Publications

Evaluation of internal teat sealant persistence in the mammary gland during the dry period

The aim of this study was to characterize the behavior of 2 commercially available internal teat sealants containing bismuth subnitrate (SOa and ORBb) during the dry- and postfresh periods in dairy cattle. Digital radiography was used to monitor location and percentage of teat cistern fill at dry-off and during the dry period. Teat-level health parameters including infection status at dry-off and post-fresh as well as incidence of clinical mastitis were also assessed. Radiographic imaging revealed that 21.1% of teats had sealant present in the gland cistern at dry-off (SO= 23.6%, ORB = 18.5%) which increased to 55.9% (SO = 59.6%, ORB = 52.2%) at pre-fresh imaging. Quarters with sealant that had migrated into the gland shed noticeable amounts of sealant for twice as long (mean 14.34 milkings), compared to quarters that did not have sealant in the gland (mean: 7.12, P < 0.001). There was no correlation between sealant location and intramammary infection at dry-off or post-fresh, nor did sea ant location impact clinical mastitis in the first 120 days in milk. Milk leakage after dry-off also was not correlated with an increased risk of intramammary infection during the dry or post-fresh periods. There was no difference between treatments in any of the parameters evaluated. Prolonged sealant shedding is a common reason that producers cite for not utilizing internal teat sealant products in their dry-off protocols. Further research is indicated to determine the optimal amount of sealant required to provide protection while minimizing post-fresh shedding.

Assessment of individual and population-based sampling for detection of Influenza A virus RNA in breeding swine herds

This study compared the probability of IAV RNA detection between selected individual and population-based samples. A 3500-sow breeding herd was sampled for matched sets (n = 57) of FOF, udder wipes, sow nasal wipes, individual piglet nasal wipes, and drinker wipes and tested by RT-rtPCR for IAV RNA detection. Overall, 57.9% (33/57) of FOF samples, 49.1% (28/57) of udder wipes, 28.1% (16/57) of sow nasal wipes, 15.8% (9/57) of drinker wipes and 66.6% (38/57) of the individual piglet nasal wipes tested positive for IAV RNA. FOF had a Kappa value of 0.81, a near-perfect agreement compared to individual piglet nasal wipes. Udder wipes revealed a Kappa value of 0.65, a substantial agreement with individual piglet nasal wipes. The other sample types had a fair agreement with individual piglet nasal wipes (Kappa values <0.28). These results validate FOF as an efficient alternative population-based sample type for IAV surveillance in the breeding herd. The proportion of positive piglets within litter by room A had 91% positivity (20/22), room B had 70% (17/24), and room C had 9% (1/11) positivity. The findings also highlight the importance of testing different farrowing rooms in the same breeding herd to strengthen IAV surveillance.

Genetic and antigenic characterization of an expanding H3 influenza A virus clade in US swine visualized by Nextstrain

