In retrospect, this was probably a clue to the growing abundance of fakes. “My estimate is that approximately 15 to 25 percent of our sales were taken away by counterfeiting,” Mr. Kelly said. “We’re talking thousands of books.”

After the guide is printed, all copies go to Sperryville. They are then shipped to wholesalers, retailers and individual buyers. The wholesalers sell the book to Amazon. Third-party sellers on Amazon acquire their stock in several ways. One seller of a counterfeit copy told Mr. Kelly that she had bought the book from Amazon in one of its periodic sell-offs of damaged and returned books.

Sellers on Amazon can pool their goods with the same exact goods offered by Amazon itself, a practice known as commingling. This has advantages for sellers — less processing is needed, so it’s cheaper — but it also explains how Amazon can unknowingly ship counterfeits despite getting stock directly from the printer.

Some of the counterfeits appear to have been copied by scanning. That process can easily introduce numerical errors, especially with a typeface as small as the handbook’s. “There are versions of our text out in the world over which we had no control,” Mr. Kelly said.

The company filed complaints with Amazon about counterfeiting last fall. The bookseller ultimately removed many of the resellers, some of whom then went to Antimicrobial Therapy and complained that they were innocent. Amazon declined to comment on the publisher.

The communications impasse between Amazon and Antimicrobial Therapy was complicated by the fact that they did not have a direct relationship. So in December, AMT opened a vendor site on Amazon, with the bookseller getting a commission of about 20 percent on each copy sold. Under this arrangement, Amazon tells Antimicrobial Therapy where the customer lives, and the publisher ships the book from Sperryville.