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Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics

https://doi.org/10.1101/180406
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The antibiotic resistome: gene flow in environments, animals and human beings
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The Developing Microbiome of the Preterm Infant
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The Microbiota of the Extremely Preterm Infant
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Recent updates of carbapenem antibiotics
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Brain Autoimmunity and Intestinal Microbiota: 100 Trillion Game Changers
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Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones
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Basic Local Alignment Search Tool
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Late-Onset Enterobacter cloacae Sepsis in Very-Low-Birth-Weight Neonates: Experience in a Medical Center
inferredcites →https://doi.org/10.1023/b:grow.0000007501.27878.aaopenalex-snapshot
ILR1 and sILR1 IAA amidohydrolase homologs differ in expression pattern and substrate specificity
inferredcites →https://doi.org/10.1038/nature11319openalex-snapshot
Gut microbiota composition correlates with diet and health in the elderly
inferredcites →https://doi.org/10.1038/nature11450openalex-snapshot
A metagenome-wide association study of gut microbiota in type 2 diabetes
inferredcites →https://doi.org/10.1038/nature12198openalex-snapshot
Gut metagenome in European women with normal, impaired and diabetic glucose control
inferredcites →https://doi.org/10.1038/nature13568openalex-snapshot
Alterations of the human gut microbiome in liver cirrhosis
inferredcites →https://doi.org/10.1038/nature16996openalex-snapshot
Real-time, portable genome sequencing for Ebola surveillance
inferredcites →https://doi.org/10.1038/nature18646openalex-snapshot
Human gut microbes impact host serum metabolome and insulin sensitivity
inferredcites →https://doi.org/10.1038/nbt.3103openalex-snapshot
MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island
inferredcites →https://doi.org/10.1038/ni.3780openalex-snapshot
Regulation of inflammation by microbiota interactions with the host
inferredcites →https://doi.org/10.1038/nmeth.3444openalex-snapshot
A complete bacterial genome assembled de novo using only nanopore sequencing data
inferredcites →https://doi.org/10.1038/nrgastro.2016.98openalex-snapshot
Understanding the mechanisms of faecal microbiota transplantation
inferredcites →https://doi.org/10.1073/pnas.0504978102openalex-snapshot
Obesity alters gut microbial ecology
inferredcites →https://doi.org/10.1080/14737159.2018.1487292openalex-snapshot
The challenge of diagnostic metagenomics
inferredcites →https://doi.org/10.1086/647952openalex-snapshot
Antimicrobial Susceptibility Testing: A Review of General Principles and Contemporary Practices
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btv540openalex-snapshot
NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles
inferredcites →https://doi.org/10.1093/cid/ciu822openalex-snapshot
Dysbiosis Anticipating Necrotizing Enterocolitis in Very Premature Infants
inferredcites →https://doi.org/10.1093/gigascience/giw015openalex-snapshot
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
inferredcites →https://doi.org/10.1093/jac/dkw397openalex-snapshot
Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing
inferredcites →https://doi.org/10.1093/jac/dkw547openalex-snapshot
Emergence of Klebsiella variicola positive for NDM-9, a variant of New Delhi metallo-β-lactamase, in an urban river in South Korea
inferredcites →https://doi.org/10.1093/jxb/erx289openalex-snapshot
A world of opportunities with nanopore sequencing
inferredcites →https://doi.org/10.1093/nar/gks1219openalex-snapshot
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
inferredcites →https://doi.org/10.1097/01.shk.0000239774.02904.65openalex-snapshot
THE ROLE OF THE INTESTINAL BARRIER IN THE PATHOGENESIS OF NECROTIZING ENTEROCOLITIS
inferredcites →https://doi.org/10.1099/mgen.0.000132openalex-snapshot
Completing bacterial genome assemblies with multiplex MinION sequencing
inferredcites →https://doi.org/10.1101/180406openalex-snapshot
Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics
inferredcites →https://doi.org/10.1101/gr.113985.110openalex-snapshot
Adaptive seeds tame genomic sequence comparison
inferredcites →https://doi.org/10.1101/gr.214270.116openalex-snapshot
Fast and accurate de novo genome assembly from long uncorrected reads
inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
