Severity and prevalence of small lungworm infection on three South Australian farms and associations with sheep carcass characteristics.

This field and abattoir study assessed the association of the severity and prevalence of small lungworm lesions with the carcass characteristics of 1332 lambs and adult sheep bred on three farms in southeast SA. Liveweight and measures of lungworm infection were measured on farm, then lung lesions and carcass characteristics assessed at slaughter. The overall prevalence of small lungworm lesions at slaughter was 79 % (928/1177; 95 % CI 76, 81), with a prevalence of 87 % (569/658; 95 % CI 84, 89) in lambs, and 69 % (359/519; 95 % CI 65, 73) in adults, respectively. Small lungworm infected lambs and adults had a similar hot standard carcass weight and dressing percentage compared to non-infected animals, both overall and within their respective cohort. Overall, the mean carcass weight for non-infected and infected lambs was 23.4 kg (95 % CI 18, 29), and 23.6 kg (95 % CI 18, 29), respectively, with a mean difference of 0.2 kg (95 % CI -0.4, 0.8; P = 0.5). Mean carcass weight for non-infected and infected adults was 21.3 kg (95 % CI 15, 28), and 21.5 kg (95 % CI 15, 28), with a mean difference of 0.2 kg (95 % CI -0.5, 0.9; P = 0.5). This study confirmed a very high prevalence of small lungworm lesions in sheep bred on farms in this region of SA, but their hot standard carcass weights were not reduced by these lesions. Additional information to compare the presence of lesions with productivity within an individual was collected at slaughter which provided more detailed information than is currently collected by routine abattoir surveillance. The limitations of the currently available diagnostic tests for small lungworm were also demonstrated. This indicated a need for the development of more sensitive tests to assess lungworm infections both on farm and at the abattoir. Currently, farmers in this region are concerned about the very high prevalence of small lungworm in their sheep, but this study provides reassurance that the presence of mild lesions does not reduce production.

The effect of pasture molluscicide on small lungworm infections and the productivity of grazing lambs.

The aim of this study was to assess the effect of pasture molluscicide treatment on the prevalence and severity of small lungworm infections, and the productivity of lambs grazing improved pastures in southeastern Australia. A randomised control field trial of 260 Merino-cross lambs was conducted on a commercially managed farm in South Australia with a history of high small lungworm prevalence. Separate groups of lambs rotationally grazed irrigated lucerne paddocks treated with iron chelate molluscicide or untreated control paddocks. Lambs were monitored every 2-6 weeks from weaning until slaughter with liveweight, lungworm and gastrointestinal nematode infection status measured. At slaughter indicators of small lungworm infection via inspection and carcass characteristics were assessed. The density of the intermediate host snail and lucerne pasture availability were also measured. There was a higher population of adult Prietocella barbara molluscs in the Control paddocks compared to the Treatment paddocks after molluscicide had been applied and prior to grazing commencing (206 vs. 14 snails/m2, respectively; P = 0.03; 95 % CI 8, 528). However, the overall mollusc density was similar between Control and Treatment. The prevalence of small lungworm infections was quite low during the trial (0-13 %), in both Control and Treatment lambs, except at day 94 when 48 % of 28 Control lambs were positive compared to none of 27 Treatment lambs (P < 0.001; 95 % CI 30, 66). A similar proportion of Treatment and Control lambs had evidence of small lungworm infection lesions at slaughter (both 67.8 %). Control lambs grew slightly faster than Treatment lambs, with an average daily gain of 202 (± 3 SEM) g/head/day for Control and 190 (± 4 SEM) for Treatment (P < 0.001) during the 112-day trial. Despite historic evidence of very high prevalence of lungworm infection in this region of southeastern Australia, iron chelate molluscicide treatment prior to lambs grazing the pasture had no demonstrable effect on the prevalence and severity of small lungworm infections, nor the productivity of lambs grazing these pastures. This study indicates that for a commercial sheep farm, additional molluscicide treatments of pastures after they are established, for the prevention of small lungworm infection, may not be warranted. Furthermore, requirements for more precisely monitoring snails are discussed.

