Altered infective competence of the human gut microbiome in COVID-19

[1]  S. Haque,et al.  Bacterial co-infections and antimicrobial resistance associated with the Coronavirus Disease 2019 infection. , 2022, Biotechnology & genetic engineering reviews.

[2]  T. Miyoshi‐Akiyama,et al.  Human Gut Microbiota and Its Metabolites Impact Immune Responses in COVID-19 and Its Complications , 2022, Gastroenterology.

[3]  Sanjay Budhdeo,et al.  COVID-19 severity is associated with population-level gut microbiome variations , 2022, Frontiers in Cellular and Infection Microbiology.

[4]  F. Islam,et al.  The impact of mucormycosis (black fungus) on SARS-CoV-2-infected patients: at a glance , 2022, Environmental Science and Pollution Research.

[5]  P. Wilmes,et al.  Long COVID Symptomatology After 12 Months and Its Impact on Quality of Life According to Initial Coronavirus Disease 2019 Disease Severity , 2022, Open forum infectious diseases.

[6]  B. Alisjahbana,et al.  MDR Pathogens Organisms as Risk Factor of Mortality in Secondary Pulmonary Bacterial Infections Among COVID-19 Patients: Observational Studies in Two Referral Hospitals in West Java, Indonesia , 2022, International journal of general medicine.

[7]  T. Borody,et al.  Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity , 2022, BMJ open gastroenterology.

[8]  S. Dutta,et al.  Role of the Microbiome in the Pathogenesis of COVID-19 , 2022, Frontiers in Cellular and Infection Microbiology.

[9]  M. Merad,et al.  The immunology and immunopathology of COVID-19 , 2022, Science.

[10]  Yang‐Yu Liu,et al.  Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes , 2022, Nature Communications.

[11]  T. Dingle,et al.  Antimicrobial resistance (AMR) in COVID-19 patients: a systematic review and meta-analysis (November 2019–June 2021) , 2022, Antimicrobial Resistance & Infection Control.

[12]  Shiraz A. Shah,et al.  Genome binning of viral entities from bulk metagenomics data , 2022, Nature Communications.

[13]  K. Stȩpniewska,et al.  Antibiotic resistance, virulence, and phylogenetic analysis of Escherichia coli strains isolated from free-living birds in human habitats , 2022, PloS one.

[14]  Meiqin Zheng,et al.  Alterations of fecal antibiotic resistome in COVID-19 patients after empirical antibiotic exposure , 2021, International Journal of Hygiene and Environmental Health.

[15]  Janet Diaz,et al.  A clinical case definition of post-COVID-19 condition by a Delphi consensus , 2021, The Lancet Infectious Diseases.

[16]  T. Dingle,et al.  Antimicrobial resistance (AMR) in COVID-19 patients: a systematic review and meta-analysis (November 2019–June 2021) , 2021, Antimicrobial Resistance & Infection Control.

[17]  L. Fang,et al.  The changing pattern of enteric pathogen infections in China during the COVID-19 pandemic: a nation-wide observational study , 2021, The Lancet Regional Health - Western Pacific.

[18]  D. Sanchez-Ramirez,et al.  Long-Term Impact of COVID-19: A Systematic Review of the Literature and Meta-Analysis , 2021, Biomedicines.

[19]  Shiraz A. Shah,et al.  Genome binning of viral entities from bulk metagenomics data , 2021, bioRxiv.

[20]  R. Pandey,et al.  Co-infections as Modulators of Disease Outcome: Minor Players or Major Players? , 2021, Frontiers in Microbiology.

[21]  E. Nweze,et al.  Nanoparticles as therapeutic options for treating multidrug-resistant bacteria: research progress, challenges, and prospects , 2021, World journal of microbiology & biotechnology.

[22]  H. Tun,et al.  Gut microbiome and resistome changes during the first wave of the COVID-19 pandemic in comparison with pre-pandemic travel-related changes , 2021, Journal of travel medicine.

[23]  S. Janković,et al.  Antimicrobial treatment of Erysipelatoclostridium ramosum invasive infections: a systematic review , 2021, Revista do Instituto de Medicina Tropical de Sao Paulo.

[24]  D. A. Santos,et al.  Fungal and bacterial coinfections increase mortality of severely ill COVID-19 patients , 2021, Journal of Hospital Infection.

[25]  Lanjuan Li,et al.  Six-month follow-up of gut microbiota richness in patients with COVID-19 , 2021, Gut.

[26]  A. Gómez-Mejia,et al.  Bacterial pulmonary superinfections are associated with longer duration of ventilation in critically ill COVID-19 patients , 2021, Cell Reports Medicine.