inferredcites →https://doi.org/10.1111/apa.13902openalex-snapshot
Probiotics for the prevention of necrotising enterocolitis in very low‐birth‐weight infants: a meta‐analysis and systematic review
inferredcites →https://doi.org/10.1111/j.1472-765x.2011.03016.xopenalex-snapshot
Identification of a novel fosfomycin resistance gene (fosA2) in Enterobacter cloacae from the Salmon River, Canada
inferredcites →https://doi.org/10.1126/science.1182395openalex-snapshot
Evolution of MRSA During Hospital Transmission and Intercontinental Spread
inferredcites →https://doi.org/10.1128/aac.00084-14openalex-snapshot
Resistance to Colistin Associated with a Single Amino Acid Change in Protein PmrB among Klebsiella pneumoniae Isolates of Worldwide Origin
inferredcites →https://doi.org/10.1128/aac.00419-13openalex-snapshot
The Comprehensive Antibiotic Resistance Database
inferredcites →https://doi.org/10.1128/aac.48.12.4778-4783.2004openalex-snapshot
Biochemical Characterization of the THIN-B Metallo-β-Lactamase of Janthinobacterium lividum
inferredcites →https://doi.org/10.1128/aem.02540-10openalex-snapshot
Insights into Physiological and Genetic Mupirocin Susceptibility in Bifidobacteria
inferredcites →https://doi.org/10.1128/cmr.00064-16openalex-snapshot
Polymyxins: Antibacterial Activity, Susceptibility Testing, and Resistance Mechanisms Encoded by Plasmids or Chromosomes
inferredcites →https://doi.org/10.1128/jb.173.2.697-703.1991openalex-snapshot
16S ribosomal DNA amplification for phylogenetic study
inferredcites →https://doi.org/10.1128/jcm.02483-16openalex-snapshot
Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples
inferredcites →https://doi.org/10.1136/archdischild-2013-304629openalex-snapshot
NICE clinical guideline: antibiotics for the prevention and treatment of early-onset neonatal infection
inferredcites →https://doi.org/10.1136/bmj.k462openalex-snapshot
First WHO antimicrobial surveillance data reveal high levels of resistance globally
inferredcites →https://doi.org/10.1146/annurev-micro-090816-093549openalex-snapshot
Microbiota-Based Therapies for Clostridium difficile and Antibiotic-Resistant Enteric Infections
inferredcites →https://doi.org/10.1186/1471-2164-12-402openalex-snapshot
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot
Versatile and open software for comparing large genomes
inferredcites →https://doi.org/10.1186/s12864-017-4229-xopenalex-snapshot
Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants
inferredcites →https://doi.org/10.1186/s13073-015-0220-9openalex-snapshot
Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
inferredcites →https://doi.org/10.1186/s13104-016-2171-7openalex-snapshot
The effect of DNA extraction methodology on gut microbiota research applications
inferredcites →https://doi.org/10.1186/s40168-017-0248-8openalex-snapshot
Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis
inferredcites →https://doi.org/10.12688/f1000research.7201.1openalex-snapshot
MinION Analysis and Reference Consortium: Phase 1 data release and analysis
inferredcites →https://doi.org/10.12998/wjcc.v5.i8.324openalex-snapshot
Treatment of sepsis: What is the antibiotic choice in bacteremia due to carbapenem resistantEnterobacteriaceae?
inferredcites →https://doi.org/10.1371/journal.pcbi.1004957openalex-snapshot
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
inferredcites →https://doi.org/10.2147/jir.s116088openalex-snapshot
The microbiota in inflammatory bowel disease: current and therapeutic insights
inferredcites →https://doi.org/10.2471/blt.15.152710openalex-snapshot
An international legal framework to address antimicrobial resistance
inferredcites →https://doi.org/10.3201/eid2202.151796openalex-snapshot
Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool
inferredcites →https://doi.org/10.3389/fimmu.2017.00729openalex-snapshot
Impact of Early-Life Exposures to Infections, Antibiotics, and Vaccines on Perinatal and Long-term Health and Disease
inferredcites →https://doi.org/10.3389/fmicb.2016.00459openalex-snapshot
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
inferredcites →https://doi.org/10.3389/fmicb.2016.01374openalex-snapshot
A Review of SHV Extended-Spectrum β-Lactamases: Neglected Yet Ubiquitous
inferredcites →https://doi.org/10.3389/fped.2017.00040openalex-snapshot
The Role of Mucosal Immunity in the Pathogenesis of Necrotizing Enterocolitis
inferredcites →https://doi.org/10.3920/bm2016.0184openalex-snapshot
Gut microbiota dysbiosis associated with glucose metabolism disorders and the metabolic syndrome in older adults

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer
inferred← citeshttps://doi.org/10.1007/978-3-030-62155-1_7openalex-snapshot
Metagenomic Applications for Infectious Disease Testing in Clinical Laboratories