Abortion and Lamb Mortality between Pregnancy Scanning and Lamb Marking for Maiden Ewes in Southern Australia.

The contribution of abortions to the overall mortality of lambs born to maiden (primiparous) ewes in Australia remains unclear. This cohort study aimed to quantify abortion and lamb mortality for ewe lambs and maiden Merino two-tooth ewes. Lamb mortality from pregnancy scanning to marking were determined for 19 ewe lamb and 11 Merino two-tooth ewe flocks across southern Australia. Average lamb mortality from scanning to marking was 35.8% (range 14.3-71.1%) for the ewe lambs and 29.4% (range 19.7-52.7%) for the two-tooth ewes. Mid-pregnancy abortion was detected in 5.7% of ewes (range 0-50%) in the ewe lamb flocks and 0.9% of ewes (range 0-4.4%) in the two-tooth ewe flocks. Mid-pregnancy abortion affecting ≥2% of ewes was observed in 6/19 ewe lamb flocks and 2/11 two-tooth ewe flocks. Lamb mortality from birth to marking represented the greatest contributor to foetal and lamb mortality after scanning, but mid-pregnancy abortion was an important contributor to lamb mortality in some ewe lamb flocks. Variability between the flocks indicates scope to improve the overall reproductive performance for maiden ewes by reducing foetal and lamb losses. Addressing mid-pregnancy abortion may improve the reproductive performance in some flocks.

Positive attitudes, positive outcomes: The relationship between farmer attitudes, management behaviour and sheep welfare.

This study examined the relationships between the attitudes and the management behaviour of the farmer and the on-farm welfare of their ewes. To our knowledge, this is the first study investigating these relationships in extensive sheep farming systems. Thirty-two sheep farmers and 6200 ewes were sampled across Victoria, Australia. Questionnaire interviews and on-farm animal welfare assessments were conducted. The ewes were assessed at two-time points, mid-pregnancy and weaning. To examine relationships between farmer and ewe variables, categorical principal component analyses, correlations and logistic regressions were used. The main findings of this study indicate relationships between farmer attitudes and management behaviour, consistent with findings from other more intensive livestock industries. Farmers were more likely to check the body condition of their ewes (Odds ratio = 2.37, P = 0.03), perform ultrasound pregnancy diagnosis (Odds ratio = 1.16, P = 0.02) and test for egg count before deworming sheep (Odds ratio = 2.88, P = 0.01) if they perceived these activities were important/valuable. In addition, farmers that performed these activities had a more active management style, and ewes in better welfare: fewer lame ewes at mid-pregnancy (r = -0.38 P = 0.04), and fewer ewes in need of further care at mid-pregnancy and weaning respectively (r = -0.47, P = 0.01; r = -0.50, P = 0.01). When combining the qualitative and quantitative analyses, behavioural attitudes (attitudes towards specific management behaviours) and perceived behavioural control (perceived barriers to performing the behaviour) emerged as the two main drivers underpinning farmer management behaviour. The results of this study indicate that the way farmers manage their ewes influences welfare outcomes, and management decisions are influenced by attitudes towards management practices. These findings demonstrate the opportunity to create change in farmer management behaviour and improve sheep welfare via targeted education programs.

Evaluating the welfare of extensively managed sheep.

