Assessing the impact of socio-demographics and farming activity on ward-level mortality patterns using farm and population decennial censuses.

INTRODUCTION AND OBJECTIVE: Farmers experience a specific set of unique dangers, which increases their risk of mortality compared with any other occupation. This study hypothesised that Northern Ireland's (NIs) agriculturally saturated Wards have a higher risk of mortality compared against non-agriculturally based Wards. DESIGN: The Population Census and Farm Census information were downloaded from the Northern Ireland Neighbourhood Service (NINIS) online depository to compile three mortality-based data sets (2001, 2011, pooled data sets). Assessing the impact of socio-demographics and farming activity on Ward-level mortality patterns using farm and population decennial censuses. This study analysed all 582 Ward areas of NI, which enclosed the entire populace of the country in 2001 and 2011. FINDINGS: Path analysis was utilised to examine direct and indirect paths linked with mortality within two census years (2001; 2011), alongside testing pathways for invariance between census years (pooled data set). Ward-level results provided evidence for exogenous variables to mortality operating through three/four endogenous variables via: (i) direct effects (age), (ii) summed indirect effects (age; males; living alone; farming profit; and deprivation) and (iii) total effects (age; males; living alone; and deprivation). Multi-group results cross-validated these cause-and-effect relationships relating to mortality. DISCUSSION AND CONCLUSION: This study demonstrated that farming intensity scores, farming profits and socio-demographics' influence on mortality risk in a Ward were dependent on the specific social-environmental characteristics within that area. In line with earlier area level research, results support the aggregated interpretation that higher levels of farming activity within a Ward increase the risk of mortality within those Wards of NI. This was an essential study to enable future tailoring of new strategies and upgrading of current policies to bring about significant mortality risk change at local level.

Ageing threatens sustainability of smallholder farming in China.

Rapid demographic ageing substantially affects socioeconomic development1-4 and presents considerable challenges for food security and agricultural sustainability5-8, which have so far not been well understood. Here, by using data from more than 15,000 rural households with crops but no livestock across China, we show that rural population ageing reduced farm size by 4% through transferring cropland ownership and land abandonment (approximately 4 million hectares) in 2019, taking the population age structure in 1990 as a benchmark. These changes led to a reduction of agricultural inputs, including chemical fertilizers, manure and machinery, which decreased agricultural output and labour productivity by 5% and 4%, respectively, further lowering farmers' income by 15%. Meanwhile, fertilizer loss increased by 3%, resulting in higher pollutant emissions to the environment. In new farming models, such as cooperative farming, farms tend to be larger and operated by younger farmers, who have a higher average education level, hence improving agricultural management. By encouraging the transition to new farming models, the negative consequences of ageing can be reversed. Agricultural input, farm size and farmer's income would grow by approximately 14%, 20% and 26%, respectively, and fertilizer loss would reduce by 4% in 2100 compared with that in 2020. This suggests that management of rural ageing will contribute to a comprehensive transformation of smallholder farming to sustainable agriculture in China.

Fatal Animal Related Incidents on Australian Farms - a 20-Year Review.

Objectives To assess demographic and causal factors of fatal farm incidents involving animals in Australia. Methods Descriptive study of the National Coronial Information System for persons fatally injured by an animal on an Australian farm over the 2001-20 period. Data were analysed in relation to age, sex, state where incident occurred, work-relatedness and causal agents. Results There has been little change in the mean number of animal-related injury deaths across Australia in the 2001-20 period (mean 6.5), however this is a 35% reduction on an earlier 1989-92 assessment (mean 10). The majority of incidents (81%) involved horses (n = 75) and cattle (n = 31). Males were involved in 86 (66%) cases, with 54 female cases. People aged 60 years and over accounted for 46% of the cases, with more than half occurring during work. Of the decedents, 85% fell from or were struck by an animal at the time of the incident, with 40% resulting in a head injury. Conclusion While annualized case numbers have decreased slightly, the leading agents remain consistent with previous studies. The lack of genuine progress in addressing fatalities related to horses and cattle, along with the representation of older persons in the cohort, require attention drawing on the Hierarchy of Controls.

IOT-Based Medical Informatics Farming System with Predictive Data Analytics Using Supervised Machine Learning Algorithms.

In the farming industry, the Internet of Things (IoT) is crucial for boosting utility. Innovative agriculture practices and medical informatics have the potential to increase crop yield while using the same amount of input. Individuals can benefit from the Internet of Things in various ways. The intelligent farms require the creation of an IoT-based infrastructure based on sensors, actuators, embedded systems, and a network connection. The agriculture sector will gain new advantages from machine learning and IoT data analytics in terms of improving crop output quantity and quality to fulfill rising food demand. This paper described an intelligent medical informatics farming system with predictive data analytics on sensing parameters, utilizing a supervised machine learning approach in an intelligent agricultural system. The four essential components of the proposed approach are the cloud layer, fog layer, edge layer, and sensor layer. The primary goal is to enhance production and provide organic farming by adjusting farming conditions as per plant needs that are considered in experimentation. The use of machine learning on acquired sensor data from a prototype embedded model is investigated for regulating the actuators in the system. Then, an analytics and decision-making system was built at the fog layer, employing two supervised machine learning approaches including classification and regression algorithms using a support vector machine (SVM) and artificial neural network (ANN) for effective computation over the cloud layer. The experimental results are evaluated and analyzed in MATLAB software, and it is found that the classification accuracy using SVM is much better as compared to ANN and other state of art methods.

Repeated cross-sectional sampling of pigs at slaughter indicates varying age of hepatitis E virus infection within and between pig farms.

Humans can become infected with hepatitis E virus (HEV) by consumption of undercooked pork. To reduce the burden of HEV in humans, mitigation on pig farms is needed. HEV is found on most pig farms globally, yet within-farm seroprevalence estimates vary considerably. Understanding of the underlying variation in infection dynamics within and between farms currently lacks. Therefore, we investigated HEV infection dynamics by sampling 1711 batches of slaughter pigs from 208 Dutch farms over an 8-month period. Four farm types, conventional, organic, and two types with strict focus on biosecurity, were included. Sera were tested individually with an anti-HEV antibody ELISA and pooled per batch with PCR. All farms delivered seropositive pigs to slaughter, yet batches (resembling farm compartments) had varying results. By combining PCR and ELISA results, infection moment and extent per batch could be classified as low transmission, early, intermediate or late. Cluster analysis of batch infection moments per farm resulted in four clusters with distinct infection patterns. Cluster 1 farms delivered almost exclusively PCR negative, ELISA positive batches to slaughter (PCR-ELISA+), indicating relatively early age of HEV infection. Cluster 2 and 3 farms delivered 0.3 and 0.7 of batches with intermediate infection moment (PCR+ELISA+) respectively and only few batches with early infection. Cluster 4 farms delivered low transmission (PCR-ELISA-) and late infection (PCR+ELISA-) batches, demonstrating that those farms can prevent or delay HEV transmission to farm compartments. Farm type partly coincided with cluster assignment, indicating that biosecurity and management are related to age of HEV infection.

A Survey of Chinese Pig Farms and Human Healthcare Isolates Reveals Separate Human and Animal Methicillin-Resistant Staphylococcus aureus Populations.

