Outbreak Investigation Using High-Throughput Genome Sequencing within a Diagnostic Microbiology Laboratory

Next-generation sequencing and its applications in molecular diagnostics

(2018) Zhenqiang Su et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

(2012) M. V. Larsen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

(2012) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy

(2011) Michael Hornsey et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Efficient Direct Extended-Spectrum  -Lactamase Detection by Multiplex Real-Time PCR: Accurate Assignment of Phenotype by Use of a Limited Set of Genetic Markers

(2011) J. Ellem et al.   JOURNAL OF CLINICAL MICROBIOLOGY

AGeS: A Software System for Microbial Genome Sequence Annotation

(2011) Kamal Kumar et al.   PLoS One

Genomic anatomy of Escherichia coli O157:H7 outbreaks

(2011) M. Eppinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput sequencing and clinical microbiology: progress, opportunities and challenges

(2010) Mark J Pallen et al.   CURRENT OPINION IN MICROBIOLOGY

Molecular epidemiology of Escherichia coli producing CTX-M β-lactamases: the worldwide emergence of clone ST131 O25:H4

(2010) Gisele Peirano et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Development of a set of multiplex PCR assays for the detection of genes encoding important β-lactamases in Enterobacteriaceae

(2010) Caroline Dallenne et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain

(2010) B. A. Rogers et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Characteristics of aac(6')-Ib-cr Gene in Extended-Spectrum β-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Chungnam Area

(2010) So Youn Shin et al.   Korean Journal of Laboratory Medicine

Derivation of Escherichia coli O157:H7 from Its O55:H7 Precursor

(2010) Zhemin Zhou et al.   PLoS One

A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the "-omics" era

(2009) Tin Tan et al.   BMC GENOMICS

Metagenomic Pyrosequencing and Microbial Identification

(2009) J. F. Petrosino et al.   CLINICAL CHEMISTRY

Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance

(2009) J. Feng et al.   GENOME RESEARCH

Analysis of the Genome of the Escherichia coli O157:H7 2006 Spinach-Associated Outbreak Isolate Indicates Candidate Genes That May Enhance Virulence

(2009) B. R. Kulasekara et al.   INFECTION AND IMMUNITY

Genomic Sequencing Reveals Regulatory Mutations and Recombinational Events in the Widely Used MC4100 Lineage of Escherichia coli K-12

(2009) T. Ferenci et al.   JOURNAL OF BACTERIOLOGY

Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3)

(2009) Haeyoung Jeong et al.   JOURNAL OF MOLECULAR BIOLOGY

Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli

(2009) Y. Ogura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

Prevalence of Plasmid-Mediated Quinolone Resistance Determinants over a 9-Year Period

(2008) H. B. Kim et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

blaIMP-4 in Different Genetic Contexts in Enterobacteriaceae Isolates from Australia

(2008) B. A. Espedido et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Complete Genome Sequence and Comparative Analysis of the Wild-type Commensal Escherichia coli Strain SE11 Isolated from a Healthy Adult

(2008) K. Oshima et al.   DNA RESEARCH

Plasmid-mediated quinolone resistance determinants among enterobacterial isolates from outpatients in Brazil

(2008) L. A. R. Minarini et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Insights into the Environmental Resistance Gene Pool from the Genome Sequence of the Multidrug-Resistant Environmental Isolate Escherichia coli SMS-3-5

(2008) W. F. Fricke et al.   JOURNAL OF BACTERIOLOGY

The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse

(2008) T. Durfee et al.   JOURNAL OF BACTERIOLOGY

Complete Genome Sequence and Comparative Genome Analysis of Enteropathogenic Escherichia coli O127:H6 Strain E2348/69

(2008) A. Iguchi et al.   JOURNAL OF BACTERIOLOGY

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY