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Chlamydia pecorum is a veterinary pathogen associated with abortions and perinatal mortality in sheep. Recent studies investigating foetal and perinatal lamb mortality in sheep from Australia and New Zealand identified C. pecorum clonal sequence type (ST)23 strains in aborted and stillborn lambs. Presently, there is limited genotypic information on C. pecorum strains associated with reproductive disease, although whole genome sequencing (WGS) of one abortigenic ST23 C. pecorum strain identified unique features, including a deletion in the CDS1 locus of the chlamydial plasmid. We applied WGS on two ST23 strains detected in aborted and stillborn lambs from Australia and used phylogenetic and comparative analyses to compare these to the other available C. pecorum genomes. To re-evaluate the genetic diversity of contemporary strains, we applied C. pecorum genotyping, and chlamydial plasmid sequencing to a range of C. pecorum positive samples and isolates from ewes, aborted foetuses and stillborn lambs, cattle and a goat from diverse geographical regions across Australia and New Zealand.The two new C. pecorum genomes are nearly identical to the genome of the Australian abortigenic strain including the unique deletion in the chlamydial plasmid. Genotyping revealed that these novel C. pecorum ST23 strains are widespread and associated with sheep abortions on Australian and New Zealand farms. In addition, a goat C. pecorum strain (denoted ST 304) from New Zealand was also characterised. This study expands the C. pecorum genome catalogue and describes a comprehensive molecular characterisation of the novel livestock ST23 strains associated with foetal and lamb mortality.

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 < 0.001). 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.

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.

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.

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 < 0.001). 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.

This case-control study investigated associations between Campylobacter fetus or Campylobacter jejuni titre and reproductive outcomes in 22 flocks of Merino and non-Merino maiden ewes aged 1–2 years old. Campylobacter titres were also determined for multiparous ewes aged 3 years or older on the same farms. C. fetus ‘positivity’ (titre ≥1:80) was detected for 12% (57/462; 95% confidence interval [95% CI] 9.6 to 15.6) of maiden ewes and 31% (65/210; 95% CI 25.0 to 37.4) of mature ewes. The odds for failing to rear a lamb in C. fetus-‘exposed’ maiden ewes (titre ≥1:10) was 2.01 times that of seronegative ewes (95% CI 1.09 to 3.77; P = 0.027), but there was no association between C. fetus-‘positivity’ (titre ≥1:80) and failure to rise (OR 1.69; 95% CI 0.77 to 3.76; P = 0.191). C. fetus abortions were confirmed with microbial culture in one maiden ewe flock. In this flock, C. fetus titres fluctuated and often waned by lamb marking, highlighting the value of necropsies during abortion investigations. C. jejuni-‘positivity’ (titre ≥1:80) was detected for 44% (204/462; 95% CI 39.7 to 48.7) maiden ewes, but odds of failing to rear were decreased for C. jejuni-‘positive’ ewes (OR 0.52; 95% CI 0.32 to 0.83; P = 0.007). The association between Campylobacter serology and the reproductive outcome was inconsistent in these flocks. Serology should be considered in the context of other risk factors and used in conjunction with other strategies to investigate the impact of Campylobacter exposure on ewe reproductive performance such as monitoring for abortions and lamb necropsies to determine aetiological diagnosis, and vaccination trials.

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.

This case-control study investigated associations between Campylobacter fetus or Campylobacter jejuni titre and reproductive outcomes in 22 flocks of Merino and non-Merino maiden ewes aged 1-2 years old. Campylobacter titres were also determined for multiparous ewes aged 3 years or older on the same farms. C. fetus 'positivity' (titre ≥1:80) was detected for 12% (57/462; 95% confidence interval [95% CI] 9.6 to 15.6) of maiden ewes and 31% (65/210; 95% CI 25.0 to 37.4) of mature ewes. The odds for failing to rear a lamb in C. fetus-'exposed' maiden ewes (titre ≥1:10) was 2.01 times that of seronegative ewes (95% CI 1.09 to 3.77; P = 0.027), but there was no association between C. fetus-'positivity' (titre ≥1:80) and failure to rise (OR 1.69; 95% CI 0.77 to 3.76; P = 0.191). C. fetus abortions were confirmed with microbial culture in one maiden ewe flock. In this flock, C. fetus titres fluctuated and often waned by lamb marking, highlighting the value of necropsies during abortion investigations. C. jejuni-'positivity' (titre ≥1:80) was detected for 44% (204/462; 95% CI 39.7 to 48.7) maiden ewes, but odds of failing to rear were decreased for C. jejuni-'positive' ewes (OR 0.52; 95% CI 0.32 to 0.83; P = 0.007). The association between Campylobacter serology and the reproductive outcome was inconsistent in these flocks. Serology should be considered in the context of other risk factors and used in conjunction with other strategies to investigate the impact of Campylobacter exposure on ewe reproductive performance such as monitoring for abortions and lamb necropsies to determine aetiological diagnosis, and vaccination trials.