Abstract Defining factors that influence spatial and temporal patterns of influenza A virus (IAV) is essential to inform vaccine strain selection and strategies to reduce the spread of potentially zoonotic swine-origin IAV. The relative frequency of detection of the H3 phylogenetic clade 1990.4.a (colloquially known as C-IVA) in US swine declined to 7% in 2017, but increased to 32% in 2019. We conducted phylogenetic and phenotypic analyses to determine putative mechanisms associated with increased detection. We created an implementation of Nextstrain to visualize the emergence, spatial spread, and genetic evolution of H3 IAV-S, identifying two C-IVA clades that emerged in 2017 and cocirculated in multiple US states. Phylodynamic analysis of the HA gene documented low relative genetic diversity from 2017 to 2019, suggesting clonal expansion. The major H3 C-IVA clade contained an N156H amino acid substitution, but HI assays demonstrated no significant antigenic drift. The minor HA clade was paired with the NA clade N2-2002B prior to 2016, but acquired and maintained N2-2002A in 2016, resulting in a loss in antigenic cross-reactivity between N2-2002B and −2002A containing H3N2 strains. The major C-IVA clade viruses acquired a nucleoprotein (NP) of the H1N1pdm09 lineage through reassortment in replacement of the North American swine lineage NP. Instead of genetic or antigenic diversity within the C-IVA HA, our data suggest that population immunity to H3 2010.1, along with antigenic diversity of the NA and acquisition of the H1N1pdm09 NP gene likely explain the re-emergence and transmission of C-IVA H3N2 in swine. Importance Genetically distinct clades of influenza A virus (IAV) in swine undermines efforts to control the disease. Swine producers commonly use vaccines, and vaccine strains are selected by identifying the most common hemagglutinin (HA) gene from viruses detected in a farm or a region. In 2019, we identified an increase in detection frequency of an H3 phylogenetic clade, C-IVA, which was previously circulating at much lower levels in U.S. swine. Our study identified genetic and antigenic factors contributing to its resurgence by linking comprehensive phylodynamic analyses with empirical wet-lab experiments and visualized these evolutionary analyses in a Nextstrain implementation. The contemporary C-IVA HA genes did not demonstrate an increase in genetic diversity nor significant antigenic changes. N2 genes did demonstrate antigenic diversity, and the expanding C-IVA clade acquired a nucleoprotein (NP) gene segment via reassortment. Virus phenotype and vaccination targeting prior dominant HA clades likely contributed to the clade’s success.

Detections of human seasonal H3N2 influenza A virus reverse-zoonoses in swine during the 2022-2024 influenza season

Phylogenetic-based methods for fine-scale classification of PRRSV-2 ORF5 sequences: a comparison of their robustness and reproducibility

Abstract Disease management and epidemiological investigations of porcine reproductive and respiratory syndrome virus-type 2 (PRRSV-2) often rely on grouping together highly related sequences. In the USA, the last five years have seen a major paradigm shift within the swine industry when classifying PRRSV-2, beginning to move away from RFLP (restriction fragment length polymorphisms)-typing and adopting the use of phylogenetic lineage-based classification. However, lineages and sub-lineages are large and genetically diverse, and the rapid mutation rate of PRRSV coupled with the global prevalence of the disease has made it challenging to identify new and emerging variants. Thus, within the lineage system, a dynamic fine-scale classification scheme is needed to provide better resolution on the relatedness of PRRSV-2 viruses to inform disease management and monitoring efforts and facilitate research and communication surrounding circulating PRRSV viruses. Here, we compare potential fine-scale systems for classifying PRRSV-2 variants (i.e., genetic clusters of closely related ORF5 sequences at finer scales than sub-lineage) using a database of 28,730 sequences from 2010 to 2021, representing &gt;55% of the U.S. pig population. In total, we compared 140 approaches that differed in their tree-building method, criteria, and thresholds for defining variants within phylogenetic trees using TreeCluster . Three approaches produced epidemiologically meaningful variants (i.e., ≥5 sequences per cluster), and resulted in reproducible and robust outputs even when the input data or input phylogenies were changed. In the three best performing approaches, the average genetic distance amongst sequences belonging to the same variant was 2.1 – 2.5%, and the genetic divergence between variants was 2.5-2.7%. Machine learning classification algorithms were also trained to assign new sequences to an existing variant with &gt;95% accuracy, which shows that newly generated sequences could be assigned without repeating the phylogenetic and clustering analyses. Finally, we identified 73 sequence-clusters (dated &lt;1 year apart with close phylogenetic relatedness) associated with circulation events on single farms. The percent of farm sequence-clusters with an ID change was 6.5-8.7% for our best approaches. In contrast, ∼43% of farm sequence-clusters had variation in their RFLP-type, further demonstrating how our proposed fine-scale classification system addresses shortcomings of RFLP-typing. Through identifying robust and reproducible classification approaches for PRRSV-2, this work lays the foundation for a fine-scale system that would more reliably group related field viruses and provide better improved clarity for decision-making surrounding disease management.

