Emergence of Enterohemorrhagic Escherichia coli Serovar O157 Strains in Clade 8 with Highly Similar Pulsed-Field Gel Electrophoresis Patterns

2011 ◽  
Vol 74 (8) ◽  
pp. 1324-1327 ◽  
Author(s):  
EIJI YOKOYAMA ◽  
YOSHIKI ETOH ◽  
SACHIKO ICHIHARA ◽  
KAZUMI HORIKAWA ◽  
NORIKO KONISHI ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gel Electrophoresis ◽  
Pulsed Field Gel Electrophoresis ◽  
Enterohemorrhagic Escherichia Coli ◽  
Common Source ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Pulsed Field ◽  
Genetic Features ◽  
Insertion Sites

Enterohemorrhagic Escherichia coli serovar O157 (O157) strains with highly similar pulsed-field gel electrophoresis (PFGE) patterns were isolated in Japan during 2007 and 2008. Several genetic features related to O157 evolution were investigated to indicate whether homoplasy might have contributed to the highly similar PFGE patterns in these strains. The O157 strains were classified in lineage I/II, as defined by a lineage-specific polymorphism assay-6 with an atypical allele in Z5935 (code: 231111). Analysis of the insertion sites of stx2 phage in these strains showed that the sites were “occupied” in yehV and “intact” in wrbA, indicating that the strains were derived from “Cluster 1” of “Subgroup C.” When a specific single-nucleotide polymorphism in ECs2357 in clade 8 strains was investigated, all of the strains in the present study were confirmed to be clade 8 strains. These results indicated that the O157 strains in this study had common genetic features, suggesting that the highly similar PFGE patterns of these strains were not due to homoplasy. Because no common source of these strains could be identified in 2007 to 2008 in Japan, these strains may have emerged from a unique O157 clade 8 clone and then spread by dissemination in Japan.

scholarly journals Produce Isolates of the Escherichia coli Ont:H52 Serotype That Carry both Shiga Toxin 1 and Stable Toxin Genes

2006 ◽  
Vol 72 (4) ◽  
pp. 3062-3065 ◽  
Author(s):  
Steven R. Monday ◽  
Christina Keys ◽  
Patricia Hanson ◽  
Yuelian Shen ◽  
Thomas S. Whittam ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Single Nucleotide Polymorphism ◽  
Shiga Toxin ◽  
Gel Electrophoresis ◽  
Pulsed Field Gel Electrophoresis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Pulsed Field ◽  
Clonal Group ◽  
Toxin Genes

ABSTRACT Produce isolates of the Escherichia coli Ont:H52 serotype carried Shiga toxin 1 and stable toxin genes but only expressed Stx1. These strains had pulsed-field gel electrophoresis profiles that were 90% homologous to clinical Ont:H52 strains that had identical phenotypes and genotypes. All Ont:H52 strains had identical single nucleotide polymorphism profiles that are suggestive of a unique clonal group.

scholarly journals Pulsed-Field Gel Electrophoresis Profile Changes Resulting from Spontaneous Chromosomal Deletions in Enterohemorrhagic Escherichia coli O157:H7 during Passage in Cattle

2009 ◽  
Vol 75 (17) ◽  
pp. 5719-5726 ◽  
Author(s):  
Noriyo Yoshii ◽  
Yoshitoshi Ogura ◽  
Tetsuya Hayashi ◽  
Takashi Ajiro ◽  
Toshiya Sameshima ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gel Electrophoresis ◽  
Pulsed Field Gel Electrophoresis ◽  
Enterohemorrhagic Escherichia Coli ◽  
Sequencing Analysis ◽  
Pulsed Field ◽  
Chromosomal Deletions ◽  
Profile Changes ◽  
Dna Sequencing Analysis ◽  
Pfge Profiles

ABSTRACT A total of 905 enterohemorrhagic Escherichia coli (EHEC) O157:H7 isolates that were recovered from experimentally infected cattle, in addition to the inoculated strain, were analyzed by pulsed-field gel electrophoresis (PFGE). Twelve PFGE profiles other than that of the inoculated strain were observed. We successfully identified five distinct chromosomal deletions that affected the PFGE profiles using whole-genome PCR scanning and DNA sequencing analysis. The changes in PFGE profiles of EHEC O157:H7 isolates after passage through the intestinal tract of cattle were partially generated by deletion of chromosomal regions.

scholarly journals A Whole-Genome Single Nucleotide Polymorphism-Based Approach To Trace and Identify Outbreaks Linked to a Common Salmonella enterica subsp. enterica Serovar Montevideo Pulsed-Field Gel Electrophoresis Type

2011 ◽  
Vol 77 (24) ◽  
pp. 8648-8655 ◽  
Author(s):  
Henk C. den Bakker ◽  
Andrea I. Moreno Switt ◽  
Craig A. Cummings ◽  
Karin Hoelzer ◽  
Lovorka Degoricija ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Gel Electrophoresis ◽  
Salmonella Enterica ◽  
Pfge Pattern ◽  
Pulsed Field Gel Electrophoresis ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type ◽  
Pulsed Field

