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

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.

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

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255612
Author(s):  
Rajesh Kumar Vaid ◽  
Zoozeal Thakur ◽  
Taruna Anand ◽  
Sanjay Kumar ◽  
Bhupendra Nath Tripathi
Keyword(s):  
Genome Analysis ◽  
Salmonella Enterica ◽  
Core Genome ◽  
Genomic Islands ◽  
Economic Losses ◽  
Genotypic Differences ◽  
Comparative Genome Analysis ◽  
Comparative Genome ◽  
Genomic Features ◽  
Antimicrobial Resistance 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.

scholarly journals Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10185
Author(s):  
Romen Singh Naorem ◽  
Jochen Blom ◽  
Csaba Fekete
Keyword(s):  
Genome Analysis ◽  
Genetic Background ◽  
Multiple Drug Resistance ◽  
Clinical Isolates ◽  
Ecological Niches ◽  
Comparative Genome Analysis ◽  
Pathogenic Potential ◽  
Comparative Genome ◽  
Pan Genome ◽  
Niche Adaptation

Staphylococcus aureus is a drug-resistant pathogen, capable of colonizing diverse ecological niches and causing a broad spectrum of infections related to a community and healthcare. In this study, we choose four methicillin-resistant S. aureus (MRSA) clinical isolates from Germany and Hungary based on our previous polyphasic characterization finding. We assumed that the selected strains have a different genetic background in terms of the presence of resistance and virulence genes, prophages, plasmids, and secondary metabolite biosynthesis genes that may play a crucial role in niche adaptation and pathogenesis. To clarify these assumptions, we performed a comparative genome analysis of these strains and observed many differences in their genomic compositions. The Hungarian isolates (SA H27 and SA H32) with ST22-SCCmec type IVa have fewer genes for multiple-drug resistance, virulence, and prophages reported in Germany isolates. Germany isolate, SA G6 acquires aminoglycoside (ant(6)-Ia and aph(3’)-III) and nucleoside (sat-4) resistance genes via phage transduction and may determine its pathogenic potential. The comparative genome study allowed the segregation of isolates of geographical origin and differentiation of the clinical isolates from the commensal isolates. This study suggested that Germany and Hungarian isolates are genetically diverse and showing variation among them due to the gain or loss of mobile genetic elements (MGEs). An interesting finding is the addition of SA G6 genome responsible for the drastic decline of the core/pan-genome ratio curve and causing the pan-genome to open wider. Functional characterizations revealed that S. aureus isolates survival are maintained by the amino acids catabolism and favor adaptation to growing in a protein-rich medium. The dispersible and singleton genes content of S. aureus genomes allows us to understand the genetic variation among the CC5 and CC22 groups. The strains with the same genetic background were clustered together, which suggests that these strains are highly alike; however, comparative genome analysis exposed that the acquisition of phage elements, and plasmids through the events of MGEs transfer contribute to differences in their phenotypic characters. This comparative genome analysis would improve the knowledge about the pathogenic S. aureus strain’s characterization, and responsible for clinically important phenotypic differences among the S. aureus strains.

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

mBio ◽  
2013 ◽  
Vol 4 (5) ◽  
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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