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

Otávio Guilherme Gonçalves De Almeida; Elaine Cristina Pereira De Martinis

doi:10.29333/ejgm/108690

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Otávio Guilherme Gonçalves De Almeida ¹, Elaine Cristina Pereira De Martinis ¹ ^*

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¹ Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Brazil^* Corresponding Author

Abstract

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.

Keywords

high-throughput DNA sequencing
microbiology
pathogen
whole-genome sequencing

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Article Type: Review Article

ELECTRON J GEN MED, Volume 16, Issue 3, June 2019, Article No: em136

https://doi.org/10.29333/ejgm/108690

Publication date: 02 May 2019

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Declaration of Conflict of Interest: No conflict of interest is declared by author(s).

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Vancouver

Almeida OGGD, Pereira De Martinis EC. Relating next-generation sequencing and bioinformatics concepts to routine microbiological testing. ELECTRON J GEN MED. 2019;16(3):em136. https://doi.org/10.29333/ejgm/108690

APA

Almeida, O. G. G. D., & Pereira De Martinis, E. C. (2019). Relating next-generation sequencing and bioinformatics concepts to routine microbiological testing. Electronic Journal of General Medicine, 16(3), em136. https://doi.org/10.29333/ejgm/108690

AMA

Almeida OGGD, Pereira De Martinis EC. Relating next-generation sequencing and bioinformatics concepts to routine microbiological testing. ELECTRON J GEN MED. 2019;16(3), em136. https://doi.org/10.29333/ejgm/108690

Chicago

Almeida, Otávio Guilherme Gonçalves De, and Elaine Cristina Pereira De Martinis. "Relating next-generation sequencing and bioinformatics concepts to routine microbiological testing". Electronic Journal of General Medicine 2019 16 no. 3 (2019): em136. https://doi.org/10.29333/ejgm/108690

Harvard

Almeida, O. G. G. D., and Pereira De Martinis, E. C. (2019). Relating next-generation sequencing and bioinformatics concepts to routine microbiological testing. Electronic Journal of General Medicine, 16(3), em136. https://doi.org/10.29333/ejgm/108690

MLA

Almeida, Otávio Guilherme Gonçalves De et al. "Relating next-generation sequencing and bioinformatics concepts to routine microbiological testing". Electronic Journal of General Medicine, vol. 16, no. 3, 2019, em136. https://doi.org/10.29333/ejgm/108690