Dear Dr Ahmed

The short answer is yes. 

Genomics can be of use to identify an unknown pathogen. They can be used to trace the origin of an outbreak. They can with some difficulty be used to estimate the reproductive number. 

They can also be used to confirm/refute theories about the origins of an outbreak. C difficle is a problem in many hospitals. Although ribotyping suggested a common epidemic strain, further sequencing has shown that there are multiple strains circulating. Another example is MRSA. Although these strains have similar phage profiles, biotypes and resistance patterns there are multiple strains in circulation rather than one or two epidemic types. Finally a paper recently reported the results of an investigation into an extended beta lactam resistant Klebsiella pneumonia that has persisted for a several years. On analysis it was found that the strain had originated several years before it was detected in the hospital. 

All this having been said isolating the genome of an unknown pathogen can be difficult. This is at the moment not really sensible. Most labs are not set up to do this in real time so for the moment it seems we are stuck with the usual methods. There has been movement in this area for TB but the jury is still out on these for the moment. Inhibitors of PCR that are not allowed for in testing systems may produce false negatives or even worse false positives. All of that having been said it seems likely that these methods will become mainstream in the not too distant future. 

If urgent action is indicated the usual methods are probably the most reliable at the moment. When possible sequencing of the pathogens responsible should be done as this provides information that may be useful or even critical and cannot be obtained in any other way. For example say there is an outbreak of Salmonella at a party. Most food associated Salmonella have the same serology and phage type. While the usual methods of identification may suggest uncooked eggs (the usual suspect) legally this may be problematic given the similarities between Salmonella and the problems with growing them from the eggs days after the party. Genomic typing may even rule the eggs out as a source.

Dear Dr Ahmed,

I would really like to upvote Dr. Mitchell's answer. 

And also for your motivation, I would request you to watch this short video https://youtu.be/lMzNL7JmHtQ to understand how rapid sequencing technology in field could accelerate diagnosis in real time. 

Also, you could watch this video https://vimeo.com/217788148 to understand how application of genomics in the field is of immense importance compared to conventional methods. 

(I understand both the videos feature Oxford Nanopore Sequencers and these are only for examples. I do not work for or support this technology or any other)

I agree with above points and add my views 

I remember a massive food-poisoning outbreak was underway in Germany emerged in early May 2011 by E. coli O157 strains and genomics of E. coli strain was very successful. 

https://www.nature.com/nbt/journal/v29/n9/full/nbt.1978.html

There are several literature available on this topic like 

https://www.ncbi.nlm.nih.gov/pubmed/25876885

http://cmr.asm.org/content/28/3/541.full

https://www.biomedcentral.com/collections/genomicsofinfectiousdiseases