I am assuming that by pathogenic you mean that the host is listed as human in NCBI Taxonomy. In such a situation, you should start at NCBI Taxonomy with the following query:
Acinetobacter baumannii[Name Tokens] AND "host human"[Properties]. You will see 312 results. Click on the drop-down list under "Find related data" and choose "SRA". This will return 208 SRA results.