[27]  Guozhong Zhang,et al.  Resident bacteria contribute to opportunistic infections of the respiratory tract , 2021, PLoS pathogens.

[28]  E. Haddad,et al.  Antibiotics in treatment of COVID-19 complications: a review of frequency, indications, and efficacy , 2021, Journal of infection and public health.

[29]  E. Haddad,et al.  Antibiotic usage in 2019 coronavirus disease (Covid-19) treatment: a rapid review on frequency, indications, and efficacy , 2021, Journal of Infection and Public Health.

[30]  M. Cavaleri,et al.  Antimicrobial multidrug resistance in the era of COVID-19: a forgotten plight? , 2021, Antimicrobial resistance and infection control.

[31]  M. Cavaleri,et al.  Antimicrobial multidrug resistance in the era of COVID-19: a forgotten plight? , 2021, Antimicrobial Resistance & Infection Control.

[32]  T. Mizutani,et al.  The human microbiome and COVID-19: A systematic review , 2021, PloS one.

[33]  Timothy L. Tickle,et al.  Multivariable association discovery in population-scale meta-omics studies , 2021, bioRxiv.

[34]  K. Chow,et al.  Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19 , 2021, Gut.

[35]  P. Póvoa,et al.  Relationship between SARS-CoV-2 infection and the incidence of ventilator-associated lower respiratory tract infections: a European multicenter cohort study , 2021, Intensive Care Medicine.

[36]  K. K. Sharma,et al.  Pathobionts: mechanisms of survival, expansion, and interaction with host with a focus on Clostridioides difficile , 2021, Gut microbes.

[37]  Y. Bi,et al.  Integrated gut virome and bacteriome dynamics in COVID-19 patients , 2021, Gut microbes.

[38]  P. Manghi,et al.  Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 , 2020, bioRxiv.

[39]  M. Wilkins,et al.  Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing , 2020, Scientific Reports.

[40]  I-Min A. Chen,et al.  IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses , 2020, Nucleic Acids Res..

[41]  J. Mossong,et al.  Protocol for a prospective, longitudinal cohort of people with COVID-19 and their household members to study factors associated with disease severity: the Predi-COVID study , 2020, BMJ Open.

[42]  N. Price,et al.  Health and disease markers correlate with gut microbiome composition across thousands of people , 2020, Nature Communications.

[43]  Felipe García,et al.  Incidence of co-infections and superinfections in hospitalized patients with COVID-19: a retrospective cohort study , 2020, Clinical Microbiology and Infection.

[44]  S. Peddada,et al.  Analysis of compositions of microbiomes with bias correction , 2020, Nature Communications.

[45]  N. Van Regenmortel,et al.  COVID-19-associated invasive pulmonary aspergillosis , 2020, Annals of Intensive Care.

[46]  S. Ng,et al.  Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization , 2020, Gastroenterology.

[47]  Zhicheng Li,et al.  A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data , 2020, bioRxiv.

[48]  B. Stecher,et al.  Label or Concept - What Is a Pathobiont? , 2020, Trends in microbiology.

[49]  W. Lim,et al.  Co-infections in people with COVID-19: a systematic review and meta-analysis , 2020, Journal of Infection.

[50]  Hans Clevers,et al.  SARS-CoV-2 productively infects human gut enterocytes , 2020, Science.

[51]  N. Shah,et al.  Rates of Co-infection Between SARS-CoV-2 and Other Respiratory Pathogens. , 2020, JAMA.

[52]  Daniel C. Baumgart,et al.  Diarrhea During COVID-19 Infection: Pathogenesis, Epidemiology, Prevention, and Management , 2020, Clinical Gastroenterology and Hepatology.

[53]  A. Heintz‐Buschart,et al.  PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data , 2020, bioRxiv.

[54]  Sunny H Wong,et al.  Covid‐19 and the digestive system , 2020, Journal of gastroenterology and hepatology.

[55]  H. Shan,et al.  Prolonged presence of SARS-CoV-2 viral RNA in faecal samples , 2020, The Lancet Gastroenterology & Hepatology.

[56]  R. Trimble COVID-19 Dashboard , 2020 .

[57]  Karthik Anantharaman,et al.  VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences , 2020, Microbiome.

[58]  Donovan H Parks,et al.  GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database , 2019, Bioinform..

[59]  Geoffrey L. Winsor,et al.  CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database , 2019, Nucleic Acids Res..

[60]  Jennifer Lu,et al.  Improved metagenomic analysis with Kraken 2 , 2019, Genome Biology.

