You only perform WGS typically after a sample has been isolated and confirmed. Through its regular method. You wouldnt just do it randomly. It is far too expensive. You can take known positives and compare them. Even save them to a database for later comparison. (How they figured out the ones in Seattle came from China)

Epis will use a mixture of surveys (what you are talking about) and lab data (WGS data) to narrow a link. If someone from city is matching in salmonella with 1 allelic difference between the 7 people sick you may not find put they all are at the same place through survey. But if you know 5 remembered then there is a good chance an Epi can identify that link.