genomic islands


Summary: Distinct units in some bacterial, bacteriophage or plasmid GENOMES that are types of MOBILE GENETIC ELEMENTS. Encoded in them are a variety of fitness conferring genes, such as VIRULENCE FACTORS (in "pathogenicity islands or islets"), ANTIBIOTIC RESISTANCE genes, or genes required for SYMBIOSIS (in "symbiosis islands or islets"). They range in size from 10 - 500 kilobases, and their GC CONTENT and CODON usage differ from the rest of the genome. They typically contain an INTEGRASE gene, although in some cases this gene has been deleted resulting in "anchored genomic islands".

Top Publications

  1. Hall R. Salmonella genomic islands and antibiotic resistance in Salmonella enterica. Future Microbiol. 2010;5:1525-38 pubmed publisher
    ..several Salmonella enterica serovars that cause gastrointestinal disease in humans is due to a set of related genomic islands carrying a class 1 integron, which carries the resistance genes...
  2. Cruickshank T, Hahn M. Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Mol Ecol. 2014;23:3133-57 pubmed publisher
    The metaphor of 'genomic islands of speciation' was first used to describe heterogeneous differentiation among loci between the genomes of closely related species...
  3. Daccord A, Mursell M, Poulin Laprade D, Burrus V. Dynamics of the SetCD-regulated integration and excision of genomic islands mobilized by integrating conjugative elements of the SXT/R391 family. J Bacteriol. 2012;194:5794-802 pubmed publisher
    Mobilizable genomic islands (MGIs) are small genomic islands that are mobilizable by SXT/R391 integrating conjugative elements (ICEs) due to similar origins of transfer...
  4. Allison S, Silphaduang U, Mascarenhas M, Konczy P, Quan Q, Karmali M, et al. Novel repressor of Escherichia coli O157:H7 motility encoded in the putative fimbrial cluster OI-1. J Bacteriol. 2012;194:5343-52 pubmed publisher
    ..This work provides insight into the mechanism by which Z0021, which we have named fmrA, represses flagellar synthesis and is the first report of a fimbrial-operon-encoded inhibitor of motility in E. coli O157:H7. ..
  5. Mazzaglia A, Studholme D, Taratufolo M, Cai R, Almeida N, Goodman T, et al. Pseudomonas syringae pv. actinidiae (PSA) isolates from recent bacterial canker of kiwifruit outbreaks belong to the same genetic lineage. PLoS ONE. 2012;7:e36518 pubmed publisher
    ..Results are interpreted in regard to the possible direction of movement of the pathogen between countries and suggest a possible Chinese origin of the European and New Zealand outbreaks...
  6. Cameron A, Dorman C. A fundamental regulatory mechanism operating through OmpR and DNA topology controls expression of Salmonella pathogenicity islands SPI-1 and SPI-2. PLoS Genet. 2012;8:e1002615 pubmed publisher
  7. de Bruin O, Duplantis B, Ludu J, Hare R, Nix E, Schmerk C, et al. The biochemical properties of the Francisella pathogenicity island (FPI)-encoded proteins IglA, IglB, IglC, PdpB and DotU suggest roles in type VI secretion. Microbiology. 2011;157:3483-91 pubmed publisher
  8. Siebor E, Neuwirth C. The new variant of Salmonella genomic island 1 (SGI1-V) from a Proteus mirabilis French clinical isolate harbours blaVEB-6 and qnrA1 in the multiple antibiotic resistance region. J Antimicrob Chemother. 2011;66:2513-20 pubmed publisher
    ..It might constitute a source of spread of resistance to other bacterial species. ..
  9. Osborne S, Coombes B. Transcriptional priming of Salmonella Pathogenicity Island-2 precedes cellular invasion. PLoS ONE. 2011;6:e21648 pubmed publisher

More Information


  1. Fischer W. Assembly and molecular mode of action of the Helicobacter pylori Cag type IV secretion apparatus. FEBS J. 2011;278:1203-12 pubmed publisher
    ..This review describes the molecular properties of the Cag-T4SS and compares these with prototypical systems of this family of protein transporters. ..
