Comparative genomics and in silico virulence assessment of nonpathogenic Avibacterium paragallinarum isolates from healthy layer chickens

Infectious coryza (IC) is a respiratory disease of chickens caused by the bacterial primary pathogen Avibacterium paragallinarum (AP). Clinical signs are characteristic and suggestive of the disease; however, diagnosis is confirmed through bacterial isolation or qPCR detection. Recently, several naïve, healthy layer (NHL) flocks, neither exposed to IC nor vaccinated against it, tested positive using current IC-specific qPCR assays. Moreover, AP isolates were recovered from these NHL flocks and were designated “non-pathogenic Avibacterium paragallinarum ” (npAP) due to the absence of clinical signs in the field and in an experimental challenge study. However, understanding the genetic basis behind this difference in pathogenicity remains unknown. Therefore, the purpose of the current study was to investigate the genetic explanations for the lack of pathogenicity in npAP. Comprehensive comparative genomic analysis was performed for 14 npAP and 87 pathogenic AP (pAP) genomes at three main levels, (a) gene presence/absence, (b) sequence variation within translated open reading frames (ORFs) across the whole genome, and (c) targeted analysis of selected virulence-associated genes. The analysis revealed four consistent features, (1) The HMTp210 gene, encoding the trimeric autotransporter adhesin HMTp210, important for serotyping and protective immunity, is 2–3 times longer in npAP compared to pAP. (2) npAP isolates exhibit either complete absence of the capsular polysaccharide locus or defective genes within the locus. (3) All npAP isolates lack both hmp and nsrR , which encode Flavohemoglobin/Nitric oxide dioxygenase protein (Hmp) and the nitrite-sensitive transcriptional repressor protein (NsrR), respectively. (4) The ftsZ gene, which is essential for cell-division, exhibits substantial allelic divergence between npAP and pAP. We hypothesize that defects or changes in HMTp210 adhesin, capsule, the nitric oxide dioxygenase system, or FtsZ contribute to the nonpathogenic phenotype of npAP in chickens. Moreover, most of npAP isolates encode a putative sialylated lipooligosaccharide which may promote a more commensal-like interaction with the host immune system, preventing an overt inflammatory response. In conclusion, our findings highlight potential virulence factors that can be involved in AP pathogenesis. Additionally, defining and understanding the role of these potential virulence factors, may open new avenues for the development of modified live vaccines against IC.