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Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks

Shannon D. Manning^*, Alifiya S. Motiwala, A. Cody Springman^*, Weihong Qi^*, David W. Lacher^*, Lindsey M. Ouellette^*, Janice M. Mladonicky^*, Patricia Somsel, James T. Rudrik, Stephen E. Dietrich, Wei Zhang, Bala Swaminathan^¶, David Alland, and Thomas S. Whittam^*,||

*Microbial Evolution Laboratory, National Food Safety and Toxicology Center, Michigan State University, East Lansing, MI 48824; Division of Infectious Diseases, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103; Bureau of Laboratories, Michigan Department of Community Health, Lansing, MI 48909; National Center for Food Safety and Technology, Illinois Institute of Technology, Summit, IL 60501; and ^¶Foodborne and Diarrheal Diseases Branch, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333

View larger version (27K): [in this window] [in a new window]   Fig. 1. Genetic relatedness of E. coli O157 among 403 O157 and closely related O55:H7 strains based on 96 SNPs. (A) The location of 83 genes within 96 SNP loci on the E. coli O157:H7 genomic map of the Sakai strain. Real-time PCR assays detected 52 loci with nonsynonymous polymorphisms (black circles), 43 loci with synonymous polymorphisms (white circles), and one locus (uidA-686) with a GG insertion (open triangle). (B) The distribution of nucleotide diversity () across 96 SNP loci. Diversity ranges from 0 for two monomorphic SNP loci to a maximum between 0.45 and 0.50 for 26 loci. The average for the 96 loci is 0.212 ± 0.199. (C) Phylogenetic relationships among SNP genotypes (SGs) using the minimum evolution algorithm based on the distance matrix of pairwise differences between SGs. The consensus tree is shown with the percentages at the nodes of the >70% bootstrap confidence values based on 1,000 replicates. Both the GUD+ and Sor+, which occur in clade 9, are negative (GUD– and Sor–) in the derived clades 1–8.

View larger version (18K): [in this window] [in a new window]   Fig. 2. The phylogenetic network applied to 48 parsimoniously informative (PI) sites using the Neighbor-net algorithm for 528 E. coli O157 strains. The colored ellipses mark clades supported in the minimum evolution phylogeny. The numbers at the nodes denote the SNP genotypes (SGs) 1–39, and the white circle nodes contain two SGs that match at the 48 PI sites. The seven SGs found among multiple continents are marked with squares.

View larger version (13K): [in this window] [in a new window]   Fig. 3. Distribution of Shiga toxin (Stx) genes in E. coli O157 clades. (A) The frequency of 528 O157 strains that were classified into one of nine clades based on SNP genotyping, ranked from left to right in the histogram by decreasing frequency. The four most common clades were clades 2 (47.6%), 8 (25.4%), 3 (10.6%), and 7 (7.3%). (B) Distribution of Shiga toxin variants (stx1, stx2, and stx2c) among 519 of the 528 O157 strains organized into nine clades. The percentage of PCR assay positive strains overall is given in parentheses.

View larger version (16K): [in this window] [in a new window]   Fig. 4. Odd ratios with 95% confidence intervals (dotted lines) highlighting the association between patient characteristics and infection with specific clades. Logistic regression models were adjusted for age, gender, bloody diarrhea, diarrhea, abdominal pain, chills, HUS, hospitalization, and body aches. Dark circles show significant associations.

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