ABSTRACTIn this study, we report a whole-genome single nucleotide polymorphism (SNP)-based evolutionary approach to study the epidemiology of a multistate outbreak ofSalmonella entericasubsp.entericaserovar Montevideo. This outbreak included 272 cases that occurred in 44 states between July 2009 and April 2010. A case-control study linked the consumption of salami made with contaminated black and red pepper to the outbreak. We sequenced, on the SOLiD System, 47 isolates with XbaI PFGE pattern JIXX01.0011, a common pulsed-field gel electrophoresis (PFGE) pattern associated with isolates from the outbreak. These isolates represented 20 isolates collected from human sources during the period of the outbreak and 27 control isolates collected from human, food, animal, and environmental sources before the outbreak. Based on 253 high-confidence SNPs, we were able to reconstruct a tip-dated molecular clock phylogeny of the isolates and to assign four human isolates to the actual outbreak. We developed an SNP typing assay to rapidly discriminate between outbreak-related cases and non-outbreak-related cases and tested this assay on an extended panel of 112 isolates. These results suggest that only a very small percentage of the human isolates with the outbreak PFGE pattern and obtained during the outbreak period could be attributed to the actual pepper-related outbreak (20%), while the majority (80%) of the putative cases represented background cases. This study demonstrates that next-generation-based SNP typing provides the resolution and accuracy needed for outbreak investigations of food-borne pathogens that cannot be distinguished by currently used subtyping methods.

Variable Number of Tandem Repeats and Pulsed-Field Gel Electrophoresis Cluster Analysis of Enterohemorrhagic Escherichia coli Serovar O157 Strains

2007 ◽  
Vol 70 (11) ◽  
pp. 2583-2588 ◽  
Author(s):  
EIJI YOKOYAMA ◽  
MASAKO UCHIMURA
Keyword(s):  
Escherichia Coli ◽  
Cluster Analysis ◽  
Gel Electrophoresis ◽  
Tandem Repeats ◽  
Variable Number ◽  
Pulsed Field Gel Electrophoresis ◽  
Enterohemorrhagic Escherichia Coli ◽  
Pulsed Field ◽  
Epidemiological Tool ◽  
Pfge Cluster

Ninety-five enterohemorrhagic Escherichia coli serovar O157 strains, including 30 strains isolated from 13 intrafamily outbreaks and 14 strains isolated from 3 mass outbreaks, were studied by pulsed-field gel electrophoresis (PFGE) and variable number of tandem repeats (VNTR) typing, and the resulting data were subjected to cluster analysis. Cluster analysis of the VNTR typing data revealed that 57 (60.0%) of 95 strains, including all epidemiologically linked strains, formed clusters with at least 95% similarity. Cluster analysis of the PFGE patterns revealed that 67 (70.5%) of 95 strains, including all but 1 of the epidemiologically linked strains, formed clusters with 90% similarity. The number of epidemiologically unlinked strains forming clusters was significantly less by VNTR cluster analysis than by PFGE cluster analysis. The congruence value between PFGE and VNTR cluster analysis was low and did not show an obvious correlation. With two-step cluster analysis, the number of clustered epidemiologically unlinked strains by PFGE cluster analysis that were divided by subsequent VNTR cluster analysis was significantly higher than the number by VNTR cluster analysis that were divided by subsequent PFGE cluster analysis. These results indicate that VNTR cluster analysis is more efficient than PFGE cluster analysis as an epidemiological tool to trace the transmission of enterohemorrhagic E. coli O157.

scholarly journals Differential Single Nucleotide Polymorphism-Based Analysis of an Outbreak Caused by Salmonella enterica Serovar Manhattan Reveals Epidemiological Details Missed by Standard Pulsed-Field Gel Electrophoresis

2015 ◽  
Vol 53 (4) ◽  
pp. 1227-1238 ◽  
Author(s):  
Erika Scaltriti ◽  
Davide Sassera ◽  
Francesco Comandatore ◽  
Marina Morganti ◽  
Carmen Mandalari ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Gel Electrophoresis ◽  
Salmonella Enterica ◽  
Pulsed Field Gel Electrophoresis ◽  
Snp Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type ◽  
Pulsed Field ◽  
Codon Positions

We retrospectively analyzed a rareSalmonella entericaserovar Manhattan outbreak that occurred in Italy in 2009 to evaluate the potential of new genomic tools based on differential single nucleotide polymorphism (SNP) analysis in comparison with the gold standard genotyping method, pulsed-field gel electrophoresis. A total of 39 isolates were analyzed from patients (n= 15) and food, feed, animal, and environmental sources (n= 24), resulting in five different pulsed-field gel electrophoresis (PFGE) profiles. Isolates epidemiologically related to the outbreak clustered within the same pulsotype, SXB_BS.0003, without any further differentiation. Thirty-three isolates were considered for genomic analysis based on different sets of SNPs, core, synonymous, nonsynonymous, as well as SNPs in different codon positions, by Bayesian and maximum likelihood algorithms. Trees generated from core and nonsynonymous SNPs, as well as SNPs at the second and first plus second codon positions detailed four distinct groups of isolates within the outbreak pulsotype, discriminating outbreak-related isolates of human and food origins. Conversely, the trees derived from synonymous and third-codon-position SNPs clustered food and human isolates together, indicating that all outbreak-related isolates constituted a single clone, which was in line with the epidemiological evidence. Further experiments are in place to extend this approach within our regional enteropathogen surveillance system.

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