Chemist/Microbiologist here. I make disinfectant cleaners for a living. The 99.9% is a specific claim, that has a specific legal connotation and a scientific basis as dictated by a test method. Bacterial kill is measured in “percent log reduction” and each 9 correlates to the degree of “%LR”. So if you start with a known amount of bacteria on a surface, apply your product and count the bacteria left via extraction, serial dilution and agar plating, you can correlate the %LR to a claim (claims can range from bacterial protection to sanitization to bacterial kill, etc).
99% is 2 logs, 99.9% is 3 logs, 99.99% is 4 logs and so on. To release a product into the consumer market, 99.9% reduction is the standard. That’s why bottles say “Kills 99.9%” – if the product yielded only a 99%LR, it would say “protects against 99% of bacteria.” Each word of the bottle is chosen very carefully based on the test method results.
You can pick and choose which microorganisms you test against but typically they are dictated by the test method. Staph, klebsiella, e.coli, e.hirae and salmonella are the most common. If you can make the claim with those, you are very likely to be effective against most other organisms. Of course there are exceptions which require different test methods but those products typically are used in hospital settings, not released to the general consumer.
You’d be surprised what you can find out by reading the fine print on the back of the bottle. Most people misuse their cleaners at home, don’t realize it and don’t get the protection they think they’re getting.
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