There has been increasing concern that the overuse of antibiotics in livestock farming is contributing to the burden of antimicrobial resistance in people. Farmed animals in Europe and North America, particularly pigs, provide a reservoir for livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA ST398 lineage) found in people. This study is designed to investigate the contribution of MRSA from Chinese pig farms to human infection. A collection of 483 MRSA are isolated from 55 farms and 4 hospitals in central China, a high pig farming density area. CC9 MRSA accounts for 97.2% of all farm isolates, but is not present in hospital isolates. ST398 isolates are found on farms and hospitals, but none of them formed part of the "LA-MRSA ST398 lineage" present in Europe and North America. The hospital ST398 MRSA isolate form a clade that is clearly separate from the farm ST398 isolates. Despite the presence of high levels of MRSA found on Chinese pig farms, the authors find no evidence of them spilling over to the human population. Nevertheless, the ST398 MRSA obtained from hospitals appear to be part of a widely distributed lineage in China. The new animal-adapted ST398 lineage that has emerged in China is of concern.

Prevalence of Bovine Rotavirus and Coronavirus in Neonatal Calves in Dairy Farms of Addis Ababa, Ethiopia: Preliminary Study.

BACKGROUND: Bovine rotavirus (BRV) and bovine coronavirus (BCoV) are the most common viral agents in neonatal calf diarrhea and result in serious economic consequences. The aim of the study was to determine the epidemiology of those viruses in randomly selected dairy farms of Addis Ababa. METHODS: A cross-sectional study was conducted from November 2018 to April 2019 using a probability proportional to size (PPS) sampling technique. A total of 110 calves, less than 30 days of age, from 57 dairy herds were involved in the study. Associated factors of herds and calves were collected using semistructured interviews from farm owners and through physical observation of selected calves. Fecal samples were collected and analyzed using the sandwich ELISA method. Data generated from both semistructured interviews and laboratory investigation were analyzed using STATA_MP version 15. RESULTS: From the total 110 calves, 42 (38.18%) had diarrhea during the survey. The prevalence of bovine rotavirus and coronavirus was 3.64% (4/110) and 0.91% (1/110), respectively. Diarrhea, feeding colostrum timing, and sex of the neonatal calves had statistically significant association with bovine rotavirus infection (p < 0.05). All rotavirus-positive neonatal calves were identified in small scale dairy farms and in dairy farms that reported mortality though they lack statistically significant association. Only one coronavirus case was detected among the neonatal calves. The case was identified among small scale herds and in a herd with diarrheal cases. The sex of the coronavirus calf was female, diarrheic, and among 11-20 days old. CONCLUSION: The prevalence of rotavirus and coronavirus infections in neonatal calves was seldom in dairy farms of the study area. Rotavirus was more common than coronavirus, and further studies should be initiated on other (infectious and noninfectious) causes of neonatal calf diarrhea in the area.

Occurrence of the Colistin Resistance Gene mcr-1 and Additional Antibiotic Resistance Genes in ESBL/AmpC-Producing Escherichia coli from Poultry in Lebanon: A Nationwide Survey.

