The evolutionary divergence of shiga toxin-producing escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition

Shuang Yin, Mark A. Jensen, Jiawei Bai, Chitrita Debroy, Rodolphe Barrangou, Edward G. Dudley

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

The Shiga toxin-producing Escherichia coli (STEC) strains, including those of O157:H7 and the "big six" serogroups (i.e., serogroups O26, O45, O103, O111, O121, and O145), are a group of pathogens designated food adulterants in the United States. The relatively conserved nature of clustered regularly interspaced short palindromic repeats (CRISPRs) in phylogenetically related E. coli strains makes them potential subtyping markers for STEC detection, and a quantitative PCR (qPCR)-based assay was previously developed for O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28, and O157:H7 isolates. To better evaluate the sensitivity and specificity of this qPCR method, the CRISPR loci of 252 O157 and big-six STEC isolates were sequenced and analyzed along with 563 CRISPR1 and 624 CRISPR2 sequences available in GenBank. General conservation of spacer content and order was observed within each O157 and big-six serogroup, validating the qPCR method. Meanwhile, it was found that spacer deletion, the presence of an insertion sequence, and distinct alleles within a serogroup are sources of false-negative reactions. Conservation of CRISPR arrays among isolates expressing the same flagellar antigen, specifically, H7, H2, and H11, suggested that these isolates share an ancestor and provided an explanation for the false positives previously observed in the qPCR results. An analysis of spacer distribution across E. coli strains provided limited evidence for temporal spacer acquisition. Conversely, comparison of CRISPR sequences between strains along the stepwise evolution of O157:H7 from its O55:H7 ancestor revealed that, over this̃7,000-year span, spacer deletion was the primary force generating CRISPR diversity.

Original languageEnglish (US)
Pages (from-to)5710-5720
Number of pages11
JournalApplied and environmental microbiology
Volume79
Issue number18
DOIs
StatePublished - Sep 23 2013

Fingerprint

Clustered Regularly Interspaced Short Palindromic Repeats
Shiga-Toxigenic Escherichia coli
Shiga toxin-producing Escherichia coli
divergent evolution
toxin
quantitative polymerase chain reaction
serotypes
divergence
ancestry
Polymerase Chain Reaction
Escherichia coli
antigen
False Negative Reactions
Inverted Repeat Sequences
adulterated products
allele
food pathogens
pathogen
assay
transposons

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Food Science
  • Applied Microbiology and Biotechnology
  • Ecology

Cite this

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title = "The evolutionary divergence of shiga toxin-producing escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition",
abstract = "The Shiga toxin-producing Escherichia coli (STEC) strains, including those of O157:H7 and the {"}big six{"} serogroups (i.e., serogroups O26, O45, O103, O111, O121, and O145), are a group of pathogens designated food adulterants in the United States. The relatively conserved nature of clustered regularly interspaced short palindromic repeats (CRISPRs) in phylogenetically related E. coli strains makes them potential subtyping markers for STEC detection, and a quantitative PCR (qPCR)-based assay was previously developed for O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28, and O157:H7 isolates. To better evaluate the sensitivity and specificity of this qPCR method, the CRISPR loci of 252 O157 and big-six STEC isolates were sequenced and analyzed along with 563 CRISPR1 and 624 CRISPR2 sequences available in GenBank. General conservation of spacer content and order was observed within each O157 and big-six serogroup, validating the qPCR method. Meanwhile, it was found that spacer deletion, the presence of an insertion sequence, and distinct alleles within a serogroup are sources of false-negative reactions. Conservation of CRISPR arrays among isolates expressing the same flagellar antigen, specifically, H7, H2, and H11, suggested that these isolates share an ancestor and provided an explanation for the false positives previously observed in the qPCR results. An analysis of spacer distribution across E. coli strains provided limited evidence for temporal spacer acquisition. Conversely, comparison of CRISPR sequences between strains along the stepwise evolution of O157:H7 from its O55:H7 ancestor revealed that, over this̃7,000-year span, spacer deletion was the primary force generating CRISPR diversity.",
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The evolutionary divergence of shiga toxin-producing escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition. / Yin, Shuang; Jensen, Mark A.; Bai, Jiawei; Debroy, Chitrita; Barrangou, Rodolphe; Dudley, Edward G.

In: Applied and environmental microbiology, Vol. 79, No. 18, 23.09.2013, p. 5710-5720.

Research output: Contribution to journalArticle

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T1 - The evolutionary divergence of shiga toxin-producing escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition

AU - Yin, Shuang

AU - Jensen, Mark A.

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