Modern pig farming in the People's Republic of China: growth and veterinary challenges

Association analysis of the sorting nexin 29 (SNX29) gene copy number variations with growth traits in Diannan small-ear (DSE) pigs

SNX29 is a potential functional gene associated with meat production traits. Previous studies have shown that SNX29 copy number variation (CNV) could be implicated with phenotype in goats. However, in Diannan small-ear (DSE) pigs, the genetic impact of SNX29 CNV on growth traits remains unclear. Therefore, this study investigated the associations between SNX29 CNVs (CNV10810 and CNV10811) and growth traits in 415 DSE pigs. The results revealed that the CNV10810 mutation was significantly associated with backfat thickness in DSE pigs at 12 and 15 months old (P < 0.05), while the CNV10811 mutation had significant effects on various growth traits at 6 and 12 months old, particularly for body weight, body height, back height and backfat thickness (P < 0.05 or P < 0.001). In conclusion, our results confirm that SNX29 CNV plays a role in regulating growth and development in pigs, thus suggesting its potential application for pig breeding programmes.

Life-cycle comparisons of economic and environmental consequences for pig production with four different models in China

China, the world's largest consumer and producer of pork in the world, is attracting increasing attention due to the environmental impacts of its pig production. Previous studies seldom comprehensively compare the environmental impacts of the pig production system with different models, resulting in different intensities of environmental impacts. We aim to comprehensively evaluate Chinese pig production with different breeding models and explore a more sustainable way for pig production. We use life cycle assessment (LCA) to evaluate and compare environmental impacts of pig production system with four main breeding models in China from 1998 to 2020: domestic breeding, small-scale breeding, medium-scale breeding, and large-scale breeding. The life cycle encompasses fertilizer production, feed production, feed processing, pig raising, waste treatment, and slaughtering. The impact categories including energy consumption (EN), global warming (GWP), acidification (AP), eutrophication (EU), water use (WD), and land occupation (LO) are expressed with "100 kg live weight of fattening pig at farm gate." The results show that driven by governmental support, growing meat demand, and cost advantage, the scale breeding especially large-scale breeding simultaneously yielded greater net economic benefit and less environmental impact compared to other breeding models especially the domestic breeding. Due to mineral fertilizer application, feed production contributed over 50% of the total environmental impacts. Notably, the composition of feeds exerted significant influence on the environmental impacts arising from fertilizer production and feed processing. Furthermore, attributable to the substantial use of electricity and heat, as well as the concomitant emissions, pig raising contributed the largest GWP, while ranking second in terms of AP and EU. Notably, waste management constituted the third-largest EU, AP, and WD. In addition to promote scale breeding, we put forth several sustainable measures encompassing feed composition, cultivation practices, fertilizer utilization, and waste management for consideration.

Development and evaluation of polyclonal antibodies based antigen capture ELISA for detection of porcine rotavirus

Rotaviruses are rising as zoonotic viruses worldwide, causing the lethal dehydrating diarrhea in children, piglets, and other livestock of economic importance. A simple, swift, cost-effective, highly specific, and sensitive antigen-capture enzyme-linked immunosorbent assay (AC-ELISA) was developed for detection of porcine rotavirus-A (PoRVA) by employing rabbit (capture antibody) and murine polyclonal antibodies (detector antibody) produced against VP6 of PoRVA (RVA/Pig-tc/CHN/TM-a/2009/G9P23). Reactivity of the both polyclonal antibodies was confirmed by using an indirect ELISA, western-blot analysis and indirect fluorescence assay against rVP6 protein and PoRVA. The detection limit of AC-ELISA was found 50 ng/ml of PoRVA protein. The relative sensitivity and specificity of this in-house AC-ELISA were evaluated for detection of PoRVA from 295 porcine diarrhea samples, and results were compared with that of RT-PCR and TaqMan RT-qPCR. The relative sensitivity and specificity of AC-ELISA compared with those of TaqMan RT-qPCR were found as 94.4 and 99.2%, respectively, with the strong agreement (κ -0.58) between these two techniques. Furthermore, AC-ELISA could not detect any cross-reactivity with porcine epidemic diarrhea virus, transmissible gastro-enteritis virus, pseudo rabies virus and porcine circovirus-2. This in-house AC-ELISA efficiently detected PoRVA from clinical samples, which suggests that this technique can be used for large-scale surveillance and timely detection of rotavirus infection in the porcine farms.

Utilizing Electrochemical Biosensors as an Innovative Platform for the Rapid and On-Site Detection of Animal Viruses

Animal viruses are a significant threat to animal health and are easily spread across the globe with the rise of globalization. The limitations in diagnosing and treating animal virus infections have made the transmission of diseases and animal deaths unpredictable. Therefore, early diagnosis of animal virus infections is crucial to prevent the spread of diseases and reduce economic losses. To address the need for rapid diagnosis, electrochemical sensors have emerged as promising tools. Electrochemical methods present numerous benefits, including heightened sensitivity and selectivity, affordability, ease of use, portability, and rapid analysis, making them suitable for real-time virus detection. This paper focuses on the construction of electrochemical biosensors, as well as promising biosensor models, and expounds its advantages in virus detection, which is a promising research direction.

Scale Difference from the Impact of Disease Control on Pig Production Efficiency

Epidemic disease prevention plays a critical role in ensuring the healthy development of livestock farming, and the subjective willingness of breeders can be affected by the cost of epidemic disease prevention. To correct the misconception that farmers regard the cost of disease control as an ineffective cost, and to promote the healthy development of the pig breeding industry, our study employed the data envelopment analysis super-efficiency model and panel threshold regression model to evaluate the combination of the cost of epidemic disease prevention and swine productivity using data collected from 1998-2018 across 30 provinces in China. The following results were obtained. (1) The cost of epidemic disease prevention generated a non-linear on swine productivity when the swine farming scale was limited; (2) When the number of animals at the beginning of the year was less than 6.0002, swine productivity was impacted negatively; (3) When the number of animals at the beginning of the year ranged between 6.0002 and 12.9994, the impact was insignificant; (4) A strong correlation was observed between the expenses of epidemic disease prevention and animal productivity when the number of animals at the beginning of the year exceeded 12.9994. These results indicate that publicity should be enhanced to elucidate the combination of epidemic disease prevention and swine productivity among breeders. In addition, the government should introduce relevant policies to encourage the development of large-scale pig farming, such as subsidies for the construction of large-scale farms and insurance.

Global prevalence, subtypes distribution, zoonotic potential, and associated risk factors of Blastocystis sp. in domestic pigs (Sus domesticus) and wild boars (Sus scrofa): A systematic review and meta-analysis

The intestinal parasite Blastocystis sp. is a widely distributed protist among humans and various animal hosts, with significant prevalence in developing countries. Due to the zoonotic nature of its subtypes (STs), we aimed at global estimation of the prevalence, STs distribution, zoonotic potential, and associated risk factors of Blastocystis sp. infection in domestic pigs (Sus domesticus) and wild pigs/wild boars (Sus scrofa). The study was designed and conducted in 2021 via searching articles in PubMed, Scopus, Google Scholar, and Web of Science databases, based on the PRISMA checklist, and meta-analysis was done using a random-effects model to calculate the weighted estimates and 95% confidence intervals (95% CIs). Totally, 43 papers (47 datasets) reported data on 7977 examined pigs in 24 countries with a total prevalence of 50.9% (95% CI: 42.8-59%). In details, prevalence was higher among domestic pigs [52.4% (95% CI: 43.9-60.7%)] than wild boars [31.2% (95% CI: 11.2-62%)], but is poorly statistically supported as far as the CIs largely overlap. Out of 28 reported STs, nine (ST1-ST7, ST10, and ST15) were reported from domestic pigs, while six (ST1, ST3-ST5, ST8, and ST15) had been isolated from wild boars. Among nine zoonotic STs (ST1-ST8, and ST12), all were identified in examined swine populations, except for ST12. As well, ST1 and ST5 were probably the most frequently circulating STs among these animals. In addition, male and older pigs showed higher Blastocystis sp. infection. Altogether, Blastocystis epidemiology and the distribution of its related STs in pigs is still open to question and requires more extensive studies, especially in the neglected regions of the world.

Characterization of smallholder pig production systems in the Western Cape, South Africa

This study set out to characterize the farming and management practices of smallholder pig production systems in the Western Cape, South Africa. Data was gathered in three municipalities: Khayelitsha (27 farmers), Mamre (26 farmers) and Malmesbury (22 farmers) with the use of a structured questionnaire through both face-to-face and telephonic interviews. The study revealed that smallholder pig farmers in the Western Cape owned on average 37.4 ± 50.5 pigs. Majority of farmers (61%) made use of tattoo markings to identify their pigs, 6% made use of ear tags and 4% clipped the ears of their pigs. More than 25% of farmers did not use any method of identification to mark their pigs. More than half of the respondents (51%) do not have formal recordkeeping systems in place. Livestock theft was found to be a major problem amongst farmers. No differences were found amongst the three study areas and the type of housing system used (P > 0.05). The most popular materials pens were constructed of across the three areas were wood (40%), corrugated iron (16%) or a combination of the two (32%); other materials used were cement blocks (5%), polystyrene (1%) or plastic (1%). Pig farmers kept 43% Large White, 43 % crossbred and 14% Landrace across the three districts. Commercial feed was used by 61% of Mamre farmers whereas Khayelitsha farmers fed an equal amount of by-products (44%) and mixed (44%) feed to their pigs, whereas Malmesbury fed 44% mixed, 33% commercial and 24% by-products obtained from factories to their pigs. Piglet mortality due to the sow lying on her piglets was experienced by 47% of farmers interviewed, whilst 29% had experienced piglet mortalities due to the cold. Perturbingly, 76% of farmers did not send dead pigs for a post-mortem, stating that they could not rely on veterinarians or afford their services. Smallholder pig farmers in Malmesbury (68%) and Khayelitsha (70%) sold their pigs to the informal market, indicating that keeping pigs provided a source of revenue. Mamre marketed 88% of their pigs as weaners, Khayelitsha marketed 73% of their pigs as growers, whereas Malmesbury kept 32% of their pigs as breeding stock. Khayelitsha and Malmesbury marketed their growers at 63.3 ± 41.2 kg and 51.5 ± 30.2 kg, respectively, to the informal market. The study highlights the farming practices of smallholder pig farmers in three districts in the Western Cape. There a few differences in the practices of these farmers, but overall, there are similar limitations that hinder them from improved production, such as limited recordkeeping, theft, lack of infrastructure and finances for post-mortem examination. Smallholder pig farmers in the Western Cape are still mainly selling to the informal market. This informal market is not fully characterized yet in the Western Cape, and more studies are needed to further determine and investigate the benefits of only selling to the informal market.