  2. Douard G, Praud K, Cloeckaert A, Doublet B. The Salmonella genomic island 1 is specifically mobilized in trans by the IncA/C multidrug resistance plasmid family. PLoS ONE. 2010;5:e15302 pubmed publisher
    ..Moreover, the increasing prevalence of IncA/C plasmids in MDR S. enterica isolates worldwide has potential implications for the epidemic success of the antibiotic resistance genomic island SGI1 and its close derivatives. ..
  3. den Bakker H, Moreno Switt A, Govoni G, Cummings C, Ranieri M, Degoricija L, et al. Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica. BMC Genomics. 2011;12:425 pubmed publisher
    ..All clade B isolates contained two pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin islet; a combination of these two islands was previously thought to ..
  4. Gonzaga A, Martin Cuadrado A, Lopez Perez M, Megumi Mizuno C, García Heredia I, Kimes N, et al. Polyclonality of concurrent natural populations of Alteromonas macleodii. Genome Biol Evol. 2012;4:1360-74 pubmed publisher
    ..51%, both AltDE and AltDE1 contained flexible genomic islands (fGIs), that is, genomic islands present in both genomes in the same genomic context but having different ..
  5. Mancilla M, Marin C, Blasco J, Zárraga A, López Goñi I, Moriyon I. Spontaneous excision of the O-polysaccharide wbkA glycosyltranferase gene is a cause of dissociation of smooth to rough Brucella colonies. J Bacteriol. 2012;194:1860-7 pubmed publisher
    ..This ISBm1-mediated wbkA excision and the different %GC levels of the excised fragment and of other wbk genes suggest that the Brucella wbk locus is the result of at least two horizontal acquisition events...
  6. Huang Q, Cheng X, Cheung M, Kiselev S, Ozoline O, Kwan H. High-density transcriptional initiation signals underline genomic islands in bacteria. PLoS ONE. 2012;7:e33759 pubmed publisher
    b>Genomic islands (GIs), frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of "alien" elements which probably undergo special temporal-spatial ..
  7. De Maayer P, Venter S, Kamber T, Duffy B, Coutinho T, Smits T. Comparative genomics of the Type VI secretion systems of Pantoea and Erwinia species reveals the presence of putative effector islands that may be translocated by the VgrG and Hcp proteins. BMC Genomics. 2011;12:576 pubmed publisher
  8. Li Z, Stevens D, Hamilton S, Parimon T, Ma Y, Kearns A, et al. Fatal S. aureus hemorrhagic pneumonia: genetic analysis of a unique clinical isolate producing both PVL and TSST-1. PLoS ONE. 2011;6:e27246 pubmed publisher
    ..Both ?PVLv68111 and SaPI68111 are fully mobilizable and therefore transmissible to other strains. Taken together, these findings suggest that hypervirulent S. aureus have the potential to emerge worldwide. ..
  9. Mijnendonckx K, Provoost A, Monsieurs P, Leys N, Mergeay M, Mahillon J, et al. Insertion sequence elements in Cupriavidus metallidurans CH34: distribution and role in adaptation. Plasmid. 2011;65:193-203 pubmed publisher
    ..The strain carries two megaplasmids specialized in the response to heavy metals and a considerable number of genomic islands, transposons and insertion sequence (IS) elements...
  10. Johnson T, Wannemuehler Y, Kariyawasam S, Johnson J, Logue C, Nolan L. Prevalence of avian-pathogenic Escherichia coli strain O1 genomic islands among extraintestinal and commensal E. coli isolates. J Bacteriol. 2012;194:2846-53 pubmed publisher
    ..coli strains, identifying 43 genomic islands. Here, the genomic islands of APEC O1 were compared to those of other sequenced E...
  11. Mulder D, Cooper C, Coombes B. Type VI secretion system-associated gene clusters contribute to pathogenesis of Salmonella enterica serovar Typhimurium. Infect Immun. 2012;80:1996-2007 pubmed publisher
    ..These data suggest that the SPI-6 T6SS has been integrated into the Salmonella Typhimurium virulence network and customized for host-pathogen interactions through the action of noncore genes. ..
