Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries

Review of guidance papers on regression modeling in statistical series of medical journals

(2022) Christine Wallisch et al.   PLoS One

Neonatal sepsis and mortality in low-income and middle-income countries from a facility-based birth cohort: an international multisite prospective observational study

(2022) Rebecca Milton et al.   Lancet Global Health

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

(2021) Kirsty Sands et al.   Nature Microbiology

Effects of antibiotic resistance, drug target attainment, bacterial pathogenicity and virulence, and antibiotic access and affordability on outcomes in neonatal sepsis: an international microbiology and drug evaluation prospective substudy (BARNARDS)

(2021) Kathryn M Thomson et al.   LANCET INFECTIOUS DISEASES

Global, regional, and national sepsis incidence and mortality, 1990–2017: analysis for the Global Burden of Disease Study

(2020) Kristina E Rudd et al.   LANCET

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines

(2020) Stephen J Bush et al.   GigaScience

High Carriage Rates of Multidrug-Resistant Gram-Negative Bacteria in Neonatal Intensive Care Units From Ghana

(2020) Appiah-Korang Labi et al.   Open Forum Infectious Diseases

The Gut of Healthy Infants in the Community as a Reservoir of ESBL and Carbapenemase-Producing Bacteria

(2020) Ali F. Saleem et al.   Antibiotics-Basel

Neonatal sepsis in South Asia: huge burden and spiralling antimicrobial resistance

(2019) Suman Chaurasia et al.   BMJ-British Medical Journal

Whole-genome sequences of multidrug-resistant Escherichia coli in South-Kivu Province, Democratic Republic of Congo: characterization of phylogenomic changes, virulence and resistance genes

(2019) Leonid M. Irenge et al.   BMC INFECTIOUS DISEASES

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

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

The Preterm Gut Microbiota: An Inconspicuous Challenge in Nutritional Neonatal Care

(2019) Jannie G. E. Henderickx et al.   Frontiers in Cellular and Infection Microbiology

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

Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth

(2019) Yan Shao et al.   NATURE

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

(2019) Andrew J. Gasparrini et al.   Nature Microbiology

Gut carriage of antimicrobial resistance genes among young children in urban Maputo, Mozambique: Associations with enteric pathogen carriage and environmental risk factors

(2019) David Berendes et al.   PLoS One

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Genome Sequencing of Extended-Spectrum β-Lactamase (ESBL)-Producing Klebsiella pneumoniae Isolated from Pigs and Abattoir Workers in Cameroon

(2018) Luria L. Founou et al.   Frontiers in Microbiology

Carbapenemase-producing Enterobacteriaceae among pregnant women and newborns in Algeria: Prevalence, molecular characterization, maternal-neonatal transmission, and risk factors for carriage

(2018) Assia Mairi et al.   AMERICAN JOURNAL OF INFECTION CONTROL

Spreading patterns of NDM-producing Enterobacteriaceae in clinical and environmental settings in Yangon, Myanmar

(2018) Yo Sugawara et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Carriage and Acquisition of Extended-spectrum β-Lactamase–producing Enterobacterales Among Neonates Admitted to Hospital in Kilifi, Kenya

(2018) Ngure Kagia et al.   CLINICAL INFECTIOUS DISEASES

Neonatal sepsis

(2017) Andi L Shane et al.   LANCET

Intense pre-admission carriage and further acquisition of ESBL-producing Enterobacteriaceae among patients and their caregivers in a tertiary hospital in Rwanda

(2017) Mathis S. E. Kurz et al.   TROPICAL MEDICINE & INTERNATIONAL HEALTH

Erratum to: Mutational landscape of mucinous ovarian carcinoma and its neoplastic precursors

(2017) Georgina L. Ryland et al.   Genome Medicine

Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic Elements In situ of the Infant Gut

(2017) Andreas Porse et al.   Frontiers in Cellular and Infection Microbiology

High Prevalence of Carbapenemase-Producing Enterobacteriaceae among Hospitalized Children in Luanda, Angola

(2016) Nicolas Kieffer et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

(2016) Philip Ewels et al.   BIOINFORMATICS

Risk factors for fecal carriage of carbapenemase producing Enterobacteriaceae among intensive care unit patients from a tertiary care center in India

(2016) Gajanand Mittal et al.   BMC MICROBIOLOGY

High rate of faecal carriage of extended-spectrum β-lactamase-producing Enterobacteriaceae in healthy children in Bangui, Central African Republic

(2016) A. Farra et al.   CLINICAL MICROBIOLOGY AND INFECTION

The global epidemiology of carbapenemase-producing Enterobacteriaceae

(2016) David van Duin et al.   Virulence

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

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

High Gastrointestinal Colonization Rate with Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae in Hospitalized Patients: Emergence of Carbapenemase-Producing K. pneumoniae in Ethiopia

(2016) Kassu Desta et al.   PLoS One

Colonization of Extended-Spectrum-β-Lactamase- and NDM-1-Producing Enterobacteriaceae among Pregnant Women in the Community in a Low-Income Country: a Potential Reservoir for Transmission of Multiresistant Enterobacteriaceae to Neonates

(2015) Fanny Chereau et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Isolates from Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community- versus Hospital-Associated Transmission in an Endemic Setting

(2014) N. Stoesser et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

High-level and novel mechanisms of carbapenem resistance in Gram-negative bacteria from tertiary hospitals in Nigeria

(2014) D.O. Ogbolu et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Prevalence of faecal carriage of NDM-1-producing bacteria among patients with diarrhoea in Bangladesh

(2014) M. A. Islam et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

(2014) Nicholas J. Croucher et al.   NUCLEIC ACIDS RESEARCH

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Frequency and factors associated with carriage of multi-drug resistant commensal Escherichia coliamong women attending antenatal clinics in Central India

(2013) Ashish Pathak et al.   BMC INFECTIOUS DISEASES

Community acquisition of β-lactamase producing Enterobacteriaceae in neonatal gut

(2013) Charu Kothari et al.   BMC MICROBIOLOGY

MLST revisited: the gene-by-gene approach to bacterial genomics

(2013) Martin C. J. Maiden et al.   NATURE REVIEWS MICROBIOLOGY

Risk of Early-Onset Neonatal Infection with Maternal Infection or Colonization: A Global Systematic Review and Meta-Analysis

(2013) Grace J. Chan et al.   PLOS MEDICINE

Prevalence and molecular characterization of Enterobacteriaceae producing NDM-1 carbapenemase at a military hospital in Pakistan and evaluation of two chromogenic media

(2012) Kathryn M. Day et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Prevalence of faecal carriage of Enterobacteriaceae with NDM-1 carbapenemase at military hospitals in Pakistan, and evaluation of two chromogenic media

(2011) J. D. Perry et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Rectal Carriage of Extended-Spectrum Beta-Lactamase-Producing Gram-Negative Bacilli in Community Settings in Madagascar

(2011) Perlinot Herindrainy et al.   PLoS One

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Natural transfer of sulphonamide and ampicillin resistance between Escherichia coli residing in the human intestine

(2008) M. Trobos et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY