Seasonal Variation in Prevalence of Mycoplasma hyopneumoniae and Other Respiratory Pathogens in Peri-Weaned, Post-Weaned, and Fattening Pigs with Clinical Signs of Respiratory Diseases in Belgian and Dutch Pig Herds, Using a Tracheobronchial Swab Sampling Technique, and Their Associations with Local Weather Conditions

Impact of porcine respiratory disease complex on carcass weight and meatiness: quantitative insights from a mixed-model analysis

BACKGROUND

Porcine respiratory disease complex (PRDC) significantly impacts the swine industry worldwide, leading to economic losses due to poor growth performance, reduced feed efficiency, higher medication costs, and adversely affecting pig welfare by causing clinical symptoms such as fever, cough, loss of appetite, lethargy, and dyspnea. Cranio-ventral pulmonary consolidation (CVPC) and pleuritis are the most frequent macroscopic lung lesions observed in PRDC and are indicators of decreased animal welfare. This study aimed to quantify the effects of CVPC and pleurisy on carcass weight, meatiness, and average daily carcass weight gain (ADCWG) in fattening pigs, thereby assessing their impact on both production and welfare. A total of 679 slaughtered pigs from seven batches (farms) were evaluated for lung lesions at slaughter. We employed a mixed-model analysis to assess the correlation between lung lesions and production parameters across the farms.

RESULTS

The mean prevalence of lesions was 23.86% for CVPC and 15.46% for pleurisy, indicating a significant presence of respiratory disease affecting animal welfare. Pigs with severe lung lesions (≥ 15.1%) exhibited significantly lower ADCWG compared to pigs without lesions (0.951 kg/day vs. 0.997 kg/day, p = 0.024), reflecting reduced growth performance and welfare. The mixed-effects model revealed that lesions in the right apical lobe and dorso-caudal pleurisy were associated with significant reductions in carcass weight (- 2.77 kg and - 2.29 kg, respectively) and carcass meat (- 1.76 kg and - 1.43 kg, respectively). An economic analysis under average market price conditions demonstrated that severe lung lesions could lead to financial losses of up to 11.53 EUR per 100 kg of meat, emphasizing the economic impact of compromised welfare due to respiratory diseases.

CONCLUSIONS

This study provides quantitative evidence of the negative impact of CVPC and pleurisy on carcass weight and meatiness in fattening pigs. The findings underscore the importance of effective respiratory disease management in swine production, highlighting potential areas for targeted interventions to improve animal health and economic outcomes.

High-throughput screening for respiratory pathogens within pigs in Denmark; analysis of circulating porcine respiratory coronaviruses and their association with other pathogens

Porcine respiratory coronavirus (PRCV) typically causes subclinical or mild respiratory infections in pigs, but may lead to more severe disease with other factors. PRCV infection in Denmark was initially detected in 1984, but data are lacking about its current prevalence and diversity. Antibodies against PRCV were detected in about 75 % of recent pig sera from Denmark. In addition, pig nasal swab samples were screened for PRCV and 12 other respiratory pathogens using a high-throughput RT-qPCR system. All targeted pathogens were detected but at different prevalences. Significant associations were found between the presence of PRCV and certain other pathogens. From PRCV positive samples, partial spike gene sequences and complete nucleocapsid coding sequences were determined. In phylogenetic analyses, these PRCVs clustered with earlier European PRCVs and were distinct from transmissible gastroenteritis virus. We conclude that PRCV is widespread within the pig population in Denmark. Further studies on the significance of PRCV are warranted.

A multiplex real-time RT-PCR system to simultaneously diagnose 16 pathogens associated with swine respiratory disease

AIMS

Swine respiratory disease (SRD) is a major disease complex in pigs that causes severe economic losses. SRD is associated with several intrinsic and extrinsic factors such as host health status, viruses, bacteria, and environmental factors. Particularly, it is known that many pathogens are associated with SRD to date, but most of the test to detect those pathogens can be normally investigated only one pathogen while taking time and labor. Therefore, it is desirable to develop rapidly and efficiently detectable methods those pathogens to minimize the damage caused by SRD.

