CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens

Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa

(2021) Lina M León et al.   NUCLEIC ACIDS RESEARCH

Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes

(2021) You Che et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Type III-A CRISPR immunity promotes mutagenesis of staphylococci

(2021) Charlie Y. Mo et al.   NATURE

Current challenges and future opportunities of phage therapy

(2020) Diana P Pires et al.   FEMS MICROBIOLOGY REVIEWS

Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance

(2020) Corneliu Ovidiu Vrancianu et al.   Frontiers in Microbiology

The Role of Integrative and Conjugative Elements in Antibiotic Resistance Evolution

(2020) João Botelho et al.   TRENDS IN MICROBIOLOGY

Machine-learning approach expands the repertoire of anti-CRISPR protein families

(2020) Ayal B. Gussow et al.   Nature Communications

CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa

(2020) Rachel M. Wheatley et al.   ISME Journal

CRISPRCasTyper: Automated Identification, Annotation, and Classification of CRISPR-Cas Loci

(2020) Jakob Russel et al.   CRISPR Journal

Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

(2019) Saadlee Shehreen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A phylogenetic test of the role of CRISPR-Cas in limiting plasmid acquisition and prophage integration in bacteria

(2019) Derek O'Meara et al.   PLASMID

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

CRISPR-Cas influences the acquisition of antibiotic resistance in Klebsiella pneumoniae

(2019) Natalie A. Mackow et al.   PLoS One

Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation

(2019) Eugenio L. Mangas et al.   Microbial Genomics

Type IV CRISPR–Cas systems are highly diverse and involved in competition between plasmids

(2019) Rafael Pinilla-Redondo et al.   NUCLEIC ACIDS RESEARCH

CRISPR-Cas antimicrobials: Challenges and future prospects

(2018) Elizabeth Pursey et al.   PLoS Pathogens

Characterization of CRISPR-Cas Systems in Clinical Klebsiella pneumoniae Isolates Uncovers Its Potential Association With Antibiotic Susceptibility

(2018) Hsin-Yu Li et al.   Frontiers in Microbiology

Discovery of widespread Type I and Type V CRISPR-Cas inhibitors

(2018) Nicole D. Marino et al.   SCIENCE

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

(2018) Meng Liu et al.   NUCLEIC ACIDS RESEARCH

Presence of Type I-F CRISPR/Cas systems is associated with antimicrobial susceptibility in Escherichia coli

(2017) Seyid Aydin et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Why Might Bacterial Pathogens Have Small Genomes?

(2017) Lucy A. Weinert et al.   TRENDS IN ECOLOGY & EVOLUTION

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

(2016) François Enault et al.   ISME Journal

Access to effective antimicrobials: a worldwide challenge

(2016) Ramanan Laxminarayan et al.   LANCET

CRISPR-Cas Systems Optimize Their Immune Response by Specifying the Site of Spacer Integration

(2016) Jon McGinn et al.   MOLECULAR CELL

Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer

(2016) Christian J. H. von Wintersdorff et al.   Frontiers in Microbiology

No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales

(2015) Uri Gophna et al.   ISME Journal

Phylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa

(2015) Alex van Belkum et al.   mBio

MCMC Methods for Multi-Response Generalized Linear Mixed Models: TheMCMCglmmRPackage

(2015) Jarrod D. Hadfield   Journal of Statistical Software

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens

(2014) Asma Hatoum-Aslan et al.   CURRENT OPINION IN MICROBIOLOGY

Whole-Genome Sequence Analysis of the Naturally Competent Acinetobacter baumannii Clinical Isolate A118

(2014) German M. Traglia et al.   Genome Biology and Evolution

Dealing with the Evolutionary Downside of CRISPR Immunity: Bacteria and Beneficial Plasmids

(2013) Wenyan Jiang et al.   PLoS Genetics

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

The Class A β-Lactamase FTU-1 Is Native to Francisella tularensis

(2011) Nuno T. Antunes et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation

(2011) Julien Guglielmini et al.   PLoS Genetics

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Correlations Between Bacterial Ecology and Mobile DNA

(2010) Irene L. G. Newton et al.   CURRENT MICROBIOLOGY

Multidrug-Resistant Enterococci Lack CRISPR-cas

(2010) K. L. Palmer et al.   mBio

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Generalized linear mixed models: a practical guide for ecology and evolution

(2009) Benjamin M. Bolker et al.   TRENDS IN ECOLOGY & EVOLUTION