Optical maps distinguish individual strains of Escherichia coli O157 : H7

Kotewicz, Michael L.; Jackson, Scott A.; LeClerc, J. Eugene; Cebula, Thomas A.

doi:10.1099/mic.0.2006/004507-0

Cited by 47 publications

(52 citation statements)

References 45 publications

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“…Small restriction fragments, ranging from 21 bp to 1.5 kb, found in the sequence-based maps are not efficiently detected in optical maps. These fragments are called dropout fragments, and their effect on the overall size determination of a 5 Mbp genome is 20-40 kb (Kotewicz et al, 2007). …”

Section: Resultsmentioning

confidence: 99%

“…Changes seen in the chromosomes of outbreak strains were the same whether their optical maps were aligned either to sequence-based in silico or to de novo optical maps of EDL933 and Sakai. The small drop-out fragments from 21 bp to 1.5 kb lost in optical maps lower the ability to detect differences only slightly (Kotewicz et al, 2007).…”

Section: Resultsmentioning

confidence: 99%

“…Variations among dozens of prophage integrations and excisions, as well as prophage deletions and substitutions, have changed restriction sites and PFGE and PCR profiles for otherwise similar E. coli O157 : H7 isolates. Notably, large, and often double, chromosomal inversions are prevalent in E. coli O157 : H7 isolates (Iguchi et al, 2006;Shima et al, 2006;Kotewicz et al, 2007) and the inversions have occurred within resident prophages.…”

Section: Introductionmentioning

confidence: 99%

“…However, PFGE has limited resolving power; other microbiological and biochemical characterizations, including single-nucleotide polymorphism (SNP) profiles and DNA microarray analysis, can provide much more detail, albeit at greater expense. For example, when applied to Escherichia coli O157 : H7, DNA microarray studies have generated a wealth of information on genome variability among isolates of this important pathogen (Fukiya et al, 2004;Wick et al, 2005;Ogura et al, 2006;Jackson et al, 2007;Zhang et al, 2006). DNA arrays, however, also have limitations in that they cannot detect the presence of new genes or novel rearrangements of genes, nor can they determine the chromosomal locations(s) of genomic elements.…”

Section: Introductionmentioning

confidence: 99%

“…The contiguous fragments of one optical map can be aligned and compared to the BamHI in silico chromosome map of a sequenced reference strain, or to the optical maps of different strains. Changes as small as 2 kb can be mapped (Lim et al, 2001;Chen et al, 2006;Kotewicz et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2008

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2008

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Physical Maps of Chromosomes

Ussery

2009

Encyclopedia of Life Sciences

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Physical maps of chromosomes are a way of visualizing the entire chromosome in a single figure. Physical maps can come in a variety of formats, including actual photographs of chromosomes, genetic maps where the relative locations of genes are mapped, restriction maps showing the location of restriction enzyme cutting sites along the deoxyribonucleic acid (DNA), and finally maps based on the known DNA sequence along the entire chromosome.

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Optical mapping of DNA: Single‐molecule‐based methods for mapping genomes

2011

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The technologies associated with DNA sequencing are rapidly evolving. Indeed, single-molecule DNA sequencing strategies are cheaper and faster than ever before. Despite this progress, every sequencing platform to date relies on reading the genome in small, abstract fragments, typically of less than 1000 bases in length. The overarching aim of the optical map is to complement the information derived from DNA sequencing by providing long-range context on which these short sequence reads can be built. This is typically done using an enzyme to target and modify at short DNA sequences of, say, six bases in length throughout the genome. By accurately placing these short pieces of sequence on long genomic DNA fragments, up to several millions of bases in length, a scaffold for sequence assembly can be obtained. This review focuses on three enzymatic approaches to optical mapping. Optical mapping was first developed using restriction enzymes to sequence-specifically cleave DNA that is immobilized on a surface. More recently, nicking enzymes have found application in the sequence-specific fluorescent labeling of DNA for optical mapping. Such covalent modification allows the DNA to be imaged in solution, and this, in combination with developing nanofluidic technologies, is enabling new high-throughput approaches to mapping. And, finally, this review will discuss the recent development of mapping with subdiffraction-limit precision using methyltransferase enzymes to label the DNA with an ultrahigh density.

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Optical maps distinguish individual strains of Escherichia coli O157 : H7

Cited by 47 publications

References 45 publications

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

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

Physical Maps of Chromosomes

Optical mapping of DNA: Single‐molecule‐based methods for mapping genomes

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