scholarly journals Comprehensive comparative genomics analysis for the emerging human pathogen Streptococcus dysgalactiae subsp. equisimilis (SDSE): A case study and Pan-subspecies genomic analysis

2021 ◽  
Author(s):  
Amr T. M. Saeb ◽  
Hamsa Tayeb
Keyword(s):  
Comparative Genomics ◽  
Virulence Factors ◽  
Genomic Analysis ◽  
Streptococcal Toxic Shock Syndrome ◽  
Human Pathogen ◽  
Streptococcus Dysgalactiae ◽  
Close Relationship ◽  
Life Threatening ◽  
Host Mortality ◽  
Comparative Genomics Analysis

Background: Streptococcus dysgalactiae subsp. equisimilis (SDSE) is the causal agent of various diseases that include wound infection, erysipelas, cellulitis, life-threatening necrotizing fasciitis, and streptococcal toxic shock syndrome. It is capable of infecting both humans and animals. In this investigation, we present a comprehensive genomic analysis for the SDSE strain SCDR1 that belongs to Lancefield group G, emm type (stG6) and (MLST) sequence type (ST44) that is the first time to be documented in Saudi Arabia and the middle east. Besides, we present the most comprehensive comparative genomics analysis for the emerging human pathogen SDSE. Methodology: We utilized next-generation sequencing techniques (NGS), bioinformatics, phylogenetic analysis, and comparative pathogenomics to characterize SCDR1 and all publicly available SDES genomes. Results: We found that SCDR1 consisted of a circular genome of 2179136 bp. Comparative analyses among bacterial genomes indicated that SCDR1 was most closely related to AC-2713 and GGS_124. Genome annotation of SCDR-1 strain showed that it contains many genes with homology to known virulence factors, including genes involved in cellular invasion, Antiphagocytosis, immune evasion, invasion of skin and soft tissue, host mortality and tissue damage, toxins, pore-forming proteins, cytotoxins, beta-hemolysis agents. Two CRISPR arrays were identified in SCDR1 that are consist of 35 CRISPR repeats and 33 CRISPR spacers. Two CAS systems were observed in the SCDR-1 genome, namely, CAS-TypeIIA and CAS-TypeIC. SDSE core Resistome is consisting of 22 genes, including folA, gyrA, gyrB, and FabK. SDSE core Virulome consisting of 38 genes including, fba, fbp54, gidA, and lsp. Conclusion: Our study confirmed that the SDSE strains possess different characteristics in producing virulence factors for pathogenicity to humans and based on its genome sequence and close relationship with GAS. Our study shed light on the proposed pathogenic mechanisms of SDSE and may form the basis of molecular epidemiological research on these highly virulent bacteria.

scholarly journals First Report and Comparative Genomics Analysis of a blaOXA-244–Harbouring Escherichia coli Isolate Recovered in American Continent

2019 ◽  
Author(s):  
Deisy J Abril ◽  
Ingrid Gisell Bustos Moya ◽  
Ricaurte Alejandro Marquez-Ortiz ◽  
Diego Fernando Josa Montero ◽  
Zayda Lorena Corredor Rozo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Comparative Genomics ◽  
Genomic Island ◽  
Genomic Analysis ◽  
American Continent ◽  
Incompatibility Group ◽  
Coli Isolate ◽  
First Report ◽  
E Coli ◽  
Comparative Genomics Analysis

The carbapenemase OXA-244 is a derivate of OXA-48, and its detection is very difficult in laboratories. Here we report the identification and genomic analysis of an Escherichia coli isolate (28Eco12) harbouring the blaOXA-244 gene identified in Colombia, South America. The 28Eco12 isolate was identified during a retrospective study and it was recovered from a patient treated in Colombia. The complete nucleotide sequence was established using the PacBio platform. A comparative genomics analysis with other blaOXA-244–harbouring Escherichia coli strains was performed. The 28Eco12 isolate belonged to sequence type (ST) 38 and its genome was composed of two molecules, a chromosome of 5,343,367 bp and a plasmid of 92,027 bp, which belonged to the incompatibility group IncY and did not harbour resistance genes. The blaOXA-244 gene was chromosomally-encoded and mobilized by an ISR1-related Tn6237 composite transposon. Notably, this transposon was inserted and located within a new genomic island. For our knowledge this is the first report of a blaOXA-244–harbouring Escherichia coli isolate in American continent.Our results suggest that the introduction of the OXA-244-producing E. coli isolate was through clonal expansion of the ST38 pandemic clone. Other isolates producing OXA-244 could be circulating silently on the American continent.