Chinese Public Attitudes towards, and Knowledge of, Animal Welfare

Food-producing animals make up the majority of animals that humans manage globally, and China has been a major producer and exporter of animal products since the late 1990s. The opinions of the population in China regarding animal welfare are not as well understood as those in Europe. In China, animal welfare as a societal concern is still at an early stage of development. This survey of Chinese attitudes aimed to understand consumer knowledge of and behaviour towards animal welfare, and to determine whether harnessing consumer interests may be a potential future influence on the development of high-welfare agricultural production. Most participants were not aware of the meaning of animal welfare, but the number of those that were aware was higher than reported previously. The welfare of wild animals was rated particularly important compared to other animals. The links between welfare and the taste and/or safety of food were considered to be important, and Chinese consumers reported a willingness to pay more for food from animals produced in good welfare conditions, although the quality of the food was considered more important than the animal suffering. A large majority of the respondents reported that there should be legislation protecting animals and certification of welfare on farms, that animals on farms should be provided with enjoyable experiences and that transportation times should be minimised. Furthermore, most respondents reported that animals should be stunned before slaughter. We conclude that animal welfare is of importance to the Chinese consumer, in particular because of its connection to food quality.

Construction and analysis for dys-regulated lncRNAs and mRNAs in LPS-induced porcine PBMCs

Long non-coding RNAs (lncRNAs) are emerging as key regulators in inflammation. However, their functions and profiles in LPS-induced inflammation in pigs are largely unknown. In this study, we profiled global lncRNA and mRNA expression changes in PBMCs treated with LPS using the lncRNA-seq technique. In total 43 differentially expressed (DE) lncRNAs and 1082 DE mRNAs were identified in porcine PBMCs after LPS stimulation. Functional enrichment analysis on DE mRNAs indicated these genes were involved in inflammation-related signaling pathways, including cytokine–cytokine receptor interaction, TNF-α, NF-κB, Jak-STAT and TLR signaling pathways. In addition, co-expression network and function analysis identified the potential lncRNAs related to inflammatory response and immune response. The expressions of eight lncRNAs (ENSSSCT00000045208, ENSSSCT00000051636, ENSSSCT00000049770, ENSSSCT00000050966, ENSSSCT00000047491, ENSSSCT00000049750, ENSSSCT00000054262 and ENSSSCT00000044651) were validated in the LPS-treated PBMCs by quantitative real-time PCR (qRT-PCR). In LPS-challenged piglets, we identified that expression of three lncRNAs (ENSSSCT00000051636, ENSSSCT00000049770, and ENSSSCT00000047491) was significantly up-regulated in liver, spleen and jejunum tissues after LPS challenge, which indicated that these lncRNAs might be important regulators for inflammation. This study provides the first lncRNA and mRNA transcriptomic landscape of LPS-mediated changes in porcine PBMCs, which might provide potential insights into lncRNAs involved in regulating inflammation in pigs.

Active regional surveillance for early detection of exotic/emerging pathogens of swine: A comparison of statistical methods for farm selection

In this study, five spatially balanced sampling methods, i.e., generalized random-tessellation stratified (GRTS), local pivotal method (LPM), spatially correlated Poisson sampling (SCPS), local cube method (LCUBE), and balanced acceptance sampling (BAS) were compared to simple random sampling (SRS) based on a livestock disease transmission model on a hypothetical region (195 km × 300 km) populated with 6000 farms in terms of the probability of detection by sample size. Given a fixed sample size, four of the five spatially balanced sampling methods provided better performance than SRS, i.e., higher probabilities of detecting at least one infected farms over a range of regional prevalence evaluated (1%-5%). That is, for any given probability of detection, spatially balanced methods required testing fewer farms than SRS. In an era of pandemics, active regional surveillance for early detection of emerging pathogens becomes urgent, yet shrinking budgets impose intractable constraints. The better performance and higher efficiency of spatially balanced sampling methods suggests a potential improvement in regional livestock disease surveillances and a partial solution to the challenge of affordable surveillance.

African Swine Fever Epidemiology and Control

African swine fever is a devastating disease that can result in death in almost all infected pigs. The continuing spread of African swine fever from Africa to Europe and recently to the high-pig production countries of China and others in Southeast Asia threatens global pork production and food security. The African swine fever virus is an unusual complex DNA virus and is not related to other viruses. This has presented challenges for vaccine development, and currently none is available. The virus is extremely well adapted to replicate in its hosts in the sylvatic cycle in East and South Africa. Its spread to other regions, with different wildlife hosts, climatic conditions, and pig production systems, has revealed unexpected epidemiological scenarios and different challenges for control. Here we review the epidemiology of African swine fever in these different scenarios and methods used for control. We also discuss progress toward vaccine development and research priorities to better understand this complex disease and improve control.

Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing

Genetic characterization of Chinese indigenous pig breeds is essential to promote scientific conservation and sustainable development of pigs. Here, we systematically surveyed the genomes of 75 unrelated Diannan small-ear (DSE) pigs from three diverse regions (Yingjiang County, Jinping County, and Sipsongpanna in Yunnan Province) to describe their population structures, genetic diversity, inbreeding coefficients, and selection signatures. First, these individuals were sequenced and genotyped using the genome reducing and sequencing (GGRS) protocol. A total of 438,038 autosomal single-nucleotide polymorphisms (SNPs) were obtained and used for subsequent statistical analysis. The results showed that these DSE pigs were clearly differentiated into three separate clades revealed by the population structure and principal component analysis, which is consistent with their geographical origins. Diannan small-ear pigs owned lower genetic diversity when compared with some other pig breeds, which demonstrated the need to strengthen the conservation strategies for DSE pigs. In addition, the inbreeding coefficients based on runs of homozygosity (ROH) length (F _ROH) were calculated in each ROH length categories, respectively. And the results indicated that the ancient (up to 50 generations ago) inbreeding had greater impacts than recent (within the last five generations) inbreeding within DSE pigs. Some candidate selection signatures within the DSE pig population were detected through the ROH islands and integrated haplotype homozygosity score (iHS) methods. And genes associated with meat quality (COL15A1, RPL3L, and SLC9A3R2), body size (PALM2-AKAP2, NANS, TRAF7, and PACSIN1), adaptability (CLDN9 and E4F1), and appetite (GRM4) were identified. These findings can help to understand the genetic characteristics and provide insights into the molecular background of special phenotypes of DSE pigs to promote conservation and sustainability of the breed.

Analysis of microRNA expression profiles in porcine PBMCs after LPS stimulation

In the present study, we used microRNA (miRNA) sequencing to discover and explore the expression profiles of known and novel miRNAs in 1000 ng/ml LPS stimulated for 8 h vis-à-vis non-stimulated (i.e. control) PBMCs isolated from the blood of healthy pigs. A total of 291 known miRNAs were bio-computationally identified in porcine PBMCs, and 228 novel miRNAs (not enlisted in the swine mirBase) were identified. Among these miRNAs, ssc-miR-148a-3p, ssc-let-7g, ssc-let-7f, 3_8760, ssc-miR-26a, ssc-miR-451, ssc-miR-21, ssc-miR-30d, ssc-miR-99a and ssc-miR-103 were the top 10 most abundant miRNAs in porcine PBMCs. Through miRNA differential analysis combined with quantitative PCR, we found the expressions of ssc-miR-122, ssc-miR-129b, ssc-miR-17-5p and ssc-miR-152 were significantly changed in porcine PBMCs after LPS stimulation. Furthermore, targets prediction and function analysis indicated a significant enrichment in gene ontology functional categories related to diseases, immunity and inflammation. In conclusion, this study on profiling of miRNAs expressed in LPS-stimulated PBMCs provides an important reference point for future studies on regulatory roles of miRNAs in porcine immune system.

Fates of antibiotic resistance genes in a distributed swine wastewater treatment plant

This study explores the prevalence, emission, and reduction of five ARGs (sulI, tetA, mphB, qnrD, and mcr-1) and integron (intI) through a distributed swine wastewater purification facility and the effluent-receiving environment. Typical metal resistance genes (MRGs), pathogenic bacterial indicators, the bacterial community, and wastewater properties were also explored to determine their effects on the fates of ARGs. Results indicated that the purification process could hardly effectively remove ARGs' prevalence. 3.1 × 10⁴ -7.1 × 10⁸  copies/L were present after purification, and 4%-57% of them persisted in the subsequent creek and adjacent soil. 16S rRNA sequencing suggested that the discharge of wastewater significantly changed the bacterial community in receiving creek and soil. Molecular ecological networks analysis detected the wide co-occurrence among ARGs, MRGs, and PBGs, which could further facilitate the propagation of antibiotic resistance. ARG incidence and specific bacterial genera were closely correlated, suggesting an extensive hosting relationship. Redundancy analyses showed wastewater organics and nutrients showed positive correlation to most ARGs' abundance, but negatively correlated to their relative abundance. PRACTITIONER POINTS: Fate of five ARGs and intI was studied in a swine wastewater treatment system. The treatment process could not effectively reduce ARGs' abundance. ARGs and pathogens in wastewater were transferred to the receiving creek and soil. The network analysis found wide co-occurrence among ARGs, metal resistance genes, and pathogens. Wastewater nutrients positively correlated to ARG's abundance but negatively correlated to their relative abundance.

Applying an environmental public health lens to the industrialization of food animal production in ten low- and middle-income countries

Background

Industrial food animal production (IFAP) is characterized by dense animal housing, high throughput, specialization, vertical integration, and corporate consolidation. Research in high-income countries has documented impacts on public health, the environment, and animal welfare. IFAP is proliferating in some low- and middle-income countries (LMICs), where increased consumption of animal-source foods has occurred alongside rising incomes and efforts to address undernutrition. However, in these countries IFAP’s negative externalities could be amplified by inadequate infrastructure and resources to document issues and implement controls.

