Optical mapping and 454 sequencing of Escherichia coli O157 : H7 isolates linked to the US 2006 spinach-associated outbreak

Abstract

Optical maps for five representative clinical, food-borne and bovine-derived isolates from the 2006 Escherichia coli O157 : H7 outbreak linked to fresh spinach in the United States showed a common set of 14 distinct chromosomal markers that define the outbreak strain. Partial 454 DNA sequencing was used to characterize the optically mapped chromosomal markers. The markers included insertions, deletions, substitutions and a simple single nucleotide polymorphism creating a BamHI site. The Shiga toxin gene profile of the spinach-associated outbreak isolates (stx1 " stx2 + stx2c + ) correlated with prophage insertions different from those in the prototypical EDL933 and Sakai reference strains (stx1 + stx2 + stx2c " ). The prophage occupying the yehV chromosomal position in the spinach-associated outbreak isolates was similar to the stx1 + EDL933 cryptic prophage V, but it lacked the stx1 gene. In EDL933, the stx2 genes are within prophage BP933-W at the wrbA chromosomal locus; this locus was unoccupied in the spinach outbreak isolates. Instead, the stx2 genes were found within a chimeric BP933-W-like prophage with a different integrase, inserted at the argW locus in the outbreak isolates. An extra set of Shiga toxin genes, stx2c, was found in the outbreak isolates within a prophage integrated at the sbcB locus. The optical maps of two additional clinical isolates from the outbreak showed a single, different prophage variation in each, suggesting that changes occurred in the source strain during the course of this widespread, multi-state outbreak.

Escherichia coli Serotype O55:H7 Diversity Supports Parallel Acquisition of Bacteriophage at Shiga Toxin Phage Insertion Sites during Evolution of the O157:H7 Lineage

“…Variants of stx 1 -containing bacteriophages have been found inserted at the yehV gene in O157:H7 and O84:H4 strains (9,26,57) and at the Z2577 gene in a O146:H21 strain (36). Variants of stx 2 -containing phages have been found in O157:H7 strains at wrbA (stx 2 ) (26, 57), at argW (stx 2 ) and sbcB (stx 2c ) in the 2006 spinach-outbreak related strains (38,39), and at yecE (stx 2 ) (10).…”

Overview of molecular typing methods for outbreak detection and epidemiological surveillance

“…Whole chromosome optical maps can be created for a few organisms within two days. Due to a very high accuracy and resolution potential, optical mapping has been used successfully in retrospective outbreak investigations to examine the genetic relatedness among isolates of several bacterial species [82][83][84]. Mellmann and colleagues [85] created for the first time whole chromosome optical maps in real-time outbreak investigations for the E. coli isolates recovered from patients in hospitals located in four different German cities during the 2011 outbreak of E. coli O104:H4.…”

Optical Mapping Reveals a Large Genetic Inversion between Two Methicillin-Resistant Staphylococcus aureus Strains

“…Genomic inversions have frequently been reported for strains of Escherichia coli, Salmonella enterica serovar Typhimurium, Yersinia sp., group A Streptococcus, and Lactococcus lactis (7-9, 18, 27, 28, 30, 37). Multiple types of chromosomal rearrangements have also been observed with food-borne strains of E. coli O157:H7 (19). A common observation with these inversions is the presence of IS elements or prophages flanking the junction sites.…”