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Review

Whole-genome sequencing in bacteriology: state of the art

Pages 115-123 | Published online: 08 Oct 2013

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Ping Xu & John Gunsolley. (2014) Application of metagenomics in understanding oral health and disease. Virulence 5:3, pages 424-432.
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Darlene D. Wagner, Rachel L. Marine, Edward Ramos, Terry Fei Fan Ng, Christina J. Castro, Margaret Okomo-Adhiambo, Krysten Harvey, Gregory Doho, Reagan Kelly, Yatish Jain, Roman L. Tatusov, Hideky Silva, Paul A. Rota, Agha N. Khan & M. Steven Oberste. (2022) VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data. Microbiology Spectrum 10:2.
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Sushant Parab, Davide Corà & Federico Bussolino. 2022. Methods in Actinobacteriology. Methods in Actinobacteriology 229 235 .
Laura A.E. Van Poelvoorde, Xavier Saelens, Isabelle Thomas & Nancy H. Roosens. (2020) Next-Generation Sequencing: An Eye-Opener for the Surveillance of Antiviral Resistance in Influenza. Trends in Biotechnology 38:4, pages 360-367.
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Zhuo Liu, Gerui Zhang, Zhao Jingyuan, Liyan Yu, Junxiu Sheng, Na Zhang & Hong Yuan. (2020) Second-Generation Sequencing with Deep Reinforcement Learning for Lung Infection Detection. Journal of Healthcare Engineering 2020, pages 1-9.
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Alisha Parveen, Sukant Khurana & Abhishek Kumar. (2019) Overview of Genomic Tools for Circular Visualization in the Nextgeneration Genomic Sequencing Era. Current Genomics 20:2, pages 90-99.
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Shuaiming Jiang, Chenchen Ma, Qiannan Peng, Dongxue Huo, Wu Li & Jiachao Zhang. (2019) Microbial Profile and Genetic Polymorphism of Predominant Species in Some Traditional Fermented Seafoods of the Hainan Area in China. Frontiers in Microbiology 10.
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Rodrigo E Mendes, Ronald N Jones, Leah N Woosley, Vincent Cattoir & Mariana Castanheira. (2019) Application of Next-Generation Sequencing for Characterization of Surveillance and Clinical Trial Isolates: Analysis of the Distribution of β-lactamase Resistance Genes and Lineage Background in the United States. Open Forum Infectious Diseases 6:Supplement_1, pages S69-S78.
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Deepak Kumar & Siddhartha Thakur. (2018) Molecular Tools To Study Preharvest Food Safety Challenges. Microbiology Spectrum 6:1.
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Azevedo Vasco. (2017) Pathogenesis of Corynebacterium diphtheriae and available vaccines: An Overview. Global Journal of Infectious Diseases and Clinical Research, pages 020-024.
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Frederico Schmitt Kremer, Alan John Alexander McBride & Luciano da Silva Pinto. (2017) Approaches for in silico finishing of microbial genome sequences. Genetics and Molecular Biology 40:3, pages 553-576.
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Francisco R. Fields, Shaun W. Lee & Michael J. McConnell. (2017) Using bacterial genomes and essential genes for the development of new antibiotics. Biochemical Pharmacology 134, pages 74-86.
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Ruud H. Deurenberg, Erik Bathoorn, Monika A. Chlebowicz, Natacha Couto, Mithila Ferdous, Silvia García-Cobos, Anna M.D. Kooistra-Smid, Erwin C. Raangs, Sigrid Rosema, Alida C.M. Veloo, Kai Zhou, Alexander W. Friedrich & John W.A. Rossen. (2017) Reprint of “Application of next generation sequencing in clinical microbiology and infection prevention”. Journal of Biotechnology 250, pages 2-10.