Methods

Using UN FAOSTAT data, we selected ten LMICs where food animal production is expanding and assessed patterns of IFAP growth. We conducted a mixed methods review to explore factors affecting growth, evidence of impacts, and information gaps; we searched several databases for sources in English, Spanish, and Portuguese. Data were extracted from 450+ sources, comprising peer-reviewed literature, government documents, NGO reports, and news articles.

Results

In the selected LMICs, not only has livestock production increased, but the nature of expansion appears to have involved industrialized methods, to varying extents based on species and location. Expansion was promoted in some countries by explicit government policies. Animal densities, corporate structure, and pharmaceutical reliance in some areas mirrored conditions found in high-income countries. There were many reported weaknesses in regulation and capacity for enforcement surrounding production and animal welfare. Global trade increasingly influences movement of and access to inputs such as feed. There was a nascent, compelling body of scientific literature documenting IFAP’s negative environmental and public health externalities in some countries.

Conclusions

LMICs may be attracted to IFAP for economic development and food security, as well as the potential for increasing access to animal-source foods and the role these foods can play in alleviating undernutrition. IFAP, however, is resource intensive. Industrialized production methods likely result in serious negative public health, environmental, and animal welfare impacts in LMICs. To our knowledge, this is the first systematic effort to assess IFAP trends through an environmental public health lens for a relatively large group of LMICs. It contributes to the literature by outlining urgent research priorities aimed at informing national and international decisions about the future of food animal production and efforts to tackle global undernutrition.

High probability areas for ASF infection in China along the Russian and Korean borders

African swine fever (ASF) is a transcontinental, contagious, fatal virus disease of pig with devastating socioeconomic impacts. Interaction between infected wild boar and domestic pig may spread the virus. The disease is spreading fast from the west of Eurasia towards ASF-free China. Consequently, prediction of the distribution of ASF along the Sino-Russian-Korean borders is urgent. Our area of interest is Northeast China. The reported ASF-locations in 11 contiguous countries from the Baltic to the Russian Federation were extracted from the archive of the World Organization for Animal Health from July 19, 2007 to March 27, 2017. The locational records of the wild boar were obtained from literature. The environmental predictor variables were downloaded from the WorldClim website. Spatial rarefication and pair-wise geographic distance comparison were applied to minimize spatial autocorrelation of presence points. Principal component analysis (PCA) was used to minimize multi-collinearity among predictor variables. We selected the maximum entropy algorithm for spatial modelling of ASF and wild boar separately, combined the wild boar prediction with the domestic pig census in a single map of suids and overlaid the ASF with the suids map. The accuracy of the models was assessed by the AUC. PCA delivered five components accounting for 95.7% of the variance. Spatial autocorrelation was shown to be insignificant for both ASF and wild boar records. The spatial models showed high mean AUC (0.92 and 0.97) combined with low standard deviations (0.003 and 0.006) for ASF and wild boar, respectively. The overlay of the ASF and suids maps suggests that a relatively short sector of the Sino-Russian border has a high probability entry point of ASF at current conditions. Two sectors of the Sino-Korean border present an elevated risk.

The Main Risk Factors of Nipah Disease and Its Risk Analysis in China

Nipah disease is a highly fatal zoonosis which is caused by the Nipah virus. The Nipah virus is a BSL-4 virus with fruit bats being its natural host. It is mainly prevalent in Southeast Asia. The virus was first discovered in 1997 in Negeri Sembilan, Malaysia. Currently, it is mainly harmful to pigs and humans with a high mortality rate. This study describes the route of transmission of the Nipah virus in different countries and analyzes the possibility of the primary disease being in China and the method of its transmission to China. The risk factors are analyzed for different susceptible populations to Nipah disease. The aim is to improve people's risk awareness and prevention and control of the disease and reduce its risk of occurring and spreading in China.

Effect of chemical clarification of oral fluids on the detection of porcine reproductive and respiratory syndrome virus IgG

Routine collection and testing of oral fluid (OF) samples facilitates porcine reproductive and respiratory syndrome virus (PRRSV) surveillance in commercial swine herds in a cost-effective, welfare-friendly fashion. However, OFs often contain environmental contaminants that may affect liquid handling and test performance. Traditional processing methods (e.g., filtration or centrifugation) are not compatible with high-throughput testing because of the burden of additional processing costs and time. OF "clarification" using chemical flocculants is an alternative approach not widely explored. Therefore, we evaluated the effect of chitosan-based clarification treatment on a commercial PRRSV OF ELISA. Serum and individual OFs were collected from vaccinated pigs ( n = 17) at -7 to 42 d post-vaccination and subdivided into 4 aliquots. Each aliquot was clarified (treatment A, B, C), with the 4th aliquot serving as untreated control. All samples were tested by PRRSV OF ELISA immediately after treatment and then were held at 4°C to be re-tested at 2, 4, 6, and 14 d post-treatment. Quantitative and qualitative treatment effects were evaluated. A Kruskal-Wallis test found no significant difference in ELISA S/P responses among treatments by days post-treatment. No difference was detected in the proportion of positive PRRSV antibody samples among treatments (Cochran Q, p > 0.05). Treatment of swine OFs using chitosan-based formulations did not affect the performance of a commercial PRRSV OF ELISA. Chitosan (or other flocculants) could improve OF characteristics and could be adapted for use in the field or in high-throughput laboratories.