scholarly journals First Report and Comparative Genomics Analysis of a blaOXA-244-Harboring Escherichia coli Isolate Recovered in the American Continent

Antibiotics ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 222 ◽  
Author(s):  
Deisy Abril ◽  
Ingrid Gisell Bustos Moya ◽  
Ricaurte Alejandro Marquez-Ortiz ◽  
Diego Fernando Josa Montero ◽  
Zayda Lorena Corredor Rozo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Comparative Genomics ◽  
Genomic Island ◽  
Genomic Analysis ◽  
American Continent ◽  
Incompatibility Group ◽  
Coli Isolate ◽  
First Report ◽  
E Coli ◽  
Comparative Genomics Analysis

The carbapenemase OXA-244 is a derivate of OXA-48, and its detection is very difficult in laboratories. Here, we report the identification and genomic analysis of an Escherichia coli isolate (28Eco12) harboring the blaOXA-244 gene identified in Colombia, South America. The 28Eco12 isolate was identified during a retrospective study, and it was recovered from a patient treated in Colombia. The complete nucleotide sequence was established using the PacBio platform. A comparative genomics analysis with other blaOXA-244–harboring Escherichia coli strains was performed. The 28Eco12 isolate belonged to sequence type (ST) 38, and its genome was composed of two molecules, a chromosome of 5,343,367 bp and a plasmid of 92,027 bp, which belonged to the incompatibility group IncY and did not harbor resistance genes. The blaOXA-244 gene was chromosomally encoded and mobilized by an ISR1-related Tn6237 composite transposon. Notably, this transposon was inserted and located within a new genomic island. To our knowledge, this is the first report of a blaOXA-244–harboring Escherichia coli isolate in America. Our results suggest that the introduction of the OXA-244-producing E. coli isolate was through clonal expansion of the ST38 pandemic clone. Other isolates producing OXA-244 could be circulating silently in America.

scholarly journals Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity

2021 ◽  
Vol 7 (5) ◽  
pp. 337
Author(s):  
Daniel Peterson ◽  
Tang Li ◽  
Ana M. Calvo ◽  
Yanbin Yin
Keyword(s):  
Comparative Genomics ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Phytopathogenic Fungi ◽  
Secreted Proteins ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Signal Peptides ◽  
Comparative Genomics Analysis

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome.

Possible antivirulent activity of some agents against clinical isolates of Pseudomonas aeruginosa

2021 ◽  
Vol 30 (2) ◽  
pp. 1-8
Author(s):  
Ahmad O. Rifai ◽  
Abeer M. Abd El-Aziz ◽  
Hany I. Kenawy
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Quorum Sensing ◽  
Virulence Factors ◽  
Therapeutic Target ◽  
Inhibitory Action ◽  
Antibacterial Agents ◽  
Mechanisms Of Resistance ◽  
Life Threatening ◽  
Pheniramine Maleate ◽  
Pyocyanin Production

Background: Pseudomonas aeruginosa has developed different mechanisms of resistance against antibiotics and became one of the most life-threatening pathogens. Fighting against its virulence Factors are an alternative therapeutic target. Objective: This study was directed towards the investigation of anti-quorum sensing activity and inhibitory action on virulence factors of different agents including antibacterial agents to which Pseudomonas aeruginosa isolates are resistant and non-antibacterial agents. Methodology: Anti-quorum sensing activity of ceftriaxone, ceftazidime (CAZ), cefepime (FEP), vancomycin (VA), paracetamol (PA), and pheniramine maleate (PHE) investigated as well as their ability to reduce other virulence factors including protease, hemolysin, and pyocyanin production. Results: This study showed that 3rd and 4th generations cephalosporins could be used as anti-quorum sensing agents effectively in the treatment of Pseudomonas aeruginosa infections, however, vancomycin, paracetamol, and pheniramine maleate had no effect on inhibiting the studied virulence factors. Conclusion: From our study we conclude that although cephalosporins at the used concentrations did not show anti-pseudomonal activity they were effective as anti virulent agents that could be utilized in therapeutically in controlling Pseudomonas aeruginosa infections.

Phylogenetic relationships of ascomycetes and basidiomycetes based on comparative genomics analysis

2017 ◽  
Vol 39 (12) ◽  
pp. 1307-1316 ◽  
Author(s):  
Xunbiao Liu ◽  
Qianqian Zhang ◽  
Xinyao Xia ◽  
Xiuyuan Liu ◽  
Lei Ge ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Phylogenetic Relationships ◽  
Comparative Genomics Analysis
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