Genomic Diversity and Chromosomal Rearrangements in Neisseria gonorrhoeae and Neisseria meningitidis

Abstract

Chromosomal rearrangements in N. gonorrhoeae and N. meningitidis were studied with the determination of mobile elements and their role in rearrangements. The results of whole-genome sequencing and de novo genome assembly for 50 N. gonorrhoeae isolates collected in Russia were compared with 96 genomes of N. gonorrhoeae and 138 genomes of N. meningitidis from the databases. Rearrangement events with the determination of the coordinates of syntenic blocks were analyzed using the SibeliaZ software v.1.2.5, the minimum number of events that allow one genome to pass into another was calculated using the DCJ–indel model using the UniMoG program v.1.0. Population-level analysis revealed a stronger correlation between changes in the gene order and phylogenetic proximity for N. meningitidis in contrast to N. gonorrhoeae. Mobile elements were identified, including Correa elements; Spencer-Smith elements (in N. gonorrhoeae); Neisserial intergenic mosaic elements; IS elements of IS5, IS30, IS110, IS1595 groups; Nf1–Nf3 prophages; NgoФ1–NgoФ9 prophages; and Mu-like prophages Pnm1, Pnm2, MuMenB (in N. meningitidis). More than 44% of the observed rearrangements most likely occurred with the participation of mobile elements, including prophages. No differences were found between the Russian and global N. gonorrhoeae population both in terms of rearrangement events and in the number of transposable elements in genomes.

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

“…DNA repeat sequences could be targeted by recombination processes leading to amplifications, deletions, and rearrangements of genetic material [47,52,53]. In this study, we identified 156 rearrangement events caused by TRIP1 repeat sequences in 6725 E. coli genomes (Figure 5).…”

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

“…A total of 29 collections were taken, including genomes of 14,763 isolates from 68 countries ( Supplementary Figure S1, Supplementary Table S1 ). The final sample also comprised 61 genomes of the Russian isolates described earlier [ 21 , 22 ].…”

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

“…The first MITEs described in Bacteria were the so called 'Correia elements' of N. gonorrhoeae and N. meningitidis (36,37), and their destabilizing role of the genome was demonstrated after the analysis of the transcriptional regulation of several Neisseria genes (38). Negative effects related to transposition events have been described so far, such as gene inactivation, alteration of gene function, genomic rearrangements, modification of the genome structure (formation of secondary structures), or genomic instability leading to accumulation of mutations (30,(39)(40)(41)(42)(43)(44)(45)(46)(47)(48)). Importantly, MITEs have been also related with the genes dispersion of antimicrobial resistance in Acinetobacter and Enterobacter cloacae (49)(50)(51)(52).…”