METHODS AND RESULTS

We designed a multiplex real-time RT-PCR (RT-qPCR) system to diagnose simultaneously 16 pathogens, including nine viruses and seven bacteria associated with SRD, on the basis of single qPCR and RT-qPCR assays reported in previous studies. Multiplex RT-qPCR system we designed had the same ability to single RT-qPCR without significant differences in detection sensitivity for all target pathogens at minimum to maximum genomic levels. Moreover, the primers and probes used in this system had highly specificity because the sets had not been detected pathogens other than the target and its taxonomically related pathogens. Furthermore, our data demonstrated that this system would be useful to detect a causative pathogen in the diagnosis using oral fluid from healthy pigs and lung tissue from pigs with respiratory disorders collected in the field.

CONCLUSIONS

The rapid detection of infected animals from the herd using our system will contribute to infection control and prompt treatment in the field.

Seasonality of antimicrobial use in Dutch food-producing animals

Due to globally increasing antimicrobial resistance (AMR), it is pivotal to understand factors contributing to antimicrobial use (AMU) to enable development and implementation of AMR-reducing interventions. Therefore, we explored seasonal variations of systemic AMU in food-producing animals in the Netherlands. Dutch surveillance data from January 2013 to December 2018 from cattle, pig, and broiler farms were used. AMU was expressed as the number of Defined Daily Dosages Animal per month (DDDA/animal-month) per farm by animal sector, antimicrobial line (first, second, and third), antimicrobial class, and farm type. Seasonality of AMU was analyzed using Generalized Additive Models (GAMs) with DDDA/animal-month as outcome variable, and year and month as independent variables. Year and month were modelled as smooth terms represented with penalized regression splines.Significant seasonality of AMU was found in the cattle and pig sectors, but not in broilers. Significant seasonality of AMU was found mainly for first-line antimicrobials. In the cattle sector, a significant increase during winter was found for the use of amphenicols (an increase of 23.8%) and long-acting macrolides (an increase of 3.4%). In the pig sector, seasonality of AMU was found for pleuromutilins (p < 0.001) with an increase of 20% in October-November. The seasonality of pleuromutilins was stronger in sows/piglets (an increase of 47%) than in fattening pigs (16% increase). Only in fattening pigs, the use of amphenicols showed a significant seasonality with an increase of 11% during winter (P < 0.001). AMU in cattle and pig sectors shows seasonal variations likely caused by seasonality of diseases. In broilers, no AMU seasonality was observed, possibly due to the controlled environment in Dutch farms. In the context of the one health concept, future studies are necessary to explore whether this seasonality is present in other populations and whether it has implications for antimicrobial resistance in humans through the food chain.

Network analysis of pig movement data as an epidemiological tool: an Austrian case study

Animal movements represent a major risk for the spread of infectious diseases in the domestic swine population. In this study, we adopted methods from social network analysis to explore pig trades in Austria. We used a dataset of daily records of swine movements covering the period 2015-2021. We analyzed the topology of the network and its structural changes over time, including seasonal and long-term variations in the pig production activities. Finally, we studied the temporal dynamics of the network community structure. Our findings show that the Austrian pig production was dominated by small-sized farms while spatial farm density was heterogeneous. The network exhibited a scale-free topology but was very sparse, suggesting a moderate impact of infectious disease outbreaks. However, two regions (Upper Austria and Styria) may present a higher structural vulnerability. The network also showed very high assortativity between holdings from the same federal state. Dynamic community detection revealed a stable behavior of the clusters. Yet trade communities did not correspond to sub-national administrative divisions and may be an alternative zoning approach to managing infectious diseases. Knowledge about the topology, contact patterns, and temporal dynamics of the pig trade network can support optimized risk-based disease control and surveillance strategies.

Determinants of farms' antibiotic consumption - A longitudinal study of pig fattening farms in Germany

As high consumption of antibiotics in livestock production poses risks to public health, Germany has implemented a monitoring system to decrease their administration to farm animals. Data from 1,984 German pig farms are used to describe prescription trends for different antibiotic subclasses between Autumn 2017 and Autumn 2019. A panel Tobit model with control function approach is implemented to identify determinants of antibiotic consumption, where variables studied include farm, farmer, and county characteristics as well as weather variables. The overall quantity of prescribed antibiotics has been stable but with seasonal fluctuations and a shift away from critically important antibiotics used. Biosecurity factors such as livestock farm density in a county and pigs per farm are shown to be important drivers of antibiotic consumption. In addition, the number of cold days within a season increases antibiotic consumption but precipitation and the number of hot days have no significant effect.

Viral and Bacterial Profiles in Endemic Influenza A Virus Infected Swine Herds Using Nanopore Metagenomic Sequencing on Tracheobronchial Swabs

Swine influenza A virus (swIAV) plays an important role in porcine respiratory infections. In addition to its ability to cause severe disease by itself, it is important in the multietiological porcine respiratory disease complex. Still, to date, no comprehensive diagnostics with which to study polymicrobial infections in detail have been offered. Hence, veterinary practitioners rely on monospecific and costly diagnostics, such as Reverse Transcription quantitative PCR (RT-qPCR), antigen detection, and serology. This prevents the proper understanding of the entire disease context, thereby hampering effective preventive and therapeutic actions. A new, nanopore-based, metagenomic diagnostic platform was applied to study viral and bacterial profiles across 4 age groups on 25 endemic swIAV-infected German farms with respiratory distress in the nursery. Farms were screened for swIAV using RT-qPCR on nasal and tracheobronchial swabs (TBS). TBS samples were pooled per age, prior to metagenomic characterization. The resulting data showed a correlation between the swIAV loads and the normalized reads, supporting a (semi-)quantitative interpretation of the metagenomic data. Interestingly, an in-depth characterization using beta diversity and PERMANOVA analyses allowed for the observation of an age-dependent interplay of known microbial agents. Also, lesser-known microbes, such as porcine polyoma, parainfluenza, and hemagglutinating encephalomyelitis viruses, were observed. Analyses of swIAV incidence and clinical signs showed differing microbial communities, highlighting age-specific observations of various microbes in porcine respiratory disease. In conclusion, nanopore metagenomics were shown to enable a panoramic view on viral and bacterial profiles as well as putative pathogen dynamics in endemic swIAV-infected herds. The results also highlighted the need for better insights into lesser studied agents that are potentially associated with porcine respiratory disease. IMPORTANCE To date, no comprehensive diagnostics for the study of polymicrobial infections that are associated with porcine respiratory disease have been offered. This precludes the proper understanding of the entire disease landscape, thereby hampering effective preventive and therapeutic actions. Compared to the often-costly diagnostic procedures that are applied for the diagnostics of porcine respiratory disease nowadays, a third-generation nanopore sequencing diagnostics workflow presents a cost-efficient and informative tool. This approach offers a panoramic view of microbial agents and contributes to the in-depth observation and characterization of viral and bacterial profiles within the respiratory disease context. While these data allow for the study of age-associated, swIAV-associated, and clinical symptom-associated observations, it also suggests that more effort should be put toward the investigation of coinfections and lesser-known pathogens (e.g., PHEV and PPIV), along with their potential roles in porcine respiratory disease. Overall, this approach will allow veterinary practitioners to tailor treatment and/or management changes on farms in a quicker, more complete, and cost-efficient way.

Porcine respiratory disease complex: Dynamics of polymicrobial infections and management strategies after the introduction of the African swine fever