  12. Nowrouzian F, Oswald E. Escherichia coli strains with the capacity for long-term persistence in the bowel microbiota carry the potentially genotoxic pks island. Microb Pathog. 2012;53:180-2 pubmed publisher
    ..Long-term persistence in the colon of pks island-containing E. coli strains may be associated with the induction of genomic mutations in the host intestine. ..
  13. Fookes M, Schroeder G, Langridge G, Blondel C, Mammina C, Connor T, et al. Salmonella bongori provides insights into the evolution of the Salmonellae. PLoS Pathog. 2011;7:e1002191 pubmed publisher
    ..This work suggests that S. bongori has inherited the ancestral Salmonella virulence gene set, but has adapted by incorporating virulence determinants that resemble those employed by EPEC. ..
  14. Lautner M, Schunder E, Herrmann V, Heuner K. Regulation, integrase-dependent excision, and horizontal transfer of genomic islands in Legionella pneumophila. J Bacteriol. 2013;195:1583-97 pubmed publisher
    ..pneumophila Corby (named trb-tra). Analogous versions of trb-tra are localized on the genomic islands Trb-1 and Trb-2...
  15. Roos T, van Passel M. A quantitative account of genomic island acquisitions in prokaryotes. BMC Genomics. 2011;12:427 pubmed publisher
    ..the introgression of single genes, but also through the acquisition of large gene clusters, which are termed Genomic Islands. Since only a small proportion of all the DNA diversity has been sequenced, it can be hard to find the ..
  16. Kittichotirat W, Bumgarner R, Asikainen S, Chen C. Identification of the pangenome and its components in 14 distinct Aggregatibacter actinomycetemcomitans strains by comparative genomic analysis. PLoS ONE. 2011;6:e22420 pubmed publisher
    ..Furthermore, 171 genomic islands were identified...
  17. Chandry P, Gladman S, Moore S, Seemann T, Crandall K, Fegan N. A Genomic Island in Salmonella enterica ssp. salamae provides new insights on the genealogy of the locus of enterocyte effacement. PLoS ONE. 2012;7:e41615 pubmed publisher
    ..Although recombination and horizontal gene transfer are important factors in the genealogy of most genomic islands, the phylogeny of the T3SS of LEE can be interpreted with a bifurcating tree...
  18. Moreno Switt A, den Bakker H, Cummings C, Rodriguez Rivera L, Govoni G, Raneiri M, et al. Identification and characterization of novel Salmonella mobile elements involved in the dissemination of genes linked to virulence and transmission. PLoS ONE. 2012;7:e41247 pubmed publisher
    ..We also identified two novel genomic islands (SGI2 and SGI3), and 42 prophages with mosaic architecture, seven of them harboring known virulence genes...
  19. Tegtmeyer N, Wessler S, Backert S. Role of the cag-pathogenicity island encoded type IV secretion system in Helicobacter pylori pathogenesis. FEBS J. 2011;278:1190-202 pubmed publisher
    ..The contribution of these signalling pathways to pathogenesis during H. pylori infections is discussed. ..
  20. Bröms J, Lavander M, Meyer L, Sjostedt A. IglG and IglI of the Francisella pathogenicity island are important virulence determinants of Francisella tularensis LVS. Infect Immun. 2011;79:3683-96 pubmed publisher
    ..Thus, IglG and IglI play key roles for modulation of the intracellular host response and also for the virulence of F. tularensis. ..
  21. Francis F, Kim J, Ramaraj T, Farmer A, Rush M, Ham J. Comparative genomic analysis of two Burkholderia glumae strains from different geographic origins reveals a high degree of plasticity in genome structure associated with genomic islands. Mol Genet Genomics. 2013;288:195-203 pubmed publisher
    ..glumae BGR1 corresponded to predicted genomic islands. In contrast, little variation was observed in known and potential virulence genes between the two genomes...
