Genomic Islets Research Articles

Extensive gene flow in secondary sympatry after allopatric speciation.

In the conventional view, species are separate gene pools delineated by reproductive isolation (RI). In an alternative view, species may also be delineated by a small set of 'speciation genes' without full RI, a view that has gained broad acceptance. A recent survey, however, suggested that the extensive literature on 'speciation with gene flow' is mostly (if not all) about exchanges in the early stages of speciation. There is no definitive evidence that the observed gene flow actually happened after speciation is completed. Here, we wish to know whether 'good species' (defined by the 'secondary sympatry' test) do continue to exchange genes and, importantly, under what conditions such exchanges can be observed. De novo whole-genome assembly and re-sequencing of individuals across the range of two closely related mangrove species (Rhizophora mucronata and R. stylosa) reveal the genomes to be well delineated in allopatry. They became sympatric in northeastern Australia but remain distinct species. Nevertheless, their genomes harbor ∼4000-10 000 introgression blocks averaging only about 3-4 Kb. These fine-grained introgressions indicate continual gene flow long after speciation as non-introgressable 'genomic islets,' ∼1.4 Kb in size, often harbor diverging genes of flower or gamete development. The fine-grained introgression in secondary sympatry may help settle the debate about sympatric vs. micro-allopatric speciation. In conclusion, true 'good species' may often continue to exchange genes but the opportunity for detection is highly constrained.

Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics

The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers ~ 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.

Virulence Gene Profiling and Pathogenicity Characterization of Non-Typhoidal Salmonella Accounted for Invasive Disease in Humans

Human infection with non-typhoidal Salmonella serovars (NTS) infrequently causes invasive systemic disease and bacteremia. To understand better the nature of invasive NTS (iNTS), we studied the gene content and the pathogenicity of bacteremic strains from twelve serovars (Typhimurium, Enteritidis, Choleraesuis, Dublin, Virchow, Newport, Bredeney, Heidelberg, Montevideo, Schwarzengrund, 9,12:l,v:- and Hadar). Comparative genomic hybridization using a Salmonella enterica microarray revealed a core of 3233 genes present in all of the iNTS strains, which include the Salmonella pathogenicity islands 1–5, 9, 13, 14; five fimbrial operons (bcf, csg, stb, sth, sti); three colonization factors (misL, bapA, sinH); and the invasion gene, pagN. In the iNTS variable genome, we identified 16 novel genomic islets; various NTS virulence factors; and six typhoid-associated virulence genes (tcfA, cdtB, hlyE, taiA, STY1413, STY1360), displaying a wider distribution among NTS than was previously known. Characterization of the bacteremic strains in C3H/HeN mice showed clear differences in disease manifestation. Previously unreported characterization of serovars Schwarzengrund, 9,12:l,v:-, Bredeney and Virchow in the mouse model showed low ability to elicit systemic disease, but a profound and elongated shedding of serovars Schwarzengrund and 9,12:l,v:- (as well as Enteritidis and Heidelberg) due to chronic infection of the mouse. Phenotypic comparison in macrophages and epithelial cell lines demonstrated a remarkable intra-serovar variation, but also showed that S. Typhimurium bacteremic strains tend to present lower intracellular growth than gastroenteritis isolates. Collectively, our data demonstrated a common core of virulence genes, which might be required for invasive salmonellosis, but also an impressive degree of genetic and phenotypic heterogeneity, highlighting that bacteremia is a complex phenotype, which cannot be attributed merely to an enhanced invasion or intracellular growth of a particular strain.

Population structure of Pseudomonas aeruginosa in CF and COPD

Chronic airway infections with Pseudomonas aeruginosa are common in individuals with bronchiectasis or cystic fibrosis (CF). P. aeruginosa can also be isolated from the sputum of adults with chronic obstructive pulmonary disease (COPD), but the role of the organism in the course of the disease is less well characterized than in other clinical settings. The population genetics of P. aeruginosa in these diseases and in acute infections was investigated by a microarray analysis representing the core genome by single nucleotide polymorphisms and the accessory genome by markers of genomic islets and islands, yielding an identification fidelity >99,8%.

Identification of the clonal complexes of Staphylococcus aureus strains by determination of the conservation patterns of small genomic islets

To investigate the clonality of Staphylococcus aureus isolates, it is important to identify their clonal complexes (CCs) with multilocus sequence typing (MLST). However, it is expensive to carry out MLST analyses for many isolates. The aim of this study, therefore, was to develop a cost-effective method to identify CCs by determining the conservation pattern of 'small genomic islets' (SGIs). SGIs are nonconserved regions between strains and have single or multiple open-reading frames (ORFs). The whole-genome sequences of nine strains were compared in order to select 16 SGIs. The conservation patterns of the 16 SGIs (islet patterns) were investigated in 136 S. aureus isolates, which were classified into 21 CCs. The islet patterns (IPs) exhibited a one-to-one correspondence with the CCs, except for isolates belonging to CC1, CC5 and CC8. The IPs typical of strains belonging to CC1, CC5 and CC8 differed between those of sequence type 1 (ST1) and ST188 (CC1), ST5 and ST6 (CC5) and ST8 and ST239 (CC8). The CCs of many isolates can be identified in an easy and inexpensive manner by detecting these 16 SGIs. Emergent clones, particularly methicillin-resistant ones, can be identified by examining numerous islets by IP analysis.

Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa.

