OTUs whose abundance is significantly higher in schistosome infected children compared to uninfected children.

<p>OTU significance was calculated using the ANOVA test after false discovery rate correction (p values <0.05).</p

The relative abundance of bacterial classes within the human gut microbiome separated into A) age range, B) sex, C) infection status.

<p>The relative abundance of bacterial classes within the human gut microbiome separated into A) age range, B) sex, C) infection status.</p

Mean relative abundance of three dominant phyla (Bacteroidetes, Firmicutes and Proteobacteria) within each category (age range, infection based on egg count, serological analysis and sex).

<p>Mean relative abundance of three dominant phyla (Bacteroidetes, Firmicutes and Proteobacteria) within each category (age range, infection based on egg count, serological analysis and sex).</p

Principal CoOrdinates Analysis of the microbial community similarity by A) age range, B) sex, C) infection status.

<p>Distances between samples were calculated using unweighted UniFrac.</p

Two-sided student’s t-test output testing the null hypothesis that there is no difference in OTU diversity for the different age, infection status, and sex categories.

<p>Two-sided student’s t-test output testing the null hypothesis that there is no difference in OTU diversity for the different age, infection status, and sex categories.</p

A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria.

We devised software tools to systematically investigate the contents and contexts of bacterial tRNA and tmRNA genes, which are known insertion hotspots for genomic islands (GIs). The strategy, based on MAUVE-facilitated multigenome comparisons, was used to examine 87 Escherichia coli MG1655 tRNA and tmRNA genes and their orthologues in E.coli EDL933, E.coli CFT073 and Shigella flexneri Sf301. Our approach identified 49 GIs occupying ∼1.7 Mb that mapped to 18 tRNA genes, missing 2 but identifying a further 30 GIs as compared with Islander [Y. Mantri and K. P. Williams (2004), Nucleic Acids Res., 32, D55–D58]. All these GIs had many strain-specific CDS, anomalous GC contents and/or significant dinucleotide biases, consistent with foreign origins. Our analysis demonstrated marked conservation of sequences flanking both empty tRNA sites and tRNA-associated GIs across all four genomes. Remarkably, there were only 2 upstream and 5 downstream deletions adjacent to the 328 loci investigated. In silico PCR analysis based on conserved flanking regions was also used to interrogate hotspots in another eight completely or partially sequenced E.coli and Shigella genomes. The tools developed are ideal for the analysis of other bacterial species and will lead to in silico and experimental discovery of new genomic islands

Schematic representation of a range of hypothetical tRNA site configurations present in the four complete genomes (MG1655, CFT073, EDL933 and Sf301) (–)

<p><b>Copyright information:</b></p><p>Taken from "A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria"</p><p>Nucleic Acids Research 2006;34(1):e3-e3.</p><p>Published online 9 Jan 2006</p><p>PMCID:PMC1326021.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> The conserved UF and DF regions flanking tRNA genes are shown as dark grey filled boxes. UF and DF boxes drawn below the line indicate inversions with respect to the reference template MG1655 ( and ). The UF and DF boxes shown in pale grey with a broken outline represent deletions with respect to MG1655 ( and ). Genomic islands, where present, are indicated as broken boxes to emphasize the relatively large size of these regions. Arrowheads shown below each sub-figure indicate the location and orientation of primers specific to the UF and DF regions. Hollow arrowheads indicate the absence of matching complementary sequence. The solid line between the arrowheads shown in () indicates a likely successful PCR amplification; while the dotted line in () indicates a successful e-PCR-based ‘amplification’ that would typically yield a product of size far in excess of that that could be generated through standard PCR. The numbers shown above each configuration after the colon symbol represent the number of examples observed in the four genomes tested based on the 87 MG1655 tRNA genes and the total complement of orthologues present in the other three genomes (). The numbers of examples observed in the five unpublished genomes ( EAEC O42, EPEC E2348/69, ETEC E24377A, HS and 53G), with respect to the subset of 20 tRNA genes only (Supplementary Table S3), are shown in parentheses. The symbols shown alongside the drawings are used in and Supplementary Table S4 to highlight tRNA loci affected by inversions and/or deletions. Examples of the various atypical configurations observed in the four genomes are shown to the right. The figure is not drawn to scale

Additional file 1: of An outbreak of pneumococcal meningitis among older children (≥5 years) and adults after the implementation of an infant vaccination programme with the 13-valent pneumococcal conjugate vaccine in Ghana

The weekly distribution of suspected meningitis cases in the hardest hit districts. (A) Jaman North District, (B) Tain District, (C) Techiman Municipal District and (D) Wenchi District. (JPG 609 kb