  22. Pezoa D, Yang H, Blondel C, Santiviago C, Andrews Polymenis H, Contreras I. The type VI secretion system encoded in SPI-6 plays a role in gastrointestinal colonization and systemic spread of Salmonella enterica serovar Typhimurium in the chicken. PLoS ONE. 2013;8:e63917 pubmed publisher
    ..The genus Salmonella contains five phylogenetically distinct T6SS encoded in differentially distributed genomic islands. S...
  23. Chu C, Doublet B, Lee Y, Cloeckaert A, Chiou C, Chen S, et al. Salmonella genomic island 1-J variants associated with change in the antibiotic resistance gene cluster in multidrug-resistant Salmonella enterica serovar Virchow isolated from humans, Taiwan, 2004-2006. Clin Microbiol Infect. 2012;18:47-53 pubmed publisher
    ..Virchow isolates collected from humans, which spread vertically. The genomic island SGI1 appears to be largely responsible for the diversity of MDR phenotypes among S. Virchow isolates in Taiwan. ..
  24. Mart nez L, Yakhnin H, Camacho M, Georgellis D, Babitzke P, Puente J, et al. Integration of a complex regulatory cascade involving the SirA/BarA and Csr global regulatory systems that controls expression of the Salmonella SPI-1 and SPI-2 virulence regulons through HilD. Mol Microbiol. 2011;80:1637-56 pubmed publisher
    ..Our results illustrate the integration of global and specific regulators into a multifactorial regulatory cascade controlling the expression of virulence genes acquired by horizontal transfer events...
  25. Almagro Moreno S, Napolitano M, Boyd E. Excision dynamics of Vibrio pathogenicity island-2 from Vibrio cholerae: role of a recombination directionality factor VefA. BMC Microbiol. 2010;10:306 pubmed publisher
    ..We demonstrate that excision of VPI-2 is induced under some environmental stress conditions and we show for the first time that an RDF encoded within a pathogenicity island in V. cholerae is required for excision of the region. ..
  26. Lopez Perez M, Gonzaga A, Martin Cuadrado A, Onyshchenko O, Ghavidel A, Ghai R, et al. Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph. Sci Rep. 2012;2:696 pubmed
    ..The genomes contain several genomic islands with different gene content...
  27. Gennari M, Ghidini V, Caburlotto G, Lleo M. Virulence genes and pathogenicity islands in environmental Vibrio strains nonpathogenic to humans. FEMS Microbiol Ecol. 2012;82:563-73 pubmed publisher
    ..The emergence of environmental bacteria with new virulence traits might constitute a direct concern for public health and a risk for human health...
  28. Zhang J, van Aartsen J, Jiang X, Shao Y, Tai C, He X, et al. Expansion of the known Klebsiella pneumoniae species gene pool by characterization of novel alien DNA islands integrated into tmRNA gene sites. J Microbiol Methods. 2011;84:283-9 pubmed publisher
    ..highly plastic architecture comprising a core genome backbone interspersed with numerous and varied alien genomic islands. In this study the size of the presently known K...
  29. Dominguez N, Hackett K, Dillard J. XerCD-mediated site-specific recombination leads to loss of the 57-kilobase gonococcal genetic island. J Bacteriol. 2011;193:377-88 pubmed publisher
    ..These data suggest a model of GGI excision and loss explaining the absence of the GGI from some gonococcal strains and the maintenance of variant GGIs in some gonococcal and meningococcal isolates. ..
  30. Ram G, Chen J, Kumar K, Ross H, Ubeda C, Damle P, et al. Staphylococcal pathogenicity island interference with helper phage reproduction is a paradigm of molecular parasitism. Proc Natl Acad Sci U S A. 2012;109:16300-5 pubmed publisher
  31. Clark L, Perrett C, Malt L, Harward C, Humphrey S, Jepson K, et al. Differences in Salmonella enterica serovar Typhimurium strain invasiveness are associated with heterogeneity in SPI-1 gene expression. Microbiology. 2011;157:2072-83 pubmed publisher
    ..The previously unrecognized strain heterogeneity in SPI-1 expression and invasiveness has important implications for studies of Salmonella infection. ..