Genetic plant improvement and climate changes

The consequences of climate change for the agribusiness in Brazil have been widely debated.The issue is discussed in this publication to show the expected problems, particularly those associated with increases in temperature and water stress.It is emphasized that the genetic improvement of plants, based on the experience in the past, has much to contribute to mitigate these problems.To invest in the breeding of new cultivars, selected under stress conditions, is certainly the best possible strategy for agriculture to cope with changes caused by climate alterations.

Investigating the uses of machine learning algorithms to inform risk factor analyses: The example of avian infectious bronchitis virus (IBV) in broiler chickens

Influência da distância no bem estar e qualidade de carne de suínos transportados em Mato Grosso

Universidade Federal de Mato Grosso (UFMT), Faculdade de Agronomia e Medicina Veterinaria, Departamento de Producao Animal, Cuiaba, MT, Brasil

Quality assessment of glucose measurement with regard to epidemiology and clinical management of diabetes mellitus in Germany

Background: During the last decade, Germany has seen an increased prevalence and a redistribution from undetected to diagnosed diabetes mellitus. Due to this substantial epidemiological development, the number of people with documented type 2 diabetes was 8.7 million in 2022. An estimated two million undiagnosed subjects are to be added. Beyond that, the life expectancy of diabetic subjects is increasing due to more responsive health systems in terms of care. Possible reasons include improved screening of at-risk individuals, the introduction of HbA1c for diagnosis in 2010, and the higher use of risk scores. Additionally, quality aspects of the laboratory methodology should be taken into consideration. Methods: Epidemiology and clinical management of diabetes in Germany are presented in the light of publications retrieved by a selective search of the PubMed database. Additionally, the data from German external quality assessment (EQA) surveys for the measurands glucose in plasma and HbA1c in whole blood, reviewed from 2010 until 2022, were evaluated. Above this, data concerning the analytical performance of near-patient glucometer devices, according to the ISO norm 15197:2013, were analyzed. Results: Two laboratory aspects are in good accordance with the observation of an increase in the diabetes mellitus prevalence when retrospectively reviewing the period 2010 to 2022: First, the analytical performance according to the ISO norm 15197:2013 of the glucometer devices widely used by patients with diabetes for the glucose self-testing, has improved during this period. Secondly, concerning the EQA program of INSTAND, the number of participating laboratories raised significantly in Germany. The spreads of variations of the specified results for plasma glucose remained unchanged between 2010 and 2022, whereas for HbA1c a significant decrease of the result scattering could be observed. Conclusion: These retrospectively established findings testify to an excellent analytical quality of laboratory diagnostics for glucose and HbA1c throughout Germany which may be involved in a better diagnosis and therapy of previously undetected diabetes mellitus.

A recombinant porcine reproductive and respiratory syndrome virus type 2 field strain derived from two PRRSV-2-modified live virus vaccines

A porcine reproductive and respiratory syndrome virus (PRRSV) type 2 (PRRSV-2) isolate was obtained from lung samples collected from a 4.5-month-old pig at a wean-to-finish site in Indiana, USA, although no gross or microscopic lesions suggestive of PRRSV infection were observed in the lung tissue. Phylogenetic and molecular evolutionary analyses based on the obtained virus sequences indicated that PRRSV USA/IN105404/2021 was a natural recombinant isolate from Ingelvac PRRS® MLV and Prevacent® PRRS, which are PRRSV-2-modified live virus vaccines commercially available in the United States. This study is the first to report the detection of a PRRSV-2 recombinant strain consisting entirely of two modified live virus vaccine strains under field conditions. Based on clinical data and the absence of lung lesions, this PRRSV-2 recombinant strain was not virulent in swine, although its pathogenicity needs to be confirmed by clinical trials.

