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Chapter 11 : Genomic and Virulence Heterogeneity of Enteroaggregative

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Abstract:

This chapter focuses on study of evolution, and examines what is understood concerning the diversity of this highly heterogeneous pathovar, recent insights from whole and partial genome sequences, and how these data may eventually be used to further clarify what factors make enteroaggregative (EAEC) pathogens. In 1999, a collaborative effort between Tom Whittam’s lab and Jim Nataro’s lab provided the first large-scale phylogenetic determination of a worldwide collection of EAEC isolates, as well as isolates previously identified as diffusely adherent (DAEC). In this study, isolates were screened by 20-locus multilocus enzyme electrophoresis (MLEE) as well as colony hybridizations to 10 plasmid-and chromosome-encoded virulence genes. These results provided for the first time a more complete picture of EAEC diversity, and several important points came to light. First, three phylogenetic groups containing EAEC strains were identified and designated EAEC1, EAEC2, and AA/DA. Second, even in cases where DAEC and EAEC strains intermingled within the same phylogenetic group, these strains were clearly distinguished by the fact that DAEC did not carry EAEC virulence determinants. Third, a few strains were classified as EAEC by the HEp-2 adherence assay but were DNA probe negative for all the screened EAEC virulence factors and clustered phylogenetically outside of EAEC1, EAEC2, and AA/DA. To date, two complete and one shotgun-assembled EAEC genome sequences are available, providing important data for comparative studies between typical and atypical EAEC, as well as EAEC from different phylogenetic groups.

Citation: Dudley E, Rasko D. 2011. Genomic and Virulence Heterogeneity of Enteroaggregative , p 181-198. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch11

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Figures

Image of Figure 1.
Figure 1.

The prototypical strain EAEC 042 adheres to cells and surfaces in a stacked-brick morphology. (A) Adherence to HEp-2 cells; note the adherence both to the cells and to the surrounding glass substratum. (B) The characteristic “honeycomb” structure formed when an EAEC isolate adheres to glass or plastic. (C) Transmission electron micrograph showing details of the honeycomb structure. (D) Higher magnification of a portion of panel C showing the AAF/II extending from the surface of the bacterium. Figures 1 A and B reprinted from reference with permission.

Citation: Dudley E, Rasko D. 2011. Genomic and Virulence Heterogeneity of Enteroaggregative , p 181-198. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch11
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Image of Figure 2.
Figure 2.

Phylogenetic analysis of EAEC isolates by two techniques. (A) MLEE analysis of EAEC and DAEC; adapted from Czeczulin et al. ( ). Strains discussed in this chapter are indicated on the tree. (B) MLST using six loci; adapted from Escobar-Paramo et al. ( ).

Citation: Dudley E, Rasko D. 2011. Genomic and Virulence Heterogeneity of Enteroaggregative , p 181-198. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch11
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Image of Figure 3.
Figure 3.

Schematic representation of the genetic organization of the AAF clusters. Arrows represent genes for the fimbriae subunits (A), putative tip adhesion (B), usher (C), and chaperone (D). The organization of genes for AAF/I, AAF/III, and AAF/IV is similar, and the range of sizes in nucleotides for the three homologs are indicated below the arrows. The four AAF/II genes are organized in two different clusters, and these are separated by 12.9 kb (indicated by break lines between and ). The size of each AAF/II gene in nucleotides is indicated.

Citation: Dudley E, Rasko D. 2011. Genomic and Virulence Heterogeneity of Enteroaggregative , p 181-198. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch11
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Image of Figure 4.
Figure 4.

Percent identity of deduced amino acid sequences of , and homologs encoded within AAF/I (genes with designation), AAF/II (), AAF/III (), and AAF/IV () clusters, as determined using BLAST with default parameters. Gene names are given on the left side of each chart, and roman numerals above indicate corresponding genes from AAF/I through AAF/IV clusters. Predicted signal sequences were removed prior to alignments. NS, no significant similarity (defined as Expect value of <0.05) was found in pairwise comparison.

Citation: Dudley E, Rasko D. 2011. Genomic and Virulence Heterogeneity of Enteroaggregative , p 181-198. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch11
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Image of Figure 5.
Figure 5.

Venn diagram of gene distribution among the EAEC, showing genomic comparisons of the complete and draft EAEC genomes to that of the commensal strain HS using the BLAST score ratio analysis ( ). Shared genes are listed in the overlapping regions of the circles, and the core genome calculated on only these four genomes is larger than when more diverse genotypes are included ( ).

Citation: Dudley E, Rasko D. 2011. Genomic and Virulence Heterogeneity of Enteroaggregative , p 181-198. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch11
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Image of Figure 6.
Figure 6.

Bioinformatic identification of a bundle-forming pilus ()-like gene cluster in 101-1. The cluster was not present in any of the other EAEC strains, but does share some similarity with the gene cluster encoded on the EPEC isolate B171 plasmid, pB171. Similarity between the two gene clusters is amino acid identity and is listed for each gene or group of genes. Attempts to identify a functional pilus in 101-1 with Bfp-reactive sera were unsuccessful.

Citation: Dudley E, Rasko D. 2011. Genomic and Virulence Heterogeneity of Enteroaggregative , p 181-198. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch11
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Tables

Generic image for table
Table 1.

Virulence genes of EAEC

Citation: Dudley E, Rasko D. 2011. Genomic and Virulence Heterogeneity of Enteroaggregative , p 181-198. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch11
Generic image for table
Table 2.

Characteristics of sequenced isolates

Citation: Dudley E, Rasko D. 2011. Genomic and Virulence Heterogeneity of Enteroaggregative , p 181-198. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch11
Generic image for table
Table 3.

Conserved and unique genes contained within EAEC strains and commensal strain HS

Citation: Dudley E, Rasko D. 2011. Genomic and Virulence Heterogeneity of Enteroaggregative , p 181-198. In Walk S, Feng P (ed), Population Genetics of Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555817114.ch11

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