4.6 Review

Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country

Related references

Note: Only part of the references are listed.
Review Biochemical Research Methods

Current challenges and best-practice protocols for microbiome analysis

Richa Bharti et al.

Summary: Analyzing the microbiome using next-generation sequencing techniques has improved our understanding of environmental microorganisms. However, analysis is affected by experimental conditions and downstream analysis, and new sequencing technologies can impact results. This work aims to review important workflows for sequencing data and provide best-practice protocols.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Biochemical Research Methods

Optimization of 16S rRNA gene analysis for use in the diagnostic clinical microbiology service

Dan Sune et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2020)

Article Multidisciplinary Sciences

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

Andrei Prodan et al.

PLOS ONE (2020)

Review Biotechnology & Applied Microbiology

Library preparation for next generation sequencing: A review of automation strategies

J. F. Hess et al.

BIOTECHNOLOGY ADVANCES (2020)

Article Biochemical Research Methods

Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads

William S. Pearman et al.

BMC BIOINFORMATICS (2020)

Article Chemistry, Analytical

Automation of Amplicon-Based Library Preparation for Next-Generation Sequencing by Centrifugal Microfluidics

Jacob Friedrich Hess et al.

ANALYTICAL CHEMISTRY (2020)

Article Infectious Diseases

Improving Diagnostic and Laboratory Capacity Helps in Control of Infection: an Indian Perspective

Sanjay Bhattacharya

CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES (2020)

Editorial Material Medicine, General & Internal

Next-Generation Sequencing of Infectious Pathogens

Marta Gwinn et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2019)

Review Genetics & Heredity

Clinical metagenomics

Charles Y. Chiu et al.

NATURE REVIEWS GENETICS (2019)

Article Multidisciplinary Sciences

The effect of 16S rRNA region choice on bacterial community metabarcoding results

Yu. S. Bukin et al.

SCIENTIFIC DATA (2019)

Letter Biotechnology & Applied Microbiology

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen et al.

NATURE BIOTECHNOLOGY (2019)

Review Infectious Diseases

Electronic Health Record Use in Public Health Infectious Disease Surveillance, USA, 2018-2019

Sarah J. Willis et al.

CURRENT INFECTIOUS DISEASE REPORTS (2019)

Article Biotechnology & Applied Microbiology

Insights into microbial community structure and diversity in oil palm waste compost

Nurshafika Abd Khalid et al.

3 BIOTECH (2019)

Editorial Material Genetics & Heredity

Strategies for Genomic Medicine Education in Low- and Middle-Income Countries

Nirmala D. Sirisena et al.

FRONTIERS IN GENETICS (2019)

Article Medical Laboratory Technology

Essential Diagnostics for the Use of World Health Organization Essential Medicines

Lee F. Schroeder et al.

CLINICAL CHEMISTRY (2018)

Review Infectious Diseases

Next-generation sequencing technologies and their application to the study and control of bacterial infections

J. Besser et al.

CLINICAL MICROBIOLOGY AND INFECTION (2018)

Article Infectious Diseases

Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics

Stefan A. Boers et al.

EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES (2018)

Editorial Material Medicine, General & Internal

Laboratory medicine in low-income and middle-income countries: progress and challenges

John N. Nkengasong et al.

LANCET (2018)

Article Microbiology

A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform

Monica Pichler et al.

MICROBIOLOGYOPEN (2018)

Article Pathology

Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection

Wei Gu et al.

Annual Review of Pathology-Mechanisms of Disease (2018)

Review Pathology

A Next-Generation Sequencing PrimerHow Does It Work and What Can It Do?

Yuriy O. Alekseyev et al.

ACADEMIC PATHOLOGY (2018)

Review Pathology

An Essential Pathology Package for Low- and Middle-Income Countries

Kenneth A. Fleming et al.

AMERICAN JOURNAL OF CLINICAL PATHOLOGY (2017)

Review Microbiology

What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015

Erik Munson et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2017)

Article Biotechnology & Applied Microbiology

16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria

G. S. Watts et al.

JOURNAL OF APPLIED MICROBIOLOGY (2017)

Article Biotechnology & Applied Microbiology

Application of next generation sequencing in clinical microbiology and infection prevention

Ruud H. Deurenberg et al.

JOURNAL OF BIOTECHNOLOGY (2017)

Article Biotechnology & Applied Microbiology

25 years of serving the community with ribosomal RNA gene reference databases and tools

Frank Oliver Gloeckner et al.

JOURNAL OF BIOTECHNOLOGY (2017)

Article Multidisciplinary Sciences

BBMerge - Accurate paired shotgun read merging via overlap

Brian Bushnell et al.

PLOS ONE (2017)

Article Medical Laboratory Technology

Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection

Robert Schlaberg et al.

ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE (2017)

Article Biotechnology & Applied Microbiology

SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare?

Monika Balvociute et al.

BMC GENOMICS (2017)

Article Medical Laboratory Technology

A Model Study of In Silico Proficiency Testing for Clinical Next-Generation Sequencing

Eric J. Duncavage et al.

ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE (2016)

Article Biochemical Research Methods

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis

Bo Yang et al.

BMC BIOINFORMATICS (2016)

Review Biotechnology & Applied Microbiology

High Throughput Sequencing: An Overview of Sequencing Chemistry

Sheetal Ambardar et al.

INDIAN JOURNAL OF MICROBIOLOGY (2016)

Article Biochemical Research Methods

DADA2: High-resolution sample inference from Illumina amplicon data

Benjamin J. Callahan et al.

NATURE METHODS (2016)

Article Microbiology

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

Juan Jovel et al.

FRONTIERS IN MICROBIOLOGY (2016)

Article Multidisciplinary Sciences

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

Patrick D. Schloss et al.

