MEGARes: an antimicrobial resistance database for high throughput sequencing

Abstract

Antimicrobial resistance has become an imminent concern for public health. As methods for detection and characterization of antimicrobial resistance move from targeted culture and polymerase chain reaction to high throughput metagenomics, appropriate resources for the analysis of large-scale data are required. Currently, antimicrobial resistance databases are tailored to smaller-scale, functional profiling of genes using highly descriptive annotations. Such characteristics do not facilitate the analysis of large-scale, ecological sequence datasets such as those produced with the use of metagenomics for surveillance. In order to overcome these limitations, we present MEGARes (https://megares.meglab.org), a hand-curated antimicrobial resistance database and annotation structure that provides a foundation for the development of high throughput acyclical classifiers and hierarchical statistical analysis of big data. MEGARes can be browsed as a stand-alone resource through the website or can be easily integrated into sequence analysis pipelines through download. Also via the website, we provide documentation for AmrPlusPlus, a user-friendly Galaxy pipeline for the analysis of high throughput sequencing data that is pre-packaged for use with the MEGARes database.

Figure 1.

(A) This annotation graph contains no cycles (is a tree), as nodes 1 and 2 do not share children and are therefore independent. (B) In contrast, node 3 and node 4 share node 5 as a child, which creates a cycle in the annotation graph and statistical dependencies between nodes 3 and 4. (C) The MEGARes annotation structure for two gene groups (rpoB and iri) that confer resistance to the rifampin class of antimicrobials. This annotation scheme contains no cycles. (D) The CARD annotation structure for the same two gene groups (rpoB and iri).

Figure 2.

A pipeline workflow diagram describing the steps involved in the AmrPlusPlus pipeline. The tan box denotes input files, blue boxes represent steps in the pipeline, green boxes denote outputs and arrows show the directionality of the workflow.