowledge gaps and future research directions in equid molecular parasitology.

Lamb survival is an important welfare and productivity issue for sheep industries worldwide. Lower lamb survival has been reported for primiparous ewes, but the causes of this are not well studied. The aim of this study was to determine causes of perinatal deaths for lambs born to primiparous ewes in Western Australia, and identify if infectious diseases are implicated. Lamb mortality from birth to marking were determined for 11 primiparous ewe flocks on 10 farms in Western Australia. Lamb mortality from birth to marking averaged 14% for single-born and 26% for multiple-born lambs. Lamb necropsies (n = 298) identified starvation–mismosthering–exposure (34%), dystocia (24%) and stillbirth (15%) as the most common causes of perinatal lamb death. There was no evidence of exotic abortigenic pathogens in aborted and stillborn lambs (n = 35). Chlamydia pecorum was detected by qPCR in 15/35 aborted and stillborn lambs on 5/6 farms. Preliminary molecular characterisation of C. pecorum detected in samples from aborted and stillborn lambs (n = 8) using both Multilocus Sequence Typing and ompA genotyping indicated all strains were genetically identical to previously described pathogenic livestock strains, denoted ST23, and dissimilar to gastrointestinal strains. High frequency of detection of a pathogenic C. pecorum strains ST23 associated with ovine abortion and stillbirth on multiple farms located across a wide geographic area has not been previously reported. Chlamydia pecorum may contribute to reproductive wastage for primiparous sheep in Western Australia. Further investigation to understand C. pecorum epidemiology and impact on sheep reproduction is warranted.

Background Toxoplasma gondii causes reproductive losses in sheep worldwide, including Australia. The reproductive performance of primiparous ewes is typically lower than for mature, multiparous ewes, and younger ewes are more likely to be immunologically naïve and therefore more susceptible to reproductive disease if T. gondii infection occurs during pregnancy. The aim of this study was to assess the impact of infection with T. gondii on the reproductive performance of primiparous ewes in southern Australia using a prospective cohort study. This will inform the need for targeted control strategies for T. gondii in Australian sheep. Results Toxoplasma gondii seropositivity using indirect ELISA was detected at 16/28 farms located across southern Australia. Apparent seropositivity to T. gondii was lower in primiparous ewes (1.1, 95% confidence interval (CI) 0.6, 1.8) compared to mature, multiparous ewes (8.1, 95% CI 6.0, 10.5; P Toxoplasma gondii seroconversion during the gestation and lambing period was confirmed for 11/1097 (1.0, 95% CI 0.5, 1.7) of pregnant primiparous ewes that failed to raise a lamb, and 1/161 (0.6, 95% CI 0.1, 2.9) primiparous ewes with confirmed mid-pregnancy abortion. Conclusions Low frequency of detection of T. gondii seroconversion during gestation and low frequency of seropositivity to T. gondii suggests that toxoplasmosis was not an important contributor to reproductive losses in primiparous ewes on farms located over a wide geographical area in southern Australia.

Coxiella burnetii can cause reproductive disease in sheep and zoonotic Q-fever infections in humans. The role of infectious diseases including coxiellosis in causing poorer reproductive performance of primiparous ewes is not well studied. The aim of this study was to determine if natural exposure to C. burnetii is associated with poor reproductive performance of primiparous ewes and compare seroprevalence of primiparous and multiparous ewes. Coxiella burnetii seroprevalence was 0.08% (95% confidence interval 0.01, 0.36) in primiparous ewes and 0.36% (0.07, 1.14) in mature ewes. Coxiella burnetii was not detected in tissue samples from aborted or stillborn lambs using molecular diagnostic tests (qPCR). These findings suggest that C. burnetii infection was unlikely to be an important contributor to abortion and perinatal mortalities observed for primiparous ewes, and exposure to C. burnetii was not widespread in ewes on farms located over wide geographical region of southern Australia.

Traditional methods of detecting Chlamydia pecorum in tissue samples such as polymerase chain reaction or cell culture are laborious and costly. We evaluated the use of a previously developed C. pecorum LAMP assay using minimally processed ovine samples. Cotyledon (n = 16), foetal liver (n = 22), foetal lung (n = 2), and vaginal (n = 6) swabs, in addition to cotyledon (n = 6) and foetal liver (n = 8) tissue samples, were rapidly processed and used for LAMP testing without DNA extraction. Overall, LAMP test results were highly congruent with the in-house reference qPCR, with 80.43% (37/46; 72.73% positive agreement (PA); 84.75% negative agreement (NA)) overall agreeance for swab samples, and 85.71% (12/14; 80% PA; 88.89% NA) overall agreeance for tissue samples. Out of the 11 total discrepant results, discrepancy was mainly observed in samples (n = 10) with less than 100 copies/µL C. pecorum DNA. While sensitivity could be improved, the simplicity, low cost, and accuracy of detection makes this test amenable for use at point-of-care for detecting C. pecorum in sheep.

The role of infectious diseases including coxiellosis in causing poorer reproductive performance of primiparous ewes are not well studied. The aims of this study were to determine if natural exposure to Coxiella burnetii is widespread in breeding ewes and whether seropositivity is associated with poor reproductive performance of primiparous ewes. Seropositivity to Coxiella burnetii was 0.08% (CI95% 0.01, 0.36) in primiparous ewes and 0.36% (CI95% 0.07, 1.14) in mature ewes. Coxiella burnetii was not detected in aborted or stillborn lambs using qPCR. These findings suggest C. burnetii infection was unlikely to be an important contributor to abortion and perinatal mortalities observed for primiparous ewe flocks, and exposure to C. burnetii was not widespread in ewes on farms located over wide geographical region of southern Australia. Whilst ewes on these farms were not an important reservoir for C. burnetii, sporadic zoonotic transmission from sheep is reported and has public health implications.

Neospora caninum has been implicated as a sporadic cause of abortion and perinatal deaths in sheep flocks globally. However, its significance as a reproductive pathogen for sheep in Australia remains unknown. The aims of this study were to (i) determine the seroprevalence of N. caninum in Australian breeding ewes and (ii) examine if natural exposure to N. caninum is associated with poor reproductive performance of primiparous ewes in southern Australia. Thirty flocks of primiparous ewes (aged 1-2 years old at lambing) from 28 farms in three states (Western Australia, South Australia and Victoria) were monitored between mating and lamb marking. Blood samples were also collected from multiparous mature ewes (aged 3 years or older) at each farm. Seroprevalence for anti-N. caninum IgG using indirect ELISA was determined for a subset of primiparous ewes that were predominantly determined to be pregnant and subsequently failed to rear a lamb (n = 1279) and randomly selected mature multiparous ewes with unknown reproductive status (n = 558). Neopsora caninum apparent seroprevalence was 0.16% (95% confidence interval 0.03%, 0.5%) in primiparous ewes, with seropositivity identified in two ewes from farms located in South Australia and Victoria. There was no evidence of seropositivity in mature ewes with apparent seroprevalence 0% (0%, 0.45%). These findings suggest that N. caninum infection was not widespread in primiparous ewes or mature multiparous ewes on these farms, and exposure to N. caninum infection was unlikely to explain abortion and perinatal mortalities observed for primiparous ewes.

Faecal egg counting techniques (FECT) form the cornerstone for the detection of gastrointestinal parasites in equines. For this purpose, several flotation, centrifugation, image- and artificial intelligence-based techniques are used, with varying levels of performance. This review aimed to critically appraise the literature on the assessment and comparison of various coprological techniques and/or modifications of these techniques used for equines and to identify the knowledge gaps and future research directions. We searched three databases for published scientific studies on the assessment and comparison of FECT in equines and included 27 studies in the final synthesis. Overall, the performance parameters of McMaster (81.5%), Mini-FLOTAC® (33.3%) and simple flotation (25.5%) techniques were assessed in most of the studies, with 77.8% of them comparing the performance of at least two or three methods. The detection of strongyle, Parascaris spp. and cestode eggs was assessed for various FECT in 70.4%, 18.5% and 18.5% studies, respectively. A sugar-based flotation solution with a specific gravity of ≥1.2 was found to be the optimal flotation solution for parasitic eggs in the majority of FECT. No uniform or standardised protocol was followed for the comparison of various FECT, and the tested sample size (i.e. equine population and faecal samples) also varied substantially across all studies. To the best of our knowledge, this is the first systematic review to evaluate studies on the comparison of FECT in equines and it highlights important knowledge gaps in the evaluation and comparison of such techniques.

Dystocia contributes to lamb and ewe mortality in the periparturient period but impacts for extensive sheep production systems remain poorly understood. Here we show that lamb and ewe mortality associated with dystocia has important impacts on sheep production in Australia and New Zealand, and quantify financial impacts for the Australian sheep industry. A systematic review of the literature identified 11 publications published since 1990 that reported sheep mortality due to dystocia in Australia or New Zealand. Assumptions for ewe breeding flock structure and reproductive performance were based on Australian sheep industry data. The proportion of lamb mortality attributable to dystocia (including stillbirths and perinatal deaths with evidence of hypoxic injury) pooled across all studies (pooled proportional mortality ratio) was 47 % (95 % Confidence Interval (CI): 38, 55). Pooled proportional mortality ratio for Australian studies was 53 % (95 %CI: 47, 60), and for New Zealand studies was 35 % (95 %CI: 19, 51). Pooled proportional mortality ratio was similar for lambs born to Merino and non-Merino ewes, although more data are needed to determine effects of ewe breed independent of other factors. Pooled proportional mortality ratio was higher for single lambs (59 %; 95 % CI: 55, 63) than twin (47 %; 41, 54) or triplet (49 %; 46, 52) lambs. However, the number of dystocia-associated mortalities is higher for twin-born lambs than for singles because total mortality is higher for twin-born lambs. It is estimated that approximately 7.7 million lamb deaths and 297,500 ewe deaths per year are attributable to dystocia in Australia for the national flock of 38 million breeding ewes. The whole-farm bio-economic Model of an Integrated Dryland Agricultural System (MIDAS) was used to determine the impacts of dystocia-associated ewe and lamb mortality on Australian farm profit. Dystocia is estimated to reduce Australian national farm profit by AU$780 million or $23.00 per ewe mated based on an assumed lamb sale price of AU$6.50 per kg carcass weight. These estimates do not include the costs of reduced productivity for surviving ewes and lambs, intervention, post-farmgate impacts, delayed genetic progress, or impacts on animal welfare and access into sheep meat and wool markets. Reducing dystocia through improved genetics and sheep management will improve animal welfare and farm profit.

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.

Associations between faecal shedding of pathogenic Yersinia enterocolitica (based on the yst virulence gene) with growth, carcass weight and diarrhoea were investigated using an observational longitudinal study of 1200 crossbred prime (meat) lambs on eight Australian farms. Live weight, breech faecal soiling score (scale 1-5) and faecal consistency score (FCS; scale 1-5) were recorded, and faecal samples collected from each lamb on three sampling occasions; weaning (≈12 weeks of age), post-weaning (≈19 weeks) and pre-slaughter (≈29 weeks). Hot standard carcass weight was measured at slaughter. Faecal samples were screened for presence and concentration of pathogenic Y. enterocolitica using quantitative PCR. Associations of pathogenic Y. enterocolitica detection and shedding intensity with lamb health and production were assessed using general linear models (carcass weight), linear mixed effects models (live weight, FCS and breech soiling score) and non-parametric tests (FCS and breech soiling score). Prevalence for non-pelleted faeces (FCS ≥ 3.0) and diarrhoea (FCS ≥ 4.0) were compared with the two-tailed z-test, odds ratios and relative risk. Lambs shedding pathogenic Y. enterocolitica were 3.78 kg lighter post-weaning (P < 0.001) and 2.61 kg lighter pre-slaughter (P = 0.035) compared to lambs in which pathogenic Y. enterocolitica was not detected. Higher faecal concentration of pathogenic Y. enterocolitica was associated with lower live weight (P < 0.001). There was no association between pathogenic Y. enterocolitica detection and carcass weight. Overall, there was no evidence of association between pathogenic Y. enterocolitica detection and diarrhoea (higher FCS, higher risk for non-pelleted faeces or diarrhoea, or higher breech soiling score). Only one flock had increased relative risk for non-pelleted faeces associated with pathogenic Y. enterocolitica detection, and one other flock had increased relative risk for diarrhoea associated with pathogenic Y. enterocolitica detection. This is the first report of an association between reduced sheep live weight and pathogenic Y. enterocolitica based on the presence of the yst gene for heat stable enterotoxin determined by qPCR in sheep. Notably, impacts on live weight were observed in the absence of diarrhoea.

Many island ecosystems are exposed to ecological threats through invasive species and the parasites they harbour. Parasites can impact endemic island populations whether they are stable populations...

Western Australian rangeland goats were surveyed for faecal carriage of Salmonella enterica and Campylobacter spp. Faecal samples were collected from 125 goats on four occasions. The first sample was collected immediately upon arrival at a commercial goat depot (feedlot). Subsequent samples were collected at one month intervals thereafter. Frequency of detection and faecal carriage intensity were determined using qPCR targeting the S. enterica outer membrane protein (ompF) and Campylobacter spp. purine biosynthesis gene (purA). Salmonella enterica were identified in 40/500 of faecal samples, with S. enterica faecal carriage detected in 30% (38/125) goats over the duration of the study. Campylobacter spp. were identified in 12/500 of samples, with Campylobacter spp. detected in 10% (12/125) goats over duration of the study. Frequency of detection was highest at the first sample collection for both S. enterica (26%) and Campylobacter spp. (8%). Repeat detection of Salmonella was observed for only a single goat (0.8%). Salmonella qPCR positive samples were characterised at ompF and invA genes as S. enterica. Further characterisation at STM2755 and STM4497 genes confirmed the isolates were S. enterica serovar Typhimurium. Characterization at the 16S rRNA and hippuricase (hipO) genes revealed all Campylobacter spp. positive samples were C. jejuni. This study demonstrates that qPCR can be used for rapid identification of faecal carriage in goat faecal samples and showed evidence of carriage of zoonotic S. Typhimurium and C. jejuni by captured rangeland goats. The findings have implications for management of goats at abattoirs and in confined feeding facilities.

Faecal shedding of Eimeria by captured rangeland goats (Capra hircus) was investigated using a longitudinal observational study. Faecal samples were collected from 125 male goats on four occasions. The first sampling occurred following capture and transport, immediately after arrival at a commercial goat depot (feedlot) in Western Australia, with subsequent 3 sample collections occurring at one month intervals thereafter. Goats were composite breed and aged approximately 9–12 months on arrival at the feedlot. Prevalence and shedding intensity (faecal oocyst concentration) for Eimeria were determined using qPCR. Species were identified from individual oocysts (isolated using micromanipulation) using molecular analysis at two loci, specifically 18S rRNA and mitochondrial cytochrome oxidase gene (COI), and confirmed by microscopy. Longitudinal prevalence (animals positive at least once) for Eimeria spp. by qPCR was 90.4%, with 60% goats shedding Eimeria spp. on more than one occasion. Point prevalence (prevalence at a single sampling occasion) ranged from 2.4% (fourth sampling) to 70.4% (second sampling). Three species were identified at the 18S rRNA locus and confirmed by microscopy: E. christenseni (longitudinal prevalence for single infection 34.4%), E. hirci (17.6%) and E. arloingi (8.8%) over the four sample collections. Mixed infections were identified in 56.8% goats (longitudinal prevalence). 18S rRNA sequences from E. christenseni and E. hirci were 100% homologous with ovine E. ahsata and E. crandallis respectively, and E. arloingi was 100% similar to caprine E. arloingi. At the COI locus, E. christenseni, E. hirci and E. arloingi grouped separately, and were closely related to ovine E. ahsata, with genetic similarities of 96.5%, 92.6% and 91.4% respectively. This is the first report for molecular characteristics of caprine-derived Eimeria spp. using a combination of 18S rRNA and COI. Molecular techniques can be used to identify Eimeria spp. in goat faecal samples, specifically through characterization at 18S locus and other gene loci when used in parallel. Molecular techniques offer some advantages over microscopy for identification of Eimeria species, particularly with respect to precision.

Objective Develop a multiplex quantitative PCR assay to investigate the prevalence and shedding of Escherichia coli O157/O145, Salmonella spp. and Campylobacter spp. in sheep at sale yards and abattoirs. Methods A qPCR for E. coli O157/O145 was developed, validated and multiplexed with an existing qPCR for Campylobacter and Salmonella enterica. The absolute numbers of E. coli O157/O145, Campylobacter and Salmonella in control samples was determined using droplet digital PCR. These were then used as the controls in the multiplex qPCR on a total of 474 sheep faecal samples collected from two saleyards over a 4-month period (April–July 2014) and 96 effluent samples from an abattoir. Results The mutiplex qPCR was specific with a sensitivity of 5 organisms/μL faecal DNA extract for Campylobacter, S. enterica and E. coli O157/O145. The overall prevalence of Campylobacter, S. enterica and E. coli O157/O145 in faecal samples was 5.7%, 3.6% and 8.4% and in effluent samples was 18.8%, 6.3% and 5.2%, respectively. The pathogen loads of Campylobacter, S. enterica and E. coli O157/O145 in faecal and effluent samples was also determined via mutiplex qPCR. Conclusions The overall prevalences of Campylobacter, S. enterica and E. coli O157/O145 were generally low (

Uninucleated Entamoeba cysts measuring 7.3 × 7.7 μm were detected in faecal samples collected from wild Rangeland goats (Capra hircus) after arrival at a commercial goat depot near Geraldton, Western Australia at a prevalence of 6.4% (8/125). Sequences were obtained at the 18S rRNA (n = 8) and actin (n = 5) loci following PCR amplification. At the 18S locus, phylogenetic analysis grouped the isolates closest with an E. bovis isolate (FN666250) from a sheep from Sweden with 99% similarity. At the actin locus, no E. bovis sequences were available, and the isolates shared 94.0% genetic similarity with E. suis from a pig in Western Japan. This is the first report to describe the morphology and molecular characterisation of Entamoeba from Rangeland goats in Western Australia and the first study to produce actin sequences from E. bovis-like Entamoeba sp.

