Genomic epidemiology of porcine Lawsonia intracellularis in China revealed by metagenome-assembled genomes and global comparative analysis

Abstract Lawsonia intracellularis , the etiological agent of porcine proliferative enteropathy, is widely distributed in swine herds and poses a significant economic burden to the global swine industry. However, its obligate intracellular lifestyle severely limits in vitro cultivation, hindering large-scale genomic surveillance and epidemiological tracking. In this study, we combined nationwide PCR-based prevalence screening with culture-independent metagenomic sequencing to characterize the molecular epidemiology and genomic features of circulating L. intracellularis strains in China. PCR screening of 1,831 clinical samples collected from 13 provinces revealed widespread circulation, with an overall individual positivity rate of 26.38%. From strongly positive specimens, nine high-quality metagenome-assembled genomes (MAGs) were successfully reconstructed. Comparative analysis against all publicly available global genomes revealed exceptionally high average nucleotide identity (> 99.9%) and limited single-nucleotide polymorphism (SNP) variation (ranging from 4 to 370). Phylogenetic reconstruction divided the strains into two major clades, within which Chinese isolates were interspersed with international strains, suggesting recent shared ancestry and potential cross-regional transmission. Pangenome analysis revealed a highly conserved core genome with restricted accessory diversity, which is consistent with the genomic architecture typical of obligate intracellular bacteria. Only a few high-confidence antimicrobial resistance determinants were identified, although several homologous loci potentially associated with resistance were detected. Notably, comparative analysis revealed four virulence-associated genes that were conserved in field isolates but highly divergent from or absent from the vaccine strain, indicating the development of a niche-specific adaptive evolution. This study establishes the first comprehensive genomic epidemiological framework for L. intracellularis in China, demonstrating the utility of metagenomics for tracking unculturable pathogens, informing regional surveillance strategies, and highlighting conserved versus variable genomic targets for future vaccine and therapeutic development.