Machine learning prediction and experimental validation of antigenic drift in H3 influenza A viruses in swine

ABSTRACT The antigenic diversity of influenza A virus (IAV) circulating in swine challenges the development of effective vaccines, increasing zoonotic threat and pandemic potential. High throughput sequencing technologies are able to quantify IAV genetic diversity, but there are no accurate approaches to adequately describe antigenic phenotypes. This study evaluated an ensemble of non-linear regression models to estimate virus phenotype from genotype. Regression models were trained with a phenotypic dataset of pairwise hemagglutination inhibition (HI) assays, using genetic sequence identity and pairwise amino acid mutations as predictor features. The model identified amino acid identity, ranked the relative importance of mutations in the hemagglutinin (HA) protein, and demonstrated good prediction accuracy. Four previously untested IAV strains were selected to experimentally validate model predictions by HI assays. Error between predicted and measured distances of uncharacterized strains were 0.34, 0.70, 2.19, and 0.17 antigenic units. These empirically trained regression models can be used to estimate antigenic distances between different strains of IAV in swine using sequence data. By ranking the importance of mutations in the HA, we provide criteria for identifying antigenically advanced IAV strains that may not be controlled by existing vaccines and can inform strain updates to vaccines to better control this pathogen.

Development of a pig wean-quality score using machine-learning algorithms to characterize and classify groups with high mortality risk under field conditions

236 Factors associated with the farrowing rate in Brazilian batch farrowing sow farms

Abstract Introduction In the Brazilian swine industry, ~50% of the farms do not reach a target farrowing rate (FR) of 90%. It is known that environmental, management, nutrition, and health-related factors impair the ability of farms to achieve the target. This study aimed to evaluate predictors in Brazilian batch farrowing (BF) farms to identify drivers of FR. Methods An observational study was conducted in 25 BF farms (3- to 4-week batch intervals) and a survey with 41 questions gathered information on management practices, infrastructure, and health procedures. Retrospective monthly production data were collected (2022-2023) covering 555 herd-months observations. The outcome was analyzed using a binomial distribution and pairwise comparisons for FR marginal means were conducted using the Tukey-Kramer test. An initial univariate analysis was performed to assess the effect of each predictor using the GLMER procedure (R-software) with farm included as a random effect. Sixteen variables with P-value lower than 0.20 were selected to build a multivariable model using forward stepwise selection. Predictors with a P-value ≤ 0.05 were retained. Results The study farms had on average 1,031sows (330-3650), being 45.9% in 3-week and 54.1% 4- BF intervals. The overall average of FR was 89.9% (q1–87.0%; median–90.6%; q3–93.3%). Seven predictors were retained: percentage of mortality and re-served sows, day of estrus detection onset post-weaning, time spent on estrus detection, timing of group housing for gestating sows, daily stimulation for sows to stand, and season. The increase of 1% in the sow mortality and the percentage of re-served sows were associated with a decrease of 2% and 1% in the odds of the FR, respectively (P≤0.01). Table 1 describes each predictor with their respective average and confidence interval. Estrus detection starting on the day of weaning increased by 3.3% on FR compared to those starting one day post-weaning (P&amp;lt; 0.01). Lower FR was observed for housing sows 3-4-weeks compared to 1-week post-insemination (P&amp;lt; 0.01). Farms spending &amp;gt;25 min/50 females for heat check had higher FR than ≤25 min/50 females (P&amp;lt; 0.01). No difference was observed between farms that expend 15-25 min compared to those using less than 15 min/50 females. The FR was lower during fall compared to other seasons (P≤0.01). Farms that implemented a standardized procedure for standing sows once daily during gestation demonstrated 2.4% increase in the FR compared to farms that did not use this practice (P≤0.01). Conclusion The duration for estrus detection, estrus detection onset, practice of standing up the sows during gestation, reduction in sow mortality and reduction in the percentage of sows re-served into the breeding group must be revisited at the farm level for improving FR. Group housing gestating sows in different weeks post-insemination was not associated with FR, compared to sows kept in stalls.

