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

Abstract

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.

MLST revisited: the gene-by-gene approach to bacterial genomics

“…The need for effective data repositories is well recognized, as is evident from the interest generated by initiatives such as the Global Microbial Identifier [63][64][65] , and the power of such infrastructure is illustrated by the success of the 16S rRNA sequence and MLST databases 20,62 . For example, there are many MLST databases available on a number of websites (see PubMLST, the MLST homepage, the MLST databases at the ERI, UCC (Environmental Research Institute, University College Cork, Ireland) and the Institut Pasteur MLST databases), and these databases enable data generated in different laboratories to be efficiently compared.…”

Le séquençage haut-débit

“…Depuis peu, la spectrométrie de masse permet, par l'analyse des empreintes spectrales des biomarqueurs, une identification rapide par comparaison avec une banque d [6]. Une réflexion sur la centralisation des données au sein de banques dédiées et sur la standardisation des formats doit également être menée, afin de regrouper efficacement les données pertinentes issues du séquençage, et améliorer nos connaissances [7]. Enfin, une fois les premières limites dépassées, les pipelines ergonomiques utilisant les banques de données nettoyées devront être intensivement testés sur de larges jeux de données cliniques avant d'être validés et adoptés dans les laboratoires cliniques [6].…”

A foresight study on emerging technologies: State of the art of Omics technologies and potential applications in food and feed safety

“…The extremely rapid advances in sequencing techniques open up new avenues for promoting microbial food safety (Abee, et al, 2004, Boxrud, 2010, Carrico, et al, 2013. Now that whole genome sequencing (WGS) can be performed for just over € 100,-per strain with the expectation that the price will soon approach € 50,-it is becoming a cost-effective technique for large scale application.…”

“…It can give information on modes of action and target organs (Ramirez et al, 2013). It can also detect the effects of endocrine disruptors, for example on steroid hormone synthesis (Rijk et al, 2012).…”

“…Metabolomics is expected to have a strong role in the identification of the potential targets of toxicants (Ramirez et al, 2013). It can give information on modes of action and target organs (Ramirez et al, 2013).…”