Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries

Neonatal sepsis in low-income countries: epidemiology, diagnosis and prevention

(2020) Constantin Radu Popescu et al.   Expert Review of Anti-Infective Therapy

Blood culture result profile and antimicrobial resistance pattern: a report from neonatal intensive care unit (NICU), Asella teaching and referral hospital, Asella, south East Ethiopia

(2019) Abebe Sorsa et al.   Antimicrobial Resistance and Infection Control

Whole-genome-based analysis reveals multiclone Serratia marcescens outbreaks in a non-Neonatal Intensive Care Unit setting in a tertiary care hospital in India

(2019) Anusha Rohit et al.   JOURNAL OF MEDICAL MICROBIOLOGY

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

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates

(2019) Michael Feldgarden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Aetiology of invasive bacterial infection and antimicrobial resistance in neonates in sub-Saharan Africa: a systematic review and meta-analysis in line with the STROBE-NI reporting guidelines

(2019) Uduak Okomo et al.   LANCET INFECTIOUS DISEASES

Dealing with Neonatal Emergencies in Low-resource Settings

(2019) Vivek Shukla et al.   Seminars in Fetal & Neonatal Medicine

The evolution and transmission of multi-drug resistant Escherichia coli and Klebsiella pneumoniae: the complexity of clones and plasmids

(2019) Steven J Dunn et al.   CURRENT OPINION IN MICROBIOLOGY

Predictors of the extended-spectrum-beta lactamases producing Enterobacteriaceae neonatal sepsis at a tertiary hospital, Tanzania

(2018) Rehema Marando et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes

(2018) Ryan R. Wick et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Effectiveness of intrapartum antibiotic prophylaxis for early-onset group B Streptococcal infection: An integrative review

(2018) Kathryn Braye et al.   Women and Birth

Outbreak of Hypervirulent Multi-Drug Resistant Klebsiella variicola causing high mortality in neonates in Bangladesh

(2018) Refath Farzana et al.   CLINICAL INFECTIOUS DISEASES

Outbreak of Yersiniabactin-Producing Klebsiella pneumoniae in a Neonatal Intensive Care Unit

(2018) Lukas Wisgrill et al.   PEDIATRIC INFECTIOUS DISEASE JOURNAL

Resistance phenotype and clinical molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae among pediatric patients in Shanghai

(2018) Dongxing Tian et al.   Infection and Drug Resistance

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Nosocomial outbreak of KPC-2- and NDM-1-producing Klebsiella pneumoniae in a neonatal ward: a retrospective study

(2016) Jing Yu et al.   BMC INFECTIOUS DISEASES

Characterisation and antimicrobial resistance of sepsis pathogens in neonates born in tertiary care centres in Delhi, India: a cohort study

(2016)   Lancet Global Health

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data

(2015) Katrine G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data

(2015) Shaokang Zhang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

Etiology of Bacteremia in Young Infants in Six Countries

(2015) Davidson H. Hamer et al.   PEDIATRIC INFECTIOUS DISEASE JOURNAL

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance inKlebsiella pneumoniae, an urgent threat to public health

(2015) Kathryn E. Holt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neonatal nosocomial bloodstream infections at a referral hospital in a middle-income country: burden, pathogens, antimicrobial resistance and mortality

(2015) Angela Dramowski et al.   Paediatrics and International Child Health

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

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

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution

(2014) Astrid von Mentzer et al.   NATURE GENETICS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

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

(2014) Michael Inouye et al.   Genome Medicine

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Klebsiella pneumoniae resistant to third-generation cephalosporins in five African and two Vietnamese major towns: multiclonal population structure with two major international clonal groups, CG15 and CG258

(2012) S. Breurec et al.   CLINICAL MICROBIOLOGY AND INFECTION

Identification of acquired antimicrobial resistance genes

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

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

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

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Population‐Based Incidence and Etiology of Community‐Acquired Neonatal Bacteremia in Mirzapur, Bangladesh: An Observational Study

(2009) Gary L. Darmstadt et al.   JOURNAL OF INFECTIOUS DISEASES