Surveillance of bacterial pathogens important to public health microbiology has traditionally relied on physiological, biochemical and phenotypic properties as markers for species identification and strain typing. In the 1930’s, serotyping based on antigen-antibody reactions was one of the first approaches to differentiate bacteria beyond the species level; this was followed by phage typing schemes in the 1950’s. It wasn’t until the 1980's, that the first bacterial strain typing methods based on nucleic acid markers were developed leading to Pulse Field Gel Electrophoresis (PFGE) as the gold standard.
Since then, many sequence-based approaches for the detection and typing of pathogens have emerged starting with multilocus sequence typing (MLST) and leading to the current gold standard approach, single nucleotide polymorphism (SNP)-based typing approaches utilising whole genome sequence data. This pathogen genomics approach has offered the opportunity to unify workflows and harmonise surveillance via global data analysis platforms. From the beginning, these various approaches have relied on characterisation of pure isolates, however, increasing diversity of microbial pathogens coupled with the use of culture independent testing compromises current genomic surveillance approaches. Sequencing strategies need to adapt to ensure they can simultaneously identify and type diverse microorganisms in complex samples with precision. Metagenomics-enabled surveillance methods offer the opportunity to improve detection of both known and yet-to-emerge pathogens.