  32. Bohlin J, van Passel M, Snipen L, Kristoffersen A, Ussery D, Hardy S. Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands. BMC Genomics. 2012;13:66 pubmed publisher
    ..We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure...
  33. Nadeau N, Whibley A, Jones R, Davey J, Dasmahapatra K, Baxter S, et al. Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing. Philos Trans R Soc Lond B Biol Sci. 2012;367:343-53 pubmed publisher
    ..We find no major structural rearrangements but many relatively large (greater than 1 kb) insertion/deletion events (including gain/loss of transposable elements) that are variable between races. ..
  34. Kirzinger M, Stavrinides J. Host specificity determinants as a genetic continuum. Trends Microbiol. 2012;20:88-93 pubmed publisher
    ..This review highlights examples of host specificity determinants of viruses, bacteria and fungi, and presents them from within a genetic continuum that spans from the single residue through to entire genomic islands.
  35. Azpiroz M, Bascuas T, Laviña M. Microcin H47 system: an Escherichia coli small genomic island with novel features. PLoS ONE. 2011;6:e26179 pubmed publisher
    b>Genomic islands are DNA regions containing variable genetic information related to secondary metabolism. Frequently, they have the ability to excise from and integrate into replicons through site-specific recombination...
  36. Wei W, Guo F. Prediction of genomic islands in seven human pathogens using the Z-Island method. Genet Mol Res. 2011;10:2307-15 pubmed publisher
    ..The Z-Island method is a theoretical method for predicting genomic islands in bacterial genomes; it consists of determination of the cumulative GC profile and computation of codon ..
  37. Yu G, Fu X, Jin K, Zhang L, Wu W, Cui Z, et al. Integrative analysis of transcriptome and genome indicates two potential genomic islands are associated with pathogenesis of Mycobacterium tuberculosis. Gene. 2011;489:21-9 pubmed publisher
    Mycobacterium tuberculosis (M.tb) is a successful human pathogen and widely prevalent throughout the world. Genomic islands (GIs) are thought to be related to pathogenicity. In this study, we predicted two potential genomic islands in M...
  38. Shaffer C, Gaddy J, Loh J, Johnson E, Hill S, Hennig E, et al. Helicobacter pylori exploits a unique repertoire of type IV secretion system components for pilus assembly at the bacteria-host cell interface. PLoS Pathog. 2011;7:e1002237 pubmed publisher
    ..In summary, these results indicate that CagH, CagI, and CagL are components of a T4SS subassembly involved in pilus biogenesis, and highlight the important role played by unique constituents of the H. pylori cag T4SS. ..
  39. Makarova K, Wolf Y, Snir S, Koonin E. Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J Bacteriol. 2011;193:6039-56 pubmed publisher
    ..statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. The defense islands are enriched in putative operons and contain numerous overrepresented gene families...
  40. Blondel C, Jimenez J, Leiva L, Alvarez S, Pinto B, Contreras F, et al. The type VI secretion system encoded in Salmonella pathogenicity island 19 is required for Salmonella enterica serotype Gallinarum survival within infected macrophages. Infect Immun. 2013;81:1207-20 pubmed publisher
    ..Our data indicate that SPI-19 T6SS corresponds to a novel tool used by Salmonella to survive within host cells. ..
  41. Butler M, Stockwell P, Black M, Day R, Lamont I, Poulter R. Pseudomonas syringae pv. actinidiae from recent outbreaks of kiwifruit bacterial canker belong to different clones that originated in China. PLoS ONE. 2013;8:e57464 pubmed publisher
    ..The Chilean strains of PSA carry a third variant of this island. These genomic islands are integrative conjugative elements (ICEs)...
  42. Del Canto F, Valenzuela P, Cantero L, Bronstein J, Blanco J, Blanco J, et al. Distribution of classical and nonclassical virulence genes in enterotoxigenic Escherichia coli isolates from Chilean children and tRNA gene screening for putative insertion sites for genomic islands. J Clin Microbiol. 2011;49:3198-203 pubmed publisher
    ..Sequencing of tDNA-associated genetic insertions might identify new ETEC virulence determinants. ..
