PorinPredict: In Silico Identification of OprD Loss from WGS Data for Improved Genotype-Phenotype Predictions of P. aeruginosa Carbapenem Resistance

Genomic Surveillance of Clinical Pseudomonas aeruginosa Isolates Reveals an Additive Effect of Carbapenemase Production on Carbapenem Resistance

(2022) Luke Diorio-Toth et al.   Microbiology Spectrum

Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae

(2022) Sophia David et al.   PLoS Pathogens

Whole-Genome Sequencing Reveals Diversity of Carbapenem-Resistant Pseudomonas aeruginosa Collected through CDC’s Emerging Infections Program, United States, 2016–2018

(2022) Richard A. Stanton et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

(2021) Michael Feldgarden et al.   Scientific Reports

Emergence of Ceftazidime- and Avibactam-Resistant Klebsiella pneumoniae Carbapenemase-Producing Pseudomonas aeruginosa in China

(2021) Yiwei Zhu et al.   mSystems

Genotypes, carbapenemase carriage, integron diversity and oprD alterations among carbapenem-resistant Pseudomonas aeruginosa from Russia

(2020) Yuliya Bocharova et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Pseudomonas aeruginosa epidemic high-risk clones and their association with horizontally-acquired β-lactamases: 2020 update

(2020) Ester del Barrio-Tofiño et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Spanish nationwide survey on Pseudomonas aeruginosa antimicrobial resistance mechanisms and epidemiology

(2019) Ester del Barrio-Tofiño et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages

(2019) Egon A Ozer et al.   Genome Biology and Evolution

Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread

(2019) Sophia David et al.   Nature Microbiology

Characterization of carbapenem-resistant and XDR Pseudomonas aeruginosa in Canada: results of the CANWARD 2007–16 study

(2019) Melissa G McCracken et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Using Genomics to Track Global Antimicrobial Resistance

(2019) Rene S. Hendriksen et al.   Frontiers in Public Health

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

(2019) James J Davis et al.   NUCLEIC ACIDS RESEARCH

Longitudinal analysis of ESBL and carbapenemase carriage among Enterobacterales and Pseudomonas aeruginosa isolates collected in Europe as part of the International Network for Optimal Resistance Monitoring (INFORM) global surveillance programme, 2013–17

(2019) Krystyna M Kazmierczak et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis

(2018) Evelina Tacconelli et al.   LANCET INFECTIOUS DISEASES

A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events

(2018) Magali Jaillard et al.   PLoS Genetics

Towards a genomics-informed, real-time, global pathogen surveillance system

(2017) Jennifer L. Gardy et al.   NATURE REVIEWS GENETICS

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Deciphering the resistome of the widespreadP. aeruginosaST175 international high-risk clone through whole genome sequencing

(2016) Gabriel Cabot et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Overexpression of MexAB-OprM efflux pump in carbapenem-resistant Pseudomonas aeruginosa

(2016) Ya-ping Pan et al.   ARCHIVES OF MICROBIOLOGY

Intraclonal Genome Stability of the Metallo-β-lactamase SPM-1-producing Pseudomonas aeruginosa ST277, an Endemic Clone Disseminated in Brazilian Hospitals

(2016) Ana P. B. Nascimento et al.   Frontiers in Microbiology

Better prediction of functional effects for sequence variants

(2015) Maximilian Hecht et al.   BMC GENOMICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Carbapenem resistance in cystic fibrosis strains of Pseudomonas aeruginosa as a result of amino acid substitutions in porin OprD

(2015) Charlotte Richardot et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain

(2012) K. A. Jolley et al.   MICROBIOLOGY-SGM

Substrate Specificity within a Family of Outer Membrane Carboxylate Channels

(2012) Elif Eren et al.   PLOS BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Classification of OprD sequence and correlation with antimicrobial activity of carbapenem agents inPseudomonas aeruginosaclinical isolates collected in Japan

(2009) Yumiko Sanbongi et al.   MICROBIOLOGY AND IMMUNOLOGY