The objective of the present study was to determine genomic characteristics of expanded-spectrum cephalosporin (ESC)-resistant Escherichia coli spreading in healthy broilers in Lebanon in 2018. Rectal swabs (n = 280) from 56 farms were screened for the presence of ESC-resistant E. coli isolates. Antimicrobial susceptibility and extended-spectrum ß-lactamase (ESBL)/AmpC production were determined by the disk diffusion method. Whole-genome sequencing (WGS) of 102 representative isolates of E. coli was performed to determine their phylogenetic diversity, serotypes, sequence types (ST), acquired resistance genes, and virulence-associated genes. Fifty-two out of 56 farms housed broilers carrying ESC-resistant E. coli isolates. These farms had large and recurrent antimicrobial practices, using, for some of them, critically important antibiotics for prophylactic and therapeutic purposes. Among the 102 sequenced multidrug-resistant (MDR) E. coli isolates, the proportion of ESBL, plasmid-mediated AmpC ß-lactamase (pAmpC) producers, and ESBL/pAmpC coproducers was 60%, 27.6%, and 12.4%, respectively. The most prevalent ESBL/pAmpC genes were blaCMY-2, blaCTX-M-3, blaCTX-M-15, blaCTX-M-27, and blaCTX-M-14b (n = 42, n = 31, n =15, n = 9, and n = 7, respectively). These ESBL/pAmpC producers were distributed in different STs, most being well-known avian-associated and sometimes pathogenic STs (ST-10, ST-48, ST-93, ST-115, ST-117, and ST-457). Phylogenetic single nucleotide polymorphism (SNP) analysis confirmed their genetic diversity and wide dispersion across the Lebanese territory. Most isolates were also resistant to ciprofloxacin (101/102 with 3 QRDR mutations), and 19/102 isolates from 11 unrelated STs also carried the mobile resistance gene mcr-1. This survey illustrates the alarming prevalence of MDR E. coli resistant to medically important antibiotics in broilers in Lebanon. This advocates the need for surveillance programs of antimicrobial resistance in Lebanon and the reduction of excessive use of antibiotics to limit the spread of MDR E. coli in food-producing animals. IMPORTANCE Poultry production is a main contributor of the global trend of antimicrobial resistance arising from food-producing animals worldwide. In Lebanon, inappropriate use of antibiotics is frequent in chickens for prophylactic reasons and to improve productivity, resulting in an alarming prevalence of extended-spectrum ß-lactamase (ESBL)/AmpC-producing Escherichia coli, also resistant to other medically important antibiotics (i.e., colistin and ciprofloxacin). Their complex genomic epidemiology highlighted by an important genetic diversity suggests that these resistance determinants are largely spreading in enteric bacteria in Lebanese poultry. Further molecular surveillance is needed to understand the country-specific epidemiology of ESBL/AmpC and mcr-1 genes in Lebanese poultry production. In addition, decisive interventions are urgently needed in order to ban the use of critically important antibiotics for human medicine in food-producing animals and limit the spread of antibiotic resistance in Lebanon.

Women's empowerment in agriculture and productivity change: The case of Bangladesh rice farms.

Using productivity change as a measure of farm economic performance, we analyze the relationship between women's empowerment in agriculture and farm productivity change and its components, which include efficiency change, technological change, and scale efficiency change. A non-parametric Malmquist approach is used to measure farm specific productivity change and its decomposition. We use a bootstrap regression to analyze factors that cause differences in productivity change and its components, testing, in particular, the role women's empowerment plays. The empirical application focuses on a sample of Bangladesh rice farms over the crop cultivation period 2011 and 2014. Results suggest that improvements in women's empowerment in agriculture were associated with higher levels of productivity change, efficiency change, and technical change, while they had no impact on scale efficiency change. We find that empowering women, specifically, improving their ability to make independent choices regarding agricultural production had a statistically significant positive association with productivity change, efficiency change, and technical change. We also find that lowering the gender parity gap is positively related with improving productivity of the sample farms.

Risk factors for poor colostrum quality and failure of passive transfer in Scottish dairy calves.

Failure of passive transfer (FPT) has health, welfare and economic implications for calves. Immunoglobulin G (IgG) concentration of 370 dairy calf serum samples from 38 Scottish dairy farms was measured via radial immunodiffusion (RID) to determine FPT prevalence. IgG concentration, total bacteria count (TBC) and total coliform count (TCC) of 252 colostrum samples were also measured. A questionnaire was completed at farm enrollment to investigate risk factors for FPT and poor colostrum quality at farm-level. Multivariable mixed effect logistic and linear regressions were carried out to determine significant risk factors for FPT and colostrum quality. Prevalence of FPT at calf level was determined to be 14.05%. Of 252 colostrum samples, 111 (44.05%) failed to meet Brix thresholds for colostrum quality. Of these 28 and 38 samples also exceeded TBC and TCC thresholds, respectively. Increased time between parturition and colostrum harvesting was numerically (non-significantly) associated with a colostrum Brix result <22%, and increased time spent in a bucket prior to feeding or storing was significantly associated with high TBC (≥100 000 cfu/ml and also ≥10 000 cfu/ml). High TBC values in colostrum were significantly associated with lower serum IgG concentrations. This study highlights associations between colostrum quality and FPT in dairy calves as well as potential risk factors for reduced colostrum quality; recommending some simple steps producers can take to maximise colostrum quality on farm.