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.

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.

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.

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.

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.

Chlamydia pecorum is an obligate intracellular pathogen with a wide host range including livestock such as sheep, cattle, goats, and pigs as well as wildlife species such as koalas. Chlamydial polyarthritis is an economically important disease resulting in swollen joints, lameness, stiffness, and weight loss in young sheep. In the present study, tissues from sheep experimentally or naturally infected with Chlamydia pecorum were assessed by histopathology and immunohistochemistry. Carpal, hock, and stifle joints as well as spleen, liver, kidney, lymph nodes, lung, and brain of 35 sheep from different inoculation groups were available. Two different C. pecorum strains (IPA and E58), different routes of administration (intraarticular or intravenous), UVA-irradiated IPA strain, and corresponding noninfected control groups were investigated. Similar investigations on tissues from 5 naturally infected sheep were performed. The most obvious inflammatory lesions were observed in synovial tissues and, notably, in the renal pelvis from the experimentally infected group and naturally infected animals. This resulted in chronic or chronic-active arthritis and pyelitis. Intralesional chlamydial inclusions could be demonstrated by immunohistochemistry in both tissues. Immunohistochemical evaluation of the presence and distribution of macrophages, T and B cells in synovial tissues revealed macrophages as the most prevalent inflammatory cell population. Previous observations indicated that C. pecorum isolates can infect circulating monocytes. Together with the finding of the histological lesions in synovial tissues and internal organs alongside the presence of C. pecorum DNA, these observations suggest chlamydial arthritis in lambs is the result of hematogeneous spread of C. pecorum.

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.

This article presents the preliminary findings of an ongoing, national project investigating the magnitude, timing and causes of reproductive wastage for maiden ewes.

This article presents the preliminary findings of an ongoing, national project investigating the magnitude, timing and causes of reproductive wastage for maiden ewes.

Resolving Orbital and Climate Keys of Earth and Extraterrestrial Environments with Dynamics (ROCKE-3D) is a three-dimensional General Circulation Model (GCM) developed at the NASA Goddard Institute for Space Studies for the modeling of atmospheres of solar system and exoplanetary terrestrial planets. Its parent model, known as ModelE2, is used to simulate modern Earth and near-term paleo-Earth climates. ROCKE-3D is an ongoing effort to expand the capabilities of ModelE2 to handle a broader range of atmospheric conditions, including higher and lower atmospheric pressures, more diverse chemistries and compositions, larger and smaller planet radii and gravity, different rotation rates (from slower to more rapid than modern Earth's, including synchronous rotation), diverse ocean and land distributions and topographies, and potential basic biosphere functions. The first aim of ROCKE-3D is to model planetary atmospheres on terrestrial worlds within the solar system such as paleo-Earth, modern and paleo-Mars, paleo-Venus, and Saturn's moon Titan. By validating the model for a broad range of temperatures, pressures, and atmospheric constituents, we can then further expand its capabilities to those exoplanetary rocky worlds that have been discovered in the past, as well as those to be discovered in the future. We also discuss the current and near-future capabilities of ROCKE-3D as a community model for studying planetary and exoplanetary atmospheres.

The Earth System Prediction Suite (ESPS) is a collection of flagship U.S. weather and climate models and model components that are being instrumented to conform to interoperability conventions, documented to follow metadata standards, and made available either under open source terms or to credentialed users.

We have modified the publicly available electromagnetic scattering code called DDSCAT to handle bigger targets with shorter execution times than the original code. A big target is one whose sphere equivalent radius is large compared to the incident wavelength. DDSCAT uses the discrete-dipole approximation and an accurate result requires the spacing between dipoles to be small relative to the wavelength. This requirement, along with the big target size, implies that the number of discrete grid cells defining the computational grid box surrounding the target must be large. The memory requirement is thus significant and the execution time long. The original version of the code cannot handle large enough targets that we would like to consider because they require memory exceeding what is available on a single node of our cluster and execution time extending to days. We have removed two limitations of the original version of the code. First, to speed up the execution involving multiple target orientations, the original code assigned one, but only one, MPI process to each independent orientation. We surmount this limitation by assigning each orientation a team of processes. Second, the original code allocated all the memory for the full problem for each MPI process. We surmount this limitation by decomposing the data structures across the members of a team. With these changes, the new version can handle much bigger targets. Moreover, it exhibits strong scaling for xed problem size. The execution time decreases very nearly 1/p as the processor count p increases. Execution time measured in days with the original code can now be reduced to fractions of an hour., See also ADA584538. Progress in Electromagnetics Research Symposium (33rd) (PIERS 2013) held in Taipei, Taiwan on 25-28 March 2013. U.S. Government or Federal Purpose Rights License