Rapid Gene Turnover as a Significant Source of Genetic Variation in a Recently Seeded Population of a Healthcare-Associated Pathogen

Prokaryote genome fluidity is dependent on effective population size

(2017) Nadia Andrea Andreani et al.   ISME Journal

Antibiotic Resistance of Gram-Negative Bacilli Isolated from Pediatric Patients with Nosocomial Bloodstream Infections in a Mexican Tertiary Care Hospital

(2017) Miguel Ángel Ares et al.   CHEMOTHERAPY

A Multicenter Study in Mexico Finds Acinetobacter baumannii Clinical Isolates Belonging to Clonal Complexes 636B(113B) and 92BHarboring OXA-72, OXA-239, and OXA-469

(2016) Ana M. Gonzalez-Villoria et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Exploring non-hospital-related settings in Angola reveals new Acinetobacter reservoirs for blaOXA-23 and blaOXA-58

(2016) Liliana Silva et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Characterization of NDM-1- and OXA-23-producing Acinetobacter baumannii isolates from inanimate surfaces in a hospital environment in Algeria

(2016) K. Zenati et al.   JOURNAL OF HOSPITAL INFECTION

Intrahost Evolution of Methicillin-ResistantStaphylococcus aureusUSA300 Among Individuals With Reoccurring Skin and Soft-Tissue Infections

(2016) Taj Azarian et al.   JOURNAL OF INFECTIOUS DISEASES

Outbreak Caused byblaOXA-72-ProducingAcinetobacter baumanniiST417 Detected in Clinical and Environmental Isolates

(2016) Elsa Tamayo-Legorreta et al.   Microbial Drug Resistance

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe

(2016) David M. Aanensen et al.   mBio

Evolution of a Sigma Factor: An All-In-One of Gene Duplication, Horizontal Gene Transfer, Purifying Selection, and Promoter Differentiation

(2016) Gamaliel López-Leal et al.   Frontiers in Microbiology

Trans-Atlantic exchanges have shaped the population structure of the Lyme disease agent Borrelia burgdorferi sensu stricto

(2016) S. Castillo-Ramírez et al.   Scientific Reports

High prevalence of oxacillinases in clinical multidrug-resistant Acinetobacter baumannii isolates from the Tshwane region, South Africa – an update

(2015) Michelle Lowings et al.   BMC INFECTIOUS DISEASES

ChlamydiaceaeGenomics Reveals Interspecies Admixture and the Recent Evolution ofChlamydia abortusInfecting Lower Mammalian Species and Humans

(2015) Sandeep J. Joseph et al.   Genome Biology and Evolution

Genetic characterisation of drug resistance and clonal dynamics of Acinetobacter baumannii in a hospital setting in Mexico

(2015) Paola Bocanegra-Ibarias et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

The impact of hospital-acquired infections with multidrug-resistant bacteria in an oncology intensive care unit

(2015) P. Cornejo-Juárez et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Prevalence of hypermutators among clinicalAcinetobacter baumanniiisolates

(2015) Patricia Komp Lindgren et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung

(2015) Julio Diaz Caballero et al.   mBio

A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii

(2015) Agnes P. Chan et al.   GENOME BIOLOGY

Population structure ofNeisseria gonorrhoeaebased on whole genome data and its relationship with antibiotic resistance

(2015) Matthew N. Ezewudo et al.   PeerJ

Acinetobacter baumannii Repeatedly Evolves a Hypermutator Phenotype in Response to Tigecycline That Effectively Surveys Evolutionary Trajectories to Resistance

(2015) Troy G. Hammerstrom et al.   PLoS One

Molecular Mechanisms Associated with Nosocomial Carbapenem-resistant Acinetobacter baumannii in Mexico

(2014) María Dolores Alcántar-Curiel et al.   ARCHIVES OF MEDICAL RESEARCH

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Mycobacterial Phylogenomics: An Enhanced Method for Gene Turnover Analysis Reveals Uneven Levels of Gene Gain and Loss among Species and Gene Families

(2014) Pablo Librado et al.   Genome Biology and Evolution

The Extent of Genome Flux and Its Role in the Differentiation of Bacterial Lineages

(2014) Reuben W. Nowell et al.   Genome Biology and Evolution

Minor Fitness Costs in an Experimental Model of Horizontal Gene Transfer in Bacteria

(2014) Anna Knöppel et al.   MOLECULAR BIOLOGY AND EVOLUTION

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Genome reduction as the dominant mode of evolution

(2013) Yuri I. Wolf et al.   BIOESSAYS

Acinetobacter baumannii Infections in a Tertiary Care Hospital in Mexico over the Past 13 Years

(2013) R. Morfín-Otero et al.   CHEMOTHERAPY

Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements

(2013) Ola Brynildsrud et al.   ISME Journal

Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

(2013) L. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Acinetobacter baumannii: evolution of a global pathogen

(2013) Luísa C.S. Antunes et al.   Pathogens and Disease

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

(2012) Franz Baumdicker et al.   Genome Biology and Evolution

Global evolution of multidrug-resistant Acinetobacter baumannii clonal lineages

(2012) Raffaele Zarrilli et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

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

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

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species

(2012) Derrick E. Fouts et al.   NUCLEIC ACIDS RESEARCH

Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus

(2012) Santiago Castillo-Ramírez et al.   GENOME BIOLOGY

BadiRate: estimating family turnover rates by likelihood-based methods

(2011) P. Librado et al.   BIOINFORMATICS

The Impact of Recombination on dN/dS within Recently Emerged Bacterial Clones

(2011) Santiago Castillo-Ramírez et al.   PLoS Pathogens

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

A Timescale for Evolution, Population Expansion, and Spatial Spread of an Emerging Clone of Methicillin-Resistant Staphylococcus aureus

(2010) Ulrich Nübel et al.   PLoS Pathogens

Factors influencing survival in patients with multi-drug-resistant Acinetobacter bacteraemia

(2009) Gokhan Metan et al.   European Journal of Internal Medicine

Genome Sequence of a Recently Emerged, Highly Transmissible, Multi-Antibiotic- and Antiseptic-Resistant Variant of Methicillin-Resistant Staphylococcus aureus, Sequence Type 239 (TW)

(2009) M. T. G. Holden et al.   JOURNAL OF BACTERIOLOGY

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach

(2009) Jing Tang et al.   PLoS Computational Biology

Factors affecting the concordance between orthologous gene trees and species tree in bacteria

(2008) Santiago Castillo-Ramírez et al.   BMC EVOLUTIONARY BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH