Apathogenic microorganism that is highly resistant to antibiotics, often causing deep-tissue nosocomial infections, and frequently found living in many areas of the hospital is:

Pseudomonas aeruginosa

Explanation:

Pseudomonas aeruginosa is a rod like shaped bacterium, a gram negative infection invading the host cells of its host(e.g human). It leave it host restless by weakening the host defense mechanisms. This pathological condition is caused by an infection called nosocomial infections. Pseudomonas aeruginosa possess an advanced resistance mechanism hence making its treatment with antibiotics difficult.