Relating next-generation sequencing and bioinformatics concepts to routine microbiological testing

Autor(es)

Goncalves De Almeida, Otavio Guilherme ^[1] ; Pereira De Martinis, Elaine Cristina ^[1]

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Fac Ciencias Farmaceut Ribeirao Preto, Sao Paulo - Brazil

• Tipo de documento: Artigo de Revisão
• Fonte: ELECTRONIC JOURNAL OF GENERAL MEDICINE; v. 16, n. 3 2019.
• Citações Web of Science: 1

Resumo

Next-Generation Sequencing (NGS) is becoming a reality in the clinical microbiology laboratory because it can speed diagnosis when compared to traditional culture based-methods and moreover, to aid in unravelling key virulence traits of important pathogens. Nonetheless, there are many limitations for its wide application in routine testing, as the requirement of high performance hardware and software to support bioinformatics analysis, as well as the expertise in different programming languages to perform the analyses. In this context, this review was drawn to synthesize some basic concepts involved in NGS for Whole-Genome Sequencing (WGS), based on two international straightforward efforts to standardize WGS data acquisition and processing in the clinical routine, the PulseNet International and the ENGAGE project, allied with other tools available for WGS analysis, beginning from the available sequencing platforms to the main user-friendly pipelines dedicated for the pathogen identification, including the use of properly databases to search for virulence factors, resistance genes and software resources for molecular typing of isolates. (AU)

• Processo FAPESP: 17/13759-6 - Prospecção metagenômica de bactérias relacionadas a quorum sensing durante a fermentação espontânea do cacau
• Beneficiário: Otávio Guilherme Gonçalves de Almeida
• Modalidade de apoio: Bolsas no Brasil - Doutorado Direto