Comparative genome analysis of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum decodes strain specific genes

Abstract

Salmonella enterica serovar Gallinarum biovar Pullorum (bvP) and biovar Gallinarum (bvG) are the etiological agents of pullorum disease (PD) and fowl typhoid (FT) respectively, which cause huge economic losses to poultry industry especially in developing countries including India. Vaccination and biosecurity measures are currently being employed to control and reduce the S. Gallinarum infections. High endemicity, poor implementation of hygiene and lack of effective vaccines pose challenges in prevention and control of disease in intensively maintained poultry flocks. Comparative genome analysis unravels similarities and dissimilarities thus facilitating identification of genomic features that aids in pathogenesis, niche adaptation and in tracing of evolutionary history. The present investigation was carried out to assess the genotypic differences amongst S.enterica serovar Gallinarum strains including Indian strain S. Gallinarum Sal40 VTCCBAA614. The comparative genome analysis revealed an open pan-genome consisting of 5091 coding sequence (CDS) with 3270 CDS belonging to core-genome, 1254 CDS to dispensable genome and strain specific genes i.e. singletons ranging from 3 to 102 amongst the analyzed strains. Moreover, the investigated strains exhibited diversity in genomic features such as virulence factors, genomic islands, prophage regions, toxin-antitoxin cassettes, and acquired antimicrobial resistance genes. Core genome identified in the study can give important leads in the direction of design of rapid and reliable diagnostics, and vaccine design for effective infection control as well as eradication. Additionally, the identified genetic differences among the S. enterica serovar Gallinarum strains could be used for bacterial typing, structure based inhibitor development by future experimental investigations on the data generated.

Hybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil

“…enterica serovar Enteritidis str. P125109 (NC_011294.1) [ 52 ]. However, the GC content of the assembled genome (52.16%) was more similar to Salmonella enterica subsp.…”

“…enterica serovar Enteritidis str. P125109 (NC_011294.1) (52.17%) [ 52 ]. HiSeq assemblies have been traditionally considered the “gold standard” because MinION sequencing could introduce high numbers of errors and consequently may interfere with high-quality genome annotations due to reduced accuracy in gene prediction, producing a large number of misannotated genes [ 53 , 54 ].…”

Emergence, Dissemination and Antimicrobial Resistance of the Main Poultry-Associated Salmonella Serovars in Brazil

“…S. Gallinarum strains also present several different genomic profiles, including lineages with several prophages, plasmids, and gene clusters coding for different AMR mechanisms [75,88]. It has also been reported that S. Gallinarum has accumulated many pseudogenes and virulence genes associated with specificity to chicken hosts [89].…”

Through the Looking Glass: Genome, Phenome, and Interactome of Salmonella enterica

“…However, egg contamination can lose its association with causing foodborne illness, as exemplified by the closely related serotypes S. gallinarum and S. pullorum . These two serotypes are host-restricted to the bird and are not a cause of human foodborne illness [ 64 ]. They are threats to food security because of high transmittance and mortality in chicks and mature birds [ 65 ].…”