Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients

Lung Microbiota Predict Clinical Outcomes in Critically Ill Patients

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Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients

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Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study

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RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak

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Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

(2020) Xianding Deng et al.   Nature Microbiology

Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization

(2020) Vikas Peddu et al.   CLINICAL CHEMISTRY

COVID-19, superinfections and antimicrobial development: What can we expect?

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Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing

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Rates of Co-infection Between SARS-CoV-2 and Other Respiratory Pathogens

(2020) David Kim et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Presenting Characteristics, Comorbidities, and Outcomes Among 5700 Patients Hospitalized With COVID-19 in the New York City Area

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Co-infections in people with COVID-19: a systematic review and meta-analysis

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Co‐infection in SARS‐CoV‐2 infected Patients: Where Are Influenza Virus and Rhinovirus/Enterovirus?

(2020) Michael D. Nowak et al.   JOURNAL OF MEDICAL VIROLOGY

Co‐detection of respiratory pathogens in patients hospitalized with Coronavirus viral disease‐2019 pneumonia

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COVID‐19: Recommended sampling sites at different stage of the disease

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Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays

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Co-infection with respiratory pathogens among COVID-2019 cases

(2020) Xiaojuan Zhu et al.   VIRUS RESEARCH

Anaerobes in cystic fibrosis patients’ airways

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Bacterial and viral respiratory tract microbiota and host characteristics in children with lower respiratory tract infections: a matched case-control study

(2019) Wing Ho Man et al.   Lancet Respiratory Medicine

The Commensal Microbiota and Viral Infection: A Comprehensive Review

(2019) Na Li et al.   Frontiers in Immunology

The microbiome of the upper respiratory tract in health and disease

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Lung Microbiota Is Related to Smoking Status and to Development of Acute Respiratory Distress Syndrome in Critically Ill Trauma Patients

(2018) Ariane R. Panzer et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Evaluation of the CosmosID Bioinformatics Platform for Prosthetic Joint-Associated Sonicate Fluid Shotgun Metagenomic Data Analysis

(2018) Qun Yan et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak

(2016) Andrea Ottesen et al.   BMC MICROBIOLOGY

Cross-talk among flesh-eatingAeromonas hydrophilastrains in mixed infection leading to necrotizing fasciitis

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Corynebacterium accolens Releases Antipneumococcal Free Fatty Acids from Human Nostril and Skin Surface Triacylglycerols

(2016) Lindsey Bomar et al.   mBio

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data

(2015) Konstantin Okonechnikov et al.   BIOINFORMATICS

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

(2015) Alexander L. Greninger et al.   Genome Medicine

Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing

(2014) Nur A. Hasan et al.   PLoS One

Longitudinal analysis of microbial interaction between humans and the indoor environment

(2014) S. Lax et al.   SCIENCE

Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples

(2014) Michael J. Strong et al.   PLoS Pathogens

Upper Respiratory Tract Microbial Communities, Acute Otitis Media Pathogens, and Antibiotic Use in Healthy and Sick Children

(2012) Melinda M. Pettigrew et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial Communities of the Upper Respiratory Tract and Otitis Media in Children

(2011) A. S. Laufer et al.   mBio

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Detection of Anaerobic Bacteria in High Numbers in Sputum from Patients with Cystic Fibrosis

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