Objectives To develop molecular tools for the investigation of the prevalence, species and faecal shedding of Yersinia in sheep. Methods A quantitative PCR (qPCR) targeting the β subunit of the Yersinia spp. RNA polymerase gene was developed and validated. The prevalence of pathogenic Y. enterocolitica was determined by screening for the virulent yst gene. These qPCR assays were used to determine Yersinia spp. prevalence and faecal shedding concentration from 3412 faecal samples collected from approximately 1189 lambs (100–180 lambs/flock) on eight farms across Australia. This was a longitudinal study, with sheep sampled on three occasions (weaning, post-weaning and pre-slaughter). A subset of up to five positive samples from each sampling on each farm (n = 111) was sequenced. Results Yersinia spp. (including both pathogenic and non-pathogenic species) were identified in all flocks, with 60.7% of lambs shedding Yersinia spp. on at least one sampling occasion. Point prevalence ranged from 4% to 91% across farms and sampling occasions. Median Yersinia spp. bacterial concentration was 1.1 × 106, 2.8 × 106 and 5.6 × 105 organisms/g faeces at weaning, post-weaning and pre-slaughter, respectively, across all farms. Pathogenic Y. enterocolitica was identified in all eight flocks sampled, with 14.8% of lambs shedding pathogenic Y. enterocolitica on at least one sampling occasion. Conclusion Yersinia spp. and pathogenic Y. enterocolitica in particular were commonly identified in a sample of Australian sheep flocks using molecular techniques. Further studies into associations between faecal shedding of pathogenic Yersinia spp. and sheep productivity or clinical disease may utilise qPCR in conjunction with other diagnostic tools.

This review aims to describe the nutritional and non-nutritional factors that may affect parturition and dystocia in sheep. Dystocia is associated with fetopelvic disproportion, uterine inertia, failure of the cervix to fully dilate, malpresentation and disease or congenital defects in lambs. Dystocia can result in lambs that are born dead, or lambs that survive parturition but sustain birth injury including central nervous system damage. Dystocia risk is increased with high or low birthweight lambs, high (fat) or low liveweight ewes, and small first parity ewes. Other factors implicated include low muscle glycogen, pregnancy toxaemia, mineral imbalance causing hypocalcaemia, and a lack of antioxidant nutrients. Addressing these risks requires differential nutritional management for single and multiple bearing ewes. There is also evidence for stress and environmentally related dystocia. The stress related hormones cortisol, adrenaline and ACTH play a major role in the initiation and control of parturition in the sheep indicating a need for adequate supervision during lambing, provision of adequate feed and shelter at the lambing site, and small flock size to reduce physical and environmental stress. Hormonal control of parturition can be further disrupted by xenoestrogens or phytoestrogens in clovers and medics. Oestrogenic plants are still widely grown in mixed pastures but should be not be grazed by pregnant ewes. There is clearly a genetic component to dystocia. This is partly explained by incompatibility in physical size and dimensions of the ram, ewe and lamb. A rapid reduction in dystocia through direct genetic selection is problematic with low heritability of dystocia and some of its indicator traits such as lambing ease. This review provides broad interpretation of the literature, but conclusions are not definitive with widespread inconsistency in reported results. Further research is required to investigate dystocia under commercial production conditions, and this should be complemented by focussed studies under controlled conditions. Priorities include defining the fitness of the ewe to lamb, the role of stress and environment on parturition and the use of indicator traits to select for ease of birth.

Diarrhoea is a common, widespread and frustrating reality for sheep enterprises in most sheep producing regions globally and of particular concern in Australia as the major risk factor for breech flystrike. Parasitic disease has long been recognised as an important factor in diarrhoea in sheep, particularly the gastrointestinal nematodes (Trichostrongylus and Teladorsagia species). This review focuses on the role of parasitic infections in causing diarrhoea in sheep, with emphasis on the epidemiology of diarrhoea outbreaks related to worms and opportunities to manage the risk of diarrhoea outbreaks in sheep related to parasitic infections. Parasitic nematodes damage the gastrointestinal tract via a complex relationship between direct impacts from worms, such as physical changes to the gut mucosa, and indirect effects largely associated with the host response. Diarrhoea associated with large worm burdens is most efficiently managed through integrated parasite management programs. Despite some limitations, measuring faecal worm egg counts remains a mainstay for assessing the contribution of worms to outbreaks of diarrhoea in sheep. Larval hypersensitivity scouring is emerging as a significant cause of worm-related diarrhoea in sheep without large adult worm burdens in some geographic locations. The syndrome describes a heightened inflammatory response to the ingestion of trichostrongylid infective larvae seen in the gut of sheep with diarrhoea, and is most effectively addressed through selecting sheep for low breech soiling ('dag scores'), as worm resistant sheep may show an increased propensity for diarrhoea, even with low rates of larval challenge. Importantly, dag should be considered as a separate trait to WEC in breeding indexes. Outbreaks of diarrhoea in young sheep are often multifactorial, and co-infections with nematodes and other infectious agents associated with diarrhoea are common. This presents challenges for the field investigation of diarrhoea in grazing sheep.

This study investigated faecal carriage and antimicrobial resistance (AMR) of Salmonella enterica recovered from rangeland goats. Faecal samples (n = 400) were collected at slaughter from four consignments of goats (n = 100 samples per consignment), each from one of four localities in Western Australia. Carriage of Salmonella spp. was detected in 106 samples (26.5%; 95% CI 22.4–31.0%). The rate of faecal carriage for each consignment ranged between 23–30%. PCR assays targeting the STM2755 and STM4497 genes revealed 84.9% (90/106) of the isolates were of serovar Typhimurium. Salmonella Chester (11/106, 10.4%) and S. Saintpaul (5/106, 4.7%) were characterised at invA and ompF genes. Antimicrobial susceptibility testing demonstrated that 84.0% of isolates were susceptible to all tested (n = 13) antimicrobials. Resistance was identified to azithromycin (14.2%), tetracycline (10.4%), ampicillin (5.7%), amoxicillin–clavulanate and cefoxitin (3.8%), trimethoprim/sulfamethoxazole (1.9%), gentamicin and streptomycin (0.9%). No isolate was resistant to four or more antimicrobials, or to critically important antimicrobials such as fluoroquinolones and extended spectrum cephalosporins. This is the first study reporting AMR in Salmonella isolates from Australian rangeland goats. The rate of detection of AMR was very low, some resistance to low-importance drugs was present in the Salmonella population, despite the absence of active selection pressure.

