An author thinks that a journal’s decision not to publish is ethically incorrect

A submitted paper reported on the investigation and management of an outbreak of a disease in a work environment (Company A). The authors acknowledged the referring physician from the workplace—who had declined on legal advice to be listed as an author—and also declared that the lead author had provided medical advice for remuneration to Company A during legal proceedings related to the outbreak discussed in the article. When the article was submitted, the outbreak was the subject of legal proceedings between Company A, where the outbreak occurred, and the company supplying the alleged causative agent of the outbreak (Company B). The lead author had signed a confidentiality agreement with Company A in regards to his/her evidence for the legal proceedings, but not for any information already known to the public through no fault of the author. The author had also added a handwritten addendum, stating s/he accepted the agreement “to the extent that my academic freedom to report findings of scientific and public health importance is not compromised.” On peer review the science of the paper was judged to be sound. The journal’s legal advisor had some concerns about publication; legal proceedings were active; the workplace physician though involved scientifically was not listed as an author; and the paper discussed the outbreak from the perspective of Company A. While the article was cogent and objective about Company A, there was no information about Company B’s knowledge of the outbreak. If the case resolved in favour of Company B, then the article would need to reflect this. The editor wrote to the authors, relaying the legal concerns and informed them that journal, on the basis of legal advice, could not publish while litigation was ongoing. The journal suggested that it would consider a revised version of the manuscript after the case had been resolved. The authors submitted a revised version of the article. As part of the revisions, the authors had deleted all references to the names and locale of the companies. The legal proceedings had been concluded with an out of court settlement; the lead author had no involvement in this. The terms of the settlement are subject to a confidentiality clause and it is not known whether liability was admitted or not. Company A does not wish the paper to be published on the grounds that this would violate the confidentiality agreement between the two parties. On the basis of legal advice from his/her institution, the author states that s/he is not bound by an agreement to which s/he was not party; that the handwritten clause in his/her agreement with Company A allows for publication of the article; and that the details of the outbreak were public as they had been presented in abstract form as well as briefly described in a local language publication. The lead author feels that the journal’s reluctance to publish on the basis of legal concerns is flawed. As originally relayed to the author, it was stated that the journal could be seen as “taking sides” in an ongoing legal dispute—a view that the author feels is “ethically unacceptable. ” Company A is threatening legal action against the authors if details of the case are published, and Company B would also potentially have an action for defamation. What should be done?