The aim of this study was to identify the main on-farm welfare issues likely to be encountered in extensive sheep farming systems. Thirty-two commercial sheep farms in Victoria, Australia were involved in this study. Of the 32 farms involved, 30 were visited twice (at mid-pregnancy and weaning), and 2 farms only once (both at weaning). In total, 62 visits were conducted and 6,200 ewes (aged 2-5 years) were examined using six animal-based indicators: body condition score (BCS), fleece condition, skin lesions, tail length, dag score and lameness. In addition, the number of ewes that needed further care (such as sick or injured sheep) was recorded and reported to the farmers. Generalised linear mixed models were conducted to investigate associations between welfare outcomes and visit, ewe breed and location, with all three, and their interactions, as fixed factors. In all instances, farm was set as a random factor to account for specific variation between farms. Overall, the welfare of the ewe flocks, based on the six indicators measured, was considered good. A total of 86.9% of the ewes were in adequate BCS (2.5-3.5), 91% had good fleece condition, 69.2% had no skin lesions, 97.1% had low dag scores, and overall lameness was 4.7%. An important and prevalent risk to welfare identified across farms was short tail length; with 85.7% of ewes having tails docked shorter than the third palpable joint. While the welfare of the flock was good, ewes in need of further care were identified at all farms. There were 185 (3.0%) cases needing further care, and the extent of welfare compromise of these animals was considered significant. Main reasons for further care were moderate/severe lameness or foot-related issues, BCS ≤ 2 and active dermatophilosis or broken wool. To our knowledge, this study constitutes the largest assessment of ewes conducted in Australia, and the findings provide valuable insight into the main welfare issues likely to be encountered in extensive sheep farming enterprises. Future studies should develop practical technologies that can assist in the detection of the welfare issues identified in this study. In addition, the thresholds identified here could be used for future comparison and sheep welfare benchmarking programs to assess farm performance and measure continuous improvements.

Epidemiology of gastrointestinal nematodes of alpacas in Australia: I. A cross-sectional study.

This study involved a national cross-sectional survey of gastrointestinal nematodes (GINs) of alpacas in Australia. A total of 1545 fresh faecal samples were collected from both sexes of alpacas and processed for faecal egg counts (FEC) and molecular identification of nematodes using the multiplexed tandem PCR assay. Based on egg morphology, the overall prevalence of GINs was 66% while that for strongyles was 59%. The overall mean FEC was 276 eggs per gram (EPG) of faeces, with the highest count of 17,415 EPG. Male alpacas had a higher prevalence (68%, 334/490) as well as mean FEC (328 ± 60 EPG) of GINs than females (63%, 602/954; 227 ± 26, respectively). Weaners had the highest prevalence (80%) whereas tuis had the highest FEC (402 EPG) of nematodes. The highest prevalence (77%, 293/383) and FEC (630 EPG) of GINs were observed in the summer rainfall zone followed by the Mediterranean-type rainfall, non-seasonal rainfall and winter rainfall zones. The characterisation of nematode DNA isolated from faeces revealed the occurrence of seven different GINs, including Camelostrongylus mentulatus, Cooperia spp., Haemonchus spp., Oesophagostomum spp., Ostertagia ostertagi, Teladorsagia circumcincta and Trichostrongylus spp. Besides, Nematodirus spp. and Trichuris spp. were also found during FECs. The prevalence of Haemonchus spp. was highest in the summer rainfall zone while that of C. mentulatus was highest in the Mediterranean-type rainfall, non-seasonal rainfall and winter rainfall zones. The findings of this study revealed that alpacas harbour many of the same nematodes as sheep and cattle.

Epidemiology of gastrointestinal nematodes of alpacas in Australia: II. A longitudinal study.

