Yes, i am using streptococcus pneumonia ATCC700669 (FM211187). I downloaded the fasta file.. made the index file by bowtie-build and then mapped using tophat2. The result that i got for the diseased sample is :

Left reads:
          Input     :    164672
           Mapped   :       540 ( 0.3% of input)
            of these:       512 (94.8%) have multiple alignments (0 have >20)
Right reads:
          Input     :    164672
           Mapped   :      1119 ( 0.7% of input)
            of these:      1057 (94.5%) have multiple alignments (0 have >20)
Unpaired reads:
          Input     :     48331
           Mapped   :       148 ( 0.3% of input)
            of these:       141 (95.3%) have multiple alignments (0 have >20)
 0.5% overall read mapping rate.

Aligned pairs:         6
     of these:         6 (100.0%) have multiple alignments
                       2 (33.3%) are discordant alignments
 0.0% concordant pair alignment rate.

And for the healthy (was just exoerimenting with the healthy sample, what comes out)

Left reads:
          Input     :   1254299
           Mapped   :       843 ( 0.1% of input)
            of these:       156 (18.5%) have multiple alignments (0 have >20)
Right reads:
          Input     :   1254299
           Mapped   :      2527 ( 0.2% of input)
            of these:      1700 (67.3%) have multiple alignments (0 have >20)
 0.1% overall read mapping rate.

Aligned pairs:       719
     of these:        45 ( 6.3%) have multiple alignments
 0.1% concordant pair alignment rate.

By just looking at the result, do you say that the bacterial genome remain are into the sample???