Pathogen detection and characterization methods in public health infectious disease surveillance rely on the identification of agents that are already known to be associated with a particular clinical syndrome. Metagenomics, as an emerging field in genomics and sequencing technology, can give a renewed impetus to pathogen detection in public health laboratories by allowing the simultaneous detection of all microorganisms in a clinical sample, without a priori knowledge of their identities, through the use of next-generation DNA sequencing. The objective remains the detection of rare and novel pathogens, and to uncover the role of dysbiotic microbiomes in infectious and chronic human disease. Advances in sequencing platforms and development of novel bioinformatics and biostatistics tools will allow metagenomics to alleviate and determine whole-genome sequences of pathogens, allowing inferences about antibiotic resistance, virulence, evolution and transmission to be made. Public health laboratories follow the trend to integrate metagenomics techniques into their diagnostic tools. Today, IonTorrent’s PGM and Proton sequencers provide the the fastest sequencing approaches with best cost-benefit results, applicable in urgent public health issues.