(1) Background: In recent years, the increasing emergence of multidrug-resistant pathogens in pig farms has begun to pose a severe threat to animal welfare and, by extension, public health. In this study, we aimed to explore the biological characteristics and genomic features of bacteriophages that are capable of lysing porcine multidrug-resistant E. coli, which was isolated from sewage. In doing so, we provided a reference for phage therapies that can be used to treat multidrug-resistant strains. (2) Method: Using the multidrug-resistant E. coli isolate sq-1 as the host bacterium, bacteriophages were isolated and purified from fecal samples using a double-layer agar plate method. The morphology was observed using a transmission electron microscope, and its host range, optimal multiplicity of infection (MOI), one-step growth curve, thermal stability, acid–base tolerance, and in vitro antibacterial ability were tested. Genomic features were analyzed using whole-genome sequencing. (3) Results: A lytic phage named vB_EcoS_Psq-1 (abbreviated as Psq-1) was successfully isolated. Electron microscopy revealed that Psq-1 belongs to the family of long-tailed phages, possessing clear and transparent plaques of approximately 1 mm in diameter. Psq-1 only lyses the host bacterium and does not affect other E. coli strains or other species of bacteria. The optimal MOI for phage Psq-1 was 0.1, with a latent period of 25 min, an exponential growth period of 25 min, and a lysis yield of 44.21 PFU/cell. Its activity remains stable at temperatures between 40 °C and 60 °C and from pH 4.0 to pH 13.0. Psq-1 exhibited a significant inhibitory effect on E. coli in liquid culture medium. The nucleic acid type of phage Psq-1 was dsDNA, with a total genome length of 44,183 bp and a GC content of 52.16%. No known resistance, lysogenic, or virulence-related genes were detected. The whole genome contains 55 open reading frames (ORFs). (4) Conclusions: This study isolated a bacteriophage that is capable of lysing multidrug-resistant E. coli. Characterized by a narrow E. coli lysis range, a long latent period, limited lytic ability, and stable biological properties, this bacteriophage can serve as a reference isolate for E. coli phages and can provide biological materials and data to support research on bacteriophages that are effective against multidrug-resistant porcine E. coli.

Background: This study aimed to analyze the antimicrobial resistance and pathogenicity of Klebsiella pneumoniae(K. pneumoniae) isolates from pigs, evaluate their potential threat to pig farming and public health, and provide a theoretical basis for controlling K. pneumoniae infections in pig farms. Methods: Nasal swabs collected from pigs were subjected to bacterial isolation, biochemical identification, species-specific PCR, and 16S rRNA sequencing to identify K. pneumoniae. Serotyping and multilocus sequence typing (MLST) were conducted using the wzi and MLST methods, respectively. Biofilm formation was assessed using crystal violet staining. Antimicrobial susceptibility was evaluated via the Kirby-Bauer disk diffusion method, and resistance and virulence genes were identified using PCR. Pathogenicity was determined through string testing and mouse infection models. Results: 21 strains of K. pneumoniae were isolated and identified from 50 swabs of pig nasal cavities. The isolates were classified into serotypes wzi 19 and wzi 81 and sequence types ST37 and ST967. Ten isolates exhibited strong biofilm-forming ability, while 11 showed moderate biofilm production. Antimicrobial susceptibility testing revealed resistance to β-lactams, aminoglycosides, quinolones, tetracyclines, sulfonamides, aminoalcohols, and glycopeptides, with sensitivity restricted to imipenem and polymyxins. Ten resistance genes and eight virulence genes were detected. Pathogenicity testing in mice revealed a moderate virulence level, with a median lethal dose (LD₅₀) of 4.0 × 10⁶ CFU/mL. Infected mice exhibited significant lesions in the liver, lungs, and small intestine. Conclusion: These findings highlight a potential risk to pig farming and public health, emphasizing the need for effective control measures against K. pneumoniae infections in pig farms.

Streptococcus suis serotype 9 is an emerging zoonotic pathogen threatening pig production and public health. Here, we combined comparative genomics of 16 strains, including clinical isolate SS2401, to elucidate the role of prophages in shaping genomic plasticity and virulence evolution. The pan-genome was open (α = 0.375), highlighting extensive genetic diversity. Prophages were prevalent (56.25% of strains), significantly correlated with larger genomes, and exhibited two integration modes: direct insertion as genomic islands and integration at recombination hotspots associated with large-scale inversions. Phylogenetic analysis of the terminase large subunit (TerL) and whole-genome sequences revealed multiple independent acquisitions, with three prophages in SS2401 originating from distinct lineages (“one strain, multiple sources”). Recombination analysis detected 1,432 events across the core genome, indicating frequent horizontal gene exchange. The virulence gene sly (suilysin) was carried as a gene cassette within prophage Phi2401a. Notably, we identified integrase-deficient but otherwise intact prophages that may function as “gene prisons,” stably fixing virulence traits. These findings demonstrate that prophages act as dual drivers of genomic architecture and as dynamic reservoirs for virulence genes, providing a framework for understanding bacterial adaptation and informing surveillance strategies in the swine industry. IMPORTANCE: Streptococcus suis serotype 9 poses a significant threat to pig farming and public health worldwide. This study reveals that prophages are not passive passengers but active architects of genomic plasticity and virulence evolution in this pathogen. We demonstrate that prophages contribute to genome expansion, facilitate large-scale chromosomal rearrangements, and carry key virulence genes such as sly . The discovery of a “one strain, multiple sources” acquisition pattern and the “gene prison” model explains how virulence traits can be stably maintained and disseminated. These findings redefine prophages as dual drivers of bacterial evolution, providing new insights for surveillance and intervention strategies in the swine industry.

