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Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/978-1-4939-7037-7_1openalex-snapshot
Whole-Genome Enrichment Using RNA Probes and Sequencing of Chlamydia trachomatis Directly from Clinical Samples
inferredcites →https://doi.org/10.1016/j.bcp.2016.12.002openalex-snapshot
Using bacterial genomes and essential genes for the development of new antibiotics
inferredcites →https://doi.org/10.1016/j.cub.2018.05.070openalex-snapshot
Cross-Contamination Explains “Inter and Intraspecific Horizontal Genetic Transfers” between Asexual Bdelloid Rotifers
inferredcites →https://doi.org/10.1016/j.ebiom.2018.10.013openalex-snapshot
The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology
inferredcites →https://doi.org/10.1016/j.mib.2014.06.002openalex-snapshot
High-throughput sequencing for the study of bacterial pathogen biology
inferredcites →https://doi.org/10.1016/s2213-2600(15)00466-xopenalex-snapshot
Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study
inferredcites →https://doi.org/10.1038/ismej.2017.69openalex-snapshot
Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations
inferredcites →https://doi.org/10.1038/ng.3148openalex-snapshot
Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis
inferredcites →https://doi.org/10.1038/nmicrobiol.2016.190openalex-snapshot
Genome-scale analysis of the non-cultivable Treponema pallidum reveals extensive within-patient genetic variation
inferredcites →https://doi.org/10.1038/nmicrobiol.2016.59openalex-snapshot
Bacterial genomics: Microbial GWAS coming of age
inferredcites →https://doi.org/10.1038/nrg3226openalex-snapshot
Transforming clinical microbiology with bacterial genome sequencing
inferredcites →https://doi.org/10.1038/nrmicro.2015.13openalex-snapshot
Within-host evolution of bacterial pathogens
inferredcites →https://doi.org/10.1073/pnas.1501049112openalex-snapshot
Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae , an urgent threat to public health
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btr708openalex-snapshot
ART: a next-generation sequencing read simulator
inferredcites →https://doi.org/10.1093/femspd/fty018openalex-snapshot
Whole-genome sequencing based characterization of antimicrobial resistance in Enterococcus
inferredcites →https://doi.org/10.1098/rspb.2015.0488openalex-snapshot
Genomic perspectives on the evolution and spread of bacterial pathogens
inferredcites →https://doi.org/10.1099/mgen.0.000205openalex-snapshot
Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages
inferredcites →https://doi.org/10.1101/gr.245373.118openalex-snapshot
Human contamination in bacterial genomes has created thousands of spurious proteins
inferredcites →https://doi.org/10.1128/aem.02020-17openalex-snapshot
Genome Sequencing Links Persistent Outbreak of Legionellosis in Sydney (New South Wales, Australia) to an Emerging Clone of Legionella pneumophila Sequence Type 211
inferredcites →https://doi.org/10.1128/jcm.00025-15openalex-snapshot
PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data
inferredcites →https://doi.org/10.1128/jcm.00119-18openalex-snapshot
Whole-Genome Sequencing of Recent Listeria monocytogenes Isolates from Germany Reveals Population Structure and Disease Clusters
inferredcites →https://doi.org/10.1128/jcm.00486-15openalex-snapshot
Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples
inferredcites →https://doi.org/10.1128/jcm.00666-18openalex-snapshot
Direct Whole-Genome Sequencing of Sputum Accurately Identifies Drug-Resistant Mycobacterium tuberculosis Faster than MGIT Culture Sequencing
inferredcites →https://doi.org/10.1128/jcm.00721-16openalex-snapshot
Whole-Genome Sequencing Elucidates Epidemiology of Nosocomial Clusters of Acinetobacter baumannii
inferredcites →https://doi.org/10.1128/jcm.00759-14openalex-snapshot
Whole-Genome Sequencing for High-Resolution Investigation of Methicillin-Resistant Staphylococcus aureus Epidemiology and Genome Plasticity
inferredcites →https://doi.org/10.1128/jcm.00831-18openalex-snapshot
Evaluation of Whole-Genome Sequencing for Identification and Typing of Vibrio cholerae
inferredcites →https://doi.org/10.1128/jcm.02116-16openalex-snapshot
Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus
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/10.1128/jcm.03534-14openalex-snapshot
Culture-Independent Genome Sequencing of Clinical Samples Reveals an Unexpected Heterogeneity of Infections by Chlamydia pecorum
inferredcites →https://doi.org/10.1128/mbio.00444-16openalex-snapshot
Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
inferredcites →https://doi.org/10.1186/s12915-017-0366-6openalex-snapshot
Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions
inferredcites →https://doi.org/10.1186/s13059-017-1196-0openalex-snapshot
The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy
inferredcites →https://doi.org/10.12688/wellcomeopenres.14265.2openalex-snapshot
Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study
inferredcites →https://doi.org/10.1371/journal.pcbi.1006277openalex-snapshot
Removing contaminants from databases of draft genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1005413openalex-snapshot
A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota
inferredcites →https://doi.org/10.1371/journal.pgen.1006724openalex-snapshot
Correction: A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota
inferredcites →https://doi.org/10.1371/journal.pmed.1001880openalex-snapshot
Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal
inferredcites →https://doi.org/10.1371/journal.pone.0164504openalex-snapshot
More than 50% of Clostridium difficile Isolates from Pet Dogs in Flagstaff, USA, Carry Toxigenic Genotypes
inferredcites →https://doi.org/10.1371/journal.pone.0184510openalex-snapshot
Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria
inferredcites →https://doi.org/10.1371/journal.ppat.1006885openalex-snapshot
When are pathogen genome sequences informative of transmission events?
inferredcites →https://doi.org/10.3201/eid2310.161248openalex-snapshot
Investigation of Outbreaks ofSalmonella entericaSerovar Typhimurium and Its Monophasic Variants Using Whole-Genome Sequencing, Denmark
inferredcites →https://doi.org/10.3389/fgene.2015.00235openalex-snapshot
Best practices for evaluating single nucleotide variant calling methods for microbial genomics
inferredcites →https://doi.org/10.7717/peerj.675openalex-snapshot
Unexpected cross-species contamination in genome sequencing projects
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1038/s41467-019-11948-6openalex-snapshot
Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex
inferred← citeshttps://doi.org/10.1038/s41579-019-0214-5openalex-snapshot
Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues
inferred← citeshttps://doi.org/10.1099/mgen.0.000418openalex-snapshot
Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences
inferred← citeshttps://doi.org/10.1099/mgen.0.000437openalex-snapshot
Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv
inferred← citeshttps://doi.org/10.1099/mgen.0.000651openalex-snapshot
Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel
inferred← citeshttps://doi.org/10.1101/2020.06.22.164186openalex-snapshot
Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv
inferred← citeshttps://doi.org/10.1101/733642openalex-snapshot
Genomic variant identification methods alter Mycobacterium tuberculosis transmission inference
inferred← citeshttps://doi.org/10.1128/msphere.00991-21openalex-snapshot
The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible
inferred← citeshttps://doi.org/10.3390/books978-3-0365-6523-1openalex-snapshot
Genomic Analysis of Antibiotics Resistance in Pathogens
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