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

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.