inferred← citeshttps://doi.org/10.1007/s12275-018-8238-5openalex-snapshot
Progress of analytical tools and techniques for human gut microbiome research
inferred← citeshttps://doi.org/10.1016/b978-0-12-801496-7.00004-6openalex-snapshot
Clinical metagenomics for infection diagnosis
inferred← citeshttps://doi.org/10.1016/b978-0-12-815249-2.00029-4openalex-snapshot
The Microbiome, Metabolome, and Proteome in Preterm Neonatal Sepsis
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Highlighting Clinical Metagenomics for Enhanced Diagnostic Decision-making: A Step Towards Wider Implementation
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Implications of Error-Prone Long-Read Whole-Genome Shotgun Sequencing on Characterizing Reference Microbiomes
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Rapid Next-Generation Sequencing–Based Diagnostics of Bacteremia in Septic Patients
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Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance
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From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic
inferred← citeshttps://doi.org/10.1038/s41587-019-0156-5openalex-snapshot
Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection
inferred← citeshttps://doi.org/10.1038/s41587-019-0191-2openalex-snapshot
Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
inferred← citeshttps://doi.org/10.1038/s41598-019-52549-zopenalex-snapshot
Rectal swabs are a reliable proxy for faecal samples in infant gut microbiota research based on 16S-rRNA sequencing
inferred← citeshttps://doi.org/10.1080/1040841x.2019.1681933openalex-snapshot
mNGS in clinical microbiology laboratories: on the road to maturity
inferred← citeshttps://doi.org/10.1089/fpd.2022.0027openalex-snapshot
Comparison Between Full-Length 16S rRNA Metabarcoding and Whole Metagenome Sequencing Suggests the Use of Either Is Suitable for Large-Scale Microbiome Studies
inferred← citeshttps://doi.org/10.1093/gigascience/giz043openalex-snapshot
Ultra-deep, long-read nanopore sequencing of mock microbial community standards
inferred← citeshttps://doi.org/10.1101/2019.12.20.884395openalex-snapshot
Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer
inferred← citeshttps://doi.org/10.1101/2019.12.21.886028openalex-snapshot
Long reads from Nanopore sequencing as a tool for animal microbiome studies
inferred← citeshttps://doi.org/10.1101/382580openalex-snapshot
Nanopore-based DNA sequencing in clinical microbiology: preliminary assessment of basic requirements
inferred← citeshttps://doi.org/10.1101/387548openalex-snapshot
Rapid Diagnosis of Lower Respiratory Infection using Nanopore-based Clinical Metagenomics
inferred← citeshttps://doi.org/10.1101/585067openalex-snapshot
Shallow metagenomics with Nanopore sequencing in canine fecal microbiota improved bacterial taxonomy and identified an uncultured CrAssphage
inferred← citeshttps://doi.org/10.1111/nyas.13672openalex-snapshot
Genomic epidemiology of multidrug‐resistant Gram‐negative organisms
inferred← citeshttps://doi.org/10.1128/genomea.01269-17openalex-snapshot
Whole-Genome Sequencing of a Human Clinical Isolate of emm28 Streptococcus pyogenes Causing Necrotizing Fasciitis Acquired Contemporaneously with Hurricane Harvey
inferred← citeshttps://doi.org/10.1183/2312508x.10015618openalex-snapshot
Applying clinical metagenomics for the detection and characterisation of respiratory infections
inferred← citeshttps://doi.org/10.1371/journal.pone.0217600openalex-snapshot
Exploration of antibiotic resistance risks in a veterinary teaching hospital with Oxford Nanopore long read sequencing
inferred← citeshttps://doi.org/10.14202/vetworld.2022.1798-1803openalex-snapshot
A preliminary metagenomics study of bacteria present in the dirt of Swiftlet farmhouses based on nitrite levels in edible bird's nest on Sumatera Island, Indonesia
inferred← citeshttps://doi.org/10.3168/jds.2019-17359openalex-snapshot
Short communication: Milk microbiota profiling on water buffalo with full-length 16S rRNA using nanopore sequencing
inferred← citeshttps://doi.org/10.33540/715openalex-snapshot
The infant gut microbiome and resistome in health and disease
inferred← citeshttps://doi.org/10.3389/fgene.2021.620009openalex-snapshot
Comprehensive Pathogen Identification, Antibiotic Resistance, and Virulence Genes Prediction Directly From Simulated Blood Samples and Positive Blood Cultures by Nanopore Metagenomic Sequencing
inferred← citeshttps://doi.org/10.70675/d91a3321z646fz4691zb1f5z1e5039b15385openalex-snapshot
Modélisation de séquences et reconstruction non supervisée de génomes microbiens à partir de donnée métagénomiques.
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