The pathogen here is not necessarily to be identified with a virus or bacteria; TCM has its own way of understanding illness, and defines the pathogen in terms of its own; a pathogen is a form of Qi which is injurious to the body in some way. In a way the pathogen includes a more subtle, energetic level than things like bacteria and viruses, so that even when the virus or bacteria is no longer present, or at least no longer detectable, the pathogen may remain. Hence despite no longer being infected, the patient does not feel properly recovered.
One reason why the body does not fully expel the pathogen, so that it takes up residence as a retained pathogenic factor, is a failure to allow enough time to recover properly, rushing back to work when not fully recovered for instance.
However, some TCM doctors also consider that antibiotics can lead to retained pathogens, in that whilst they kill the bacteria, they do not expel the pathogenic Qi, and indeed can ‘lock’ it inside the body. So that whilst a course of antibiotics helps the patient recover from an initial bacterial infection, they do not get back to full fitness and tend to suffer from recurrent symptoms. In western terms, this may relate to the way in which broad spectrum antibiotics attack the beneficial bacteria in the digestive tract (shock horror, not all bacteria are bad!), one consequence of which may be an overgrowth of yeasts which are normally kept in check by these bacteria, causing candidiasis for instance.
This is something to bear in mind when taking antibiotics, and is why some people suggest taking probiotics to recolonize the digestive tract with beneficial bacteria during or after a course of antibiotics. It is also something to bear in mind if you are tempted to rush back to work before being fully recovered. If you do find yourself with symptoms suggestive of a retained pathogen, feeling you have never been right since you had the ‘flu or glandular fever or something similar, acupuncture can be helpful in expelling the pathogen and restoring you to your former glory.