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Molecular Microbiology News Vol.2/2018 |
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Hot Topic: Whole Genome Sequencing in Clinical Routine Infection Diagnosis |
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New Publications: 1. Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing (Leo et al. 2017) 2. Messages from the First International Conference on Clinical Metagenomics (Ruppé et al. 2017) 3. Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis (Thoendel et al. 2017) Product Highlights: · Ultra-Deep Microbiome Prep Kit for microbial DNA enrichment and isolation from fluid and tissue specimens, removal of non-target host DNA · DNA-free Water Ultra-pure, DNA-free water for precise molecular analysis |
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New Publications |
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1. Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing (Leo et al. 2017) The applications of whole-metagenome shotgun sequencing in routine clinical analysis are still limited. In this study the authors extracted DNA from broncho-alveolar lavage samples with protocols based either on sequential lysis of human and bacterial cells or on the mechanical disruption of all cells. Metagenomic libraries were sequenced on Illumina HiSeq platforms. Results were compared to those obtained by conventional clinical culture and molecular methods. Compared to mechanical cell disruption, a sequential lysis protocol resulted in a significantly increased proportion of bacterial DNA over human DNA and higher sequence coverage of bacteria reported by clinical microbiology tests. |
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2. Messages from the First International Conference on Clinical Metagenomics (Ruppé et al. 2017) Metagenomics is recently entering clinical microbiology. An increasing number of diagnostic laboratories are proposing the sequencing and annotation of bacterial genomes and/or the analysis of clinical samples by direct or PCR-based metagenomics with short time-to-results. In this context, the first International Conference on Clinical Metagenomics (ICCMg) was held in Geneva in October 2016. Several key aspects were discussed, including, among others: the need for improved resolution, the importance of interpretation given the common occurrence of sequence contaminants and the bottleneck of DNA extraction. The authors concluded that further efforts are necessary to reduce turnaround time, improve data quality and lower costs to warrant full translation of metagenomics into clinical applications. |
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3. Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis (Thoendel et al. 2017) Whole-genome amplification (WGA) is a useful tool for amplification of very small quantities of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis. Depending on the application, background DNA from WGA kits can be problematic. The authors tested three WGA kits for their utility in a metagenomics approach to identify the pathogens in sonicate fluid that comprised of biofilms and other materials dislodged by sonication from the surfaces of explanted prosthetic joints. The results were then compared to those obtained with a library preparation without prior WGA using a NEBNext Ultra II paired-end kit, which requires a very small amount of input DNA. The findings highlight the impact of WGA on metagenomic analysis of low-biomass samples and the importance of careful consideration of the implications if using these tools. |
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Product Highlights |
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Ultra-Deep Microbiome Prep Microbial DNA enrichment and isolation from fluid and tissue specimens, removal of non-target host DNA Molzym’s Ultra-Deep Microbiome Prep kit is the perfect tool for microbiome studies allowing significantly deeper sequencing compared with conventional DNA isolation systems. Product features: · Isolation of enriched microbiome DNA · Removal of non-target human/animal DNA (MolYsis™-technology) · Broad-range lysis of bacteria and fungi · Small and large volumes: 0.2 to 10ml liquid samples and tissues · Contamination-free DNA isolation reagents, buffers and spin columns · Automation available |
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DNA-free Water Ultra-pure, DNA-free water for precise molecular analysis Molecular analysis can be prone to false-positive results due to reagent-based contaminations with microbial DNA. DNA-free water is ideally suited to be used in all kind of molecular microbiology applications. Product features: · Sterile, PCR-grade water · Guaranteed microbial DNA-free · PCR and Real-Time PCR tested (≥40 cycles) · High and consistent product quality |
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The following complementary resources are available online: · Product brochure on MolYsis™ kits >>Download · Product brochure on DNA-free PCR reagents >>Download · Application Note: Applications of MolYsis™ Human DNA Removal and Pathogen DNA Isolation for Molecular Analysis >>Download |
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Dear reader, Welcome to this edition of Molecular Microbiology News. With this newsletter we want to keep you updated on the latest developments in molecular detection of microbial infections. Best regards, Michael Lorenz, Ph. D. (Editor in Chief) |
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P.S.: Please forward this e-mail on to interested colleagues of yours. |
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