Genome Sequence of Neisseria meningitidis Serogroup B Strain H44/76

Abstract

Neisseria meningitidis is an obligate human pathogen. While it is a frequent commensal of the upper respiratory tract, in some individuals the bacterium spreads to the bloodstream, causing meningitis and/or sepsis, which are serious conditions with high morbidity and mortality. Here we report the availability of the genome sequence of the widely used serogroup B laboratory strain H44/76.

TEXT

Neisseria meningitidis resides in the nasopharynx of approximately 10 to 30% of the human population. However, in some individuals this pathogen results in invasive disease, leading to life-threatening septicemia and meningitis (4, 14). The factors triggering meningococcal pathogenic outbreaks have not yet been elucidated, but several host and bacterium factors have been proposed (2, 8, 13).

To date seven complete N. meningitidis genomes have been deposited with GenBank (1, 10–12, 15), of which only one is serogroup B. Here we present the sequence of N. meningitidis serogroup B strain H44/76, which is related to the sequenced serogroup B strain MC58 (GenBank accession no. AE002098) and belongs to the same clonal complex 32 (16). N. meningitidis H44/76 is widely used in molecular genetics studies, including those related to serogroup B vaccine development, because of its favorable natural transformation efficiency.

Whole genomic DNA of an H44/76 culture that only had six plate culture passages since its isolation from a patient in Norway in 1976 was sequenced (5). Sequencing was performed using shotgun 454 Titanium (Roche) pyrosequencing according to the manufacturer's recommendations. The coverage was 20-fold with a median read length of 403 nucleotides. De novo and reference mapping assemblies were performed with Newbler (version 2.3; 454 Life Sciences, Branford, CT). The final assembly, containing 46 contigs, was obtained by combining both assemblies using Aligner software (version 3.5; CodonCode Corp., Dedham, MA). Investigation of the regions surrounding contig boundaries showed that further reduction of the number of contigs was hampered due to misassembly of repetitive sequences and duplicated genes, like transposases, rRNA/tRNA regions, two-partner secretion systems, and type IV pili (9).

Annotation was performed using the annotation engine at the Institute for Genome Sciences (University of Maryland, Baltimore, MD [http://ae.igs.umaryland.edu/cgi/index.cgi]). We compared the sequences of 21 gene fragments of abcZ, adk, aroE, fumC, gdh, pdhC, pgm, aspA, carB, dhpS, glnA, gpm, mtgA, pilA, pip, ppk, pykA, rpiA, serC, talA, porA, and porB of the currently sequenced H44/76 genome with those sequences of H44/76 previously submitted to the Neisseria Multi Locus Sequence Typing database (6). All 11,549 compared nucleotides were identical, indicating a high quality of our H44/76 genome. Comparative genome analysis of strain H44/76 and MC58 (recently reannotated [12]) was performed using BLAT (7) and progressiveMauve (3).

The genome size of H44/76 is 2.18 Mb, and 2,480 open reading frames (ORFs) were annotated, compared to 2.27 Mb and 2,465 ORFs for MC58. Both strains have a GC content of 51.5%. Comparative analysis showed that four genes are uniquely present in H44/76 and nine genes are only present in MC58. Of all ORFs in H44/76, 2,317 (93%) show more than 99% sequence identity. Of the 18 least-similar genes (90 to 95% sequence identity), 3 [hmbR, tbp1, and an iron(III) ABC transporter] are associated with iron acquisition from the host.

In the genome sequence of MC58, an ∼32-kb region (NMB1124 to NMB1159) is duplicated (NMB1162 to NMB1197), while this region occurs only once in H44/76 (verified by PCR and 454 read coverage analysis). Obviously, the erythromycin cassette that truncates the siaD gene in MC58 (17) is not present in H44/76.

Nucleotide sequence accession number.

The information reported here from the Whole Genome Shotgun project has been deposited with DDBJ/EMBL/GenBank under accession number AEQZ00000000.