Genomic Diversity and Chromosomal Rearrangements in &lt;em&gt;Neisseria Gonorrhoeae&lt;/em&gt; and &lt;em&gt;Neisseria Meningitidis&lt;/em&gt;

Shaskolskiy, Boris; Kravtsov, Dmitry; Kandinov, Ilya; Dementieva, Ekaterina; Gryadunov, Dmitry

doi:10.20944/preprints202211.0228.v1

Cited by 3 publications

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

Bridging Viruses and Prokaryotic Host through Miniature Inverted-repeat Transposable Elements (MITEs)

Nadal-Molero,

Roselli,

Garcia-Juan

et al. 2024

Preprint

View full text Add to dashboard Cite

Transposable elements (TEs) have a pivotal role in the evolution of genomes across all life domains. 'Miniature Inverted-repeat Transposable-Elements' (MITEs) are non-autonomous TEs mainly located in intergenic regions, relying on external transposases for mobilization. The boundaries of MITEs' mobilome were explored across nearly 1700 prokaryotic genera, 183232 genomes, revealing a widespread distribution. MITEs were identified in 56.5% of genomes, totaling over 1.4 million cMITEs (cellular). Cluster analysis revealed that a significant 97.4% of cMITEs were conserved within genera boundaries, with up to 23% being species-specific. Subsequently, this genus-specificity was evaluated as a tool to link microbial host to their viruses. A total of 51655 cMITEs had counterparts in viral sequences, termed vMITE (viral), resulting in the identification of 2798 viral sequences with vMITEs. Among these, 1501 sequences were positively assigned to a previously known host (41.8% were isolated virus, and 12.3% were assigned through CRISPR data), while 379 new host-virus associations were predicted. Deeper analysis in Neisseria and Bacteroidetes groups allowed the association of 242 and 530 new additional viral sequences, respectively. Given the abundance of non-culturable virus sequences accumulated in databases lacking affiliations with their microbial targets, MITEs are proposed as a novel approach to establishing valid virus-host relationships.

show abstract

Bridging Viruses and Prokaryotic Host through Miniature Inverted-repeat Transposable Elements (MITEs)

Nadal-Molero,

Roselli,

Garcia-Juan

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Diversity, Distribution, and Chromosomal Rearrangements of TRIP1 Repeat Sequences in Escherichia coli

Li,

Liu,

Ning

et al. 2024

Genes

View full text Add to dashboard Cite

The bacterial genome contains numerous repeated sequences that greatly affect its genomic plasticity. The Escherichia coli K-12 genome contains three copies of the TRIP1 repeat sequence (TRIP1a, TRIP1b, and TRIP1c). However, the diversity, distribution, and role of the TRIP1 repeat sequence in the E. coli genome are still unclear. In this study, after screening 6725 E. coli genomes, the TRIP1 repeat was found in the majority of E. coli strains (96%: 6454/6725). The copy number and direction of the TRIP1 repeat sequence varied in each genome. Overall, 2449 genomes (36%: 2449/6725) had three copies of TRIP1 (TRIP1a, TRIP1b, and TRIP1c), which is the same as E. coli K-12. Five types of TRIP1 repeats, including two new types (TRIP1d and TRIP1e), are identified in E. coli genomes, located in 4703, 3529, 5741, 1565, and 232 genomes, respectively. Each type of TRIP1 repeat is localized to a specific locus on the chromosome. TRIP1 repeats can cause intra-chromosomal rearrangements. A total of 156 rearrangement events were identified, of which 88% (137/156) were between TRIP1a and TRIP1c. These findings have important implications for future research on TRIP1 repeats.

show abstract

Gonococcal Genetic Island in the Global Neisseria gonorrhoeae Population: A Model of Genetic Diversity and Association with Resistance to Antimicrobials

2023

Self Cite

View full text Add to dashboard Cite

The aim of this work was to study the genetic diversity of the gonococcal genetic island (GGI) responsible for the type IV secretion system (T4SS) and the association of a functionally active GGI with antimicrobial resistance. An analysis of the GGI in a sample of 14,763 genomes of N. gonorrhoeae isolates from the Pathogenwatch database collected in 1996–2019 from 68 countries was performed. A model of GGI’s genetic diversity that divides the global gonococcal population into fifty-one GGI clusters and three GGI superclusters based on the allele type of the traG gene and substitutions of the atlA and ych genes for eppA and ych1 has been proposed, reflecting differences among isolates in the T4SS functionality. The NG-MAST and MLST typing schemes (with accuracies of 91% and 83%, respectively) allowed the determination of both the presence of a GGI and the GGI cluster and, correspondingly, the structure of the GGI and the ability to secrete DNA. A statistically significant difference in the proportion of N. gonorrhoeae isolates resistant to ciprofloxacin, cefixime, tetracycline, and penicillin was found when comparing populations with a functional and a non-functional GGI. The presence of a functional GGI did not affect the proportion of azithromycin-resistant isolates.

show abstract

Genomic Diversity and Chromosomal Rearrangements in <em>Neisseria Gonorrhoeae</em> and <em>Neisseria Meningitidis</em>

Cited by 3 publications

References 51 publications

Bridging Viruses and Prokaryotic Host through Miniature Inverted-repeat Transposable Elements (MITEs)

Bridging Viruses and Prokaryotic Host through Miniature Inverted-repeat Transposable Elements (MITEs)

Diversity, Distribution, and Chromosomal Rearrangements of TRIP1 Repeat Sequences in Escherichia coli

Gonococcal Genetic Island in the Global Neisseria gonorrhoeae Population: A Model of Genetic Diversity and Association with Resistance to Antimicrobials

Contact Info

Product

Resources

About