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Ruud H. Deurenberg, Erik Bathoorn, Monika A. Chlebowicz, Natacha Couto, Mithila Ferdous, Silvia García-Cobos, Anna M.D. Kooistra-Smid, Erwin C. Raangs, Sigrid Rosema, Alida C.M. Veloo, Kai Zhou, Alexander W. Friedrich & John W.A. Rossen. (2017) Application of next generation sequencing in clinical microbiology and infection prevention. Journal of Biotechnology 243, pages 16-24.
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Jozef Dingemans, Pieter Monsieurs, Sung-Huan Yu, Aurélie Crabbé, Konrad U. Förstner, Anne Malfroot, Pierre Cornelis & Rob Van Houdt. (2016) Effect of Shear Stress on Pseudomonas aeruginosa Isolated from the Cystic Fibrosis Lung. mBio 7:4.
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William H. Broach, Andy Weiss & Lindsey N. Shaw. (2016) Transcriptomic analysis of staphylococcal sRNAs: insights into species-specific adaption and the evolution of pathogenesis. Microbial Genomics 2:7.
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Jin-Hong Yoo. (2016) The Recent Trend and Perspective of Infection Control in the Republic of Korea. Korean Journal of Nosocomial Infection Control 21:1, pages 1.
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Matteo Ramazzotti, Luisa Berná, Claudio Donati & Duccio Cavalieri. (2015) riboFrame: An Improved Method for Microbial Taxonomy Profiling from Non-Targeted Metagenomics. Frontiers in Genetics 6.
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Howard E Takiff & Oscar Feo. (2015) Clinical value of whole-genome sequencing of Mycobacterium tuberculosis. The Lancet Infectious Diseases 15:9, pages 1077-1090.
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Rika A. Furuta, Hirotaka Sakamoto, Ayumu Kuroishi, Kazuta Yasiui, Harumichi Matsukura & Fumiya Hirayama. (2015) Metagenomic profiling of the viromes of plasma collected from blood donors with elevated serum alanine aminotransferase levels. Transfusion 55:8, pages 1889-1899.
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Alexander Schifrin, Thuy T. B. Ly, Nils Günnewich, Josef Zapp, Verena Thiel, Stefan Schulz, Frank Hannemann, Yogan Khatri & Rita Bernhardt. (2015) Characterization of the Gene Cluster CYP264B1- geo A from Sorangium cellulosum So ce56: Biosynthesis of (+)-Eremophilene and Its Hydroxylation . ChemBioChem 16:2, pages 337-344.
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Jacques Izard. 2015. Metagenomics for Microbiology. Metagenomics for Microbiology 1 23 .
Basil Britto Xavier, Julia Sabirova, Moons Pieter, Jean-Pierre Hernalsteens, Henri de Greve, Herman Goossens & Surbhi Malhotra-Kumar. (2014) Employing whole genome mapping for optimal de novo assembly of bacterial genomes. BMC Research Notes 7:1.
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Hanna Woksepp, Anna Ryberg, Hanna Billström, Anita Hällgren, Lennart E. Nilsson, Britt-Inger Marklund, Barbro Olsson-Liljequist & Thomas Schön. (2014) Evaluation of High-Resolution Melting Curve Analysis of Ligation-Mediated Real-Time PCR, a Rapid Method for Epidemiological Typing of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter Species) Pathogens. Journal of Clinical Microbiology 52:12, pages 4339-4342.
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Juan Carlos Palomino, Peter Vandamme & Anandi Martin. (2014) Classical and new assays for detecting drug resistance in tuberculosis. Biomarkers in Medicine 8:9, pages 1105-1114.
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Céline Lucchetti-Miganeh, David Redelberger, Gaël Chambonnier, François Rechenmann, Sylvie Elsen, Christophe Bordi, Katy Jeannot, Ina Attrée, Patrick Plésiat & Sophie de Bentzmann. (2014) Pseudomonas aeruginosa Genome Evolution in Patients and under the Hospital Environment. Pathogens 3:2, pages 309-340.
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David R. Arahal. 2014. New Approaches to Prokaryotic Systematics. New Approaches to Prokaryotic Systematics 103 122 .