Cryptosporidium and Giardia are common parasites of ruminant livestock worldwide. These parasites are associated with diarrhoea outbreaks in young goats (pre-weaning), but the impacts on health and productivity for older goats (post-weaning) are not well understood. Here we show Cryptosporidium faecal shedding is associated with reduced growth and diarrhoea in goats aged approximately 9-15 months. Goats were sampled four times at one-month intervals. Faecal shedding for a range of pathogens were determined using quantitative PCR and sequencing (Cryptosporidium, Giardia, Eimeria, Salmonella, Campylobacter), and microscopy (trichostrongylid nematode worm egg count and Entamoeba). Cryptosporidium faecal shedding was associated with 1.5 kg lower growth for the one-month period following sampling. Specifically, C. xiaoi was associated with 1.9 kg lower growth in the following month. This is the first report of production impacts associated with C. xiaoi in ruminants older than 3 months of age. Cryptosporidium shedding was associated with an over 4-fold increase in risk of diarrhoea, with C. parvum associated with 10-fold and C. ubiquitum associated with 16-fold increase in risk of diarrhoea. Notably, C. xiaoi shedding was not associated with increased risk of diarrhoea. Giardia shedding was associated with looser faecal consistency, but not diarrhoea. Higher Eimeria oocyst counts were weakly associated with lower live weight, poorer body condition and looser faecal consistency. Shedding of other enteric pathogens were not associated with impacts on live weight, growth or diarrhoea risk. This study challenges the two notions that Cryptosporidium infections only impact health and productivity of goats during the pre-weaning period, and that Cryptosporidium (and specifically C. xiaoi) infections in the absence of diarrhoea are asymptomatic. Recognising the potential for impacts of Cryptosporidium infection on growth rates in the absence of diarrhoea will support improved design for experiments testing impacts of Cryptosporidium on ruminant health and production. Improved understanding of the role of protozoan infections on animal health has implications for the management of goats in order to reduce adverse impacts on farm profitability, animal welfare and public health risk.

This study aimed to establish whether sheep flock production losses due to nematode (worm) infections are typically greater in mature sheep selected for anthelmintic treatment at random compared to sheep selected for treatment based on low (poorer) body condition score (BCS). The study also examined the proportion of sheep in flocks that could be left untreated before production losses became evident, and projected worm egg pasture contamination. Sheep were monitored at two experimental sites in Western Australia (Mediterranean climate). Sheep were stratified for BCS, liveweight and faecal worm egg count (WEC) and allocated into treatment groups (treated or untreated), with equal numbers for each. Liveweight, BCS and WEC measurements were taken on 6 occasions at Farm A and 10 occasions at Farm B. Comparisons of sheep production (liveweight and BCS change) and pasture contamination potential (WEC) were conducted by generating "virtual flocks" of varying proportions sheep untreated (10%, 20%, 30%, 40%, and 50% untreated). For the comparison of the selection mode of sheep for treatment, the untreated sheep were either selected at random, or as the highest BCS animals at the commencement of observations. Univariate general linear models with least square difference post-hoc tests were used to examine differences between flocks for liveweight, BCS and WEC, and regression analysis was used to examine relationships between BCS and WEC, and liveweight and WEC. No difference in body weights was observed between flocks with varying proportions of ewes notionally left untreated at Farm B, and until more than 30% were left untreated at Farm A. There was no difference in BCS between flocks with varying proportions of ewes left untreated at either site. At no point were there differences in cumulative liveweight change or BCS between selection methods (BCS versus random) where the same proportion of sheep in virtual flocks were left untreated, suggesting that effort committed to individual BCS assessment would be of no benefit under these circumstances except for identifying low BCS sheep at risk of falling below critical limits associated with health or welfare risks. No consistent relationship between WEC and BCS or bodyweight was observed, indicating that BCS selection would have no lesser or greater impact on worm pasture contamination compared to random selection. Summer treatments based on a random selection index (with a minimum BCS limit), with up to 30% of adult sheep untreated can be expected to delay the development of anthelmintic resistance, with minimal adverse effect on sheep health or production.

The investigation aimed to assess factors affecting the uptake of novel targeted selective treatment (TST) strategies by sheep farmers in Western Australia where the most common nematode species present were Teladosagia circumcincta, Trichostrongylus spp. and Nematodirus spp. ("scour worms"). The study used a questionnaire format with questions concentrated on current worm control practices and farmers' current understanding and adoption of putative TST strategies. Participants represented a range of environments (derived from four farming regions) and sheep management situations, and it is therefore likely that the results of this investigation will apply in other locations where scour worms predominate. Sixty-five percent of participants were aware of the TST concept and 25% had implemented it in some form. The awareness of the TST approach was greatest where sheep farmers were concerned about anthelmintic resistance, where tools such as worm egg counts and faecal worm egg count resistance tests were employed, and where professional advisers were consulted regarding worm control. Respondents that sought advice chiefly from rural merchandise retailers were considerably less (0.1-0.6 times) likely to be aware of these management tools or to be aware of TST approaches. The findings indicated that the adoption of TST strategies will require greater use of professional advisers for worm control advice by sheep farmers, and that advisers are conversant with TST concepts.

The prevalence of Cryptosporidium and Giardia in faeces collected from sheep at sale yards in Western Australia and for abattoir effluent was determined using a quantitative multiplex PCR (qPCR). A total of 474 faecal samples were collected from sheep at two saleyards on four occasions (April-July 2014) and 96 effluent samples were collected from an abattoir over a four month period (April-July). The overall prevalence of Cryptosporidium in sheep faeces was 6.5% (31/474), with the zoonotic species Cryptosporidium parvum and Cryptosporidium ubiquitum accounting for 54.2% of the typed positive samples. Subtyping of the C. parvum and C. ubiquitum positives at the gp60 locus identified four C. parvum positives as IIdA18G1 and nine C. ubiquitum isolates as the XIId subtype. The overall prevalence of Giardia in sheep faeces was 6.3% (30/474), with the non-zoonotic assemblage E responsible for the majority (81.5%) of positive isolates typed. Median Cryptosporidium and Giardia oo/cyst concentrations in positive faecal samples were 1.7×103 oocysts g-1 (range 32-3.7×106 oocysts g-1) and 2.5×103 cysts g-1 (range 143-7.5×105 cysts g-1) respectively. Cryptosporidium and Giardia were identified in 10.4% (10/96) and 5.2% (5/96) of abattoir effluent samples (respectively). Median Cryptosporidium and Giardia oo/cyst concentrations in positive effluent samples was 1.3×103 cysts g-1 (range 393-1.5×104) and 1.5×104 oocysts g-1 (range 759-4.8×103) respectively. These findings have important implications for the sheep meat industry because Cryptosporidium and Giardia have both been associated with reduced carcase productivity in sheep, and the contamination of lamb carcases and watersheds with zoonotic species have important public health consequences.

