Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory

Dunne, W. Michael; Westblade, Lars F.; Ford, Bradley

doi:10.1007/s10096-012-1641-7

Cited by 143 publications

(91 citation statements)

References 69 publications

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“…The development of nextgeneration sequencing technique has revolutionized our ability to discover emerging pathogens, especially new viruses [7]. However, the clinical applications of next-generation sequencing for the diagnosis of infectious diseases are still to be explored [8].…”

Section: Archives Of Clinical Microbiology Issn 1989-8436mentioning

confidence: 99%

A Severe Leptospira interrogans Serovar Copenhageni Infection Diagnosed by Next- Generation Sequencing and Treated with Corticosteroids

Zeng¹,

Liu²,

Yuhai³

et al. 2017

Arch Clin Microbiol

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Section: Archives Of Clinical Microbiology Issn 1989-8436mentioning

confidence: 99%

A Severe Leptospira interrogans Serovar Copenhageni Infection Diagnosed by Next- Generation Sequencing and Treated with Corticosteroids

Zeng¹,

Liu²,

Yuhai³

et al. 2017

Arch Clin Microbiol

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“…In general, studies have demonstrates the prospect of metagenomics as a possible tool for clinical diagnosis. Surveillance and discovery efforts have been focused in studies of normal physiology as well as in the investigation of acute diseases like diarrhea, hemorrhagic fevers, pneumonia, among others classic infectious diseases (26)(27)(28)(29) .…”

Section: Metagenomic: Application In Clinical Contextmentioning

confidence: 99%

Metagenomic approach to study biofilm in medical context

Ribeiro

Castro

Franco

2017

MRAJ

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Microbial organization in biofilms plays an important role in health and disease. This microbial lifestyle can protect its host against pathogens and contribute to the metabolism of nutrients. On the other hand, pathogenic biofilms can increase the morbidity and mortality of patients, raising the economic cost of infections. Here, we describe how biofilm is organized, its role in different scenarios in the human body and discuss how metagenomic studies has contributed to understand the microbial diversity that interact with the host. It is currently known that many biofilms in the human body may have a polymicrobial composition. In the context of infectious diseases, this composition may limit therapeutic approaches to combat biofilms even more. Thus, describing microbial diversity could help to guide therapeutic decisions.

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“…Since the technology has been in constant evolution and the algorithms are evolving with it, there is currently no stable pipeline for the analysis of NGS data [68]. Due to limited availability of expertise in this area, centralised hubs for NGS application in diagnosis and public health have been proposed [69].…”

Section: Bioinformatics For Molecular Epidemiology: the Way Forwardmentioning

confidence: 99%

Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution

et al. 2013

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Advances in typing methodologies have been the driving force in the field of molecular epidemiology of pathogens. The development of molecular methodologies, and more recently of DNA sequencing methods to complement and improve phenotypic identification methods, was accompanied by the generation of large amounts of data and the need to develop ways of storing and analysing them. Simultaneously, advances in computing allowed the development of specialised algorithms for image analysis, data sharing and integration, and for mining the ever larger amounts of accumulated data. In this review, we will discuss how bioinformatics accompanied the changes in bacterial molecular epidemiology. We will discuss the benefits for public health of specialised online typing databases and algorithms allowing for real-time data analysis and visualisation. The impact of the new and disruptive next-generation sequencing methodologies will be evaluated, and we will look ahead into these novel challenges.

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Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory

Cited by 143 publications

References 69 publications

A Severe Leptospira interrogans Serovar Copenhageni Infection Diagnosed by Next- Generation Sequencing and Treated with Corticosteroids

A Severe Leptospira interrogans Serovar Copenhageni Infection Diagnosed by Next- Generation Sequencing and Treated with Corticosteroids

Metagenomic approach to study biofilm in medical context

Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution

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