Occurrence and aetiology of subclinical mastitis in water buffalo in Bangladesh.

Subclinical mastitis (SCM) in water buffalo is a production disease associated with decreased milk yield and impaired milk quality and safety. Water buffalo is an important livestock species in Bangladesh, but information about the occurrence and aetiology of SCM in this species is scarce. A cross-sectional study was conducted as part of the Udder Health Bangladesh Programme to (i) determine the occurrence of SCM and bulk milk somatic cell count (SCC) in water buffalo in Bangladesh, (ii) identify pathogens causing SCM and (iii) evaluate penicillin resistance in isolated staphylococci strains. Sixteen buffalo farms in the Bagerhat and Noakhali regions of Bangladesh were selected for study and a bulk milk sample was collected from each farm. In addition, 299 udder quarter milk samples were collected from 76 animals. The bulk milk samples were assessed by direct SCC and the quarter milk samples by California mastitis test (CMT). The occurrence of SCM calculated at quarter and animal level was 42.5 and 81.6%, respectively. Milk samples from 108 CMT-positive quarters in 48 animals and 38 randomly selected CMT-negative quarters in 24 animals were investigated using bacteriological culture. Estimated mean bulk milk SCC was 195 000 cells/ml milk (range 47 000- 587 000 cells/ml milk). On culture, estimated quarter-level intramammary infection (IMI) was 40.4%. The identity of isolated bacteria was confirmed by MALDI-TOF mass spectrometry. Non-aureus staphylococci (NAS) were the most common pathogens (24.7%) and, among 36 NAS tested, 36.1% were resistant to penicillin. Thus there was high occurrence of SCM on the study farms, with relatively high penicillin resistance in NAS. Further studies are needed to identify underlying risk factors and develop an udder health control strategy for water buffalo in Bangladesh.

A Mortality-Based Description of EHDV and BTV Prevalence in Farmed White-Tailed Deer (Odocoileus virginianus) in Florida, USA.

Hemorrhagic disease (HD) caused by bluetongue virus (BTV) and epizootic hemorrhagic disease virus (EHDV) is the most important viral disease of farmed and wild white-tailed deer (WTD; Odocoileus virginianus) and can cause substantial mortality in susceptible hosts. Captive cervid farming is an emerging industry in Florida, an HD-enzootic region. Morbidity and mortality due to HD are major concerns among deer farmers, but the impact of HD on Florida's cervid farming industry is unknown. Our primary objective was to determine the prevalence of epizootic hemorrhagic disease virus (EHDV) and bluetongue virus (BTV) among WTD submitted to the University of Florida Institute of Food and Agricultural Sciences Cervidae Health Research Initiative (CHeRI) for post-mortem diagnostics. Our secondary objectives were to identify the predominant circulating EHDV serotypes during each sampling year and to determine the age class with the greatest proportion of EHDV- and BTV-positive post-mortem specimens. From 2016 to 2020, spleen samples from 539 farmed WTD with unexplained mortality were tested for the presence of EHDV and BTV by RT-qPCR. Overall, the prevalence of EHDV, BTV, or EHDV/BTV coinfection was 26%, 16%, and 10%, respectively, and 44% of deer (237/539) were diagnosed with HD by RT-qPCR. The predominant circulating EHDV serotype varied by year. Overall, EHDV-2 was the most commonly identified serotype (55% of PCR-positive cases), and EHDV-1 was the least frequently identified serotype (16% of PCR-positive cases). The greatest proportion of EHDV/BTV positives among mortality cases was observed in young WTD aged 3-6 months (50%-82% positive). There was a significant difference in the prevalence of EHDV/BTV by age when comparing specimens from WTD over 1 year old (p = 0.029, n = 527). Among these samples, the number of reported mortalities and the prevalence of EHDV/BTV were highest in yearling animals (56%). These data provide the first estimate of EHDV and BTV prevalence and virus serotypes among farmed WTD in Florida, identify the WTD age groups with the greatest proportions of EHDV- and BTV-positive specimens, and suggest that HD caused by these two viruses may be a major source of mortality challenging the captive cervid farming industry in Florida.

