Location: Virus and Prion Research
2025 Annual Report
Objectives
Objective 1: Investigate the role of virulence mechanisms and impact on the swine respiratory microbiota of priority, emerging or re-emerging pathogens such as Glaesserella parasuis and Streptococcus suis. This includes evaluating the presence and mechanisms of transfer of antimicrobial resistance (AMR) genes harbored by these bacterial pathogens.
Subobjective 1.1: Identify genetic determinants contributing to the virulence of G. parasuis and S. suis through the use of comparative genomics, functional genomics, and proteomics.
Subobjective 1.2: Evaluate the presence of AMR genes, determine the genomic location of identified AMR genes, and determine which specific type of MGEs most abundantly contain AMR genes harbored by priority, emerging or re-emerging swine bacterial pathogens.
Subobjective 1.3: Determine the impact of infection with priority swine pathogens on the respiratory microbiota and development of secondary bacterial infections.
Objective 2: Develop and evaluate novel non-antibiotic intervention and management strategies to control priority bacterial diseases in swine, including vaccine platforms and therapeutics.
Subobjective 2.1: Develop novel vaccines and therapeutics to prevent clinical disease or decrease colonization caused by priority, emerging or re-emerging swine bacterial pathogens.
Subobjective 2.2: Evaluate the host response to vaccination or infection with bacterial pathogens such as G. parasuis or S. suis to identify mechanisms of cross protective immunity.
Approach
The first goal for this research plan is to investigate the role of virulence mechanisms and impact on the swine respiratory microbiota of priority, emerging or re-emerging pathogens such as Glaesserella parasuis and Streptococcus suis. This includes evaluating the presence and mechanisms of transfer of antimicrobial resistance (AMR) genes harbored by these bacterial pathogens. First, we will use genome sequence data to identify genes encoding virulence factors and compare population structure of isolates, determine whether and how bacterial gene and protein expression responds to mammalian host signals, and determine which genes enable bacteria to colonize the swine respiratory tract and cause invasive disease. Next, we will compare the whole genome sequences of swine bacterial pathogens to identify AMR genes and determine whether or not identified AMR genes are located within mobile genetic elements (MGEs) such as plasmids, prophages, integrative and conjugative elements (ICEs), insertion sequences, and transposons. Finally, we will determine whether and how the microbiota changes following infection with swine respiratory pathogens and whether changes contribute to enhanced disease and evaluate the impact of pathogen-pathogen interactions occurring during infections with G. parasuis or S. suis. The second goal for this research plan is to develop and evaluate novel non-antibiotic intervention and management strategies to control priority bacterial diseases in swine, including vaccine platforms and therapeutics. First, we will develop novel vaccines that can prevent clinical disease with priority bacterial pathogens of swine, such as G. parasuis and S. suis. Examples of these novel vaccines include a G. parasuis capsule mutant bacterin, protein subunit vaccines for S. suis and G. parasuis, a S. suis capsule mutant, a conjugated capsule vaccine for G. parasuis, and a SEZ bacterin vaccine. We will additionally isolate bacteriophages active against swine LA-MRSA ST398 isolates and evaluate the use of bacteriophage treatment to reduce colonization. Finally, we will identify immunogenic, protective, and conserved outer membrane proteins of G. parasuis through immunoproteomics that will be cross protective against multiple serotypes.
Progress Report
Subobjective 1.1: The goal of this subobjective is to use genome sequence data to identify genes encoding virulence factors and compare population structure of isolates, determine whether and how bacterial gene and protein expression responds to host or swine signals, and determine which genes enable bacteria to colonize the swine respiratory tract and cause invasive disease. Analysis of data arising from gene and protein expression analysis from samples collected from pigs during S. suis-induced disease have been conducted. This analysis will enable the identification of Streptococcus suis gene transcripts and proteins expressed during respiratory tract colonization and systemic disease that can be used in further virulence and vaccine studies. Whole-genome sequencing and analysis for Actinobacillus suis and Actinobacillus pleuropneumoniae isolates obtained from swine production facilities within the U.S. have been completed. These genome sequences are currently being screened for genes encoding putative factors that could increase the capacity of these isolates to cause disease using both publicly available databases as well as published literature detailing experimentally verified virulence factors.
Subobjective 1.2: The goal of this subobjective is to compare the whole genome sequences of swine bacterial pathogens to identify antimicrobial resistance genes and determine whether any of the identified antimicrobial resistance genes are located within mobile genetic elements, which can be easily transferred to other bacteria. Antimicrobial susceptibility testing has been performed and completed for Actinobacillus suis and Actinobacillus pleuropneumoniae isolates obtained from within the U.S. Additionally, A. suis and A. pleuropneumoniae genome sequences are currently being screened for AMR genes, and to determine if any of the AMR genes are located within MGEs.
Subobjective 2.1: The goal of this subobjective is to develop novel vaccines that can prevent clinical disease with priority bacterial pathogens of swine that pose the greatest threat, such as Glaesserella parasuis and Streptococcus suis. Genomic and in vitro assessment of Glaesserella parasuis isolates have been undertaken. This information currently being used to identify virulence factors and conserved proteins that could be used as vaccines. Samples have been collected from pigs during Glaesserella parasuis- induced disease and are being used to evaluate gene expression responses at different host sites, including joints, cerebrospinal fluid, and the lung. Additional techniques are being tested for the purpose of optimizing sample recovery for the purpose of increasing detection of when and where specific virulence factors are expressed, which will increase effectiveness of novel vaccines.
