Use of optical mapping to sort uropathogenic Escherichia coli strains into distinct subgroups

Optical maps were generated for 33 uropathogenic Escherichia coli (UPEC) isolates. For individual genomes, the NcoI restriction fragments aligned into a unique chromosome map for each individual isolate, which was then compared with the in silico restriction maps of all of the sequenced E. coli and Shigella strains. All of the UPEC isolates clustered separately from the Shigella strains as well as the laboratory and enterohaemorrhagic E. coli strains. Moreover, the individual strains appeared to cluster into distinct subgroups based on the dendrogram analyses. Phylogenetic grouping of these 33 strains showed that 32/33 were the B2 subgroup and 1/33 was subgroup A. To further characterize the similarities and differences among the 33 isolates, pathogenicity island (PAI), haemolysin and virulence gene comparisons were performed. A strong correlation was observed between individual subgroups and virulence factor genes as well as haemolysis activity. Furthermore, there was considerable conservation of sequenced-strain PAIs in the specific subgroups. Strains with different antibiotic-resistance patterns also appeared to sort into separate subgroups. Thus, the optical maps distinguished the UPEC strains from other E. coli strains and further subdivided the strains into distinct subgroups. This optical mapping procedure holds promise as an alternative way to subgroup all E. coli strains, including those involved in infections outside of the intestinal tract and epidemic strains with distinct patterns of antibiotic resistance

Whole-genome shotgun optical mapping of rhodospirillumrubrum

Rhodospirillum rubrum is a phototrophic purple non-sulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems, and as a source of hydrogen and biodegradable plastics production. To better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction maps (Xba I, Nhe I, and Hind III) of R. rubrum strain ATCC 11170 were created by optical mapping. Optical mapping is a system for creating whole-genome ordered restriction maps from randomly sheared genomic DNA molecules extracted directly from cells. During the sequence finishing process, all three optical maps confirmed a putative error in sequence assembly, while the Hind III map acted as a scaffold for high resolution alignment with sequence contigs spanning the whole genome. In addition to highlighting optical mapping's role in the assembly and validation of genome sequence, our work underscores the unique niche in resolution occupied by the optical mapping system. With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a ''molecular cytogenetics'' approach to solving problems in genomic analysis

Whole-Genome Shotgun Optical Mapping of Rhodospirillum rubrum

Rhodospirillum rubrum is a phototrophic purple nonsulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems and as a source of hydrogen and biodegradable plastic production. To better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction endonuclease maps (XbaI, NheI, and HindIII) of R. rubrum strain ATCC 11170 were created by optical mapping. Optical mapping is a system for creating whole-genome ordered restriction endonuclease maps from randomly sheared genomic DNA molecules extracted from cells. During the sequence finishing process, all three optical maps confirmed a putative error in sequence assembly, while the HindIII map acted as a scaffold for high-resolution alignment with sequence contigs spanning the whole genome. In addition to highlighting optical mapping's role in the assembly and confirmation of genome sequence, this work underscores the unique niche in resolution occupied by the optical mapping system. With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a “molecular cytogenetics” approach to solving problems in genomic analysis

script

A Python script to construct FASTA files containing reconstructed genome sequences of evolved clones after DNA rearrangements

Scanning the Landscape of Genome Architecture of Non-O1 and Non-O139 <i>Vibrio cholerae</i> by Whole Genome Mapping Reveals Extensive Population Genetic Diversity

<div><p>Historically, cholera outbreaks have been linked to <i>V</i>. <i>cholerae</i> O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 <i>V</i>. <i>cholerae</i> in causing cholera and the lack of genomic sequences of such strains from around the world. Here we address these gaps by scanning a global collection of <i>V</i>. <i>cholerae</i> strains as a first step towards understanding the population genetic diversity and epidemic potential of non O1/non-O139 strains. Whole Genome Mapping (Optical Mapping) based bar coding produces a high resolution, ordered restriction map, depicting a complete view of the unique chromosomal architecture of an organism. To assess the genomic diversity of non-O1/non-O139 <i>V</i>. <i>cholerae</i>, we applied a Whole Genome Mapping strategy on a well-defined and geographically and temporally diverse strain collection, the Sakazaki serogroup type strains. Whole Genome Map data on 91 of the 206 serogroup type strains support the hypothesis that <i>V</i>. <i>cholerae</i> has an unprecedented genetic and genomic structural diversity. Interestingly, we discovered chromosomal fusions in two unusual strains that possess a single chromosome instead of the two chromosomes usually found in <i>V</i>. <i>cholerae</i>. We also found pervasive chromosomal rearrangements such as duplications and indels in many strains. The majority of <i>Vibrio</i> genome sequences currently in public databases are unfinished draft sequences. The Whole Genome Mapping approach presented here enables rapid screening of large strain collections to capture genomic complexities that would not have been otherwise revealed by unfinished draft genome sequencing and thus aids in assembling and finishing draft sequences of complex genomes. Furthermore, Whole Genome Mapping allows for prediction of novel <i>V</i>. <i>cholerae</i> non-O1/non-O139 strains that may have the potential to cause future cholera outbreaks.</p></div

Pulse field gel electrophoresis of chromosomal DNAs of <i>V</i>. <i>cholerae</i> 1154–74 (O49) and 10432–62 (O27) strains.

<p>PFGE of intact <i>V</i>. <i>cholerae</i> DNA isolated from different <i>V</i>. <i>cholerae</i> strains. Lanes from left to right: 1) Molecular weight marker (Mbases) <i>H</i>. <i>wingeii</i> chromosomes, 2) <i>V</i>. <i>cholerae</i> O1 N16961 (the bands corresponding to Chr I and Chr II are marked by an asterisk), 3) <i>V</i>. <i>cholerae</i> 10432–62 (O27) and 4) <i>V</i>. <i>cholerae</i> 1154–74 (O49). In lanes 3 and 4, the band corresponding to the single chromosome is marked by a triangle.</p