Prospective surveillance for influenza. virus in Chinese swine farms

Pork production in China is rapidly increasing and swine production operations are expanding in size and number. However, the biosecurity measures necessary to prevent swine disease transmission, particularly influenza A viruses (IAV) that can be zoonotic, are often inadequate. Despite this risk, few studies have attempted to comprehensively study IAV ecology in swine production settings. Here, we present environmental and animal sampling data collected in the first year of an ongoing five-year prospective epidemiological study to assess IAV ecology as it relates to swine workers, their pigs, and the farm environment. From March 2015 to February 2016, we collected 396 each of environmental swab, water, bioaerosol, and fecal/slurry samples, as well as 3300 pig oral secretion samples from six farms in China. The specimens were tested with molecular assays for IAV. Of these, 46 (11.6%) environmental swab, 235 (7.1%) pig oral secretion, 23 (5.8%) water, 20 (5.1%) bioaerosol, and 19 (4.8%) fecal/slurry specimens were positive for influenza A by qRT-PCR. Risk factors for IAV detection among collected samples were identified using bivariate logistic regression. Overall, these first year data suggest that IAV is quite ubiquitous in the swine production environment and demonstrate an association between the different types of environmental sampling used. Given the mounting evidence that some of these viruses freely move between pigs and swine workers, and that mixing of these viruses can yield progeny viruses with pandemic potential, it seems imperative that routine surveillance for novel IAVs be conducted in commercial swine farms.

Revised methane emissions factors and spatially distributed annual carbon fluxes for global livestock

BACKGROUND

Livestock play an important role in carbon cycling through consumption of biomass and emissions of methane. Recent research suggests that existing bottom-up inventories of livestock methane emissions in the US, such as those made using 2006 IPCC Tier 1 livestock emissions factors, are too low. This may be due to outdated information used to develop these emissions factors. In this study, we update information for cattle and swine by region, based on reported recent changes in animal body mass, feed quality and quantity, milk productivity, and management of animals and manure. We then use this updated information to calculate new livestock methane emissions factors for enteric fermentation in cattle, and for manure management in cattle and swine.

RESULTS

Using the new emissions factors, we estimate global livestock emissions of 119.1 ± 18.2 Tg methane in 2011; this quantity is 11% greater than that obtained using the IPCC 2006 emissions factors, encompassing an 8.4% increase in enteric fermentation methane, a 36.7% increase in manure management methane, and notable variability among regions and sources. For example, revised manure management methane emissions for 2011 in the US increased by 71.8%. For years through 2013, we present (a) annual livestock methane emissions, (b) complete annual livestock carbon budgets, including carbon dioxide emissions, and (c) spatial distributions of livestock methane and other carbon fluxes, downscaled to 0.05 × 0.05 degree resolution.

CONCLUSIONS

Our revised bottom-up estimates of global livestock methane emissions are comparable to recently reported top-down global estimates for recent years, and account for a significant part of the increase in annual methane emissions since 2007. Our results suggest that livestock methane emissions, while not the dominant overall source of global methane emissions, may be a major contributor to the observed annual emissions increases over the 2000s to 2010s. Differences at regional and local scales may help distinguish livestock methane emissions from those of other sectors in future top-down studies. The revised estimates allow improved reconciliation of top-down and bottom-up estimates of methane emissions, will facilitate the development and evaluation of Earth system models, and provide consistent regional and global Tier 1 estimates for environmental assessments.

Pig empire under infectious threat: risk of African swine fever introduction into the People's Republic of China

Pig production and pork consumption are very important to the People's Republic of China for both economic and cultural reasons. The incursion and spread of a disease such as African swine fever (ASF), which emerged in Eastern Europe in 2007, could have devastating socioeconomic consequences for both the Chinese and the global pig industry. The Chinese government consequently attributes a very high priority to ASF and is actively seeking to improve its preparedness. This paper discusses different drivers and pathways of potential emergence of ASF in China in light of the country's specificities, including international movements of people, pigs and pig products, swill feeding practices and wild boar populations. It suggests that effective ASF risk management in China will require a comprehensive and integrated approach linking science and policy and will need to involve all relevant stakeholders to develop realistic policies.

Building bridges to operationalise one health - A Sino-Swedish collaboration to tackle antibiotic resistance

Antibiotic resistance is a complex global health challenge. The recent Global Action Plan on antimicrobial resistance highlights the importance of adopting One Health approaches that can cross traditional disciplinary boundaries. We report on the early experiences of a multisectoral Sino-Swedish research project that aims to address gaps in our current knowledge and seeks to improve the situation through system-wide interventions. Our research project is investigating antibiotic use and resistance in a rural area of China through a combination of epidemiological, health systems and laboratory investigations. We reflect here on the challenges inherent in conducting long distance cross-disciplinary collaborations, having now completed data and sample collection for a baseline situation analysis. In particular, we recognise the importance of investing in aspects such as effective communication, shared conceptual frameworks and leadership. We suggest that our experiences will be instructive to others planning to develop similar international One Health collaborations.

