Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome

Probiotics for preterm infants: A National Retrospective Cohort Study

(2019) Balpreet Singh et al.   Journal of Perinatology

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

(2018) Kelly L .Wyres et al.   CURRENT OPINION IN MICROBIOLOGY

Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery

(2018) Michael Kriss et al.   CURRENT OPINION IN MICROBIOLOGY

Association between duration of intravenous antibiotic administration and early-life microbiota development in late-preterm infants

(2018) Romy D Zwittink et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Maturation of the gut microbiome and risk of asthma in childhood

(2018) Jakob Stokholm et al.   Nature Communications

Cryptic transmission of ST405 Escherichia coli carrying bla NDM-4 in hospital

(2018) Xiaoxia Zhang et al.   Scientific Reports

Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome Between Neonatal Intensive Care Unit (NICU) Environments

(2018) Suchitra K. Hourigan et al.   Frontiers in Microbiology

Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

(2018) Sumayah F. Rahman et al.   mSystems

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements

(2018) Katariina Pärnänen et al.   Nature Communications

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Next-generation approaches to understand and combat the antibiotic resistome

(2017) Terence S. Crofts et al.   NATURE REVIEWS MICROBIOLOGY

Early life antibiotic use and the risk of asthma and asthma exacerbations in children

(2017) Fariba Ahmadizar et al.   PEDIATRIC ALLERGY AND IMMUNOLOGY

Antibiotic resistance potential of the healthy preterm infant gut microbiome

(2017) Graham Rose et al.   PeerJ

Proteobacteria explain significant functional variability in the human gut microbiome

(2017) Patrick H. Bradley et al.   Microbiome

Gut microbiota in early pediatric multiple sclerosis: a case−control study

(2016) H. Tremlett et al.   EUROPEAN JOURNAL OF NEUROLOGY

Elevated Blood Pressure with Reduced Left Ventricular and Aortic Dimensions in Adolescents Born Extremely Preterm

(2016) Remi R. Kowalski et al.   JOURNAL OF PEDIATRICS

Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study

(2016) Barbara B Warner et al.   LANCET

Global, regional, and national causes of under-5 mortality in 2000–15: an updated systematic analysis with implications for the Sustainable Development Goals

(2016) Li Liu et al.   LANCET

Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice

(2016) Joseph D. Planer et al.   NATURE

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

(2016) Molly K. Gibson et al.   Nature Microbiology

Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice

(2016) Alexandra E. Livanos et al.   Nature Microbiology

Detection and genetic characterization of β-lactamases in Prevotella intermedia and Prevotella nigrescens isolated from oral cavity infections and peritonsillar abscesses

(2015) Liliana Fernández-Canigia et al.   ANAEROBE

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Preterm infant gut colonization in the neonatal ICU and complete restoration 2 years later

(2015) L. Moles et al.   CLINICAL MICROBIOLOGY AND INFECTION

The effect of past antibiotic exposure on diabetes risk

(2015) B. Boursi et al.   EUROPEAN JOURNAL OF ENDOCRINOLOGY

Gut Colonization of Healthy Children and Their Mothers With Pathogenic Ciprofloxacin-ResistantEscherichia coli

(2015) Emily A. Gurnee et al.   JOURNAL OF INFECTIOUS DISEASES

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Early infancy microbial and metabolic alterations affect risk of childhood asthma

(2015) Marie-Claire Arrieta et al.   Science Translational Medicine

Antibiotics in neonatal life increase murine susceptibility to experimental psoriasis

(2015) Peter Zanvit et al.   Nature Communications

Preterm gut microbiota and metabolome following discharge from intensive care

(2015) Christopher J. Stewart et al.   Scientific Reports

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

Involvement of the iNKT Cell Pathway Is Associated With Early-Onset Eosinophilic Esophagitis and Response to Allergen Avoidance Therapy

(2014) Willem S Lexmond et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Antibiotics Associated With Increased Risk of New-Onset Crohn’s Disease But Not Ulcerative Colitis: A Meta-Analysis

(2014) Ryan Ungaro et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences

(2014) Laura M. Cox et al.   CELL

Sepsis From the Gut: The Enteric Habitat of Bacteria That Cause Late-Onset Neonatal Bloodstream Infections