A few decades ago, porcine respiratory disease complex (PRDC) exerted a major economic impact on the global swine industry, particularly due to the adoption of intensive farming by the latter during the 1980's. Since then, the emerging of porcine reproductive and respiratory syndrome virus (PRRSV) and of porcine circovirus type 2 (PCV2) as major immunosuppressive viruses led to an interaction with other endemic pathogens (e.g., Mycoplasma hyopneumoniae, Actinobacillus pleuropneumoniae, Streptococcus suis, etc.) in swine farms, thereby exacerbating the endemic clinical diseases. We herein, review and discuss various dynamic polymicrobial infections among selected swine pathogens. Traditional biosecurity management strategies through multisite production, parity segregation, batch production, the adoption of all-in all-out production systems, specific vaccination and medication protocols for the prevention and control (or even eradication) of swine diseases are also recommended. After the introduction of the African swine fever (ASF), particularly in Asian countries, new normal management strategies minimizing pig contact by employing automatic feeding systems, artificial intelligence, and robotic farming and reducing the numbers of vaccines are suggested. Re-emergence of existing swine pathogens such as PRRSV or PCV2, or elimination of some pathogens may occur after the ASF-induced depopulation. ASF-associated repopulating strategies are, therefore, essential for the establishment of food security. The "repopulate swine farm" policy and the strict biosecurity management (without the use of ASF vaccines) are, herein, discussed for the sustainable management of small-to-medium pig farms, as these happen to be the most potential sources of an ASF re-occurrence. Finally, the ASF disruption has caused the swine industry to rapidly transform itself. Artificial intelligence and smart farming have gained tremendous attention as promising tools capable of resolving challenges in intensive swine farming and enhancing the farms' productivity and efficiency without compromising the strict biosecurity required during the ongoing ASF era.

Prevalence and phylogenetic analysis of porcine circovirus type 2 (PCV2) and type 3 (PCV3) in the Southwest of China during 2020-2022

Introduction

Porcine circovirus type 2 (PCV2) is considered one of the viruses with substantial economic impact on swine industry in the word. Recently, porcine circovirus type 3 (PCV3) has been found to be associated with porcine dermatitis and nephropathy syndrome (PDNS)-like disease. And the two viruses were prone to co-infect clinically.

Methods

To further investigate the prevalence and genetic diversity of the two viruses, 257 pig samples from 23 different pig farms in southwest China with suspected PCVAD at different growth stages were analyzed by real-time PCR between 2020 and 2022 to determine the presence of PCV2 and PCV3.

Results

Results showed high prevalence of PCV2 and PCV3: 26.46% samples were PCV2 positive and 33.46% samples were PCV3 positive. The coinfection rate was doubled from 2020 (5.75%) to 2022 (10.45%). Subsequently, the whole genome sequences of 13 PCV2 and 18 PCV3 strains were obtained in this study. Of these, 1 strain was PCV2a, 5 strains were PCV2b and 7 strains were PCV2d, indicating that PCV2d was the predominant PCV2 genotype prevalent in the Southwest of China.

Discussion

In addition, the phylogenetic analysis of PCV3 showed high nucleotide homology (>98%) between the sequences obtained in this study and reference sequences. And 3 mutations (A24V, R27K and E128D) were found in PCV3 antibody recognition domains, which might be related to the mechanism of viral immune escape. Thus, this study will enhance our understanding of the molecular epidemiology and evolution of PCV2 and PCV3, which are conducive to the further study of the genotyping, immunogenicity and immune evasion of PCVs.

Detection of Porcine Circovirus Type 2a and Pasteurella multocida Capsular Serotype D in Growing Pigs Suffering from Respiratory Disease

In order to diagnose a respiratory disease in a pig farm, the lungs, spleen, and lymph nodes of three dead pigs were collected for pathogen detection by PCR and isolation on the basis of preliminary clinical diagnosis. The virus isolate was identified by gene sequence analysis and Immunoperoxidase monolayer assay (IPMA). The bacterial isolate was identified by biochemical tests, 16S rDNA sequence analysis, and species- and serotype-specific PCR, and the pathogenicity was analyzed. Porcine circovirus type 2a (PCV2a) genotype from the lungs, spleen, and lymph nodes and Pasteurella (P.) multocida capsular serotypes D from the lungs were found. The PCV2a isolates could specifically bound the anti-PCV2-Cap polyclonal antibody. The 16S rDNA sequence of P. multocida isolates had 99.9% identity with that of the strain from cattle, and the isolate was highly pathogenic to mice. The results showed that the co-infection of PCV2a and P. Multocida capsular serotypes D should be responsible for the disease. The uncommon PCV2a is still prevalent in some pig farms besides the dominant PCV2d genotype. This study could provide important etiological information for effective control and treatment of the disease in pig farms.