Chronic Wasting Disease Transmission Risk Assessment for Farmed Cervids in Minnesota and Wisconsin.

CWD (chronic wasting disease) has emerged as one of the most important diseases of cervids and continues to adversely affect farmed and wild cervid populations, despite control and preventive measures. This study aims to use the current scientific understanding of CWD transmission and knowledge of farmed cervid operations to conduct a qualitative risk assessment for CWD transmission to cervid farms and, applying this risk assessment, systematically describe the CWD transmission risks experienced by CWD-positive farmed cervid operations in Minnesota and Wisconsin. A systematic review of literature related to CWD transmission informed our criteria to stratify CWD transmission risks to cervid operations into high-risk low uncertainty, moderate-risk high uncertainty, and negligible-risk low uncertainty categories. Case data from 34 CWD-positive farmed cervid operations in Minnesota and Wisconsin from 2002 to January 2019 were categorized by transmission risks exposure and evaluated for trends. The majority of case farms recorded high transmission risks (56%), which were likely sources of CWD, but many (44%) had only moderate or negligible transmission risks, including most of the herds (62%) detected since 2012. The presence of CWD-positive cervid farms with only moderate or low CWD transmission risks necessitates further investigation of these risks to inform effective control measures.

Rural landscape dynamics over time and its consequences for habitat preference patterns of the grey partridge Perdix perdix.

Intensification of agricultural practices has drastically shaped farmland landscapes and generally caused a decline in spatial and temporal heterogeneity, thus leading to changes in habitat quality and food resources and a decline for most farmland birds Europe-wide. The relationship between complex landscape changes and habitat preferences of animals still remains poorly understood. Particularly, temporal and spatial changes in diversity may affect not only habitat choice but also population sizes. To answer that question, we have looked into a severely declining typical farmland bird species, the grey partridge Perdix perdix in a diverse farmland landscape near Vienna to investigate the specific habitat preferences in respect to the change of agricultural landscape over two decades and geographic scales. Using a dataset collected over 7.64 km² and between 2001 and 2017 around Vienna, we calculated Chesson's electivity index to study the partridge's change of habitat selection over time on two scales and between winter and spring in 2017. Although the farmland landscape underwent an ongoing diversification over the two decades, the grey partridges declined in numbers and shifted habitat use to less diverse habitats. During covey period in winter, partridges preferred also human infrastructure reservoirs such as roads and used more diverse areas with smaller fields than during breeding where they selected harvested fields but surprisingly, avoided hedges, fallow land and greening. Known as best partridge habitats, those structures when inappropriately managed might rather function as predator reservoirs. The avoidance behaviour may further be a consequence of increasing landscape structuring and edge effects by civilisation constructions. Besides, the loss in size and quality of partridge farmland is altered by crop choice and pesticides reducing plant and insect food. With declining breeding pairs, the grey partridge does not seem to adjust to these unsustainable landscape changes and farmland practices.

Genomic analysis of extra-intestinal Campylobacter jejuni and Campylobacter coli isolated from commercial chickens.