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Antibiotic resistance is a complex global health challenge

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One Health approaches are needed to facilitate understanding and action

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China is one of the largest producers and consumers of antibiotics in the world

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China is giving attention to antibiotic resistance at the highest political level

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We report on the early stages of a Sino-Swedish One Health research programme

Reducing the land use of EU pork production: where there's swill, there's a way

Livestock production occupies approximately 75% of agricultural land, consumes 35% of the world's grain, and produces 14.5% of anthropogenic greenhouse gas emissions. With demand for meat and dairy products forecast to increase 60% by 2050, there is a pressing need to reduce the footprint of livestock farming. Food wastes have a long history as a source of environmentally benign animal feed, but their inclusion in feed is currently banned in the EU because of disease control concerns. A number of East Asian states have in the last 20 years, however, introduced regulated, centralised systems for safely recycling food wastes into animal feed. This study quantifies the land use savings that could be realised by changing EU legislation to promote the use of food wastes as animal feed and reviews the policy, public, and industry barriers to the use of food waste as feed. Our results suggest that the application of existing technologies could reduce the land use of EU pork (20% of world production) by one fifth, potentially saving 1.8 million hectares of agricultural land. While swill presents a low-cost, low-impact animal feed, widespread adoption would require efforts to address consumer and farmer concerns over food safety and disease control.

Microbial population dynamics in response to increasing loadings of pre-hydrolyzed pig manure in an expanded granular sludge bed

In recent years, pig manure (PM) has been regarded as a valuable substrate for energy and resource recovery via bioprocesses such as anaerobic digestion (AD), however, the efficiency of digesting raw PM is limited by the presence of refractory compounds. In this study, we applied a series of pretreatment on raw PM, consisting of subsequent thermochemical pretreatment, enzymatic hydrolysis, tyndallization and filtration. The liquid PM hydrolysates were fed to an expanded granular sludge bed (EGSB) for the production of biogas. The general performance and population dynamics of the EGSB reactor were assessed during an extended operational period of 339 days. An efficient and stable digestion process was achieved under high organic loading rates (OLRs) up to 21 kg-COD/(m(3)·d), agreeing with a sludge loading rate of 0.75 kg-COD/(kg-VSS·d), 1600 mg-NH4(+)-N/L and 17 mg/L of free ammonia nitrogen. The tyndallization decreased the total amount of active cells from 1 × 10(8) to 1 × 10(2) CFU/ml. Hence, bio-augmentation with pigs' intestinal microbiota was absent and the community dynamics were mainly credited to the composition of the substrate (i.e. PM hydrolysates) and the environmental conditions inside the reactor. The results showed the influence of both the seed community and the imposed loading rates on the evolutionary trajectory of the EGSB microbial community. Four bacterial genera (Clostridium, Cytophaga, Bacillus and Bacteroides) and two methanogenic genera (Methanosaeta and Methanobacterium) dominated the communities. An obvious shift from aceticlastic Methanosaeta to hydrogenotrophic Methanobacterium appeared when the OLR was increased to over 10 kg-COD/(m(3)·d).

Spatiotemporal trends in the discovery of new swine infectious agents

A literature review was conducted to assess the spatiotemporal trend and diversity of infectious agents that were newly found in pigs between 1985 and 2010. We identified 173 new variants from 91 species, of which 73 species had not been previously described in pigs. These new species, of which one third was zoonotic, were taxonomically diverse. They were identified throughout the study period, predominantly in the main pork producing countries, with the rate of discovery of new virus variants doubling within the last 10 years of the study period. Whilst infectious agent species newly detected in high-income countries were more likely to be associated with higher virulence, zoonotic agents prevailed in low- and middle-income countries. Although this trend is influenced by factors conditioning infectious agent detection – diagnostic methods, surveillance efforts, research interests –, it may suggest that different scales and types of production systems promote emergence of certain types of infectious agents. Considering the rapid transformation of the swine industry, concerted efforts are needed for improving our understanding of the factors influencing the emergence of infectious agents. This information then needs to inform the design of risk-based surveillance systems and strategies directly mitigating the risk associated with these factors.

A 25 years experience of group-housed sows-reproduction in animal welfare-friendly systems

Since January 1 2013, group housing of sows has been compulsory within the European Union (EU) in all pig holdings with more than ten sows. Sows and gilts need to be kept in groups from 4 weeks after service to 1 week before the expected time of farrowing (Article 3(4) of Directive 2008/120/EC on the protection of pigs). The legislation regarding group housing was adopted already in 2001 and a long transitional period was allowed to give member states and producers enough time for adaptation. Even so, group housing of sows still seems to be uncommon in the EU, and is also uncommon in commercial pig farming systems in the rest of the world. In this review we share our experience of the Swedish 25 years of animal welfare legislation stipulating that sows must be loose-housed which de facto means group housed. The two most important concerns related to reproductive function among group-housed sows are the occurrence of lactational oestrus when sows are group-housed during lactation, and the stress that is associated with group housing during mating and gestation. Field and clinical observations in non-lactating, group-housed sows in Sweden suggest that by making basic facts known about the pig reproductive physiology related to mating, we might achieve application of efficient batch-wise breeding without pharmacological interventions. Group housing of lactating sows has some production disadvantages and somewhat lower productivity would likely have to be expected. Recordings of behavioural indicators in different housing systems suggest a lower welfare level in stalled animals compared with group-housed ones. However, there are no consistent effects on the reproductive performance associated with different housing systems. Experimental studies suggest that the most sensitive period, regarding disturbance of reproductive functions by external stressors, is the time around oestrus. We conclude that by keeping sows according to the pig welfare-friendly Directive 2008/120/EC, it is possible to combine group-housing of sows with good reproductive performance and productivity. However, substantially increased research and development is needed to optimize these systems.