Characterising the epidemiology of influenza A viruses at the swine-human interface: Study Protocol of the PigFluCam+ project in Cambodia (Preprint)

<sec> <title>UNSTRUCTURED</title> Influenza A viruses are a significant cause of global morbidity, mortality and economic losses. Swine are considered an important host for pandemic emergence; however, knowledge on the ecology and evolution of swine influenza viruses in relation to pig production and exchange systems is limited. The PigFluCam+ project was first initiated in 2019 as a One Health-focussed research collaboration between public and animal health stakeholders. The primary goal of the project was to characterise the risk of zoonotic influenza arising from the rapidly changing pig sectors in Cambodia. This paper outlines the detailed methods and approaches used by the project, serving as a resource for future research initiatives with similar aims. These approaches consist of systematic sample collections and survey studies. Serological and virological investigations were conducted over a two-year period through nasal swab and blood sampling in pigs at multiple slaughterhouses across various provinces. Cross-sectional surveys were conducted to characterise pig production practices and trading networks. In parallel, a cohort study was carried out involving households with and without occupational exposure to live pigs to compare the seroprevalence of influenza A viruses among different swine-associated occupational groups. Despite disruptions caused by the COVID-19 pandemic and the introduction of African Swine Fever into the region, the project has successfully generated a wealth of data on the epidemiology of influenza at the human-swine interface and provided phylogenetic inferences into the evolutionary and transmission dynamics of swine influenza viruses in pigs. This project has developed surveillance protocols and modern technologies for establishing active zoonotic disease surveillance. These efforts support the region’s capability to effectively identify zoonotic pathogens and enhance the prediction and response to zoonotic outbreaks and pandemic risk associated with pig production systems in the Lower Mekong region. </sec>

Veterinarian perceptions and practices in prevention and control of influenza virus in the Midwest United States swine farms

Influenza A virus (IAV) is an endemic respiratory pathogen affecting swine worldwide and is a public health concern as a zoonotic pathogen. Veterinarians may respond to IAV infection in swine with varied approaches depending on their perception of its economic impact on human and animal health. This study considered three primary veterinary practice categories: swine exclusive veterinary practitioner, large animal practitioner, which corresponds to veterinarians that work predominantly with food animals including but not exclusively porcine, and mixed animal practitioner, which corresponds to veterinarians working with companion and food animals. This survey aimed to assess U.S. veterinarian perceptions, biosecurity practices, and control methods for IAV in swine. In this study, 54.5% (188/345) of the veterinarians that were targeted responded to all portions of the survey. The study results presented different perceptions regarding IAV among veterinarians in different types of veterinary practices and the current IAV mitigation practices implemented in swine farms based on strategic decisions. Collectively, this study also revealed the veterinarians' perceptions that IAV as a health problem in swine is increasing, IAV has a moderate economic impact, and there is a high level of concern regarding IAV circulating in swine. These findings highlight the need for IAV surveillance data, improved vaccine strategies, as well as important opportunities regarding methods of control and biosecurity. Additionally, results of this survey suggest biosecurity practices associated with the veterinarian's swine operations and prevention of zoonotic diseases can be strengthened through annual IAV vaccination of humans and support of sick leave policies for farm workers.

Evaluating stillborn and litter size as indicators of PRRSV detection in live piglets and the use of stillborn tongue fluids as risk-based samples for PRRSV monitoring

A risk-based approach to animal selection for sampling enhances pathogen detection by increasing the probability of selecting an animal harboring the pathogen while requiring a smaller sample size. Postmortem tongue fluids (TF) have emerged as a promising risk-based approach, with a PRRSV RNA positivity rate similar to serum, processing fluids, and family oral fluids. Thus, this study assessed the effect of stillborn presence, litter size, and PRRSV RNA detection by RT-qPCR in stillborn TF on the probability of having viremic piglets within the litter. Samples from 130 litters were collected within 12 hours after farrowing from two breeding herds. TF and intracardiac blood were collected from stillborns, and tail blood swabs were collected from liveborn littermates within the selected litters. Samples were individually tested for PRRSV RNA detection by RT-qPCR. Litters with ≤ 11 liveborn piglets were defined as small. Generalized linear regression models were used to evaluate the litter size, presence of stillborns, and stillborn PRRSV results on the probability that a litter or at least one liveborn littermate would test PRRSV-positive. The live piglets' mean positivity within the litter was 5.0%, while the total born was 4.6%. Litters with at least one stillborn had 12.5 times higher odds of having a PRRSV-positive result, and 4.8 times higher odds of having at least one viremic liveborn piglet. In small litters, the odds of having a PRRSV-positive result increased 12.2 times, whereas the odds of having a viremic liveborn littermate increased 10.8 times. When the stillborn TF was positive, the odds of having a viremic liveborn littermate increased 17.6 times. In conclusion, stillborn TFs were a reliable indicator of PRRSV status among litters. Liveborn piglets from litters with PRRSV-positive stillborn TF or small litters had greater odds of testing PRRSV-positive. Therefore, stillborn TF collection and targeting small litters improve PRRSV detection and support farrowing room biocontainment strategies.

