Study Info
INDA Accessions: INRP000245
INSDC Accessions: PRJEB83778, ERP167352
- Title: Ecoli-WGS
- Data Type : Whole Genome Sequencing
- Descriptive Title: Whole genome analysis of five multi drug resistance Escherichia coli clinical isolates reveals presence of multi AMR and virulence genes
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Organism:
Scientific Name(Taxon Id): Escherichia coli (562) Common Name: E. coli
Other Info
- Abstract: Urinary tract infections are a significant health concern, particularly among women, contributing substantially to both community acquired and hospital acquired infections. The increasing prevalence of multidrug resistant Escherichia coli strains especially uropathogenic strains poses a challenge to UTI treatment and management. This study investigates the prevalence of biofilm formation and antibiotic resistance patterns among UPEC isolates from a tertiary care hospital in Odisha eastern India. A prospective cross sectional study was conducted involving non catheterized and catheterized patients with UTIs excluding those who had taken antibiotics in the past week and individuals under 18 years of age. Urine samples were cultured, and UPEC isolates were subjected to biofilm detection using the Tissue Culture Plate and Congo Red Agar methods. Antibiotic susceptibility testing was performed using the Kirby Bauer disk diffusion method following CLSI 2023 guidelines. Whole genome sequencing was carried out on the Illumina NovaSeq 6000 platform for five E. coli isolates showing resistance to antibiotics. The genomic data underwent quality control, genome assembly and annotation using FastQC Fastp SPAdes and Prokka tools respectively. Further analyses included multilocus sequence typing serotype determination and the identification of virulence and antibiotic resistance genes through the Centre for Genomic Epidemiologys online tools. Antimicrobial resistance genes were identified using the Comprehensive Antibiotic Resistance Database and ResFinder while virulence genes were screened with VirulenceFinder. Human pathogenicity was evaluated using PathogenFinder. The findings revealed significant biofilm formation capabilities among the UPEC isolates contributing to enhanced antibiotic resistance. WGS data provided insights into genetic factors underlying resistance including specific mutations and mobile genetic elements. This study underscores the importance of early susceptibility testing and targeted antibiotic therapies in managing MDR infections and highlights the genetic mechanisms driving UPEC pathogenicity in the Odisha region with implications for future surveillance and treatment strategies.
- Linked publications:
- Center Name: Institute of Life Sciences, Bhubaneswar
- Number of Base(Total) Mbp: 285,569,109
- Size in bytes(Total): 1,107,357,401
- Number of sample:
- Number of Runs:
- Number of Sequences:
- Number of Assembly:
- Number of Variant files:
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