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He doesn't need to say anything to his employer. DOT rules require any lab confirmed positive to be reported to the MRO. The MRO will contact him to interview him. Anything he tells the MRO can be used to make the decision. Since the presence of codeine could be from taking codeine OR from eating poppy seeds, unless the level was very high (unlikely), then unless there is clinical evidence of abuse - the MRO would have to report as negative.
Since any information provided to the MRO could be provided to the employer - telling the MRO that he made a "honest mistake" could be detrimental.
Since codeine from poppy seeds (a muffin, pastry etc) would appear in urine exactly the same a codeine from a pill - the MRO could not prove that the codeine did not come from poppy seeds.
If the level is above 15,000 ng/ml - very high levels, the MRO must report it as positive unless there is a valid medical explanation - poppy seeds would not explain this high of a level. Before admitting to taking codeine - he should ask what the level was. Unless the level is above 15,000 - poopy seeds would be considered a potential cause.