Glaesserella parasuis (formerly Haemophilus parasuis, HPS), Actinobacillus pleuropneumoniae (APP), Streptococcus suis (SS), and Pasteurella multocida (PM) are common bacterial pathogens associated with Porcine Respiratory Disease Complex (PRDC), a major cause of economic losses in the swine industry. To address this, a cross-sectional study was conducted across 27 large-scale swine farms in Xinjiang, China (October 2024–May 2025). A total of 1239 clinical samples were analyzed by species-specific PCR, and positive samples were further serotyped. Overall, SS and HPS were the predominant pathogens, with higher detection rates in winter and spring. Notably, SS and HPS were most frequent in nasal swabs, while APP and PM predominated in tissue samples. Furthermore, co-infections were common, with HPS + SS being the most prevalent. Serotyping revealed dominance of HPS serotype 12, APP serotype 12, SS serotype 3, and PM serotypes A and B (serotypes E and F not detected). In addition, SS was also detected in environmental samples and farm workers’ nasal swabs. These findings suggest that future prevention and control strategies should focus on developing multivalent vaccines targeting the predominant serotypes identified, implementing regular serotype surveillance to guide precision immunization protocols, and strengthening environmental disinfection and biosecurity practices to reduce co-infections and occupational exposure risks.

Porcine reproductive and respiratory syndrome virus 1 (PRRSV-1) has emerged as a critical pathogen that threatens swine herds across China. In this study, a novel PRRSV-1 strain, designated XJEU2308, was isolated from a PRRSV outbreak in a previously confirmed PRRSV-negative (both RNA and antibody negative) swine herd in Xinjiang, China. During the outbreak surveillance period, production records revealed a mean stillbirth rate of 12.19% and a suckling piglet mortality rate of 56.07%. Phylogenetic analysis on the basis of the ORF5 gene classified XJEU2308 as a BJEU06-1-like strain, whereas whole-genome analysis clustered it within the newly identified "New subgroup 1" of Chinese PRRSV-1. Notably, this strain carried a unique 3-amino acid deletion (at positions 693–695) in nonstructural protein 2 (NSP2). In challenge experiments, XJEU2308 induced typical clinical symptoms and exhibited moderate pathogenicity. Importantly, the implementation of the load-close-exposure (LCE) strategy combined with field virus (FLV) exposure successfully restored the herd to a provisional PRRSV-negative status. Overall, this study isolated a new subgroup 1-like PRRSV-1 strain from a swine farm that experienced a reproductive failure outbreak; the strain is characterized by a unique 3-amino-acid deletion in the NSP2 gene and moderate pathogenicity. Additionally, this study validated the effectiveness of the LCE-FLV strategy for containing PRRSV-1.

The emergence of antimicrobial resistance in extraintestinal pathogenic Escherichia coli (ExPEC) necessitates alternative therapies for swine. Two lytic phages, vB_EcoM_S37 and vB_EcoP_S37A, were isolated from swine wastewater and characterized for morphology, stability, host range, antibacterial efficacy, and whole-genome features. Optimal multiplicities of infection were 0.01 and 0.1, respectively. Both phages remained stable at pH 4.0–11.0 and 40–60 °C. vB_EcoM_S37 lysed 43.55% (27/62) of tested E. coli strains, with a 5-min latent period and 1173 PFU/cell burst size, and suppressed bacterial growth for 12 h in vitro. vB_EcoP_S37A lysed 6.45% (4/62) of strains, exhibited a 10-min latent period and 210 PFU/cell burst size, and maintained inhibition for 8 h. Genomic analysis revealed that both phages have linear dsDNA genomes devoid of virulence or antibiotic resistance genes. vB_EcoM_S37 (173,927 bp, 37.42% GC) belongs to the genus Mosigvirus (family Straboviridae), whereas vB_EcoP_S37A (38,725 bp, 48.64% GC) represents a novel species within the genus Teseptimavirus (family Autotranscriptaviridae). These findings support both phages as stable, safe, and promising candidates for non-antibiotic biocontrol of ExPEC infections in livestock.