Campylobacter jejuni and Campylobacter coli have commonly been considered harmless commensal inhabitants of the chicken gut; however, these Campylobacter spp. are known to be able to multiply in the gut and invade other tissues, negatively affecting host health and performance. In this study, fourteen Campylobacter spp. were isolated from chickens showing foci of necrosis on the liver surface resembling lesions observed in cases of avian vibrionic hepatitis/spotty liver disease. The whole genome sequences of the fourteen isolates were analysed and their virulomes compared to those of Campylobacter reference sequences, aiming to investigate the possible association between virulence genes and the observed pathological lesions. Nine C. jejuni and five C. coli were studied. These Campylobacter shared twelve virulence factors with other isolates originated from chicken livers and hosted a higher number of virulence-associated genes in comparison to the reference genomes, including genes encoding for factors involved in adherence to and invasion of the intestinal epithelial cells. Our findings seem to point out that these twelve common virulence-associated genes, together with the presence of a high number of virulence factors involved in adherence, invasion and motility, might be responsible for the extra-intestinal spread of our isolates and the colonization of parenchymatous tissues, possibly causing the pathological lesions observed.

From gene banks to farmer's fields: using genomic selection to identify donors for a breeding program in rice to close the yield gap on smallholder farms.

KEY MESSAGE: Despite phenotyping the training set under unfavorable conditions on smallholder farms in Madagascar, we were able to successfully apply genomic prediction to select donors among gene bank accessions. Poor soil fertility and low fertilizer application rates are main reasons for the large yield gap observed for rice produced in sub-Saharan Africa. Traditional varieties that are preserved in gene banks were shown to possess traits and alleles that would improve the performance of modern variety under such low-input conditions. How to accelerate the utilization of gene bank resources in crop improvement is an unresolved question and here our objective was to test whether genomic prediction could aid in the selection of promising donors. A subset of the 3,024 sequenced accessions from the IRRI rice gene bank was phenotyped for yield and agronomic traits for two years in unfertilized farmers' fields in Madagascar, and based on these data, a genomic prediction model was developed. This model was applied to predict the performance of the entire set of 3024 accessions, and the top predicted performers were sent to Madagascar for confirmatory trials. The prediction accuracies ranged from 0.10 to 0.30 for grain yield, from 0.25 to 0.63 for straw biomass, to 0.71 for heading date. Two accessions have subsequently been utilized as donors in rice breeding programs in Madagascar. Despite having conducted phenotypic evaluations under challenging conditions on smallholder farms, our results are encouraging as the prediction accuracy realized in on-farm experiments was in the range of accuracies achieved in on-station studies. Thus, we could provide clear empirical evidence on the value of genomic selection in identifying suitable genetic resources for crop improvement, if genotypic data are available.

Genetic evidence substantiates transmission of Trichinella spiralis from one swine farm to another.

BACKGROUND: Trichinella spiralis ranks seventh in the risk posed by foodborne parasites. It causes most human cases of trichinellosis and is the most frequent cause of Trichinella outbreaks on pig farms and in wild boar, worldwide. Veterinary inspectors seek the source of outbreaks in hopes of limiting the spread. Established molecular tools are inadequate for distinguishing among potential T. spiralis infection sources because genetic variability in these zoonotic pathogens is limited in Europe. Microsatellite markers proved successful in tracing an outbreak of T. britovi, a related parasite harboring much more genetic variation. Here, we successfully employed microsatellite markers to determine the genetic structure of T. spiralis isolates from two pig outbreaks, discovering notable uniformity among parasites within each farm and discovering an epidemiological link between these two outbreaks. METHODS: The individual larvae from five isolates of T. spiralis from two pig farms and from ten wild boars were genotyped using nine microsatellite markers to examine their genetic structure. RESULTS: Notably uniform parasite populations constituted each farm outbreak, and the parasites from the first and second outbreaks resembled each other to a notable degree, indicating an epidemiological link between them. Wild boar harbored more genetically variable larval cohorts, distinguishing them from parasites isolated from domestic pigs. CONCLUSIONS: Microsatellite markers succeeded in distinguishing isolates of the highly homogeneous T. spiralis, aiding efforts to track transmission. Each outbreak was composed of a homogenous group of parasites, suggesting a point source of contamination.

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.

Detection and distribution of haematophagous flies and lice on cattle farms and potential role in the transmission of Theileria orientalis.

