ABSTRACT
Whole-genome sequencing (WGS) using next-generation sequencing (NGS) approaches is the primary requisite for establishment of genetic linkages and detection of genes of interest. Considering foodborne microbial strains of clinical relevance, it is observed that the whole world is suffering from foodborne pathogenesis. Hence, researches have been conducted in the past to decipher the pathophysiology of foodborne pathogens, using WGS and NGS tools, but skewing mostly toward bacterial strains. Both gram-positive and gram-negative bacteria associated with foodborne diseases are subjected to WGS and pertinent annotations. However, certain bacteria, like Shigella sp., which are not consistent with particular gene expression are yet to be genetically defined by WGS. In addition, filamentous fungal strains surviving in food stuffs express toxins and cause fatality; still, the whole genomic studies of candidate fungal strains are yet to be exploited using NGS contrivances. The possible reason behind this phenomenon could be due to longer generation time and the dimorphism of fungal pathogens. Likewise, the foodborne viral strains (bacteriophages) are also ignored, not being considered for whole-genome sequencings (possibly due to frequent mutations conferred by bacteriophages). In conclusion, it is urged that continuous efforts be made to identify and annotate the genes or gene clusters of all foodborne microbes using WGS and NGS approaches.