Pseudomonas aeruginosa isolates have a highly conserved core genome representing up to 90% of the total genomic sequence with additional variable accessory genes, many of which are found in genomic islands or islets. The identification of the Liverpool Epidemic Strain (LES) in a children's cystic fibrosis (CF) unit in 1996 and its subsequent observation in several centers in the United Kingdom challenged the previous widespread assumption that CF patients acquire only unique strains of P. aeruginosa from the environment. To learn about the forces that shaped the development of this important epidemic strain, the genome of the earliest archived LES isolate, LESB58, was sequenced. The sequence revealed the presence of many large genomic islands, including five prophage clusters, one defective (pyocin) prophage cluster, and five non-phage islands. To determine the role of these clusters, an unbiased signature tagged mutagenesis study was performed, followed by selection in the chronic rat lung infection model. Forty-seven mutants were identified by sequencing, including mutants in several genes known to be involved in Pseudomonas infection. Furthermore, genes from four prophage clusters and one genomic island were identified and in direct competition studies with the parent isolate; four were demonstrated to strongly impact on competitiveness in the chronic rat lung infection model. This strongly indicates that enhanced in vivo competitiveness is a major driver for maintenance and diversifying selection of these genomic prophage genes.

Adaptive expression of foreign genes in the clonal variants of bacteria: From proteomics to clinical application

Clonal variants of bacteria are able to colonize environmental niches and patients. The factors, that determine the interplay between the colonization of diverse habitats and adaptation, are acquired through horizontal gene transfer. Elucidation of mechanisms, which lead to the prevalence of dominant bacterial clones in patients and the environment, requires the knowledge of complex phenotypes. It was found in the genomes of most bacteria, that upon a conserved chromosomal backbone there were regions of plasticity achieved by insertions, deletions and rearrangements of genomic islands and islets as well as large chromosomal inversions. However, it had been shown that environmental and clinical isolates are indistinguishable in certain pathogenic and biodegradative properties. For example, clonal variants of Pseudomonas aeruginosa exhibit convergent phenotypes despite the presence of numerous DNA insertions in the genome. Apart from this feature, expression of a few genes from the acquired genetic material is important for niche-based adaptation of this organism. Protein expression patterns at the cellular and sub-cellular levels showed common virulence factors and novel drug targets among clonal variants of bacteria. This review will give a short overview on proteomics of different clonal variants of bacteria with respect to clinical applications.

Population structure of Pseudomonas aeruginosa

The metabolically versatile Gram-negative bacterium Pseudomonas aeruginosa inhabits terrestrial, aquatic, animal-, human-, and plant-host-associated environments and is an important causative agent of nosocomial infections, particularly in intensive-care units. The population genetics of P. aeruginosa was investigated by an approach that is generally applicable to the rapid, robust, and informative genotyping of bacteria. DNA, amplified from the bacterial colony by circles of multiplex primer extension, is hybridized onto a microarray to yield an electronically portable binary multimarker genotype that represents the core genome by single nucleotide polymorphisms and the accessory genome by markers of genomic islets and islands. The 240 typed P. aeruginosa strains of diverse habitats and geographic origin segregated into two large nonoverlapping clusters and 45 isolated clonal complexes with few or no partners. The majority of strains belonged to few dominant clones widespread in disease and environmental habitats. The most frequent genotype was represented by the sequenced strain PA14. Core and accessory genome were found to be nonrandomly assembled in P. aeruginosa. Individual clones preferred a specific repertoire of accessory segments. Even the most promiscuous genomic island, pKLC102, had integrated preferentially into a subset of clones. Moreover, some physically distant loci of the core genome, including oriC, showed nonrandom associations of genotypes, whereas other segments in between were freely recombining. Thus, the P. aeruginosa genome is made up of clone-typical segments in core and accessory genome and of blocks in the core with unrestricted gene flow in the population.

Structure of Pseudomonas aeruginosa populations analyzed by single nucleotide polymorphism and pulsed-field gel electrophoresis genotyping.

Pseudomonas aeruginosa has a wide ecological distribution that includes natural habitats and clinical settings. To analyze the population structure and distribution of P. aeruginosa, a collection of 111 isolates of diverse habitats and geographical origin, most of which contained a genome with a different SpeI macrorestriction profile, was typed by restriction fragment length polymorphism based on 14 single nucleotide polymorphisms (SNPs) located at seven conserved loci of the core genome (oriC, oprL, fliC, alkB2, citS, oprI, and ampC). The combination of these SNPs plus the type of fliC present (a or b) allowed the assignment of a genetic fingerprint to each strain, thus providing a simple tool for the discrimination of P. aeruginosa strains. Thirteen of the 91 identified SNP genotypes were found in two or more strains. In several cases, strains sharing their SNP genotype had different SpeI macrorestriction profiles. The highly virulent CHA strain shared its SNP genotype with other strains that had different SpeI genotypes and which had been isolated from nonclinical habitats. The reference strain PAO1 also shared its SNP genotype with other strains that had different SpeI genotypes. The P. aeruginosa chromosome contains a conserved core genome and variable amounts of accessory DNA segments (genomic islands and islets) that can be horizontally transferred among strains. The fact that some SNP genotypes were overrepresented in the P. aeruginosa population studied and that several strains sharing an SNP genotype had different SpeI macrorestriction profiles supports the idea that changes occur at a higher rate in the accessory DNA segments than in the conserved core genome.