[61]  B. Liu,et al.  Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing , 2019, bioRxiv.

[62]  Feng Li,et al.  MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies , 2019, PeerJ.

[63]  D. Graham,et al.  Clinical Spectrum , 2018, A Clinician's Guide to Progressive Supranuclear Palsy.

[64]  M. Bassetti,et al.  Multidrug-resistant Klebsiella pneumoniae: challenges for treatment, prevention and infection control , 2018, Expert review of anti-infective therapy.

[65]  E. Pamer,et al.  Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them , 2018, Mucosal Immunology.

[66]  Fengzhu Sun,et al.  Identifying viruses from metagenomic data by deep learning. , 2018, 1806.07810.

[67]  Alexander J Probst,et al.  Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy , 2017, Nature Microbiology.

[68]  E. Garner,et al.  DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data , 2018, Microbiome.

[69]  Andrzej Dziembowski,et al.  PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures , 2018, Nucleic acids research.

[70]  Lenwood S. Heath,et al.  DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data , 2017, bioRxiv.

[71]  A. Heintz‐Buschart,et al.  IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses , 2016, Genome Biology.

[72]  A. Heintz‐Buschart,et al.  IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses , 2016, Genome Biology.

[73]  A. Heintz‐Buschart,et al.  Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes , 2016, Nature Microbiology.

[74]  Måns Magnusson,et al.  MultiQC: summarize analysis results for multiple tools and samples in a single report , 2016, Bioinform..

[75]  Alexey A. Gurevich,et al.  MetaQUAST: evaluation of metagenome assemblies , 2016, Bioinform..

[76]  Blake A. Simmons,et al.  MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets , 2016, Bioinform..

[77]  Brian D. Ondov,et al.  Mash: fast genome and metagenome distance estimation using MinHash , 2015, Genome Biology.

[78]  Connor T. Skennerton,et al.  CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.

[79]  E. Bornberg-Bauer,et al.  Host–Pathogen Coevolution: The Selective Advantage of Bacillus thuringiensis Virulence and Its Cry Toxin Genes , 2015, PLoS biology.

[80]  Matthew B. Sullivan,et al.  VirSorter: mining viral signal from microbial genomic data , 2015, PeerJ.

[81]  Kunihiko Sadakane,et al.  MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..

[82]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[83]  J. Martínez Short-sighted evolution of bacterial opportunistic pathogens with an environmental origin , 2014, Front. Microbiol..

[84]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[85]  Brian Bushnell,et al.  BBMap: A Fast, Accurate, Splice-Aware Aligner , 2014 .

[86]  Luis Miguel Rodriguez-Rojas,et al.  Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets , 2014, Bioinform..

[87]  S. Rampelli,et al.  Inflammation and colorectal cancer, when microbiota-host mutualism breaks. , 2014, World journal of gastroenterology.

[88]  C. Buffie,et al.  Microbiota-mediated colonization resistance against intestinal pathogens , 2013, Nature Reviews Immunology.

[89]  G. Bou,et al.  Antimicrobial Resistance and Virulence: a Successful or Deleterious Association in the Bacterial World? , 2013, Clinical Microbiology Reviews.

[90]  Hélène Touzet,et al.  SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data , 2012, Bioinform..

[91]  G. B. Golding,et al.  Antibiotic resistance is ancient , 2011, Nature.

[92]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[93]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[94]  C. Waldner,et al.  Associations between Antimicrobial Resistance Phenotypes, Antimicrobial Resistance Genes, and Virulence Genes of Fecal Escherichia coli Isolates from Healthy Grow-Finish Pigs , 2009, Applied and Environmental Microbiology.

[95]  B. Finlay,et al.  Crossing the Line: Selection and Evolution of Virulence Traits , 2006, PLoS pathogens.

[96]  Jun Yu,et al.  VFDB: a reference database for bacterial virulence factors , 2004, Nucleic Acids Res..

[97]  Vincent Burrus,et al.  Shaping bacterial genomes with integrative and conjugative elements. , 2004, Research in microbiology.

[98]  S. Weber,et al.  Rotavirus infection in adults , 2004, The Lancet Infectious Diseases.

[99]  Fernando Baquero,et al.  Interactions among Strategies Associated with Bacterial Infection: Pathogenicity, Epidemicity, and Antibiotic Resistance , 2002, Clinical Microbiology Reviews.

[100]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[101]  Sven Rahmann,et al.  Genome analysis , 2022 .

[102]  S. McIlroy,et al.  DNA and RNA extraction , 2010 .