title: Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis.
abstract: Adherent-invasive Escherichia coli (AIEC) strains are detected more frequently within mucosal lesions of patients with Crohn's disease (CD). The AIEC phenotype consists of adherence and invasion of intestinal epithelial cells and survival within macrophages of these bacteria in vitro. Our aim was to identify candidate transcripts that distinguish AIEC from non-invasive E. coli (NIEC) strains and might be useful for rapid and accurate identification of AIEC by culture-independent technology. We performed comparative RNA-Sequence (RNASeq) analysis using AIEC strain LF82 and NIEC strain HS during exponential and stationary growth. Differential expression analysis of coding sequences (CDS) homologous to both strains demonstrated 224 and 241 genes with increased and decreased expression, respectively, in LF82 relative to HS. Transition metal transport and siderophore metabolism related pathway genes were up-regulated, while glycogen metabolic and oxidation-reduction related pathway genes were down-regulated, in LF82. Chemotaxis related transcripts were up-regulated in LF82 during the exponential phase, but flagellum-dependent motility pathway genes were down-regulated in LF82 during the stationary phase. CDS that mapped only to the LF82 genome accounted for 747 genes. We applied an in silico subtractive genomics approach to identify CDS specific to AIEC by incorporating the genomes of 10 other previously phenotyped NIEC. From this analysis, 166 CDS mapped to the LF82 genome and lacked homology to any of the 11 human NIEC strains. We compared these CDS across 13 AIEC, but none were homologous in each. Four LF82 gene loci belonging to clustered regularly interspaced short palindromic repeats region (CRISPR)--CRISPR-associated (Cas) genes were identified in 4 to 6 AIEC and absent from all non-pathogenic bacteria. As previously reported, AIEC strains were enriched for pdu operon genes. One CDS, encoding an excisionase, was shared by 9 AIEC strains. Reverse transcription quantitative polymerase chain reaction assays for 6 genes were conducted on fecal and ileal RNA samples from 22 inflammatory bowel disease (IBD), and 32 patients without IBD (non-IBD). The expression of Cas loci was detected in a higher proportion of CD than non-IBD fecal and ileal RNA samples (p <0.05). These results support a comparative genomic/transcriptomic approach towards identifying candidate AIEC signature transcripts.
authors.affiliation: Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America.
authors.forename: Yuanhao
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America.
authors.forename: Leahana
authors.initials: L
authors.lastname: Rowehl
authors.affiliation: Department of Pediatrics, Stony Brook University, Stony Brook, New York, United States of America.
authors.forename: Julia M
authors.initials: JM
authors.lastname: Krumsiek
authors.affiliation: Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America.
authors.forename: Erika P
authors.initials: EP
authors.lastname: Orner
authors.affiliation: Department of Pediatrics, Washington University St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Nurmohammad
authors.initials: N
authors.lastname: Shaikh
authors.affiliation: Department of Pediatrics, Washington University St. Louis, St. Louis, Missouri, United States of America; Department of Molecular Microbiology, Washington University St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Phillip I
authors.initials: PI
authors.lastname: Tarr
authors.affiliation: The Genome Institute, Washington University St. Louis, St. Louis, Missouri, United States of America.
authors.forename: Erica
authors.initials: E
authors.lastname: Sodergren
authors.affiliation: The Genome Institute, Washington University St. Louis, St. Louis, Missouri, United States of America.
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
authors.affiliation: Department of Medicine, University of New Mexico, Albuquerque, New Mexico, United States of America.
authors.forename: Edgar C
authors.initials: EC
authors.lastname: Boedeker
authors.affiliation: Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Canada.
authors.forename: Xuejian
authors.initials: X
authors.lastname: Xiong
authors.affiliation: Department of Biochemistry & Molecular and Medical Genetics, University of Toronto, Toronto, Canada.
authors.forename: John
authors.initials: J
authors.lastname: Parkinson
authors.affiliation: Department of Medicine, University of Colorado, Denver, Colorado, United States of America.
authors.forename: Daniel N
authors.initials: DN
authors.lastname: Frank
authors.affiliation: Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America.
authors.forename: Ellen
authors.initials: E
authors.lastname: Li
authors.affiliation: Department of Pediatrics, Stony Brook University, Stony Brook, New York, United States of America.
authors.forename: Grace
authors.initials: G
authors.lastname: Gathungu
mesh_terms: D001422:Bacterial Adhesion / Q000235:genetics*; D003424:Crohn Disease / Q000382:microbiology; D015536:Down-Regulation / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D004927:Escherichia coli Infections / Q000382:microbiology*; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D006801:Humans; D007082:Ileum / Q000382:microbiology; D007413:Intestinal Mucosa / Q000382:microbiology; D008264:Macrophages / Q000382:microbiology; D012329:RNA, Bacterial / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*; D015854:Up-Regulation / Q000235:genetics
chemical_list: D012329:RNA, Bacterial