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Understanding the host-adapted state of Citrobacter rodentium by transcriptomic analysis

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Abstract

Citrobacter rodentium (Cr) is a mouse pathogen that mimics many aspects of enteropathogenic Escherichia coli infections including producing attaching and effacing (A/E) lesions. Host-adapted (HA) Cr cells that are shed at the peak of infection have been reported to be hyper-infective. The exact mechanism underlying this phenomenon has remained elusive since the pathogen loses its HA ‘status’ immediately upon subculturing in laboratory media. We sequenced the entire transcriptome of Cr directly from the feces of infected mice and analyzed the gene expression pattern. We observed that the entire transcriptional machinery as well as several transcriptional regulators to be differentially expressed when compared with the transcriptome of cells grown on laboratory media. Major adhesion and effector genes, tir and eae, were highly expressed in HA along with many genes located on all five loci of enterocyte effacement regions (LEE 1–5). Notable absent among the HA expressed genes were 19 fimbrial operons and non-fimbrial adhesions and several non-LEE encoded effectors. These results demonstrate that host-adapted Cr has a unique transcriptome that is associated with increased host transmission.

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Authors and Affiliations

  1. Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, 10300 Baltimore Ave., B307C, Rm. 228, BARC-E, Beltsville, MD, 20705, USA

    Allen D. Smith, Celine Chen & Harry D. Dawson

  2. Environmental, Microbial, and Food Safety Laboratory, Beltsville Agriculture Research Center, USDA-ARS, Beltsville, MD, USA

    Xianghe Yan & Arvind A. Bhagwat

Authors
  1. Allen D. Smith
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  2. Xianghe Yan
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  3. Celine Chen
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  4. Harry D. Dawson
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  5. Arvind A. Bhagwat
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Correspondence to Allen D. Smith.

Additional information

Communicated by Erko Stackebrandt.

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203_2016_1191_MOESM1_ESM.pptx

Principle component analysis of RNAseq samples. Cr was grown under three conditions: aerobic LB media grown cells, host-adapted cells, and anaerobic fecal media grown cells (n=3/group). A 3D plot was generated for comparison of all three growth conditions using the coefficient of variation of the eigenvalues of the PCA analysis. Hierarchical clustering of genes of Cr revealed the spatial partitioning of sample replicates across growth conditions indicating that unique gene expression patterns were present in each group (PPTX 74 kb)

203_2016_1191_MOESM2_ESM.pptx

Comparison of gene expression levels by RNASeq and qRT-PCR. The figure compares the mean fold change in gene expression obtained from RNAseq vs. qRT-PCR data under host-adapted and LB conditions (n=3-4). Primers used for individual genes are as indicated in Table S1. Regression analysis was done using SigmaPlot version 11 (Systat Software, Germany) (PPTX 55 kb)

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Smith, A.D., Yan, X., Chen, C. et al. Understanding the host-adapted state of Citrobacter rodentium by transcriptomic analysis. Arch Microbiol 198, 353–362 (2016). https://doi.org/10.1007/s00203-016-1191-y

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  • DOI: https://doi.org/10.1007/s00203-016-1191-y

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