PEERJ (2016)

Article Biotechnology & Applied Microbiology

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

Nam-Phuong Nguyen et al.

NPJ BIOFILMS AND MICROBIOMES (2016)

Article Multidisciplinary Sciences

Helicobacter pylori Eradication Causes Perturbation of the Human Gut Microbiome in Young Adults

Theresa Wan-Chen Yap et al.

PLOS ONE (2016)

Article Health Policy & Services

Key success factors behind electronic medical record adoption in Thailand

Kanida Narattharaksa et al.

JOURNAL OF HEALTH ORGANIZATION AND MANAGEMENT (2016)

Article Emergency Medicine

Electronic Medical Records in low to middle income countries: The case of Khayelitsha Hospital, South Africa

Emmanuel C. Ohuabunwa et al.

AFRICAN JOURNAL OF EMERGENCY MEDICINE (2016)

Article Biochemical Research Methods

PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm

Yun-Lung Li et al.

BMC BIOINFORMATICS (2015)

Review Microbiology

Current and Past Strategies for Bacterial Culture in Clinical Microbiology

Jean-Christophe Lagier et al.

CLINICAL MICROBIOLOGY REVIEWS (2015)

Review Microbiology

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

Jean-Christophe Lagier et al.

CLINICAL MICROBIOLOGY REVIEWS (2015)

Review Genetics & Heredity

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

Alejandra Escobar-Zepeda et al.

FRONTIERS IN GENETICS (2015)

Review Biochemistry & Molecular Biology

Next generation sequencing technology: Advances and applications

H. P. J. Buermans et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2014)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Computer Science, Interdisciplinary Applications

Improving the work efficiency of healthcare-associated infection surveillance using electronic medical records

Yu-Sheng Lo et al.

COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE (2014)

Article Biochemistry & Molecular Biology

Ribosomal Database Project: data and tools for high throughput rRNA analysis

James R. Cole et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

Dramatic reduction of culture time of Mycobacterium tuberculosis

Ramzi Ghodbane et al.

SCIENTIFIC REPORTS (2014)

Review Genetics & Heredity

Clinical detection and characterization of bacterial pathogens in the genomics era

Pierre-Edouard Fournier et al.

GENOME MEDICINE (2014)

Review Biotechnology & Applied Microbiology

A commentary on the role of molecular technology and automation in clinical diagnostics

Ciara O'Connor et al.

BIOENGINEERED (2014)

Article Microbiology

Outbreak Investigation Using High-Throughput Genome Sequencing within a Diagnostic Microbiology Laboratory

Norelle L. Sherry et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2013)

Article Biochemistry & Molecular Biology

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Christian Quast et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing

Hanyoup Kim et al.

PLOS ONE (2013)

Article Critical Care Medicine

Characteristics and outcomes of culture-negative versus culture-positive severe sepsis

Jason Phua et al.

CRITICAL CARE (2013)

Article Mathematical & Computational Biology

Palindromic sequence impedes sequencing-by-ligation mechanism

Yu-Feng Huang et al.

BMC SYSTEMS BIOLOGY (2012)

Article Medicine, General & Internal

Does This Adult Patient With Suspected Bacteremia Require Blood Cultures?

Bryan Coburn et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2012)

Article Biochemistry & Molecular Biology

The NCBI Taxonomy database

Scott Federhen

NUCLEIC ACIDS RESEARCH (2012)

Article Medicine, Research & Experimental

Experience of quality management system in a clinical laboratory in Nigeria

Rosemary A. Audu et al.

AFRICAN JOURNAL OF LABORATORY MEDICINE (2012)

Article Biotechnology & Applied Microbiology

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

Andrea K. Bartram et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)

Article Multidisciplinary Sciences

Microbial Dysbiosis in Colorectal Cancer (CRC) Patients

Iradj Sobhani et al.

PLOS ONE (2011)

Article Pathology

The Role of Standards and Training in Preparing for Accreditation

Sheila Woodcock et al.

AMERICAN JOURNAL OF CLINICAL PATHOLOGY (2010)

Editorial Material Biotechnology & Applied Microbiology

Genome sequencing on nanoballs

Gregory J. Porreca

NATURE BIOTECHNOLOGY (2010)

Letter Biochemical Research Methods

QIIME allows analysis of high-throughput community sequencing data

J. Gregory Caporaso et al.

NATURE METHODS (2010)

Review Biotechnology & Applied Microbiology

DNA, RNA, and Protein Extraction: The Past and The Present

Siun Chee Tan et al.

JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY (2009)

Article Multidisciplinary Sciences

Real-Time DNA Sequencing from Single Polymerase Molecules

John Eid et al.

SCIENCE (2009)

Article Infectious Diseases

Comparison of 3 swab transport systems for direct release and recovery of aerobic and anaerobic bacteria

Kenneth G. Van Horn et al.

DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE (2008)

Article Biochemical Research Methods

A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria

Soumitesh Chakravorty et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2007)

Article Biotechnology & Applied Microbiology

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

T. Z. DeSantis et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)

Review Biochemical Research Methods

Bioinformatics for whole-genome shotgun sequencing of microbial communities

K Chen et al.

PLOS COMPUTATIONAL BIOLOGY (2005)

Article Multidisciplinary Sciences

Cultivating the uncultured

K Zengler et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Medicine, General & Internal

Unculturable bacteria - the uncharacterized organisms that cause oral infections

W Wade

JOURNAL OF THE ROYAL SOCIETY OF MEDICINE (2002)

Article Immunology

A flea-associated rickettsia pathogenic for humans

D Raoult et al.

EMERGING INFECTIOUS DISEASES (2001)