On the Northern Tablelands of New South Wales, Australia, endemic Theileria orientalis infection of cattle has been reported on farms where no ticks have been observed, raising the question of how Theileria is transmitted in these areas. To investigate the potential role of mechanical transmission by insects, the present study investigated the seasonal dynamics of biting fly species trapped between December 2017 and May 2019 on six cattle farms in the region where the presence of Theileria was confirmed. These flies, sucking lice collected from these farms and pools of Culicoides species affecting cattle also trapped in the region were subjected to qPCR detection of T. orientalis. Eleven species from eight genera of biting flies were collected using unbaited Nzi traps. Tabanid species were present in all farms, with Dasybasis oculata (43.6 %) and D. circumdata (27.6 %) being the most abundant and widespread species. The effect of season on the mean count per trapping event was statistically significant and highest in the summer months for Lilaea fuliginosa and D. oculata, and the autumn months for D. circumdata, with no seasonal effect on the abundance of the undescribed Dasybasis spp. No biting flies were trapped during the winter months. Sucking (Linognathus vituli and Haematopinus eurysternus) and biting (Bovicola bovis) cattle lice were also collected from all farms with the latter detected in only one farm. PCR screening for T. orientalis of trapped hematophagous insects resulted in parasite detection in the tabanid and Stomoxyini flies, biting midges and sucking lice with the highest proportion of positive samples for Haematopinus eurysternus (4/4 pools) and H. irritans exigua (6/15 individuals). The detection of the parasite in these potential vectors indicates a possible role in the mechanical transmission of T. orientalis and may partly explain the ubiquitous presence of Theileria in areas where ticks are absent.

Surveillance on respiratory diseases reveals enzootic circulation of both H5 and H9 avian influenza viruses in small-scale commercial layer farms of Bangladesh.

Poultry production in Bangladesh has been experiencing H5N1 highly pathogenic avian influenza (HPAI) and H9N2 low pathogenic avian influenza (LPAI) for the last 14 years. Vaccination of chickens against H5 HPAI is in practice since the end of 2012. Subsequently, the official reporting of HPAI outbreaks gradually decreased. However, the true extent of circulation of avian influenza virus (AIV) in commercial poultry production is not clear. To explore this, we conducted active surveillance in 422 small-scale commercial layer farms in 20 villages of Mymensingh and Tangail districts of Bangladesh during 2017 and 2018 for the presence of diseases with respiratory signs. A total of 88 farms with respiratory disease problems were identified and investigated during the surveillance. In addition, 22 small-scale commercial layer farms in the neighbouring areas with respiratory disease problem were also investigated on request from the farmers. Pooled samples of oropharyngeal swabs from live birds or respiratory tissues from dead birds of the farm suffering from respiratory disease problem were tested for molecular detection of avian influenza virus (AIV), Newcastle disease virus (NDV), infectious bronchitis virus (IBV), infectious laryngotracheitis virus (ILTV), Mycoplasma gallisepticum and Avibacterium paragallinarum. A total of 110 farms (88 in the surveillance site and 22 in the neighbouring region) were investigated, and one or more respiratory pathogens were detected from 89 farms. AIV was detected in 57 farms often concurrently with other pathogens. Among these 57 farms, H5, H9, both H5 and H9 or non-H5 and non-H9 AIV were detected in 28, 9, 13 or 7 farms, respectively. Birds of most of the H5 AIV-positive farms did not present typical clinical signs or high mortality. Twenty such farms were observed longitudinally, which had only 1.05%-5.50% mortality but a marked drop in egg production. This widespread circulation of H5 AIV along with H9 AIV and other pathogens in small-scale commercial layer farms, often with low mortality, reaffirms the enzootic circulation of AIV in Bangladesh, which may escape syndromic surveillance focused on unusual mortality only. To reduce public health risks, strengthening of the control programme with comprehensive vaccination, enhanced biosecurity, improved surveillance and outbreak response is suggested.