I have, however, not looked into the details of the available tests, so I am speaking from general knowledge.
Assuming the proper isolation procedures have been identified and protocols have been established, these can be conducted using highly automated equipment. This is the type of equipment that was developed in the 1990's for the human genome project.
It has advanced so far that there is even discussion of sequencing the entire genome of the ocean, as discussed in this talk that I attended some years ago, 2014.
Prof. Kay Bidle, Rutgers University: The Invisible World of Marine Microbes: How Earths Smallest Living Things Have the Biggest Impact on How Our Ocean Works
I would imagine that the test requires looking for a specific single nucleic acid sequence, which is greatly simplified in comparison to mapping the genome of an entire organism or ecosystem.
The seriousness of the contamination is not to be minimized; however our worldwide scientific community is not totally disarmed. The real problem is not having equipment to run the tests, but the logistics of getting the test materials to the machines and having the machines correctly programmed to obtain results, have the results subject to quality assurance, and reporting the results.
While overall the response in this country has been abysmal, there are many talented people of good will working to respond to this crisis.