Biology subjects

Saeb, A. T. M.

Publications and source records attributed to Saeb, A. T. M..

4 recordsLinked to original sources

bioRxiv2021

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

BackgroundStreptococcus 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. MethodologyWe utilized next-generation sequencing techniques (NGS), bioinformatics, phylogenetic analysis, and comparative pathogenomics to characterize SCDR1 and all publicly available SDES genomes. ResultsWe 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. ConclusionOur 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.

microbiology↗

bioRxiv2021

Comparative investigation of the Diabetic foot ulcer microbiome

BackgroundMany factors may affect wound healing in Diabetic foot ulcer, namely, microbial density, microorganisms, microbial synergy, the host immune response, and infected tissue quality. MethodologyThis study used a cross-sectional design. We assessed 38 Subjects with DFUs, 23 neuroischaimic, and 15 neuropathic, for microbiota colonizing the DFU utilizing traditional cultures and 16S gene sequencing methods. All the relevant clinical factors were collected. Wound swabs were collected for both traditional microbiological analysis, direct swab (DSM), and cultured (CM) microbiome analysis. DNA isolation, and 16SrRNA hypervariable regions were amplified. Bioinformatics analysis was performed using IonReporter Software, statistical analysis, and diversity indices were computed with vegan R-package. ResultsThe traditional microbiological method was able to detect a maximum of one or two pathogens, and, in some cases, no pathogen was detected. The total number of the observed species was 176. The number of identified species was higher in the cultured microbiome (155) than the direct swab microbiome (136). Diversity analysis indicated that biological diversity is higher in the cultured microbiome compared with the DSM. The Shannon H index was 2.75 for the cultured microbiome and 2.63 for DSM. We observed some differences in the major bacterial taxa amongst neuroischaimic and neuropathic DFU microbiomes. ConclusionsCultured microbiome is superior to both the traditional method and direct swab microbiome. The Neuroischaimic group showed higher values for the tested diversity indices than the Neuroischaimic group. Neither Cluster Analysis nor Principal Component Analysis showed apparent clustering amongst the two types of ulcers.

microbiology↗

bioRxiv2018

Relative Reduction of the Biological and phylogenetic diversity of oral microbiome in diabetic and pre-diabetic subjects

BackgroundThere is a suggested reciprocal relationship between oral health and systemic disease such as type 2 diabetes. In this relationship, a systemic disease predisposing to oral infection, and when that infection is present, the oral infection aggravates the progression of the systemic disease. Several studies suggested that some oral microbiome constituents are linked to both diabetes, metabolic syndrome and obesity. This study aims to compare the microbial diversity and population structure of oral microbiome among normoglycemic, impaired glucose tolerance (IGT) and diabetic subjects.\n\nMethodologyThis study followed a case-control design (15 T2D patients, 10 IGTs and, 19 controls). Patient records were screened as per the inclusion and exclusion criteria. Assessment of periodontitis and oral health was performed to all subjects. DNA Isolation purification and quantification from collected Saliva samples were performed. 16SrRNA hypervariable regions were amplified and sequenced. Generated sequences were subjected to bioinformatics analysis. Statistical analysis and diversity indices were computed with the statistical software R, the vegan R-package, and Past318 software.\n\nResultsA total observed number of 551 OTUs. A clear reduction of the number of species (OTUs) was observed in both IGT (412) and diabetic group (372) compared with the normoglycemic group (502). This was associated with a similar pattern of biological diversity among the three groups. Phylogenetic diversity (PD-SBL) value in the normoglycemic group was higher than the diabetic group. The diabetic group had the highest evenness value and the highest microbiome bacterial pathogenic content.\n\nConclusionWe observed a clear reduction in the biological and phylogenetic diversity in the diabetic and pre-diabetic oral microbiome in comparison with the normoglycemic oral microbiome. However, this reduction was associated with an increase in the pathogenic content of the hyperglycemic microbiomes.

microbiology↗

bioRxiv2016

Genome sequencing and analysis of the first spontaneous Nanosilver resistant bacterium Proteus mirabilis strain SCDR1

BackgroundP. mirabilis is a common uropathogenic bacterium that can cause major complications in patients with long-standing indwelling catheters or patients with urinary tract anomalies. In addition, P. mirabilis is a common cause of chronic osteomyelitis in Diabetic foot ulcer (DFU) patients. We isolated P. mirabilis SCDR1 from a Diabetic ulcer patient. We examined P. mirabilis SCDR1 levels of resistance against Nano-silver colloids, the commercial Nano-silver and silver containing bandages and commonly used antibiotics. We utilized next generation sequencing techniques (NGS), bioinformatics, phylogenetic analysis and pathogenomics in the characterization of the infectious pathogen.\n\nResultsP. mirabilis SCDR1 is a multi-drug resistant isolate that also showed high levels of resistance against Nano-silver colloids, Nano-silver chitosan composite and the commercially available Nano-silver and silver bandages. The P. mirabilis -SCDR1 genome size is 3,815,621 bp. with G+C content of 38.44%. P. mirabilis-SCDR1 genome contains a total of 3,533 genes, 3,414 coding DNA sequence genes, 11, 10, 18 rRNAs (5S, 16S, and 23S), and 76 tRNAs. Our isolate contains all the required pathogenicity and virulence factors to establish a successful infection. P. mirabilis SCDR1 isolate is a potential virulent pathogen that despite its original isolation site, wound, it can establish kidney infection and its associated complications. P. mirabilis SCDR1 contains several mechanisms for antibiotics and metals resistance including, biofilm formation, swarming mobility, efflux systems, and enzymatic detoxification.\n\nConclusionP. mirabilis SCDR1 is the first reported spontaneous Nanosilver resistant bacterial strain. P. mirabilis SCDR1 possesses several mechanisms that may lead to the observed Nanosilver resistance.

microbiology↗