randomized equivalence study evaluating the efficacy of two commercially available teat sealants in dairy cows

Use of internal teat sealants is common in the U.S. to prevent new intramammary infections during the dry period. The objective of this study was to compare the efficacy of a new internal teat sealant containing bismuth subnitrate (SOa) to the first product introduced to the U.S. dairy industry (ORBb). The hypothesis was completed using a multi-site randomized, positively controlled equivalence evaluation of new intramammary infection risk difference over the dry period. At dry-off, milk samples were collected for culture and then cloxacillin benzathinec was administered, followed by the randomly assigned internal teat sealant (SO = 404 cows; ORB = 418 cows). After calving, repeat milk samples were collected. The effect of treatment on quarter-level new intramammary infection risk, cured intramammary infection risk, and risk of presence of intramammary infection post-calving was determined using generalized linear mixed models. The effects of treatment on cow-level outcomes, including incidence of clinical mastitis, culling and death, and performance in early lactation based on test-day milk production and somatic cell count, were also evaluated. The dry period new intramammary infection adjusted risk difference (SO minus ORB) was -1.60% (95% CI -5.62, 2.42). Final models demonstrated that there was no difference in risk rates of quarter-level outcomes between treatment groups. Analysis of cow-level factors, including clinical mastitis, culling and death rate within the first 120 DIM, also revealed no differences. Results of this study indicate that SO was equivalent to ORB for dry period new intramammary infection risk when utilizing blanket dry cow therapy.

Assessment of Changes in Antibiotic Use in Grow-Finish Pigs after the Introduction of Prrsv in a Naïve Farrow-to-Finish System

Responsible antibiotic usage (ABU) is crucial for both animal and human health and requires constant improvement of antimicrobial stewardship (AMS). The presence of porcine reproductive and respiratory syndrome virus (PRRSV), a viral pathogen with immunosuppressive effects on swine, can intensify bacterial co-infections, alter antibiotic pharmacokinetics, and potentially lead to increased ABU. This study aimed to measure ABU changes in the grow-finish population associated with PRRSV infection and describe the antibiotic classes employed to manage clinical signs from a farrow-to-finish genetic multiplier system. Three PRRSV statuses (naïve, positive epidemic, and positive endemic) were established to classify the lots based on PRRSV circulation, with a total of 135,063 animals evaluated. The number of pig treatments per animal days at risk (PTDR) was calculated by administration route to quantify ABU across PRRSV status using negative binomial regression or non-parametric tests (P-value < 0.05). In the nursery phase, there was a statistically significant difference between PRRSV statuses for the overall PTDR for the injectable and water routes of administration, with an ABU increase of 3.79 and 2.51 times the naïve PTDR for positive epidemic and endemic status, respectively. For the finishing phase, there was a statistically significant difference between PRRSV statuses in the injectable PTDR, with an ABU increase of 2.74 and 2.28 times the naïve PTDR level for positive epidemic and endemic statuses, respectively. The most frequently injected antibiotic in the nursery phase was ampicillin, with 49% of total injections, followed by lincomycin (31%) and enrofloxacin (20%), and in the finishing phase, 72% of injections were lincomycin, followed by enrofloxacin (28%). The results highlight that the PRRSV outbreak in the source was associated with a grow-finish ABU increase, revealing the importance of preventing PRRSV infection to potentially decrease ABU and improve AMS within swine production systems.