Subobjective 2.2: The goal of this subobjective is to identify immunogenic, protective, and conserved proteins of Glaesserella parasuis or Streptococcus suis that will be cross protective against multiple serotypes. Previously, the protein LppA from Glaesserella parasuis was identified as important to the protective immune response. This protein has been tested as a vaccine and was able to protect pigs from severe disease. LppA has also been screened for cross reactivity with other strains of Glaesserella parasuis to predict its ability to protect against different strains of Glaesserella parasuis.
Accomplishments
1. Assessment of protection and cross reactivity of a new vaccine candidate for Glaesserella parasuis disease in pigs. Glaesserella parasuis is a bacterial pathogen that causes severe disease in pigs and can lead to significant economic losses to swine producers. Producers often use killed vaccines to prevent disease with G. parasuis, but these products often cause strain or serotype specific responses. ARS researchers in Ames, Iowa, tested a new vaccine that targets a surface protein (LppA) on Glaesserella parasuis. This vaccine protected pigs against infection with two strains of Glaesserella parasuis. It also showed cross reactivity with >40 strains of Glaesserella parasuis isolated from commercial swine farms. This work demonstrated the potential for LppA to act as a broadly effective vaccine against Glaesserella parasuis. The prevention of Glaesserella parasuis disease will improve swine health and reduce antibiotic usage in swine production, enabling the swine industry to be more prosperous.
2. Three newly discovered novel non-pathogenic bacterial strains within the genus Streptococcus were identified. Streptococcus suis is a bacterial pathogen that causes several serious diseases in pigs and results in large economic losses in the U.S. swine industry. Due to the lack of commercially available vaccines, innovative therapies are needed. ARS researchers in Ames, Iowa, identified and characterized three novel non-pathogenic bacterial species within the genus Streptococcus that can potential be used to exclude Streptococcus suis. The complete genome sequence of each strain was attained and results from multiple analyses indicate that each of the three strains represent novel species within the genus Streptococcus that have a high potential to be utilized as an innovative therapy, such as a probiotic or vaccine candidate to mitigate Streptococcus suis infections and disease, enabling the swine industry to be safer and more prosperous.
3. Streptococcus suis is a zoonotic swine pathogen capable of causing a spectrum of disease outcomes in both pigs and humans and contributes to significant economic losses to the swine industry worldwide. Additionally, Streptococcus suis is regarded as a reservoir for antimicrobial resistance genes that can be easily transferred to other bacteria. Recent studies investigating Streptococcus suis isolates from U.S. swine herds identified a gene predicted to encode a bleomycin antibiotic resistance protein in every isolate evaluated. ARS researchers in Ames, Iowa, demonstrated that Streptococcus suis predicted bleomycin resistance proteins do not have sequence similarity to other well-characterized bleomycin resistance proteins and, more importantly, do not encoded a functional bleomycin resistance protein capable of conferring resistance to bleomycin or bleomycin-like drugs. These results highlight the importance of functionally testing annotation predictions and directly address potential public health risks associated with occupational exposure to Streptococcus suis. These deliverables benefit the swine industry because they help to maintain public confidence in the safety of swine farming and pork products.
Review Publications
Hau, S.J., Fittipaldi, N., Payen, S., Grenier, D.W., Nielsen, D.W., Brockmeier, S., Gottschalk, M. 2025. Protection induced in pigs previously infected by the non-virulent strain 1330 of Streptococcus suis serotype 2 is not due to the secretion of the bacteriocin suicin. PLOS ONE. 20(5). Article e0323370. https://doi.org/10.1371/journal.pone.0323370.
Nielsen, D.W., Sarlo Davila, K.M., Brockmeier, S., Hau, S.J. 2025. Transcriptional profile of Glaesserella parasuis in swine serosal and joint fluids. Frontiers in Veterinary Science. 12. Article 1452973. https://doi.org/10.3389/fvets.2025.1452973.
Hau, S.J., Luan, S., Weinert, L.A., Langford, P.R., Rycroft, A., Wren, B.W., Maskell, D.J., Tucker, A.W., Brockmeier, S. 2025. Capsular immunity is necessary for protection against some but not all strains of Glaesserella parasuis. Veterinary Microbiology. https://doi.org/10.1016/j.vetmic.2025.110509.
Nicholson, T.L., Shore, S. 2024. Comparative analysis of antimicrobial resistance and genetic diversity of Bordetella bronchiseptica isolates obtained from swine within the United States. Frontiers in Microbiology. 15. Article 1501373. https://doi.org/10.3389/fmicb.2024.1501373.
Nicholson, T.L., Stuart, K.L., Bayles, D.O. 2025. Streptococcus suivaginalis sp. nov., Streptococcus iners sp. nov. and Streptococcus iners subsp. hyiners subsp. nov. isolated from pigs. International Journal of Systematic and Evolutionary Microbiology. 75(1). https://doi.org/10.1099/ijsem.0.006631.
Hau, S.J., Eberle, K.C., Nally, J.E., Nielsen, D.W., Lippolis, J.D., Brockmeier, S. 2025. Identification of candidate vaccine antigens using 2-D gel electrophoresis and immunoproteomics for cross protection against Glaesserella parasuis. Veterinary Microbiology. 307. Article 110594. https://doi.org/10.1016/j.vetmic.2025.110594.