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

Besser, John M.; Carleton, Heather; Gerner‐Smidt, Peter; Lindsey, Rebecca L.; Trees, Eija

doi:10.1016/j.cmi.2017.10.013

Cited by 397 publications

(302 citation statements)

References 48 publications

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“…Table summarizes the most commonly used sequencing technologies in phylogenomics. For more details on these different technologies see the Beginner's Handbook of Next Generation Sequencing by Genohub (https://genohub.com/next-generation-sequencing-handbook/ ) (see also Ambardar, ; Besser et al ., , and references therein). Choosing the appropriate sequencing technology for a phylogenomic study has important effects on downstream workflows, especially in terms of read length, as library preparation in some phylogenomic techniques (e.g.…”

Section: What Is Phylogenomics?mentioning

confidence: 99%

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

Young

Gillung

2019

Systematic Entomology

155

104

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Section: What Is Phylogenomics?mentioning

confidence: 99%

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

Young

Gillung

2019

Systematic Entomology

155

104

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“…NGS technology is an effective approach for laboratory management and microbe monitoring [26]. In this study, we carried out a holistic assessment of the biological background in the environment of a microbiology laboratory.…”

Section: Discussionmentioning

confidence: 99%

Application of next generation sequencing technology on contamination monitoring in microbiology laboratory

Xiao

Zhang

Yang

et al. 2019

Biosafety and Health

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The surveillance and prevention of pathogenic microbiological contamination are the most important tasks of biosafety management in the lab. There is an urgent need to establish an effective and unbiased method to evaluate and monitor such contamination. This study aims to investigate the utility of next generation sequencing (NGS) method to detect possible contamination in the microbiology laboratory. Environmental samples were taken at multiple sites at the lab including the inner site of centrifuge rotor, the bench used for molecular biological tests, the benches of biosafety cabinets used for viral culture, clinical sample pre-treatment and nucleic acids extraction, by scrubbing the sites using sterile flocked swabs. The extracted total nucleic acids were used to construct the libraries for deep sequencing according to the protocol of Ion Torrent platform. At least 1G raw data was obtained for each sample. The reads of viruses and bacteria accounted for 0.01 ± 0.02%, and 77.76 ± 12.53% of total reads respectively. The viral sequences were likely to be derived from gene amplification products, the nucleic acids contaminated in fetal bovine serum. Reads from environmental microorganisms were also identified. Our results suggested that NGS method was capable of monitoring the nucleic acids contaminations from different sources in the lab, demonstrating its promising utility in monitoring and assessing the risk of potential laboratory contamination. The risk of contamination from reagents, remnant DNA and environment should be considered in data analysis and results interpretation.

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“…The Sanger method ("first generation" technology) was the main sequencing technology used between 1975 and 2005 for microbial WGS [87]. It produces long (500-1000 bp), high-quality sequencing reads and has been regarded as the gold standard for sequencing DNA.…”

Section: Next Generation Sequencing Platformsmentioning

confidence: 99%

“…However, when both technologies are used in combination to close genomes, also known as hybrid sequencing, the short reads generate good quality contigs while the long reads can close the gaps that are between the contigs during scaffold assembly. For more information on the main sequencing platforms and their performance, refer to the brief summary (see Table 2; [87]) and the details [77,94,95] that are described in above cited excellent recent reviews.…”

Section: Next Generation Sequencing Platformsmentioning

confidence: 99%

Food Security: Microbiological and Chemical Risks

Schlundt

Tay

et al. 2020

Advanced Sciences and Technologies for Security Applications

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

Cited by 397 publications

References 48 publications

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

Application of next generation sequencing technology on contamination monitoring in microbiology laboratory

Food Security: Microbiological and Chemical Risks

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