Abstract
Serogroup A meningococci are a leading cause of bacterial meningitis in children and young adults worldwide. However, the genetic basis of serogroup A strains' virulence and their epidemiological properties remain poorly understood. Therefore, we sequenced the complete genome of the transformable Neisseria meningitidis serogroup A strain WUE2594.
Serogroup A strains of Neisseria meningitidis cause large epidemics of acute bacterial meningitis particularly in sub-Saharan Africa (13). Whereas five complete genome sequences are available for serogroup B and C strains (2, 7, 12, 15, 19), which are endemic predominantly in industrialized countries (6), only a single serogroup A strain has so far been sequenced (11). However, the fact that the sequenced serogroup A strain Z2491 is not transformable in vitro has severely hindered the experimental analysis of serogroup A virulence and epidemiology. Here, we provide the complete genome of the serogroup A strain WUE2594 from sequence type 5 (ST5), which was isolated in Germany in 1991 from a patient suffering from acute bacterial meningitis (8). Using standard protocols (4), WUE2594 could easily be transformed with plasmid and genomic DNA irrespective of the serogroup or ST of the donor strain.
For de novo sequencing of the WUE2594 genome at 22-fold coverage, Roche/454 sequencing of 3.5-kb paired-end and shotgun libraries (262,751 reads, 73,081,503 bases) using Roche/454 GS FLX Titanium chemistry (Roche Diagnostics, Penzberg, Germany) was combined with Sanger sequencing of PCR products for gap closure on an ABI 3730XL sequencer (Applied Biosystems, CA). Celera assembler version 6.1 (10) and Gap4 (18) were used for de novo assembly, and Mira (version 2.9.26x3; http://www.chevreux.org/projects_mira.html) was used for contig mapping against the Z2491 reference genome (GenBank accession no. AL157959.1). Annotation of the WUE2594 genome was performed with GenDB (9), using the NeMeSys database annotation (15) of Z2491 as a reference.
The genome of WUE2594 contains 2,227,256 bp and has an average G+C content of 51.8%. It contains four rRNA operons and codes for 55 tRNAs, 1,941 protein-coding sequences (CDSs), and 135 pseudogenes. In line with a clonal population structure of serogroup A meningococci (1), the WUE2594 genome has the highest similarity to the genome of Z2491 among the seven so far completely sequenced meningococcal strains (2, 7, 11, 12, 15, 16, 19). Both share 1,857 CDSs, with an average nucleotide sequence identity of 98.6%, and are highly colinear, with only one inversion spanning the capsule locus regions A, C, and E (5). Compared to Z2491, the WUE2594 genome has a rearranged pilE/S locus encoding the major pilin subunit of the type IV pilus, which resembles the pilE/S locus of the serogroup C strain FAM18 (2). Compatible with an open meningococcal pan-genome (17), WUE2594 harbors a Mu-like prophage 42 kb in size that is absent in all completely sequenced meningococcal genomes, and it also contains a specific type II restriction modification system on the minimal mobile element MMEsucD uvrA, which was possibly acquired via horizontal gene transfer from Leptotrichia buccalis (REBASE entry LbuDORF1152P) (14). Among others, WUE2594 in turn lacks the Nf1 prophage, which was found to be associated with hyperinvasive lineages (3) and which has been replaced in WUE2594 by insertion sequence element IS1655, emphasizing the high mobility of these genetic elements in meningococci.
Nucleotide sequence accession number.
The genome sequence of N. meningitidis WUE2594 has been assigned GenBank accession no. FR774048.
ACKNOWLEDGMENTS
The funding for this sequencing project was provided by the German Federal Ministry of Education and Research (BMBF) within the PathoGenoMik funding initiative (grant no. 0313134).
Footnotes
Published ahead of print on 4 February 2011.
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