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

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.

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

10.21203/rs.3.rs-112825/v1 ◽

2020 ◽

Author(s):

Rajesh Kumar Vaid ◽

Zoozeal Thakur ◽

Taruna Anand ◽

Sanjay Kumar ◽

Bhupendra Nath Tripathi

Keyword(s):

Genome Analysis ◽

Salmonella Enterica ◽

Genomic Islands ◽

Economic Losses ◽

Genotypic Differences ◽

Comparative Genome Analysis ◽

Comparative Genome ◽

Genomic Features ◽

Niche Adaptation ◽

Antimicrobial Resistance 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 with a focus on identification of candidate virulence factors. 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 genomic islands, prophage regions, toxin-antitoxin cassettes, and acquired antimicrobial resistance genes. The identified genetic differences among the S. enterica serovar Gallinarum strains could be used for bacterial typing, design of rapid and reliable diagnostics, structure based inhibitor development and vaccine design for effective infection control as well as eradication and will also form basis for future experimental investigations.

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Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted Salmonella enterica Serovar Typhimurium Pathovar

mBio ◽

10.1128/mbio.00565-13 ◽

2013 ◽

Vol 4 (5) ◽

Cited By ~ 34

Author(s):

Robert A. Kingsley ◽

Sally Kay ◽

Thomas Connor ◽

Lars Barquist ◽

Leanne Sait ◽

...

Keyword(s):

Genome Analysis ◽

Salmonella Enterica ◽

Host Adaptation ◽

Whole Genome ◽

Comparative Genome Analysis ◽

Comparative Genome ◽

Content Type ◽

Serovar Typhimurium ◽

Genetic Signatures

ABSTRACTSalmonella entericaserovar Typhimurium definitive type 2 (DT2) is host restricted toColumba livia(rock or feral pigeon) but is also closely related toS. Typhimurium isolates that circulate in livestock and cause a zoonosis characterized by gastroenteritis in humans. DT2 isolates formed a distinct phylogenetic cluster withinS. Typhimurium based on whole-genome-sequence polymorphisms. Comparative genome analysis of DT2 94-213 andS. Typhimurium SL1344, DT104, and D23580 identified few differences in gene content with the exception of variations within prophages. However, DT2 94-213 harbored 22 pseudogenes that were intact in other closely relatedS. Typhimurium strains. We report a novelin silicoapproach to identify single amino acid substitutions in proteins that have a high probability of a functional impact. One polymorphism identified using this method, a single-residue deletion in the Tar protein, abrogated chemotaxis to aspartatein vitro. DT2 94-213 also exhibited an altered transcriptional profile in response to culture at 42°C compared to that of SL1344. Such differentially regulated genes included a number involved in flagellum biosynthesis and motility.IMPORTANCEWhereasSalmonella entericaserovar Typhimurium can infect a wide range of animal species, some variants within this serovar exhibit a more limited host range and altered disease potential. Phylogenetic analysis based on whole-genome sequences can identify lineages associated with specific virulence traits, including host adaptation. This study represents one of the first to link pathogen-specific genetic signatures, including coding capacity, genome degradation, and transcriptional responses to host adaptation within aSalmonellaserovar. We performed comparative genome analysis of reference and pigeon-adapted definitive type 2 (DT2)S. Typhimurium isolates alongside phenotypic and transcriptome analyses, to identify genetic signatures linked to host adaptation within the DT2 lineage.

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Pathogenic and antimicrobial resistance genes in Streptococcus oralis strains revealed by comparative genome analysis

Genomics ◽

10.1016/j.ygeno.2020.04.014 ◽

2020 ◽

Vol 112 (5) ◽

pp. 3783-3793

Author(s):

Jiannan Zhou ◽

Tianyong Sun ◽

Wenyan Kang ◽

Di Tang ◽

Qiang Feng

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Genome Analysis ◽

Comparative Genome Analysis ◽

Comparative Genome ◽

Streptococcus Oralis ◽

Antimicrobial Resistance Genes

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Comparative genome analysis of IncHI2 VIM-1 carbapenemase-encoding plasmids of Escherichia coli and Salmonella enterica isolated from a livestock farm in Germany

Veterinary Microbiology ◽

10.1016/j.vetmic.2015.09.001 ◽

2017 ◽

Vol 200 ◽

pp. 114-117 ◽

Cited By ~ 23

Author(s):

Linda Falgenhauer ◽

Hiren Ghosh ◽

Beatriz Guerra ◽

Yancheng Yao ◽

Moritz Fritzenwanker ◽

...

Keyword(s):

Escherichia Coli ◽

Genome Analysis ◽

Salmonella Enterica ◽

Comparative Genome Analysis ◽

Comparative Genome ◽

Livestock Farm

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Comparative genome analysis of Corynebacterium species: The underestimated pathogens with high virulence potential

Infection Genetics and Evolution ◽

10.1016/j.meegid.2021.104928 ◽

2021 ◽

pp. 104928

Author(s):

Fouzia Nasim ◽

Arijit Dey ◽

Insaf Ahmed Qureshi

Keyword(s):

Genome Analysis ◽

Comparative Genome Analysis ◽

Comparative Genome ◽

Virulence Potential ◽

Corynebacterium Species ◽

High Virulence

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Synteny Conservation and Chromosome Rearrangements During Mammalian Evolution

Genetics ◽

10.1093/genetics/147.1.289 ◽

1997 ◽

Vol 147 (1) ◽

pp. 289-296 ◽

Cited By ~ 2

Author(s):

Jason Ehrlich ◽

David Sankoff ◽

Joseph H Nadeau

Keyword(s):

Genome Analysis ◽

Systematic Errors ◽

Chromosome Rearrangements ◽

Mammalian Evolution ◽

Comparative Genome Analysis ◽

Reciprocal Translocations ◽

Comparative Genome ◽

Strong Selection ◽

Synteny Conservation

Abstract An important problem in comparative genome analysis has been defining reliable measures of synteny conservation. The published analytical measures of synteny conservation have limitations. Nonindependence of comparisons, conserved and disrupted syntenies that are as yet unidentified, and redundant rearrangements lead to systematic errors that tend to overestimate the degree of conservation. We recently derived methods to estimate the total number of conserved syntenies within the genome, counting both those that have already been described and those that remain to be discovered. With this method, we show that ~65% of the conserved syntenies have already been identified for humans and mice, that rates of synteny disruption vary ~25-fold among mammalian lineages, and that despite strong selection against reciprocal translocations, inter-chromosome rearrangements occurred approximately fourfold more often than inversions and other intra-chromosome rearrangements, at least for lineages leading to humans and mice.

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