Even though we say that one who recites the Shema' in his mind alone, with no sound emanating from his mouth, has not fulfilled his obligation of reading the Shema', nevertheless, if he is unable to read it aloud because he is ill, or for some other reason out of his control, he does fulfill his obligation.
As a matter of fact, he should read it in his mind only, even initially, if he is in an unclean place, assuming that he is unable to clean it (or go elsewhere). This is considered to be "Oness" (being out of one's control). If one is able to read it again later in a clean place, before the time for its recitation has passed, one should do so.
If, however, the place is not just unclean, but contains actual filth of the type where one is forbidden to even think of words of Torah, then one may not recite the Shema' in one's mind. In such a case, if the person desires to recite the Shema' and is pained at not being able to do so, G-d considers it as if he had recited it.
(See Shulhan 'Arukh, with Rama, 62:4. Kaf Hahayyim, ibid, Oth 8. Mishnah Berurah, ibid., 9)
Shema' Yisrael, Shma Yisroel, Reciting the Shema in a dirty place