The National Archives in Record Group 109 holds a register of patients, Jan. 1, 1864 - June 12, 1865, for the General Hospital, Shreveport, La (ch. VI, vol. 297)

I do not find any records for the Jefferson Texas Hospital.

[The Confederacy, A Guide to the Archives of the Government of the Confederate States of America, National Archives and Records Administration, Washington, DC]

I have never researched these types of records and do not know to what detail they include, such as symptoms, treatment, etc. you

This site may be helpful in your search:

http://www.archives.gov/publications/prologue/1994/spring/confederate-medical-personnel.html