Leptospirosis is a neglected, re-emerging bacterial disease with both zoonotic and conservation implications. Rats and livestock are considered the usual sources of human infection, but all mammalian species are capable of carrying Leptospira spp. and transmitting pathogenic leptospires in their urine, and uncertainty remains about the ecology and transmission dynamics of Leptospira in different regions. In light of a recent case of human leptospirosis on tropical Christmas Island, this study aimed to investigate the role of introduced animals (feral cats and black rats) as carriers of pathogenic Leptospira spp. on Christmas Island and to compare this with two different climatic regions of Western Australia (one island and one mainland). Kidney samples were collected from black rats (n = 68) and feral cats (n = 59) from Christmas Island, as well as feral cats from Dirk Hartog Island (n = 23) and southwest Western Australia (n = 59). Molecular (PCR) screening detected pathogenic leptospires in 42.4% (95% confidence interval 29.6-55.9) of cats and 2.9% (0.4-10.2) of rats from Christmas Island. Sequencing of cat- and rat-positive samples from Christmas Island showed 100% similarity for Leptospira interrogans. Pathogenic leptospires were not detected in cats from Dirk Hartog Island or southwest Western Australia. These findings were consistent with previous reports of higher Leptospira spp. prevalence in tropical regions compared with arid and temperate regions. Despite the abundance of black rats on Christmas Island, feral cats appear to be the more important reservoir species for the persistence of pathogenic L. interrogans on the island. This research highlights the importance of disease surveillance and feral animal management to effectively control potential disease transmission.

Sheep nematode control utilising refugia-based strategies have been shown to delay anthelmintic resistance, but the optimal indices to select individuals to be left untreated under extensive sheep grazing conditions are not clear. This experiment tested the hypothesis that high body condition can indicate ability of mature sheep to better cope with worms and therefore remain untreated in a targeted treatment programme. Adult Merino ewes from flocks on two private farms located in south-west Western Australia (Farm A, n = 271, and Farm B, n = 258) were measured for body condition score (BCS), body weight and worm egg counts (WEC) on four occasions between May and December (pre-lambing, lamb marking, lamb weaning and post-weaning). Half of the ewes in each flock received anthelmintic treatments to suppress WEC over the experimental period and half remained untreated (unless critical limits were reached). Response to treatment was analysed in terms of BCS change and percentage live weight change. No effect of high or low initial WEC groups was shown for BCS response, and liveweight responses were inconsistent. A relatively greater BCS response to treatment was observed in ewes in low BCS pre-lambing compared to better-conditioned ewes on one farm where nutrition was sub-optimal and worm burdens were high. Sheep in low body condition pre-lambing were more than three times more likely to fall into a critically low BCS (

Faecal excretion of Campylobacter spp. and Salmonella enterica in sheep in Australia was determined using a quantitative multiplex PCR (qPCR) targeting the Campylobacter spp. purine biosynthesis gene (PurA) and the S. enterica outer membrane protein (ompF). The mutiplex qPCR was specific and Campylobacter spp. and S. enterica were each detected with a sensitivity of 5 organisms/µL faecal DNA extract. This multiplex qPCR was used to determine the prevalence and concentration of Campylobacter spp. and S. enterica in 3412 faecal samples collected from 1189 lambs on eight farms across South Australia (n = 2 farms), New South Wales (n = 1), Victoria (n = 2) and Western Australia (n = 3) at three sampling periods (weaning, post-weaning and pre-slaughter). The overall prevalences of Campylobacter spp. and S. enterica were 13.3% and 5.0%, respectively, with the highest prevalence for Campylobacter spp. in South Australia and the highest prevalence for S. enterica in New South Wales. Campylobacter jejuni was the only Campylobacter sp. identified from a subset of 120 positive samples sequenced at the 16S locus. S. enterica serovar Typhimurium was the only serovar of S. enterica identified from a subset of 120 positive samples sequenced at the ompF locus. Across all states, Campylobacter spp. had the highest median bacterial concentration in faeces at weaning and post-weaning (medians of 3.4 × 10(6) and 1.1 × 10(5), respectively), whereas S. enterica had the highest median bacterial concentration at pre-slaughter (1.8 × 10(5)/g faeces).

The prevalence of Cryptosporidium in sheep in the eastern states of Australia has not been well described, therefore a study of the prevalence, oocyst concentration, species and subtypes of Cryptosporidium were assessed from lamb faecal samples at three sampling periods (weaning, post-weaning and pre-slaughter) from eight farms across South Australia, New South Wales, Victoria and Western Australia. A total of 3412 faecal samples were collected from approximately 1182 lambs across the four states and screened for the presence of Cryptosporidium using a quantitative PCR (qPCR) at the actin locus. Positives were typed at the 18S locus and at a second locus using C. parvum and C. hominis specific qPCR primers. The overall prevalence was 16.9% (95% CI: 15.6–18.1%) and of the 576 positives, 500 were successfully genotyped. In general, the prevalence of Cryptosporidium was higher in WA than the eastern states. Cryptosporidium prevalence peaked at 43.9% and 37.1% at Pingelly (WA2) and Arthur River (WA1), respectively during weaning and at Pingelly (WA2) during pre-slaughter (36.4%). The range of oocyst shedding at weaning overall across all states was 63–7.9 × 106 and the median was 3.2 × 104 oocysts g−1. The following species were identified; C. xiaoi (69%—345/500), C. ubiquitum (17.6%—88/500), C. parvum (9.8%—49/500), C. scrofarum (0.8%—4/500), mixed C. parvum and C. xiaoi (2.4%—12/500), C. andersoni (0.2%—1/500) and sheep genotype 1 (0.2%—1/500). Subtyping of C. parvum and C. ubiquitum isolates identified IIa and IId subtype families within C. parvum (with IId as the dominant subtype) and XIIa within C. ubiquitum. This is the first published description of C. parvum subtypes detected in lambs in Australia.

