Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care

Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei

(2020) Leah W. Roberts et al.   Nature Communications

Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive

(2020) Kelly L. Wyres et al.   Microbial Genomics

Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines

(2020) Silvia Argimón et al.   Nature Communications

Hospitalization costs for patients colonized with carbapenemase-producing Enterobacterales during an Australian outbreak

(2020) A.J. Rodriguez-Acevedo et al.   JOURNAL OF HOSPITAL INFECTION

Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene–based approaches

(2018) A.C. Schürch et al.   CLINICAL MICROBIOLOGY AND INFECTION

Analysis of global prevalence of antibiotic resistance in Acinetobacter baumannii infections disclosed a faster increase in OECD countries

(2018) Ruiqiang Xie et al.   Emerging Microbes & Infections

Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak

(2018) Jason C. Kwong et al.   PeerJ

Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens

(2018) Sharon J. Peacock et al.   MICROBIOLOGY-SGM

Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions

(2018) James Stimson et al.   MOLECULAR BIOLOGY AND EVOLUTION

High incidence of pandrug-resistant Acinetobacter baumannii isolates collected from patients with ventilator-associated pneumonia in Greece, Italy and Spain as part of the MagicBullet clinical trial

(2017) J Nowak et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Cost-effectiveness of Ward Closure to Control Outbreaks of Norovirus Infection in United Kingdom National Health Service Hospitals

(2016) Zia Sadique et al.   JOURNAL OF INFECTIOUS DISEASES

The Cost of Responding to anAcinetobacterOutbreak in Critically Ill Surgical Patients

(2016) Yushan Jiang et al.   Surgical Infections

Bacterial diguanylate cyclases: Structure, function and mechanism in exopolysaccharide biofilm development

(2015) Chris G. Whiteley et al.   BIOTECHNOLOGY ADVANCES

Fatal Outbreak of an Emerging Clone of Extensively Drug-ResistantAcinetobacter baumanniiWith Enhanced Virulence

(2015) Crystal L. Jones et al.   CLINICAL INFECTIOUS DISEASES

Whole-Genome Sequencing in Outbreak Analysis

(2015) Carol A. Gilchrist et al.   CLINICAL MICROBIOLOGY REVIEWS

Molecular Epidemiology and Mechanisms of Carbapenem Resistance ofAcinetobacterspp. in Asia and Oceania

(2015) Witchuda Kamolvit et al.   Microbial Drug Resistance

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

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

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

(2014) Michael Inouye et al.   Genome Medicine

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME 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

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

OmpA Is the Principal Nonspecific Slow Porin of Acinetobacter baumannii

(2012) E. Sugawara et al.   JOURNAL OF BACTERIOLOGY

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

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

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Control of an Outbreak of Carbapenem-Resistant Acinetobacter baumannii in Australia after Introduction of Environmental Cleaning with a Commercial Oxidizing Disinfectant

(2010) Michelle Doidge et al.   INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY

The Population Structure of Acinetobacter baumannii: Expanding Multiresistant Clones from an Ancestral Susceptible Genetic Pool

(2010) Laure Diancourt et al.   PLoS One

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Nosocomial Outbreak of Infection With Pan–Drug-Resistant Acinetobacter baumannii in a Tertiary Care University Hospital

(2009) Raquel Valencia et al.   INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY

Acinetobacter baumannii: Emergence of a Successful Pathogen

(2008) A. Y. Peleg et al.   CLINICAL MICROBIOLOGY REVIEWS