Functional categories of differentially expressed genes between the <i>ptxP1</i> and <i>ptxP3</i> strains.

<p>The gene count (absolute number of genes) of differentially expressed genes per category (blue). And the gene count of differentially expressed genes relative to the total number of genes (red) present in the genomes of the analyzed strains.</p

Genes from the vir-core regulon were significantly upregulated in the <i>ptxP3</i> strains compared to the <i>ptxP1</i> strains.

<p>Genes from the vir-core regulon were significantly upregulated in the <i>ptxP3</i> strains compared to the <i>ptxP1</i> strains.</p

Differentially expressed genes in <i>ptxP3</i> vs. <i>ptxP1 Bordetella pertussis</i> strains.

<p>Differentially expressed genes in <i>ptxP3</i> vs. <i>ptxP1 Bordetella pertussis</i> strains.</p

Role of the <i>ptxP3</i> and <i>ptxP1</i> mutations and the genetic background of <i>ptxP1</i> and <i>ptxP3</i> strains in colonizing the trachea (A) and lungs (B) in mice.

<p>Mice were intranasally infected with the wildtype <i>ptxP1</i> strain, the <i>ptxP3</i> strain, isogenic strains carrying the <i>ptxP3</i> allele in the <i>ptxP1</i> genetic background (P1 gb:<i>ptxP3</i>) or the <i>ptxP1</i> allele in the <i>ptxP3</i> genetic background (P3 gb:<i>ptxP1</i>). CFUs were determined in the trachea and lungs four days post-infection. The mean is indicated by a thin line. P-values (uncorrected for multiple tests) were shown if greater than 0.05. The experiment was performed two times representative result is shown.</p

Genome-Wide Gene Expression Analysis of <i>Bordetella pertussis</i> Isolates Associated with a Resurgence in Pertussis: Elucidation of Factors Involved in the Increased Fitness of Epidemic Strains

<div><p><i>Bordetella pertussis (B. pertussis)</i> is the causative agent of whooping cough, which is a highly contagious disease in the human respiratory tract. Despite vaccination since the 1950s, pertussis remains the most prevalent vaccine-preventable disease in developed countries. A recent resurgence pertussis is associated with the expansion of <i>B. pertussis</i> strains with a novel allele for the pertussis toxin (ptx) promoter <i>ptxP3</i> in place of resident <i>ptxP1</i> strains. The recent expansion of <i>ptxP3</i> strains suggests that these strains carry mutations that have increased their fitness. Compared to the <i>ptxP1</i> strains, <i>ptxP3</i> strains produce more Ptx, which results in increased virulence and immune suppression. In this study, we investigated the contribution of gene expression changes of various genes on the increased fitness of the <i>ptxP3</i> strains. Using genome-wide gene expression profiling, we show that several virulence genes had higher expression levels in the <i>ptxP3</i> strains compared to the <i>ptxP1</i> strains. We provide the first evidence that wildtype <i>ptxP3</i> strains are better colonizers in an intranasal mouse infection model. This study shows that the <i>ptxP3</i> mutation and the genetic background of <i>ptxP3</i> strains affect fitness by contributing to the ability to colonize in a mouse infection model. These results show that the genetic background of <i>ptxP3</i> strains with a higher expression of virulence genes contribute to increased fitness.</p></div

Relative differences in gene expression between <i>ptxP3</i> and <i>ptxP1</i> strains, as detected by microarrays and Q-PCR.

<p>Relative differences in gene expression between <i>ptxP3</i> and <i>ptxP1</i> strains, as detected by microarrays and Q-PCR.</p

Non-synonymous nucleotide sequence variations of HPV-18 L1.

<p>Non-synonymous nucleotide sequence variations of HPV-18 L1.</p

Maximum parsimony tree based on nucleotide sequences of L1 HPV-16 gene.

<p>Study sequences of 241 HPV-16 positive samples collected in 2009 and 2011 are shown in blue. Reference sequences of European/A lineages (GenBank reference AF536179 K02718 = NC001526, HQ644236, AF534061) are shown in green, African/B lineages (GenBank references AF472508, HQ644298 and AF536180) in brown. African-2/C lineage GenBank reference AF472509 is shown in pink. References sequences from lineage D are shown in purple HQ644257 (sublineage D1-North American), AY686579-(sublineage D2, Asian-American) AF402678 (sublineage D3, Asian-American). HPV-16 variant used in the vaccine (GenBank reference AF043286) is shown in red. The number given in each circle indicates the number of viral strains with the same sequence.</p

Comparison of gene expression measurements by microarray hybridization and quantitative real-time PCR.

<p>Log-transformed (in base 10) fold change values of the Q-PCR data (y-axis) were plotted against the log-transformed fold change values of microarray data (x-axis). The coefficient of determination (R 2) is given.</p

Characteristics of <i>ptxP1</i> and <i>ptxP3</i> strains used in this study.

<p>Characteristics of <i>ptxP1</i> and <i>ptxP3</i> strains used in this study.</p