We conducted a longitudinal survey on 13 alpaca farms in four climatic zones of Australia to understand the epidemiology of gastrointestinal nematodes (GINs) of alpacas. A total of 1688 fresh faecal samples were collected from both sexes of alpacas from May 2015 to April 2016 and processed for faecal egg counts (FEC) and molecular identification of eggs using the multiplexed-tandem PCR assay. Based on egg morphology, the overall prevalence of GINs was 61% while that for strongyles was 53%. The overall mean FEC was 168 eggs per gram (EPG) of faeces, with the highest count of 15,540 EPG. Weaners had the highest prevalence (73%) and mean FEC (295 EPG) of GINs followed by tuis, crias and adults. Alpacas in the winter rainfall zone had the highest prevalence (68%) as well as FEC (266 EPG) followed by Mediterranean-type, non-seasonal and summer rainfall zones. Trichostrongylus spp. (83%, 89/107), Haemonchus spp. (71%, 76/107) and Camelostrongylus mentulatus (63%, 67/107) were the three most common GINs of alpacas across all climatic zones. The mixed-effects zero-inflated negative binomial regression model used in this study showed that it could help to design parasite control interventions targeted at both the herd level and the individual alpaca level. The findings of this study showed that the epidemiology of GINs of alpacas is very similar to those of cattle and sheep, and careful attention should be paid when designing control strategies for domestic ruminants co-grazing with alpacas.

An assessment of worm control practices used by alpaca farmers in Australia.

This study aimed to assess current worm control practices used by Australian alpaca farmers with an online questionnaire survey. The questionnaire contained questions about farm demography and general husbandry practices, farmers' knowledge about gastrointestinal nematodes (GINs) and their importance, the use of worm control strategies and anthelmintics, and grazing management. A link for the questionnaire survey was sent to all (n = 954) registered members of the Australian Alpaca Association in July 2015. The response rate for the questionnaire was 25% (239/954). The majority of respondents were from small (≤ 50 alpacas; 64%, 153/239) followed by medium (50-100 alpacas; 24%, 57/239) and large (>100 alpacas; 12%, 29/239) farms. Findings revealed that the majority of respondents kept Huacaya alpacas to produce high-quality fibre and alpacas were usually kept with other domestic ruminants (e.g. cattle and sheep). Although half of alpaca farmers (114/220) perceived that GINs were an important health problem of alpacas, with Haemonchus spp. being the most common nematode, the majority of them (174/220) used anthelmintics for nematode control. Macrocyclic lactones, a commercial combination of four anthelmintics (abamectin, albendazole, closantel and levamisole) and monepantel were the three most commonly used dewormers by Australian alpaca farmers. Although a significant proportion (166/213) of respondents used a quarantine drench for alpacas, very few respondents were aware of strategic deworming and the issue of anthelmintic resistance. Alpaca farmers mostly used anthelmintics at the dose rate recommended for sheep (47%, 79/167) and cattle (9%, 15/167), though some used 1.5 (31%, 51/167) and 2 (13%, 22/167) times the dose rate recommended for sheep. The majority of small herds used anthelmintics at the dose rate recommended for sheep and cattle while medium and large herds used anthelmintics at 1.5 to 2 times the dose rate recommended for sheep. This study provides invaluable insights into the demography of alpaca farms in Australia, husbandry practices used by alpaca farmers and their knowledge about worms and their control, thereby paving the way for developing guidelines for the control of GINs of alpacas.

Using longitudinal syndromic surveillance to describe small ruminant health in village production systems in Myanmar.

A novel syndromic surveillance approach was used to describe small ruminant health in Myanmar, to help overcome limitations in disease diagnosis common in many parts of the world, especially in low and middle income countries (LMICs). Observations were made from July 2015 to June 2016 of ten clinical syndromes in 12 goat herds and sheep flocks owned by smallholders in the Central Dry Zone. Strengths and weaknesses to using syndromic surveillance in a village setting were identified using a formal surveillance evaluation framework, 'SERVAL'. Larger reporting teams made disproportionately more reports than smaller ones (86% compared to 14% of all reports, with a reporting rate ratio of 4.3 95% CI 3.5-5.4), which may have affected surveillance sensitivity. The benefits of the syndromic surveillance included its relatively low cost and ability to produce quantitative disease estimates that could be used to prioritise further disease investigation and extension activities. In particular, significant mortality was observed, with monthly mortality of 3.0% (95% CI 2.5-3.7%) and 0.28% (0.15-0.53%) in young and adult animals, respectively, and a population attributable fraction of mortality for young animals of 82% (68-91%). Mortality was associated with ill-thrift in young animals but had not previously been considered an important production-limiting condition in Myanmar. This information contributes to an understanding of the prevalence of excessive mortality in smallholder goat and sheep production systems. It is a practical example of the use of syndromic surveillance in a LMIC livestock production system, the results of which can direct future disease research, treatment and prevention to improve the health and productivity of small ruminants in Myanmar.

Anthelmintic resistance in gastrointestinal nematodes of alpacas (Vicugna pacos) in Australia.

BACKGROUND: Gastrointestinal nematodes (GINs) can cause significant economic losses in alpacas due to lowered production of fibre and meat. Although no anthelmintics are registered for use in alpacas, various classes of anthelmintics are frequently used to control parasitic gastroenteritis in alpacas in Australia and other countries. Very little is known about the current worm control practices as well as the efficacy of anthelmintics used against common GINs of alpacas. This study aimed to assess the existing worm control practices used by Australian alpaca farmers and to quantify the efficacy of commonly used anthelmintics against GINs of alpacas. METHODS: An online questionnaire survey was conducted to assess current worm control practices on 97 Australian alpaca farms, with an emphasis on the use of anthelmintics. Of this group of 97 alpaca farms, 20 were selected to assess the efficacy of eight anthelmintics and/or their combinations (closantel, fenbendazole ivermectin, monepantel, moxidectin and a combination of levamisole, closantel, albendazole, abamectin) using the faecal egg count reduction test (FECRT). A multiplexed-tandem PCR (MT-PCR) was used to identify the prevalent nematode genera/species. RESULTS: The response rate for the questionnaire was 94% (91/97). Almost half of the respondents kept alpacas with sheep and cattle, and 26% of respondents allowed alpacas to co-graze with these ruminants. Although only 63% respondents perceived worms to be an important health concern for alpacas, the majority of respondents (89%) used anthelmintics to control GINs of alpacas. The commonly used anthelmintics were macrocyclic lactones, monepantel, benzimidazoles, levamisole, closantel and their combinations, and they were typically administered at the dose rate recommended for sheep. The FECRT results showed that a combination of levamisole, closantel, albendazole and abamectin was the most effective dewormer followed by single drugs, including monepantel, moxidectin, closantel, fenbendazole and ivermectin. Haemonchus spp. were the most commonly resistant nematodes followed by Trichostrongylus spp., Camelostrongylus mentulatus, Ostertagia ostertagi and Cooperia spp. CONCLUSIONS: This is the first study aimed at assessing worm control practices and efficacy of commonly used anthelmintics in alpacas in Australia. Our findings document the extent of anthelmintics resistance on Australian alpaca farms and identify those anthelmintics that are still effective against GINs of alpacas.

Comparison of McMaster and FECPAKG2 methods for counting nematode eggs in the faeces of alpacas.

This study aimed to compare the FECPAKG2 and the McMaster techniques for counting of gastrointestinal nematode eggs in the faeces of alpacas using two floatation solutions (saturated sodium chloride and sucrose solutions). Faecal eggs counts from both techniques were compared using the Lin's concordance correlation coefficient and Bland and Altman statistics. Results showed moderate to good agreement between the two methods, with better agreement achieved when saturated sugar is used as a floatation fluid, particularly when faecal egg counts are less than 1000 eggs per gram of faeces. To the best of our knowledge this is the first study to assess agreement of measurements between McMaster and FECPAKG2 methods for estimating faecal eggs in South American camelids.

Faecal shedding of pathogenic Yersinia enterocolitica determined by qPCR for yst virulence gene is associated with reduced live weight but not diarrhoea in prime lambs.

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.

Sample size considerations for livestock movement network data.

