Molecular Identification and Genetic Diversity of Avibacterium paragallinarum Isolated from Chickens with Infectious Coryza in Bogor, Indonesia

Infectious coryza, a respiratory disease caused by Avibacterium paragallinarum (A. paragallinarum), poses a major threat to poultry health and productivity, particularly in tropical countries such as Indonesia. This study aimed to isolate, molecularly identify, and characterize the genetic diversity of A. paragallinarum from chickens exhibiting clinical symptoms of coryza. A total of 60 infraorbital sinus swab samples were aseptically collected from commercial layer and broiler chickens in Bogor Regency, West Java, Indonesia. The method consists of phenotypic identification (culture on Nicotinamide Adenine Dinucleotide [NAD], Gram staining, and biochemical tests) and molecular confirmation using Polymerase Chain Reaction (PCR) HPG-2, Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR, and 16S rRNA sequencing. Eight field isolates were successfully cultured on NAD-supplemented blood agar, Gram-negative, catalase and oxidase-negative. Molecular confirmation was conducted using species-specific HPG-2, with all isolates amplifying the expected 500 bp product. The evaluation of genetic diversity was conducted through ERIC-PCR, which identified five unique clusters among the isolates, demonstrating considerable genomic variation. Furthermore, partial 16S rRNA gene sequences were amplified and analyzed through phylogenetic tree construction and BLAST comparison. Sequence analysis revealed 95.7–99.2% homology with reference A. paragallinarum strains in GenBank, and 96.5–99.2% homology among the study isolates themselves. The phylogenetic tree highlighted a close relationship among the local isolates, yet also indicated a distinct genetic lineage from several international reference strains, suggesting possible regional specificity. This study provided the first detailed genetic characterization of A. paragallinarum field isolates in Indonesia using 16S rRNA sequencing. These findings highlighted the need for continuous molecular surveillance to guide accurate diagnosis. Keywords: 16S rRNA sequencing, Avibacterium paragallinarum, Field isolate, Molecular identification