A Real-Time PCR Assay for Detection of Low Pneumocystis jirovecii Levels.

Here we report a new real-time PCR assay using SYBR Green which provides higher sensitivity for the specific detection of low levels of Pneumocystis jirovecii. To do so, two primer sets were designed, targeting the family of genes that code for the most abundant surface protein of Pneumocystis spp., namely the major surface glycoproteins (Msg), and the mitochondrial large subunit rRNA (mtLSUrRNA) multicopy gene, simultaneously detecting two regions. PCR methods are instrumental in detecting these low levels; however, current nested-PCR methods are time-consuming and complex. To validate our new real-time Msg-A/mtLSUrRNA PCR protocol, we compared it with nested-PCR based on the detection of Pneumocystis mitochondrial large subunit rRNA (mtLSUrRNA), one of the main targets used to detect this pathogen. All samples identified as positive by the nested-PCR method were found positive using our new real-time PCR protocol, which also detected P. jirovecii in three nasal aspirate samples that were negative for both rounds of nested-PCR. Furthermore, we read both rounds of the nested-PCR results for comparison and found that some samples with no PCR amplification, or with a feeble band in the first round, correlated with higher Ct values in our real-time Msg-A/mtLSUrRNA PCR. This finding demonstrates the ability of this new single-round protocol to detect low Pneumocystis levels. This new assay provides a valuable alternative for P. jirovecii detection, as it is both rapid and sensitive.

Optimized DNA extraction and purification method for characterization of bacterial and fungal communities in lung tissue samples.

Human lungs harbor a scarce microbial community, requiring to develop methods to enhance the recovery of nucleic acids from bacteria and fungi, leading to a more efficient analysis of the lung tissue microbiota. Here we describe five extraction protocols including pre-treatment, bead-beating and/or Phenol:Chloroform:Isoamyl alcohol steps, applied to lung tissue samples from autopsied individuals. The resulting total DNA yield and quality, bacterial and fungal DNA amount and the microbial community structure were analyzed by qPCR and Illumina sequencing of bacterial 16S rRNA and fungal ITS genes. Bioinformatic modeling revealed that a large part of microbiome from lung tissue is composed of microbial contaminants, although our controls clustered separately from biological samples. After removal of contaminant sequences, the effects of extraction protocols on the microbiota were assessed. The major differences among samples could be attributed to inter-individual variations rather than DNA extraction protocols. However, inclusion of the bead-beater and Phenol:Chloroform:Isoamyl alcohol steps resulted in changes in the relative abundance of some bacterial/fungal taxa. Furthermore, inclusion of a pre-treatment step increased microbial DNA concentration but not diversity and it may contribute to eliminate DNA fragments from dead microorganisms in lung tissue samples, making the microbial profile closer to the actual one.

Dental Forensic Kit (DFK®) and Quick Extract™ FFPE DNA extraction kit, a new workflow for obtaining dental DNA for human genetic identity.

BACKGROUND: Most of the protocols described for obtaining DNA from dental tissues are methods that involve major laboratory equipment and many hours of work. They are also methodologies that almost destroy the tooth. AIM: Our aim was to develop an innovative workflow for optimizing dental DNA extraction from teeth. Our methodological proposal is a new workflow for obtaining dental DNA for human genetic identity using Dental Forensic Kit (DFK®) and Formalin-Fixed Paraffin-Embedded (FFPE™) DNA extraction kit. METHODS: Two different dental samples groups were assayed with DFK® and FFPE™. The first group corresponded to extracted teeth from living donors and the second group was considered in real conditions with challenging teeth from corpses. Genomic Dental DNA was amplified and genotyped with platforms Identifiler Plus™, Power Plex 21™ and Global Filer ™ kits. RESULTS: Our workflow was useful in obtaining dental DNA and partial and complete genetic profiles, from teeth of both study groups. DFK® kit worked in a conservative treatment of teeth generating dental tissues (pulp and cement) and FFPE™ for DNA extraction was a very cheap, quick and easy method for obtaining genomic dental DNA. CONCLUSIONS: The innovative method and the workflow proposed herein allows obtaining robust and reliable genetic profiles, from dental tissues. DFK® kit works optimizing the treatment of dental tissues and FFPE™ demonstrates a new use in forensic genetics.