{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T08:06:34Z","timestamp":1791273994739,"version":"4.1.0"},"reference-count":58,"publisher":"Microbiology Society","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,12,1]]},"abstract":"<jats:p>To better understand<jats:italic>Neisseria meningitidis<\/jats:italic>genomes and virulence, microarray comparative genome hybridization (mCGH) data were collected from one<jats:italic>Neisseria cinerea<\/jats:italic>, two<jats:italic>Neisseria lactamica<\/jats:italic>, two<jats:italic>Neisseria gonorrhoeae<\/jats:italic>and 48<jats:italic>Neisseria meningitidis<\/jats:italic>isolates. For<jats:italic>N. meningitidis<\/jats:italic>, these isolates are from diverse clonal complexes, invasive and carriage strains, and all major serogroups. The microarray platform represented<jats:italic>N. meningitidis<\/jats:italic>strains MC58, Z2491 and FAM18, and<jats:italic>N. gonorrhoeae<\/jats:italic>FA1090. By comparing hybridization data to genome sequences, the core<jats:italic>N. meningitidis<\/jats:italic>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<jats:italic>N. lactamica<\/jats:italic>and<jats:italic>N. meningitidis<\/jats:italic>. However, island acquisition occurs infrequently, such that the genomic-level relationship is not obscured within clonal complexes. The<jats:italic>N. meningitidis<\/jats:italic>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.<\/jats:p>","DOI":"10.1099\/mic.0.29261-0","type":"journal-article","created":{"date-parts":[[2006,12,12]],"date-time":"2006-12-12T08:28:10Z","timestamp":1165912090000},"page":"3733-3749","source":"Crossref","is-referenced-by-count":95,"title":["Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes"],"prefix":"10.1099","volume":"152","author":[{"given":"Julie C. 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Neisseriaceae","volume-title":"Bergey's Manual of Systematic Bacteriology","author":"Bovre","year":"1984"},{"key":"R6","doi-asserted-by":"crossref","first-page":"2203","DOI":"10.1099\/00221287-147-8-2203","article-title":"The methylcitric acid pathway in Ralstonia eutropha : new genes identified involved in propionate metabolism","volume":"147","author":"Bra\u0308mer","year":"2001","journal-title":"Microbiology"},{"key":"R7","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.1128\/JB.182.5.1296-1303.2000","article-title":"Differential distribution of novel restriction-modification systems in clonal lineages of Neisseria meningitidis","volume":"182","author":"Claus","year":"2000","journal-title":"J Bacteriol"},{"key":"R8","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1046\/j.1365-2958.2003.03819.x","article-title":"Genetics of capsule O-acetylation in serogroup C, W-135 and Y meningococci","volume":"51","author":"Claus","year":"2004","journal-title":"Mol Microbiol"},{"key":"R9","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1084\/jem.20020407","article-title":"NadA, a novel vaccine candidate of Neisseria meningitidis","volume":"195","author":"Comanducci","year":"2002","journal-title":"J Exp Med"},{"key":"R10","doi-asserted-by":"crossref","first-page":"5476","DOI":"10.1128\/JB.173.17.5476-5486.1991","article-title":"Physical map of the chromosome of Neisseria gonorrhoeae FA1090 with locations of genetic markers, including opa and pil genes","volume":"173","author":"Dempsey","year":"1991","journal-title":"J Bacteriol"},{"key":"R11","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1128\/JB.185.1.155-164.2003","article-title":"Transcriptome analysis of Neisseria meningitidis during infection","volume":"185","author":"Dietrich","year":"2003","journal-title":"J Bacteriol"},{"key":"R12","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1086\/374740","article-title":"Genetic basis for nongroupable Neisseria meningitidis","volume":"187","author":"Dolan-Livengood","year":"2003","journal-title":"J Infect Dis"},{"key":"R13","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1146\/annurev.micro.53.1.43","article-title":"Addiction modules and programmed cell death and antideath in bacterial cultures","volume":"53","author":"Engelberg-Kulka","year":"1999","journal-title":"Annu Rev Microbiol"},{"key":"R14","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1046\/j.1365-2958.2003.03313.x","article-title":"Unraveling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica","volume":"47","author":"Eriksson","year":"2003","journal-title":"Mol Microbiol"},{"key":"R15","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1007\/BF02202111","article-title":"A comparison of the nucleotide sequences of the adk and recA genes of pathogenic and commensal Neisseria species: evidence for extensive interspecies recombination within 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