Characterization of 3 Megabase-Sized Circular Replicons from<i>Vibrio cholerae</i>

Okada, Kazuhisa; Natakuathung, Wirongrong; Na-Ubol, Mathukorn; Roobthaisong, Amonrattana; Wongboot, Warawan; Maruyama, Fumito; Nakagawa, Ichirô; Chantaroj, Siriporn; Hamada, Shigeyuki

doi:10.3201/eid2107.141055

Cited by 7 publications

(6 citation statements)

References 10 publications

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“…None of these isolates contained a third replicon, as has been reported elsewhere in other V . cholerae 33 . In order to estimate genetic distance, we mapped each sample’s corresponding short-read data 18 to the 7PET reference genome N16961 and called single nucleotide variants (SNVs) between the mapped reads for these isolates and N16961.…”

Section: Resultsmentioning

confidence: 99%

High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139

Dorman

Domman

Uddin

et al. 2019

Sci Rep

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Toxigenic Vibrio cholerae of the O139 serogroup have been responsible for several large cholera epidemics in South Asia, and continue to be of clinical and historical significance today. This serogroup was initially feared to represent a new, emerging V . cholerae clone that would lead to an eighth cholera pandemic. However, these concerns were ultimately unfounded. The majority of clinically relevant V . cholerae O139 isolates are closely related to serogroup O1, biotype El Tor V . cholerae , and comprise a single sublineage of the seventh pandemic El Tor lineage. Although related, these V . cholerae serogroups differ in several fundamental ways, in terms of their O-antigen, capsulation phenotype, and the genomic islands found on their chromosomes. Here, we present four complete, high-quality genomes for V . cholerae O139, obtained using long-read sequencing. Three of these sequences are from toxigenic V . cholerae , and one is from a bacterium which, although classified serologically as V . cholerae O139, lacks the CTXφ bacteriophage and the ability to produce cholera toxin. We highlight fundamental genomic differences between these isolates, the V . cholerae O1 reference strain N16961, and the prototypical O139 strain MO10. These sequences are an important resource for the scientific community, and will improve greatly our ability to perform genomic analyses of non-O1 V . cholerae in the future. These genomes also offer new insights into the biology of a V . cholerae serogroup that, from a genomic perspective, is poorly understood.

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Section: Resultsmentioning

confidence: 99%

High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139

Dorman

Domman

Uddin

et al. 2019

Sci Rep

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“…The two strains ( ) and ( ), for instance, underwent the process of chromosomal fusion and possess only one Mb long circular chromosome, which shows a high degree of synteny with the two chromosomes of the more common strains 36 . The strain ( ), on the other hand, besides having the original two chromosomes, also contains an additional Mb long replicon, which does not share any conserved region with Chr1 and Chr2 37 . For these reasons, we expect the single- and two-chromosome strains to be phylogenetically closer to each other than to the three-chromosome strain, which contains the extra replicon.…”

Section: Resultsmentioning

confidence: 99%

Intraspecies characterization of bacteria via evolutionary modeling of protein domains

Budimir

Giampieri

Saccenti

et al. 2022

Sci Rep

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The ability to detect and characterize bacteria within a biological sample is crucial for the monitoring of infections and epidemics, as well as for the study of human health and its relationship with commensal microorganisms. To this aim, a commonly used technique is the 16S rRNA gene targeted sequencing. PCR-amplified 16S sequences derived from the sample of interest are usually clustered into the so-called Operational Taxonomic Units (OTUs) based on pairwise similarities. Then, representative OTU sequences are compared with reference (human-made) databases to derive their phylogeny and taxonomic classification. Here, we propose a new reference-free approach to define the phylogenetic distance between bacteria based on protein domains, which are the evolving units of proteins. We extract the protein domain profiles of 3368 bacterial genomes and we use an ecological approach to model their Relative Species Abundance distribution. Based on the model parameters, we then derive a new measurement of phylogenetic distance. Finally, we show that such model-based distance is capable of detecting differences between bacteria in cases in which the 16S rRNA-based method fails, providing a possibly complementary approach , which is particularly promising for the analysis of bacterial populations measured by shotgun sequencing.

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“…A notable exception was the genome of TSY216, which contained more strain-specific genes. In addition to harboring two pairs of chromosomes, strain TSY216 also harbors a giant replicon that could explain its high strain-specificity relative to the others (46).…”

Section: Discussionmentioning

confidence: 99%

Pan-Genome Analysis of Vibrio cholerae and Vibrio metschnikovii Strains Isolated From Migratory Birds at Dali Nouer Lake in Chifeng, China

et al. 2021

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Migratory birds are recently recognized as Vibrio disease vectors, but may be widespread transporters of Vibrio strains. We isolated Vibrio cholerae (V. cholerae) and Vibrio metschnikovii (V. metschnikovii) strains from migratory bird epidemic samples from 2017 to 2018 and isolated V. metschnikovii from migratory bird feces in 2019 from bird samples taken from the Inner Mongolia autonomous region of China. To investigate the evolution of these two Vibrio species, we sequenced the genomes of 40 V. cholerae strains and 34 V. metschnikovii strains isolated from the bird samples and compared these genomes with reference strain genomes. The pan-genome of all V. cholerae and V. metschnikovii genomes was large, with strains exhibiting considerable individual differences. A total of 2,130 and 1,352 core genes were identified in the V. cholerae and V. metschnikovii genomes, respectively, while dispensable genes accounted for 16,180 and 9,178 of all genes for the two strains, respectively. All V. cholerae strains isolated from the migratory birds that encoded T6SS and hlyA were non-O1/O139 serotypes without the ability to produce CTX. These strains also lacked the ability to produce the TCP fimbriae nor the extracellular matrix protein RbmA and could not metabolize trimetlylamine oxide (TMAO). Thus, these characteristics render them unlikely to be pandemic-inducing strains. However, a V. metschnikovii isolate encoding the complete T6SS system was isolated for the first time. These data provide new molecular insights into the diversity of V. cholerae and V. metschnikovii isolates recovered from migratory birds.

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Characterization of 3 Megabase-Sized Circular Replicons fromVibrio cholerae

Cited by 7 publications

References 10 publications

High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139

High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139

Intraspecies characterization of bacteria via evolutionary modeling of protein domains

Pan-Genome Analysis of Vibrio cholerae and Vibrio metschnikovii Strains Isolated From Migratory Birds at Dali Nouer Lake in Chifeng, China

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