Socio-economic, industrial and cultural parameters of pig-borne infections

The pork-processing industry has been possibly the fastest growing sector of the food industry in recent years. Specialization, genetic homogenization of the pig population, high density of the breeding population, reduced human-animal interactions, slaughter at a lower age and increased international trade of live animals and pork are parameters that affect, positively or negatively, the emergence of novel pig-borne pathogens, many of which are pig-specific, and many of which have significant zoonotic potential, as observed in recent outbreaks of Nipah virus and Streptococcus suis in Southeast Asia and China, respectively. Numerous other pathogens are transmitted to humans through direct contact with or consumption of pig products, and globalization trends in trade and human population movements have resulted in outbreaks of pig-borne diseases even in Muslim countries and in Israel, where pork consumption is religiously prohibited. The role of pigs as potential reservoirs of antibiotic-resistant pathogens or genes encoding resistance, and the role of feral pigs as a reservoir of zoonotic disease, are scientific fields in direct need of further research.

Inferring patterns of influenza transmission in swine from multiple streams of surveillance data

Swine populations are known to be an important source of new human strains of influenza A, including those responsible for global pandemics. Yet our knowledge of the epidemiology of influenza in swine is dismayingly poor, as highlighted by the emergence of the 2009 pandemic strain and the paucity of data describing its origins. Here, we analyse a unique dataset arising from surveillance of swine influenza at a Hong Kong abattoir from 1998 to 2010. We introduce a state-space model that estimates disease exposure histories by joint inference from multiple modes of surveillance, integrating both virological and serological data. We find that an observed decrease in virus isolation rates is not due to a reduction in the regional prevalence of influenza. Instead, a more likely explanation is increased infection of swine in production farms, creating greater immunity to disease early in life. Consistent with this, we find that the weekly risk of exposure on farms equals or exceeds the exposure risk during transport to slaughter. We discuss potential causes for these patterns, including competition between influenza strains and shifts in the Chinese pork industry, and suggest opportunities to improve knowledge and reduce prevalence of influenza in the region.

Characterization of the methanogen community in a household anaerobic digester fed with swine manure in China

Household anaerobic digesters have been installed across rural China for biogas production, but information on methanogen community structure in these small biogas units is sparsely available. By creating clone libraries for 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes, we investigated the methanogenic consortia in a household biogas digester treating swine manure. Operational taxonomic units (OTUs) were defined by comparative sequence analysis, seven OTUs were identified in the 16S rRNA gene library, and ten OTUs were identified in the mcrA gene library. Both libraries were dominated by clones highly related to the type strain Methanocorpusculum labreanum Z, 64.0 % for 16S rRNA gene clones and 64.3 % for mcrA gene clones. Additionally, gas chromatography assays showed that formic acid was 84.54 % of the total volatile fatty acids and methane was 57.20 % of the biogas composition. Our results may help further isolation and characterization of methanogenic starter strains for industrial biogas production.

Reactomes of porcine alveolar macrophages infected with porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome (PRRS) has devastated pig industries worldwide for many years. It is caused by a small RNA virus (PRRSV), which targets almost exclusively pig monocytes or macrophages. In the present study, five SAGE (serial analysis of gene expression) libraries derived from 0 hour mock-infected and 6, 12, 16 and 24 hours PRRSV-infected porcine alveolar macrophages (PAMs) produced a total 643,255 sequenced tags with 91,807 unique tags. Differentially expressed (DE) tags were then detected using the Bayesian framework followed by gene/mRNA assignment, arbitrary selection and manual annotation, which determined 699 DE genes for reactome analysis. The DAVID, KEGG and REACTOME databases assigned 573 of the DE genes into six biological systems, 60 functional categories and 504 pathways. The six systems are: cellular processes, genetic information processing, environmental information processing, metabolism, organismal systems and human diseases as defined by KEGG with modification. Self-organizing map (SOM) analysis further grouped these 699 DE genes into ten clusters, reflecting their expression trends along these five time points. Based on the number one functional category in each system, cell growth and death, transcription processes, signal transductions, energy metabolism, immune system and infectious diseases formed the major reactomes of PAMs responding to PRRSV infection. Our investigation also focused on dominant pathways that had at least 20 DE genes identified, multi-pathway genes that were involved in 10 or more pathways and exclusively-expressed genes that were included in one system. Overall, our present study reported a large set of DE genes, compiled a comprehensive coverage of pathways, and revealed system-based reactomes of PAMs infected with PRRSV. We believe that our reactome data provides new insight into molecular mechanisms involved in host genetic complexity of antiviral activities against PRRSV and lays a strong foundation for vaccine development to control PRRS incidence in pigs.