Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data

Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli

(2020) Derek R MacFadden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform

(2020) Christian Munck et al.   Nature Communications

VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning

(2020) Jiwoong Kim et al.   PLoS Computational Biology

Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance

(2020) Kihyun Lee et al.   Microbiome

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing

(2020) Karel Břinda et al.   Nature Microbiology

The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography

(2020) Tayte P. Campbell et al.   ISME Journal

Prediction of Antimicrobial Resistance in Gram-Negative Bacteria From Whole-Genome Sequencing Data

(2020) Pieter-Jan Van Camp et al.   Frontiers in Microbiology

Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities

(2020) Maria-Elisabeth Böhm et al.   Microbiome

ResFinder 4.0 for predictions of phenotypes from genotypes

(2020) Valeria Bortolaia et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

metaFlye: scalable long-read metagenome assembly using repeat graphs

(2020) Mikhail Kolmogorov et al.   NATURE METHODS

Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C

(2020) Alyssa G. Kent et al.   Nature Communications

The Most Frequently Used Sequencing Technologies and Assembly Methods in Different Time Segments of the Bacterial Surveillance and RefSeq Genome Databases

(2020) Bo Segerman   Frontiers in Cellular and Infection Microbiology

Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes

(2019) Ankita Kothari et al.   mBio

Fast and flexible bacterial genomic epidemiology with PopPUNK

(2019) John A. Lees et al.   GENOME RESEARCH

High diversity and rapid spatial turnover of integron gene cassettes in soil

(2019) Timothy M. Ghaly et al.   ENVIRONMENTAL MICROBIOLOGY

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Identification and reconstruction of novel antibiotic resistance genes from metagenomes

(2019) Fanny Berglund et al.   Microbiome

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

(2019) Martin Steinegger et al.   NATURE METHODS

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy

(2019) Jan P. Meier-Kolthoff et al.   Nature Communications

Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges

(2019) Keira A. Cohen et al.   Genome Medicine

Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates

(2019) Michael Feldgarden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

(2019) Sion C Bayliss et al.   GigaScience

Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome

(2019) Andrew J. Gasparrini et al.   Nature Microbiology

Redistribution of intracellular and extracellular free & adsorbed antibiotic resistance genes through a wastewater treatment plant by an enhanced extracellular DNA extraction method with magnetic beads

(2019) Qing-Bin Yuan et al.   ENVIRONMENT INTERNATIONAL

Database resources of the National Center for Biotechnology Information

(2019) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

(2019) Zhemin Zhou et al.   GENOME RESEARCH

ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes

(2018) Xiaole Yin et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes

(2018) Ryan R. Wick et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The global distribution and spread of the mobilized colistin resistance gene mcr-1

(2018) Ruobing Wang et al.   Nature Communications

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data

(2018) Gustavo Arango-Argoty et al.   Microbiome

Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection

(2018) An Ni Zhang et al.   Microbiome

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Bayesian inference of ancestral dates on bacterial phylogenetic trees

(2018) Xavier Didelot et al.   NUCLEIC ACIDS RESEARCH

Predicting bacterial resistance from whole-genome sequences using k-mers and stability selection

(2018) Pierre Mahé et al.   BMC BIOINFORMATICS

ICEberg 2.0: an updated database of bacterial integrative and conjugative elements

(2018) Meng Liu et al.   NUCLEIC ACIDS RESEARCH

Prediction of the intestinal resistome by a three-dimensional structure-based method

(2018) Etienne Ruppé et al.   Nature Microbiology

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens

(2017) Ea Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

The chromosomal organization of horizontal gene transfer in bacteria

(2017) Pedro H. Oliveira et al.   Nature Communications

FARME DB: a functional antibiotic resistance element database

(2017) James C. Wallace et al.   Database-The Journal of Biological Databases and Curation

Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance GeneblaKPC

(2016) Anna E. Sheppard et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Mobile genes in the human microbiome are structured from global to individual scales

(2016) I. L. Brito et al.   NATURE

The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies

(2016) Catherine E. Yoshida et al.   PLoS One

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

(2015) Sarah J Spencer et al.   ISME Journal

Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data

(2015) Katrine G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

(2015) Phelim Bradley et al.   Nature Communications

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Detection of recombination events in bacterial genomes from large population samples

(2011) Pekka Marttinen et al.   NUCLEIC ACIDS RESEARCH

Mugsy: fast multiple alignment of closely related whole genomes

(2010) Samuel V. Angiuoli et al.   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One