Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes.
To better understand Neisseria meningitidis genomes and virulence, microarray comparative genome hybridization (mCGH) data were collected from one Neisseria cinerea, two Neisseria lactamica, two Neisseria gonorrhoeae and 48 Neisseria meningitidis isolates. For N. meningitidis, these isolates are from diverse clonal complexes, invasive and carriage strains, and all major serogroups. The microarray platform represented N. meningitidis strains MC58, Z2491 and FAM18, and N. gonorrhoeae FA1090. By comparing hybridization data to genome sequences, the core N. meningitidis genome and insertions/deletions (e.g. capsule locus, type I secretion system) related to pathogenicity were identified, including further characterization of the capsule locus, bioinformatics analysis of a type I secretion system, and identification of some metabolic pathways associated with intracellular survival in pathogens. Hybridization data clustered meningococcal isolates from similar clonal complexes that were distinguished by the differential presence of six distinct islands of horizontal transfer. Several of these islands contained prophage or other mobile elements, including a novel prophage and a transposon carrying portions of a type I secretion system. Acquisition of some genetic islands appears to have occurred in multiple lineages, including transfer between N. lactamica and N. meningitidis. However, island acquisition occurs infrequently, such that the genomic-level relationship is not obscured within clonal complexes. The N. meningitidis genome is characterized by the horizontal acquisition of multiple genetic islands; the study of these islands reveals important sets of genes varying between isolates and likely to be related to pathogenicity.
Hotopp
Julie C Dunning
JCD
The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA.
Grifantini
Renata
R
Novartis Vaccines and Diagnostics Ltd, Via Fiorentina 1, 53100 Siena, Italy.
Kumar
Nikhil
N
The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA.
Tzeng
Yih Ling
YL
Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30322 and Research Service, VA Medical Center, Decatur, GA 30033, USA.
Fouts
Derrick
D
The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA.
Frigimelica
Elisabetta
E
Novartis Vaccines and Diagnostics Ltd, Via Fiorentina 1, 53100 Siena, Italy.
Draghi
Monia
M
Novartis Vaccines and Diagnostics Ltd, Via Fiorentina 1, 53100 Siena, Italy.
Giuliani
Marzia Monica
MM
Novartis Vaccines and Diagnostics Ltd, Via Fiorentina 1, 53100 Siena, Italy.
Rappuoli
Rino
R
Novartis Vaccines and Diagnostics Ltd, Via Fiorentina 1, 53100 Siena, Italy.
Stephens
David S
DS
Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30322 and Research Service, VA Medical Center, Decatur, GA 30033, USA.
Grandi
Guido
G
Novartis Vaccines and Diagnostics Ltd, Via Fiorentina 1, 53100 Siena, Italy.
Tettelin
Hervé
H
The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA.
D016667:Bacterial Capsules / Q000235:genetics; D001692:Biological Transport / Q000235:genetics; D016000:Cluster Analysis; D004251:DNA Transposable Elements; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D044404:Genomic Islands; D023281:Genomics; D020071:Interspersed Repetitive Sequences; D042804:Neisseria cinerea / Q000235:genetics; D009344:Neisseria gonorrhoeae / Q000235:genetics; D042806:Neisseria lactamica / Q000235:genetics; D009345:Neisseria meningitidis / Q000235:genetics* / Q000472:pathogenicity; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D039002:Prophages / Q000235:genetics; D026801:Synteny; D014774:Virulence / Q000235:genetics
D004251:DNA Transposable Elements