Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042.
BACKGROUND
Escherichia coli can experience a multifaceted life, in some cases acting as a commensal while in other cases causing intestinal and/or extraintestinal disease. Several studies suggest enteroaggregative E. coli are the predominant cause of E. coli-mediated diarrhea in the developed world and are second only to Campylobacter sp. as a cause of bacterial-mediated diarrhea. Furthermore, enteroaggregative E. coli are a predominant cause of persistent diarrhea in the developing world where infection has been associated with malnourishment and growth retardation.


METHODS
In this study we determined the complete genomic sequence of E. coli 042, the prototypical member of the enteroaggregative E. coli, which has been shown to cause disease in volunteer studies. We performed genomic and phylogenetic comparisons with other E. coli strains revealing previously uncharacterised virulence factors including a variety of secreted proteins and a capsular polysaccharide biosynthetic locus. In addition, by using Biolog Phenotype Microarrays we have provided a full metabolic profiling of E. coli 042 and the non-pathogenic lab strain E. coli K-12. We have highlighted the genetic basis for many of the metabolic differences between E. coli 042 and E. coli K-12.


CONCLUSIONS
This study provides a genetic context for the vast amount of experimental and epidemiological data published thus far and provides a template for future diagnostic and intervention strategies.
Chaudhuri
Roy R
RR
Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.
Sebaihia
Mohammed
M
Hobman
Jon L
JL
Webber
Mark A
MA
Leyton
Denisse L
DL
Goldberg
Martin D
MD
Cunningham
Adam F
AF
Scott-Tucker
Anthony
A
Ferguson
Paul R
PR
Thomas
Christopher M
CM
Frankel
Gad
G
Tang
Christoph M
CM
Dudley
Edward G
EG
Roberts
Ian S
IS
Rasko
David A
DA
Pallen
Mark J
MJ
Parkhill
Julian
J
Nataro
James P
JP
Thomson
Nicholas R
NR
Henderson
Ian R
IR
D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry; D001483:Base Sequence; D002244:Carbon / Q000378:metabolism; D017931:DNA Primers; D004926:Escherichia coli / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D004927:Escherichia coli Infections / Q000382:microbiology; D029968:Escherichia coli Proteins / Q000737:chemistry; D016680:Genome, Bacterial; D054884:Host-Pathogen Interactions; D006801:Humans; D007501:Iron / Q000378:metabolism; D008826:Microbial Sensitivity Tests; D008969:Molecular Sequence Data; D010802:Phylogeny
D000900:Anti-Bacterial Agents; D001425:Bacterial Outer Membrane Proteins; D017931:DNA Primers; D029968:Escherichia coli Proteins; C517387:YtfM protein, E coli; D002244:Carbon; D007501:Iron