Pathogen–host interaction plays an essential role in pathogenicity. In this study, we investigated transcriptomes of one Streptococcus pneumoniae TIGR4-derived unencapsulated strain upon exposure to THP-1 human macrophage-like cells for 0.5 h, 1 h and 3 h, respectively. Expression of most genes was up-regulated and the changes of selected genes were validated by qRT-PCR. To characterize the functions of the identified genes, one locus of genes (SP1057–SP1063) was deleted in TIGR4 by insertion replacement mutagenesis. Compared to the wild-type strain, the constructed mutant exhibited lower binding and internalization activities to the THP-1 macrophages at early incubation time periods (0.5 h and/or 1 h) but not at 3 h. However, no change was observed in the intracellular survival assays. These data indicate that the SP1057–SP1063 locus is involved in the early stage of interaction with host macrophages. Further sequence and PCR analyses suggest that the SP1057–SP1063 locus was acquired by lateral transfer.