Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful?

Frontiers in Microbiology
Ilya B SlizovskiyNoelle R Noyes

Abstract

Antimicrobial resistance (AMR) poses a global human and animal health threat, and predicting AMR persistence and transmission remains an intractable challenge. Shotgun metagenomic sequencing can help overcome this by enabling characterization of AMR genes within all bacterial taxa, most of which are uncultivatable in laboratory settings. Shotgun sequencing, therefore, provides a more comprehensive glance at AMR "potential" within samples, i.e., the "resistome." However, the risk inherent within a given resistome is predicated on the genomic context of various AMR genes, including their presence within mobile genetic elements (MGEs). Therefore, resistome risk stratification can be advanced if AMR profiles are considered in light of the flanking mobilizable genomic milieu (e.g., plasmids, integrative conjugative elements (ICEs), phages, and other MGEs). Because such mediators of horizontal gene transfer (HGT) are involved in uptake by pathogens, investigators are increasingly interested in characterizing that resistome fraction in genomic proximity to HGT mediators, i.e., the "mobilome"; we term this "colocalization." We explored the utility of common colocalization approaches using alignment- and assembly-based techniques, on cl...Continue Reading

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Datasets Mentioned

BETA
PRJEB20800
PRJNA309291
ERP022986
PRJNA309391

Methods Mentioned

BETA
Illumina sequencing
ICE

Software Mentioned

+ BLAST
MetaSPAdes
PlasmidFinder
MEM
- - Aligner ( BWA )
UD
InteractiVenn
UA Assembly
Assembly
PATRIC

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