A novel quantitative PCR (qPCR) for Giardia at the glutamate dehydrogenase (gdh) locus was developed and validated. The qPCR was used to screen a total of 3412 lamb faecal samples collected from approximately 1189 lambs at three sampling periods (weaning, post-weaning and pre-slaughter) from eight farms across South Australia (SA), New South Wales (NSW), Victoria (Vic) and Western Australia (WA). The overall prevalence was 20.2% (95% CI 18.9-21.6) and of the 690 positives, 473 were successfully typed. In general, the prevalence of Giardia varied widely across the different farms with the highest prevalence in one WA farm (42.1%) at pre-slaughter sampling and the lowest prevalence in one Victorian farm (7.2%) at weaning. The range of cyst shedding at weaning, post-weaning and pre-slaughter overall across all states was 63-1.3×10(9) cysts g(-1) (median=1.7×10(4)), 63-1.1×10(9) cysts g(-1) (median=9.6×10(3)), 63-4.7×10(9) cysts g(-1) (median=8.1×10(4)) respectively. Assemblage specific primers at the triose phosphate isomerase (tpi) locus identified assemblage A in 22.4% (106/473) of positive samples typed, assemblage E in 75.9% (359/473) and mixed A and E assemblages in 1.7% (8/473) of samples. A subset of representative samples from the 8 farms (n=32) were typed at both the gdh and beta-giardin loci and confirmed these results and identified sub-assemblage AII in 16 representative assemblage A isolates across the 8 farms. This demonstrates a prevalence of Giardia previously not recognised in Australian sheep, highlighting a need for further research to quantify the production impacts of this protozoan parasite.

Faecal shedding of Cryptosporidium and Giardia by captured rangeland goats was investigated using a longitudinal study with four faecal samples collected from 125 male goats once monthly for four months, commencing immediately after capture and transport to a commercial goat depot (feedlot). Goats were composite breed and aged approximately 9-12months on arrival. Faecal samples were screened for Cryptosporidium and Giardia presence and concentration using quantitative PCR and sequencing at the 18S ribosomal RNA locus (Cryptosporidium), and glutamate dehydrogenase and β-giardin loci (Giardia). Longitudinal prevalence for Cryptosporidium was 27.2% (point prevalence range 3-14%) with 3 species identified: C. xiaoi (longitudinal prevalence 13.6%), C. ubiquitum (6.4%) and C. parvum (3.2%). Sub-typing at the gp60 locus identified C. ubiquitum XIIa, C. parvum IIaA17G2R1 and C. parvum IIaA17G4R1. This is the first report of the zoonotic C. parvum subtype IIaA17G4R1 in goats. The pattern of genotypes shed in faeces changed over the duration of study with C. ubiquitum identified only at the first and second samplings, and C. parvum identified only at the fourth sampling. Longitudinal prevalence for Giardia duodenalis was 29.6% (point prevalence range 4-12%) with all positives sub-typed as assemblage E. Only 2/125 goats were identified to be shedding Cryptosporidium or Giardia on more than one occasion. This is the first report of Cryptosporidium and Giardia genotypes in captured rangeland goats. Faecal shedding of zoonotic Cryptosporidium spp. and potentially zoonotic G.duodenalis has implications for food safety and effluent management. Keywords: Cryptosporidium; Giardia; Rangeland goats; zoonotic.

Bacteria of the genus Bartonella have been described in multiple mammalian hosts with many species capable of causing disease in humans. Cats and various species of rats have been reported to play a role as vertebrate hosts to a number of Bartonella spp. This study aimed to identify Bartonella spp. in Western Australia, Dirk Hartog Island (DHI), and Christmas Island (CI) and to investigate the presence of potential arthropod vectors. Feral cats were collected from CI (n = 35), DHI (n = 23) and southwest Western Australia (swWA; n = 58), and black rats were collected from CI (n = 48). Individuals were necropsied, ectoparasites were collected by external examination of carcasses, and splenic tissue was collected for polymerase chain reaction analysis to detect Bartonella DNA. Bartonella henselae DNA was detected from two cats and Bartonella koehlerae DNA from one cat in southwest WA, but Bartonella DNA was not identified in cats on DHI or CI. Bartonella phoceensis (28/48 = 58.3%) and a novel Bartonella genotype (8/48 = 16.7%) based on the internal transcribed space region were detected in the spleens of black rats on CI. Detection of Bartonella spp. in each location corresponded to the presence of ectoparasites. Cats from southwest WA harbored four species of fleas, including Ctenocephalides felis, and black rats on CI were infested with multiple species of ectoparasites, including mites, fleas, and lice. Conversely, cats on Dirk Hartog and CI were free of ectoparasites. This study has identified the DNA of Bartonella species from island and mainland swWA with some (B. henselae and B. koehlerae) of known zoonotic importance. This study further extends the geographical range for the pathogenic B. koehlerae. The association of Bartonella with ectoparasites is unsurprising, but little is known about the specific vector competence of the ectoparasites identified in this study.

Associations between intensity and frequency of Cryptosporidium and Giardia shedding with growth, carcase weight and dressing% were investigated using a longitudinal study of 1182 lambs on eight Australian farms. Live weight was recorded and faecal samples were collected on three sampling occasions; weaning (approximately 12 weeks of age), post-weaning (approximately 19 weeks) and pre-slaughter (approximately 29 weeks). Hot standard carcase weight (HSCW) and dressing% were measured at slaughter. Faecal samples were screened for presence and concentration of Cryptosporidium, Giardia and Haemonchus oocysts using a quantitative PCR. Trichostrongylid eggs were quantified with modified McMaster faecal worm egg count (WEC). Protozoan shedding intensity was categorised as high (above median oocyst concentration in positive sheep), low (below median oocyst concentration in positive sheep) or not detected. Shedding was also categorised for shedding type (no shedding, single Giardia infection, single Cryptosporidium infection, concurrent Giardia and Cryptosporidium infection) and lambs were categorised for frequency of shedding (shedding identified on 0, 1, 2 or 3 occasions). Associations of parasite shedding intensity category, shedding type, shedding frequency, WEC and Haemonchus status (positive or negative) with lamb production were assessed using general linear models (HSCW and dressing%) and linear mixed effects models (live weight). High Cryptosporidium parvum shedding was associated with lower live weight, ranging 2.31–4.52 kg over the 3 sampling occasions. Cryptosporidium parvum shedding was associated with less HSCW in high (3.22 kg less) and low (3.22 kg less) shedding lambs post-weaning, and high (2.21 kg less) and low (2.60 kg less) shedding lambs pre-slaughter as well as lower dressing% (2.7% lower in high shedding lambs post-weaning). Cryptosporidium (all species) shedding pre-slaughter was associated with reduced dressing% in both high (1.25% lower) and low (1.21% lower) shedding lambs. Giardia shedding pre-slaughter was associated with 0.59 kg less HSCW in high shedding lambs. Increased frequency of C. parvum and Giardia shedding in a specific animal (repeated detection) were associated with reduced HSCW and dressing%. Concurrent Giardia and Cryptosporidium shedding pre-slaughter was associated with reduced dressing%. No statistically significant main effects for either WEC (P > 0.05) or Haemonchus status (P > 0.05) were identified for any of the sheep meat productivity measures (live weight, HSCW and dressing%). The findings suggest naturally acquired Cryptosporidium and Giardia infections in grazing sheep are associated with depressed growth, carcase weight and dressing efficiency beyond the neonatal period in sheep representing a range of genetic backgrounds and different sheep production environments.

