Of the transcript.DiscussionWe have analyzed in this study, for the first time, expression of important order JSI-124 pneumococcal genes when S. pneumoniae is present in the CB5083 nasopharynx of healthy children. Our results clearly point towards active production of the autolysins LytC and LytA that can be implicated in either fratricide (killing of non-competent pneumococci or other species) or in biofilm formation. We have also demonstrated that transcripts for a vaccine candidate, Ply [22,47] and an adhesin implicated in carriage and virulence, PavA [48], are detected in pneumoccocal cells residing in the humannasopharynx. We were unable, however, to evaluate mRNA levels of genes encoding other vaccine candidates such as PsaA due to the presence of similar sequences in other species found in the nasopharynx. Even when we selected NP samples with the highest possible density of pneumococci, the concentration of RNA obtained from our preparations was usually ,500 pg/ml. For research purposes, NP swabs collected to detect the pneumococcus are stored in 1 ml of transport medium (STGG) whereby less than 500 ng of bacterial RNA can be obtained with protocols described in this manuscript. As demonstrated, our RNA preparations had enough quality to generate cDNA and analyze expression of a set of selected genes by quantitative RT-PCR. The yield 16985061 of RNA is, however, an important limitation to the use of bacterial RNA extracted from NP samples for gene expression studies utilizing high-throughput technology (i.e. microarrays, RNA sequencing). This work provides a panel of primers that were validated against several related strains, most of which are present in the human respiratory tract. Although in silico studies were helpful in determining the specificity of primers designed to amplify pneumococcal genes, studies with DNA purified from those 20 related species revealed more nonspecific products which indicates the need for in vitro studies to validate in silico analyzes. These pneumococcus-specific primers can be utilized to evaluate gene expression in RNA purified from sterile sites (i.e. blood or cerebrospinal fluid) or non-sterile sites (middle ear fluid or bronchoalveolar lavage). 23148522 For example, a recent study changed our view of the lung microbiome by demonstrating that, although detected with a low density, lungs contain a similar bacterial flora to those of the nasopharynx [49]. Expression of genes in patients experiencing pneumococcal otitis media may also be obtained and compared to those being expressed in the nasopharynx. This information may reveal significant changes in gene expression allowing the pneumococcus to colonize other anatomic sites and to cause disease. These studies are underway in our laboratory. Studies utilizing conventional PCR and DNA from NP samples to detect pneumococcal genes, correlated with findings utilizing DNA extracted from the strains. For example, the lytA gene could be amplified by PCR in all samples whereas ,90 of NP samples were positive for the ply gene. qPCR studies found, however, more positive samples for most of the target genes. The more strikingFigure 4. Gene expression studies. RNA was obtained from a set of NP samples; cDNA was generated and utilized in quantitative PCR reactions targeting pneumococcal genes. The graphic was adjusted to show a log2 scale of copies of mRNA/ml of the indicated gene. A red bar represent more than 104 copies/ml, yellow bars correspond to those expressing .103,104 copies/ml wher.Of the transcript.DiscussionWe have analyzed in this study, for the first time, expression of important pneumococcal genes when S. pneumoniae is present in the nasopharynx of healthy children. Our results clearly point towards active production of the autolysins LytC and LytA that can be implicated in either fratricide (killing of non-competent pneumococci or other species) or in biofilm formation. We have also demonstrated that transcripts for a vaccine candidate, Ply [22,47] and an adhesin implicated in carriage and virulence, PavA [48], are detected in pneumoccocal cells residing in the humannasopharynx. We were unable, however, to evaluate mRNA levels of genes encoding other vaccine candidates such as PsaA due to the presence of similar sequences in other species found in the nasopharynx. Even when we selected NP samples with the highest possible density of pneumococci, the concentration of RNA obtained from our preparations was usually ,500 pg/ml. For research purposes, NP swabs collected to detect the pneumococcus are stored in 1 ml of transport medium (STGG) whereby less than 500 ng of bacterial RNA can be obtained with protocols described in this manuscript. As demonstrated, our RNA preparations had enough quality to generate cDNA and analyze expression of a set of selected genes by quantitative RT-PCR. The yield 16985061 of RNA is, however, an important limitation to the use of bacterial RNA extracted from NP samples for gene expression studies utilizing high-throughput technology (i.e. microarrays, RNA sequencing). This work provides a panel of primers that were validated against several related strains, most of which are present in the human respiratory tract. Although in silico studies were helpful in determining the specificity of primers designed to amplify pneumococcal genes, studies with DNA purified from those 20 related species revealed more nonspecific products which indicates the need for in vitro studies to validate in silico analyzes. These pneumococcus-specific primers can be utilized to evaluate gene expression in RNA purified from sterile sites (i.e. blood or cerebrospinal fluid) or non-sterile sites (middle ear fluid or bronchoalveolar lavage). 23148522 For example, a recent study changed our view of the lung microbiome by demonstrating that, although detected with a low density, lungs contain a similar bacterial flora to those of the nasopharynx [49]. Expression of genes in patients experiencing pneumococcal otitis media may also be obtained and compared to those being expressed in the nasopharynx. This information may reveal significant changes in gene expression allowing the pneumococcus to colonize other anatomic sites and to cause disease. These studies are underway in our laboratory. Studies utilizing conventional PCR and DNA from NP samples to detect pneumococcal genes, correlated with findings utilizing DNA extracted from the strains. For example, the lytA gene could be amplified by PCR in all samples whereas ,90 of NP samples were positive for the ply gene. qPCR studies found, however, more positive samples for most of the target genes. The more strikingFigure 4. Gene expression studies. RNA was obtained from a set of NP samples; cDNA was generated and utilized in quantitative PCR reactions targeting pneumococcal genes. The graphic was adjusted to show a log2 scale of copies of mRNA/ml of the indicated gene. A red bar represent more than 104 copies/ml, yellow bars correspond to those expressing .103,104 copies/ml wher.