(2014) Mike A. Carl et al.   CLINICAL INFECTIOUS DISEASES

Infant antibiotic exposure and the development of childhood overweight and central adiposity

(2014) M B Azad et al.   INTERNATIONAL JOURNAL OF OBESITY

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

MLST reveals potentially high-risk international clones of Enterobacter cloacae*

(2014) R. Izdebski et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Early Empiric Antibiotic Use in Preterm Infants Is Associated with Lower Bacterial Diversity and Higher Relative Abundance of Enterobacter

(2014) Corryn Greenwood et al.   JOURNAL OF PEDIATRICS

Persistent gut microbiota immaturity in malnourished Bangladeshi children

(2014) Sathish Subramanian et al.   NATURE

Patterned progression of bacterial populations in the premature infant gut

(2014) P. S. La Rosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enterococcus faecium AND Enterococcus faecalis IN BLOOD OF NEWBORNS WITH SUSPECTED NOSOCOMIAL INFECTION

(2014) Isabela Furtado et al.   REVISTA DO INSTITUTO DE MEDICINA TROPICAL DE SAO PAULO

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

(2014) Brandon Brooks et al.   Microbiome

Medication Use in the Neonatal Intensive Care Unit

(2013) Emily Hsieh et al.   AMERICAN JOURNAL OF PERINATOLOGY

Preterm birth and subsequent insulin sensitivity: a systematic review

(2013) R. Tinnion et al.   ARCHIVES OF DISEASE IN CHILDHOOD

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Low gut microbiota diversity in early infancy precedes asthma at school age

(2013) T. R. Abrahamsson et al.   CLINICAL AND EXPERIMENTAL ALLERGY

Biphasic assembly of the murine intestinal microbiota during early development

(2013) Ida Gisela Pantoja-Feliciano et al.   ISME Journal

The gut microbiota — masters of host development and physiology

(2013) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

Committee Opinion No 579

(2013)   OBSTETRICS AND GYNECOLOGY

Preterm Birth and the Metabolic Syndrome in Adult Life: A Systematic Review and Meta-analysis

(2013) J. R. C. Parkinson et al.   PEDIATRICS

High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin

(2012) Fiona Fouhy et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma

(2012) Shannon L Russell et al.   EMBO REPORTS

Infant antibiotic exposures and early-life body mass

(2012) L Trasande et al.   INTERNATIONAL JOURNAL OF OBESITY

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

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

National, regional, and worldwide estimates of preterm birth rates in the year 2010 with time trends since 1990 for selected countries: a systematic analysis and implications

(2012) Hannah Blencowe et al.   LANCET

Antibiotics in early life alter the murine colonic microbiome and adiposity

(2012) Ilseung Cho et al.   NATURE

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Antibiotic Exposure and IBD Development Among Children: A Population-Based Cohort Study

(2012) M. P. Kronman et al.   PEDIATRICS

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

Risk of Hypertension Among Young Adults Who Were Born Preterm: A Swedish National Study of 636,000 Births

(2011) C. Crump et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Low diversity of the gut microbiota in infants with atopic eczema

(2011) Thomas R. Abrahamsson et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Meta-analysis of the association between preterm delivery and intelligence

(2011) C. O. Kerr-Wilson et al.   JOURNAL OF PUBLIC HEALTH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Risk of Asthma in Young Adults Who Were Born Preterm: A Swedish National Cohort Study

(2011) C. Crump et al.   PEDIATRICS

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Association Between the Use of Antibiotics in the First Year of Life and Pediatric Inflammatory Bowel Disease

(2010) Souradet Y Shaw et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Nature and severity of lung function abnormalities in extremely pre-term children at 11 years of age

(2010) S. Lum et al.   EUROPEAN RESPIRATORY JOURNAL

Antibiotic use and inflammatory bowel diseases in childhood

(2010) A. Hviid et al.   GUT

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

oqxAB Encoding a Multidrug Efflux Pump in Human Clinical Isolates of Enterobacteriaceae

(2009) H. B. Kim et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Academic attainment and special educational needs in extremely preterm children at 11 years of age: the EPICure study

(2009) S Johnson et al.   Archives of Disease in Childhood-Fetal and Neonatal Edition