Mouse bone marrow-derived macrophages infected with E. coli strains UTI89 and ABU83972 Transcriptome or Gene expression

Urinary tract infections (UTI) are among the most common infections in humans and are a major cause of morbidity and mortality. Uropathogenic Escherichia coli (UPEC) can invade and replicate within bladder epithelial cells, and recent evidence demonstrates that some UPEC strains can also survive within macrophages. To understand the UPEC transcriptional program associated with intramacrophage survival, we performed host–pathogen co-transcriptome analyses using RNA sequencing. Mouse bone morrow-derived macrophages (BMMs) were challenged over a 24 h time course with two UPEC reference strains that possess contrasting intramacrophage phenotypes: UTI89, which survives in BMMs, and 83972, which is killed by BMMs. Using open-source tools, we developed an effective computational framework that simultaneously separated, annotated, and quantified the mammalian and bacterial transcriptomes.