| 1. |
- Stenmark, Bianca, 1987-, et al.
(author)
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Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease
- 2020
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 10:1
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Journal article (peer-reviewed)abstract
- Invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis emerged in Europe during the 2000s. Draft genomes of serogroup Y isolates in Sweden revealed that although the population structure of these isolates was similar to other serogroup Y isolates internationally, a distinct strain (YI) and more specifically a sublineage (1) of this strain was responsible for the increase of serogroup Y IMD in Sweden. We performed single molecule real-time (SMRT) sequencing on eight serogroup Y isolates from different sublineages to unravel the genetic and epigenetic factors delineating them, in order to understand the serogroup Y emergence. Extensive comparisons between the serogroup Y sublineages of all coding sequences, complex genomic regions, intergenic regions, and methylation motifs revealed small point mutations in genes mainly encoding hypothetical and metabolic proteins, and non-synonymous variants in genes involved in adhesion, iron acquisition, and endotoxin production. The methylation motif CACNNNNNTAC was only found in isolates of sublineage 2. Only seven genes were putatively differentially expressed, and another two genes encoding hypothetical proteins were only present in sublineage 2. These data suggest that the serogroup Y IMD increase in Sweden was most probably due to small changes in genes important for colonization and transmission.
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| 2. |
- Stenmark, Bianca, 1987-, et al.
(author)
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Genome-wide methylome analysis of two strains belonging to the hypervirulent Neisseria meningitidis serogroup W ST-11 clonal complex
- 2021
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 11:1
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Journal article (peer-reviewed)abstract
- A rising incidence of meningococcal serogroup W disease has been evident in many countries worldwide. Serogroup W isolates belonging to the sequence type (ST)-11 clonal complex have been associated with atypical symptoms and increased case fatality rates. The continued expansion of this clonal complex in the later part of the 2010s has been largely due to a shift from the so-called original UK strain to the 2013 strain. Here we used single-molecule real-time (SMRT) sequencing to determine the methylomes of the two major serogroup W strains belonging to ST-11 clonal complex. Five methylated motifs were identified in this study, and three of the motifs, namely 5'-GATC-3', 5'-GAAGG-3', 5'-GCGCGC-3', were found in all 13 isolates investigated. The results showed no strain-specific motifs or difference in active restriction modification systems between the two strains. Two phase variable methylases were identified and the enrichment or depletion of the methylation motifs generated by these methylases varied between the two strains. Results from this work give further insight into the low diversity of methylomes in highly related strains and encourage further research to decipher the role of regions with under- or overrepresented methylation motifs.
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| 3. |
- Stenmark, Bianca, 1987-, et al.
(author)
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Methylome comparison of two meningococcal sub-lineages of serogroup Y cc23
- 2018
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Conference paper (peer-reviewed)abstract
- Introduction: A significant increase in invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis (MenY) ST-23 clonal complex (cc23) emerged in the United States during the 1990s, spreading to Europe shortly thereafter. The largest increase was observed in Sweden with incidence proportions up to 53%. Genome analysis of all MenY isolates causing IMD between 1995 to 2012 in Sweden revealed that a distinct strain (YI) and more specifically a subtype (1) of this strain was found to be responsible for the increase of MenY IMD in Sweden [1]. In this study, we compared the methylomes of subtype 1 to the less successful subtype 2, using Single Molecule Real-Time (SMRT) sequencing technology.Methods: Ten genomes belonging to subtype 1 (n=7) and 2 (n=3) and one MenY genome without connection to a specific lineage were sequenced using SMRT sequencing on a PacBio®RS II. The analysis platform SMRT Portal v2 was used to identify modified positions and for the genome-wide analysis of modified motifs. DNA methyltransferase genes associated with the different methyltransferase recognition motifs identified were searched using SEQWARE. The modification-dependent restriction endonucleases MspJI and FspEI were used to determine the m5C recognition sites of the active m5C methylases in the strains.Results: The genome-wide analysis of the methylomes identified two m6A modified motifs: GATC and CACNNNNNTAC, but the latter was only found in isolates belonging to subtype 2 due to a transposase inserted in the candidate gene in subtype 1 strains: a Type I restriction system specificity protein (NEIS2535). The motif CACNNNNNTAC was only found in one other meningococcal isolate in REBASE, belonging to cc23, suggesting that this is a cc23 specific motif. Eleven putative restriction modification (RM) systems were found when comparing the sequences of all 11 genomes to DNA methyltransferase genes in REBASE. Five m5C genes were predicted, however, only three of these corresponding to the motifs: GCRYGC, GGNNCC and CCAGR were confirmed as active using MspJI and FspEI cleavage. The apparent CCAGR motif may be the result of two methylases, one recognizing CCWGG and the other CCAGA, but this will have to be verified.Conclusion: These results are consistent with previous studies [2] that have shown that the composition of different RM systems are clade specific suggesting that the unique RM system of cc23 isolates will most likely result in a specific DNA methylation pattern unique to this particular cc. However, although the majority of methyltransferases were shared between the two subtypes, there was one difference in a m6A modified motif between these two highly similar cc23 subtypes, which may lead to an altered gene expression pattern.
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