  43. Wang D, Wang H, Zhou Y, Zhang Q, Zhang F, Du P, et al. Genome sequencing reveals unique mutations in characteristic metabolic pathways and the transfer of virulence genes between V. mimicus and V. cholerae. PLoS ONE. 2011;6:e21299 pubmed publisher
    ..cholerae and V. mimicus. Horizontal transfers of virulence-related genes from an uncommon clone of V. cholerae, rather than the seventh pandemic strains, have generated the pathogenic V. mimicus strain carrying cholera toxin genes...
  44. Chen Y, Stine O, Badger J, Gil A, Nair G, Nishibuchi M, et al. Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence. BMC Genomics. 2011;12:294 pubmed publisher
    ..The sixth pandemic strain sequenced in this study was serotype O4:K68...
  45. Teixidó L, Carrasco B, Alonso J, Barbe J, Campoy S. Fur activates the expression of Salmonella enterica pathogenicity island 1 by directly interacting with the hilD operator in vivo and in vitro. PLoS ONE. 2011;6:e19711 pubmed publisher
    ..Together, these results present the first evidence that Fur·Mn(2+), by binding to the upstream BoxA sequence, directly stimulates the expression of hilD in S. enterica. ..
  46. Waldor M. Mobilizable genomic islands: going mobile with oriT mimicry. Mol Microbiol. 2010;78:537-40 pubmed
    Many bacterial chromosomes contain genomic islands, large DNA segments that became incorporated into the chromosome following their horizontal transmission...
  47. Seth Smith H, Fookes M, Okoro C, Baker S, Harris S, Scott P, et al. Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae. J Bacteriol. 2012;194:1494-504 pubmed publisher
    ..We present a growing family of SPI-7-related ICEs whose mobility, abundance, and cargo variability indicate that these elements may have had a large impact on the evolution of the Enterobacteriaceae. ..
  48. O Connor T, Adepoju Y, Boyd D, Isberg R. Minimization of the Legionella pneumophila genome reveals chromosomal regions involved in host range expansion. Proc Natl Acad Sci U S A. 2011;108:14733-40 pubmed publisher
    ..pneumophila chromosome has a modular architecture consisting of several large genomic islands that are dispensable for growth in bacteriological culture. Strains lacking six of these regions, and thus 18...
  49. Lovell H, Jackson R, Mansfield J, Godfrey S, Hancock J, Desikan R, et al. In planta conditions induce genomic changes in Pseudomonas syringae pv. phaseolicola. Mol Plant Pathol. 2011;12:167-76 pubmed publisher
    ..These results shed more light onto the plasticity of the bacterial genome as it is influenced by in planta conditions. ..
  50. Smits T, Rezzonico F, Kamber T, Blom J, Goesmann A, Ishimaru C, et al. Metabolic versatility and antibacterial metabolite biosynthesis are distinguishing genomic features of the fire blight antagonist Pantoea vagans C9-1. PLoS ONE. 2011;6:e22247 pubmed publisher
  51. Queiroz M, Madrid C, Paytubi S, Balsalobre C, Juárez A. Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1, hilA. Microbiology. 2011;157:2504-14 pubmed publisher
    ..Band-shift assays and in vitro transcription data showed that for hilA induction under certain growth conditions, IHF is required to alleviate H-NS-mediated silencing. ..
  52. Du P, Yang Y, Wang H, Liu D, Gao G, Chen C. A large scale comparative genomic analysis reveals insertion sites for newly acquired genomic islands in bacterial genomes. BMC Microbiol. 2011;11:135 pubmed publisher
    ..Interestingly, newly acquired genomic islands (GIs) from horizontal transfer between different bacteria strains were found in Vibrio cholerae, ..
  53. Zheng X, Zheng H, Lan R, Ye C, Wang Y, Zhang J, et al. Identification of genes and genomic islands correlated with high pathogenicity in Streptococcus suis using whole genome tiling microarrays. PLoS ONE. 2011;6:e17987 pubmed publisher
    ..are absent in two or more strains and defined as regions of difference (RDs), among which 26 are putative genomic islands (GIs)...