The movement of animals between farms contributes to infectious disease spread in production animal populations, and is increasingly investigated with social network analysis methods. Tangible outcomes of this work include the identification of high-risk premises for targeting surveillance or control programs. However, knowledge of the effect of sampling or incomplete network enumeration on these studies is limited. In this study, a simulation algorithm is presented that provides an estimate of required sampling proportions based on predicted network size, density and degree value distribution. The algorithm may be applied a priori to ensure network analyses based on sampled or incomplete data provide population estimates of known precision. Results demonstrate that, for network degree measures, sample size requirements vary with sampling method. The repeatability of the algorithm output under constant network and sampling criteria was found to be consistent for networks with at least 1000 nodes (in this case, farms). Where simulated networks can be constructed to closely mimic the true network in a target population, this algorithm provides a straightforward approach to determining sample size under a given sampling procedure for a network measure of interest. It can be used to tailor study designs of known precision, for investigating specific livestock movement networks and their impact on disease dissemination within populations.

Longitudinal prevalence, faecal shedding and molecular characterisation of Campylobacter spp. and Salmonella enterica in sheep.

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).

Longitudinal prevalence, oocyst shedding and molecular characterisation of Eimeria species in sheep across four states in Australia.

The prevalence of Eimeria in sheep in Australia has not been well described, therefore a quantitative PCR (qPCR) was developed, validated and used to study the prevalence and oocyst concentration in 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 4 states and screened for the presence of Eimeria using this qPCR at the 18S ribosomal RNA (rRNA) locus. A subset of positives was typed by sequence analysis at the 18S locus. The overall prevalence was 18.1% (95% CI 16.8-19.3%) and of the 616 positives, 118 were successfully genotyped. The prevalence of Eimeria was highest in NSW and peaked at 70% during the post-weaning period. The range of oocyst shedding per gram of faeces (g(-1)) at weaning, post-weaning and pre-slaughter overall across all states was 23-2.1×10(7), 23-1.3×10(7) and 23-2.1×10(5), respectively. Median Eimeria shedding g(-1) was higher during post-weaning (1.1×10(3)) and pre-slaughter (1.1×10(3)) than during weaning (206). The following species were identified: Eimeria crandallis, Eimeria ahsata, Eimeria ovinoidalis, Eimeria weybridgensis and Eimeria cylindrica. Of these, E. crandallis and E. ovinoidalis, the most pathogenic species in sheep were responsible for 58.5% of infections typed. This highlights a need for further research to quantify the production impacts of Eimeria in sheep.

Longitudinal prevalence and faecal shedding of Chlamydia pecorum in sheep.

The prevalence and faecal shedding of Chlamydia spp. in sheep in Australia has not been well described. Two species-specific quantitative PCRs (qPCRs) targeting the chlamydial outer membrane protein cell surface antigen gene (ompA) were validated and used to determine the prevalence and faecal shedding of C. abortus and C. pecorum from faecal samples of lambs at three sampling times (weaning, post-weaning and pre-slaughter) from eight farms in South Australia, New South Wales, Victoria and Western Australia. A total of 3412 faecal samples were collected and screened from approximately 1189 lambs across the four states. C. abortus was not detected in any of the samples screened. The overall prevalence of C. pecorum was 1027/3412 (30.1%) and median bacterial concentrations at weaning, post-weaning and pre-slaughter were 1.8 × 10(7), 1.2 × 10(7) and 9.6 × 10(5)/g faeces, respectively. A subset of C. pecorum positive samples from each farm, (n = 48) was sequenced to confirm their identity. The present study demonstrates that C. pecorum is prevalent in Australian sheep, highlighting a need for further research on the impact of this bacterium on production.

Longitudinal prevalence, oocyst shedding and molecular characterisation of Cryptosporidium species in sheep across four states in Australia.

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 63-7.9×10(6) and the median was 3.2 × 10(4) 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.

Development of a quantitative PCR (qPCR) for Giardia and analysis of the prevalence, cyst shedding and genotypes of Giardia present in sheep across four states 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.