Diarrhoea is a widespread problem for sheep enterprises worldwide. A cross-sectional epidemiological study was conducted using a questionnaire to determine the prevalence of diarrhoea and associated risk factors where there was evidence of recent diarrhoea (active diarrhoea or fresh faecal soiling of breech fleece) for meat lambs on farms in southern Western Australia during 2010. The response rate was 41.4% (139/336). Evidence of recent diarrhoea was reported on 64.8% of farms, with a mean of 6.9% lambs affected per farm. Location of a farm and a higher annual rainfall were associated with an increased diarrhoea prevalence. Binary logistic regression analysis suggested that the drinking water source was associated with the incidence of diarrhoea, since lamb flocks supplied with dam water were 117 times (95% CI: 18.2, 754.8) more likely to have observed diarrhoea or fresh breech fleece faecal soiling than lamb flocks supplied with other sources of water. Faecal worm egg counts were used by 65% of respondents to determine whether an anthelmintic treatment was warranted and 74% of respondents administered a treatment to their meat lambs. In response to a range of diarrhoea scenarios presented to respondents (5%, 25% and 50% of the flock with evidence of recent diarrhoea), 15.1% would have elected to administer an anthelmintic treatment regardless of differences in prevalence.

On two separate sampling occasions, faecal samples were collected from lambs (2-5 months of age) grazing pasture on two separate sheep farms in southern Western Australia. Live weight, body condition score (BCS), faecal consistency score (FCS) and faecal dry matter percentage (DM%) were measured. Faecal samples were screened by PCR for Cryptosporidium (18S rRNA, actin and 60 kDa glycoprotein [gp60] loci), Giardia duodenalis (glutamate dehydrogenase [gdh] and β-giardin) and patent strongylid nematode infections (ITS-2 nuclear ribosomal DNA for Haemonchus contortus, Teladorsagia circumcincta, Trichostrongylus spp. Chabertia ovina and Oesophagostomum spp.). Faecal worm egg counts (WECs) were performed using a modified McMaster WEC technique. The WECs were adjusted for FCS and transformed using log(10)(adjusted WEC+25) prior to statistical analyses. Cryptosporidium, Giardia and Trichostrongylus spp. detected by PCR were associated with an increased risk of non-pelleted faeces (FCS ≥ 3.0) for both flocks. Cryptosporidium-positive lambs were 2.8-11.6 times more likely to have non-pelleted faeces and Giardia-positive lambs were 2.4-14.0 times more likely to have non-pelleted faeces compared to lambs negative for each respective parasite. Lambs positive for both Cryptosporidium and Giardia were 2.9-11.8 times more likely to have non-pelleted faeces than lambs positive for only one or neither of these parasites. Mixed internal parasite infections were found to have greater impacts on FCS and BCS than single infections. A higher number of internal parasites detected per lamb was associated with lower BCS and more loose faeces. The relationship between parasite detection and live weight or growth rate were inconsistent for both flocks. Adjusted WEC was correlated with FCS and faecal DM% for one flock only, although little or no correlation was found with live weight and growth rate for both flocks. Cryptosporidium ubiquitum and Cryptosporidium parvum were the most prevalent Cryptosporidium species isolated in the two flocks. Giardia assemblage E was the most commonly isolated genotype assemblage from both flocks, while assemblage A was isolated almost as frequently as assemblage E in the one flock. One flock was a potential source of zoonotic Cryptosporidium and the other flock was a potential source of zoonotic Giardia.

Patent strongylid nematode infections were identified using McMaster worm egg counts (WEC) and PCR assays (ITS-2 nuclear ribosomal DNA) to screen genomic DNA extracted directly from lamb faecal samples. Lambs from four different farms in southern Western Australia were sampled rectally on two separate occasions, with McMaster WECs and PCRs conducted on a total of 858 samples. Negative controls (n=96) (WEC

Effects of gastrointestinal parasitism on sheep productivity are usually described using live weight change, however carcass productivity is more accurately described using dressing percentage (carcass weight as a proportion of live weight). This experiment had a 2 × 2 × 2 factorial design whereby 10-month-old Merino wethers were fed lucerne (Medicago sativa) diets (fresh lucerne or lucerne chaff) with 2 levels of carboxymethycellulose (CMC) inclusion (0% or 8% CMC) and nematode larval challenge (no larval challenge or 10,000 Teladorsagia circumcincta and 10,000 Trichostrongylus colubriformis per week). Sheep were weighed and euthanased 50 or 51 days after larval challenge and CMC supplementation commenced. Weight of the carcass (hot standard carcass weight) and gastrointestinal organs (full and empty) were recorded and expressed as a proportion of live weight. Larval challenged sheep had a worm egg count (mean ± standard error) of 173 ± 38 eggs per gram of faeces and total worm count of 30,237 ± 2013 at slaughter. Larval challenged sheep had 1.3% lower dressing percentage (p = 0.048), and 2% heavier full (p = 0.007) and 1.2% heavier empty gastrointestinal tracts (p = 0.012) compared to unchallenged sheep. There was no effect of CMC inclusion or lucerne type (fresh or chaff) on gastrointestinal tract weight or dressing percentage. Larval challenged sheep had 1.1% heavier full (p < 0.001) and 0.6% heavier empty (p < 0.001) small intestines, and 0.6% heavier full (p = 0.005) and 0.3% heavier empty (p = 0.026) large intestines compared to unchallenged sheep. Use of live weight change or other measures based on live weight (e.g. feed conversion efficiency) to assess the impact of nematode challenge in sheep may underestimate carcass productivity losses associated with larval challenge in sheep even at moderate levels of larval intake and without overt clinical signs of parasitism. Measurement of carcass weight and/or lean meat yield may better reflect the true economic effects of parasitism in sheep