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Antibiotic resistance is a major public health concern that arises when bacteria evolve mechanisms to withstand the effects of antibiotic treatments. This resistance can be intrinsic, acquired through genetic mutations, or transferred between bacteria via horizontal gene transfer. The development of antibiotic resistance poses significant challenges in treating bacterial infections and necessitates ongoing research to develop new therapeutic strategies.Intrinsic resistance occurs when bacterial...
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Isolation and Identification of Waterborne Antibiotic-Resistant Bacteria and Molecular Characterization of their Antibiotic Resistance Genes
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Functional Metagenomics to Study Antibiotic Resistance.

Bejan Mahmud1, Manish Boolchandani1, Sanket Patel1,2

  • 1The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.

Methods in Molecular Biology (Clifton, N.J.)
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Summary

Researchers developed a method to find new antibiotic resistance genes (ARGs) using fecal DNA. This involved creating and screening metagenomic libraries, followed by DNA sequencing and computational analysis.

Keywords:
Antibiotic resistance genesFunctional metagenomicsFunctional selectionsHigh-throughput assemblyMassively parallel DNA sequencingPARFuMSProfile HMM-based annotationResfamsResistome

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Metagenomic expression libraries offer a powerful approach for discovering novel genes with specific functions.
  • Identifying antibiotic resistance genes (ARGs) is crucial for combating antimicrobial resistance.

Purpose of the Study:

  • To describe a comprehensive workflow for the construction and screening of metagenomic libraries derived from fecal DNA.
  • To identify novel antibiotic resistance genes (ARGs) using functional selection and high-throughput sequencing.

Main Methods:

  • Metagenomic library construction from fecal DNA.
  • Screening of libraries for functional identification of antibiotic resistance genes (ARGs).
  • Massively parallel DNA sequencing and computational analysis for assembly and annotation.

Main Results:

  • Successful construction and screening of metagenomic libraries from fecal samples.
  • Identification of DNA fragments conferring antibiotic resistance.
  • Establishment of a computational pipeline for processing and analyzing sequencing data.

Conclusions:

  • The described methodology enables efficient discovery of novel ARGs from complex metagenomic samples.
  • This approach has broad applicability for identifying genes with various desired functions from environmental DNA.