Analyzing Pathogenic Clinical Isolates Genomes to Identify Horizontal Gene Transfer of Antibiotic-Resistance Genes

Project Information

big-data, bioinformatics, hpc-storage
Project Status: Complete
Project Region: Northeast
Submitted By: Larry Whitsel
Project Email: larry.feinstein@maine.edu
Project Institution: University of Maine at Presque Isle
Anchor Institution: NE-University of Maine
Project Address: 181 Main St.
Presque Isle, Maine. 04769

Mentors: Larry Whitsel
Students: Kendra Batchelder

Project Description

Antibiotic-resistance bacteria is a growing concern and challenge for public health. Pathogenic bacteria have developed resistance mechanisms that allow them to survive and grow when antibiotics are present. Specific genes have been identified that are associated with bacteria gaining resistance to antibiotics and they are able to share this harmful genetic information with other species and genera through mobile genetic elements (MGEs). This contributes to the spread of antibiotic resistance. DNA from 28 clinical isolates has been extracted from Enterobacter, Escherichia, Pseudomonas, Staphylococcus, Klebsiella, and Stenotrophomonas species to identify antibiotic-resistance genes (ARGs) and their resistance mechanisms. After sequencing, the resulting raw-read files and the SPAdes (3.10.0) assembled contig files need further analysis to identify the MGEs present in the bacterial genomes and ARGs that are currently at risk of being transferred to other bacteria.

Project Information

big-data, bioinformatics, hpc-storage
Project Status: Complete
Project Region: Northeast
Submitted By: Larry Whitsel
Project Email: larry.feinstein@maine.edu
Project Institution: University of Maine at Presque Isle
Anchor Institution: NE-University of Maine
Project Address: 181 Main St.
Presque Isle, Maine. 04769

Mentors: Larry Whitsel
Students: Kendra Batchelder

Project Description

Antibiotic-resistance bacteria is a growing concern and challenge for public health. Pathogenic bacteria have developed resistance mechanisms that allow them to survive and grow when antibiotics are present. Specific genes have been identified that are associated with bacteria gaining resistance to antibiotics and they are able to share this harmful genetic information with other species and genera through mobile genetic elements (MGEs). This contributes to the spread of antibiotic resistance. DNA from 28 clinical isolates has been extracted from Enterobacter, Escherichia, Pseudomonas, Staphylococcus, Klebsiella, and Stenotrophomonas species to identify antibiotic-resistance genes (ARGs) and their resistance mechanisms. After sequencing, the resulting raw-read files and the SPAdes (3.10.0) assembled contig files need further analysis to identify the MGEs present in the bacterial genomes and ARGs that are currently at risk of being transferred to other bacteria.