Environmental

Oral

397426 - Comparative Study of Sequence Aligners for Detecting Antibiotic Resistance in Bacterial Metagenomes

Tuesday, June 5
8:30 AM - 10:00 AM
Location: Lakeshore B
Co-Authors: Irene Xagoraraki, 1449 Engineering Research Ct., East Lansing, MI 48824 – Michigan State University

Antibiotic resistance genes (ARGs) are pollutants known to persist in surface waters, soils, and wastewater treatment plants among other environments. Thus, methods for detecting these genes have become increasingly relevant. Next generation sequencing has brought about a host of sequence alignment tools that provide a comprehensive look into antimicrobial resistance in environmental samples. We aim to compare the performance of sequence aligners Bowtie2, BWA-MEM, BLASTN, and BLASTX when aligning bacterial metagenomes against the Comprehensive Antibiotic Resistance Database (CARD). Simulated reads with and without sequencing errors were used to evaluate the performance of each aligner under four performance criteria: correctly mapped, false positives, multi-reads, and partials. BLASTN mapped with greater accuracy among the four alignment tools followed by Bowtie2. In general, the introduction of sequencing errors had little effect on alignment results when aligning against the CARD. Given each performance criteria, BLASTN was found to be the optimal alignment approach and was therefore used to assess resistance genes in sewage samples collected after the disinfection process of two wastewater treatment plants. Beta-lactam and aminoglycoside were found to be the most abundant classes of ARGs in each sample. Our study provides sequence alignment results of synthetic, and authentic bacterial metagenomes mapped against an ARG database using multiple alignment tools, and the best practice for detecting ARGs in environmental samples.

Specific findings to present:
Sequence alignment results of simulated reads with and without sequencing errors for each alignment tool
Detected antibiotic resistance genes found in each sample.

Importance:
Findings may assist in determining what tool to use in ARG metagenomic studies

Camille McCall, PhD

PhD Student
Michigan State University

Presentation(s):

Send Email for Camille McCall


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397426 - Comparative Study of Sequence Aligners for Detecting Antibiotic Resistance in Bacterial Metagenomes



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