Molzym Blog

Latest Blog Posts

Here you find our latest blog posts. Enjoy reading!

 

Urinary Tract Microbiome Analysed Despite Low Bacterial Load

Urinary tract infections and bacterial biofilms on urinary stents are typically diagnosed by culture. Buhmann et al. [1] analysed the bacterial communities of encrustations on urinary stents after indwelling of 3-6 weeks by molecular methods and could reveal different urotypes at, in general, low bacterial loads.

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16S rDNA PCR and Sequencing Diagnosis of Bone and Joint Infections

PCR and sequencing analysis of pathogens without cultivation is an integral part of routine diagnosis. It rapidly uncovers microorganisms that do not grow in culture because of inhibition by antibiotics or fastidious growth requirements. Thereby, PCR/sequencing significantly contributes to the management of patients with bone and joint infections.

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Oral Microbiome Changes from Healthy to Carious Teeth

Abood [1] used whole genome metagenomic sequencing to precisely characterize microbial populations and their metabolic functions involved in the transition to caries. By reduction of up to 99 % human DNA background bioinformatic characterization of a complex bacterial and fungal microbiome and its change was possible.

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Highlights from ASM Microbe 2019 in San Francisco, CA

We had a great time exhibiting at this year’s ASM Microbe Meeting held from 20th to 24th of June 2019 in San Francisco, CA. Here we want to share two of our highlights from the poster sessions demonstrating the outstanding performance of Molzym’s solutions for deep microbiome/metagenomics analysis.

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Molecular Characterisation of Low Load Bacterial Samples

Molecular analysis of low microbial load samples is challenging because of the risk of contamination from ubiquitous bacterial DNA. In a recent publication, a workflow for molecular analysis was applied to fingerprint community changes in carious dentine samples before and after dental therapy.

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Diagnosis of Rare Pathogens by Direct 16S Sequencing

Infections of sterile body sites are caused by a great variety of microorganisms, including common as well as rare and unusual bacteria. This whitepaper discusses advantages of rRNA gene sequencing diagnosis performed directly on clinical materials in view of obstacles connected with the identification of infrequent pathogens by phenotypic markers.

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Critical Impact of DNA Contamination on Molecular Microbe Analysis

Contaminations by bacterial DNA in DNA extraction kits and amplification reagents can disturb 16S rRNA PCR and shotgun metagenomics analysis of samples with low loads of bacteria. Read about how to reduce contaminations, why negative controls are important and when ultra-clean reagents are indispensible for proper analysis.

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Meet Molzym at ECCMID 2019 in Amsterdam

The 29th European Congress on Clinical Microbiology and Infectious Diseases attracts specialists from all over the world to discuss the latest results in clinical diagnostics. Our Molzym experts will present solutions for the culture-independent molecular diagnosis of pathogens and the unique automated pathogen enrichment and DNA extraction robot SelectNA™plus.

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Join the Molzym Workshop at REMMDI on 11th of April

At the approaching REMMDI Meeting in Regensburg from 11th to 13th of April 2019, the Molzym experts invite you to our workshop covering in-depth insights of implementation of culture-independent analysis of pathogens by broad-range PCR in clinical routine. Learn about the benefit of Micro-Dx™ and SepsiTest™-UMD in exciting case studies. Safe your seat!

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Metagenomics for Infectious Disease Diagnostics

Next Generation Sequencing approaches for pathogen identification in clinical diagnostic routine lack FDA-cleared test systems so far. But technological improvements made in the last years are promising. One hurdle is the vast excess of human DNA compared to microbial DNA. Learn more about the problem and possible solutions.

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16S Pathogen Diagnosis of Culture-Negative Infections

Cultures of clinical specimens often are negative due to prior antibiotic treatment, fastidious growth requirements or viable but non-culturable pathogens. Stavnsbjerg et al. compared two commercial broad-range 16S rDNA PCR assays, MicroSeq® ID and UMD-SelectNA™, regarding their capacity of identifying bacteria in culture-negative samples.

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16S rDNA PCR Detection of Salmonella enterica in Blood

Salmonella enterica causes high morbidity and mortality worldwide. Culture detection is limited and affects timely antibiotic treatment. Masek et al. differentiated 9 serovars by 16S rDNA PCR and melt analysis. This and the high analytic sensitivity of the method (<10 cfu/ml) directly in blood promise to enhance current diagnosis of S. enterica.

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PCR and Sequencing Diagnosis of Infective Endocarditis

The diagnostic value of rDNA PCR and sequencing is discussed referring to clinical evaluations of infective endocarditis. The overall positivity of PCR/sequencing was notably higher than culture, in particular of heart valves. Common and rare aetiologies were similar with both systems, whereas mixed infections were more diverse by PCR/sequencing.

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SepsiTest™-UMD: Unbiased rDNA PCR Pathogen Diagnosis

Rapid pathogen detection is essential for timely patient treatment. In contrast to culture, molecular methods provide results within hours. Molzym’s highly sensitive approach combines a unique DNA extraction technique with 16S and 18S rRNA gene PCR and amplicon sequencing for the identification of bacterial and fungal infections. See how it works.

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Optimal DNA Extraction for Molecular Pathogen Analysis

Direct molecular diagnosis of pathogens is a helpful adjunct to culturing. An important factor influencing assay performance is the isolation of microbial DNA. Notable differences in Real-Time PCR assay sensitivity were observed with DNAs extracted from mock blood samples of bacteria and yeast using 7 manual and 3 automated DNA isolation kits.

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Reagent Contaminations in Microbiome Analysis

Structures of microbial communities can be distorted by reagent contaminations, especially in samples with low microbial loads as the placenta. Leon et al. used 16S targeted amplicon sequencing to examine the impact of potential contaminations on the microbiome analysis of spontaneous preterm, non-spontaneous preterm and term delivered placenta.

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16S rDNA PCR Diagnosis of Bacterial Pyomyositis

Pyomyositis is a bacterial infection of skeletal muscles, and antibiotic treatment leads to delayed or negative culture results. Gabas et al. [3] identified bacteria in all 10 patients by 16S rDNA PCR and sequencing, while culture was positive with 4 patients only. Antibiotic treatment was changed in all cases resulting in 90% recovery of patients.

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Vol 5/2018 - Infective Endocarditis - 16S/18S rDNA Diagnosis

Standard diagnosis of infective endocarditis (IE) is based on blood culturing which is limited by its high false negative rate. 16S/18S broad-range rDNA PCR analysis has a higher positivity due to, among others, the detection of mixed infections and fastidious organisms. The recent newsletter focusses on new results from IE comparative studies.

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Remove Host DNA and Use Your Validated Extraction System!

In pathogen diagnosis, establishment of DNA isolation systems needs extensive validation processes. Usually, the eluate contains a mixture of microbial and host DNA, whereby the latter negatively influences downstream analysis, especially at low load samples. Molzym’s MolYsis™ Basic kits deplete host DNA in samples prior to standard DNA extraction.

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Vol 4/2018 - New Solutions for 16S Metagenomic Sequencing

Are you using next generation sequencing and looking for reagents and methods for infection diagnosis by microbiome analysis? The new NGSeq 16S V3/V4 is a master mix for the Amplicon PCR as part of the library preparation for 16S metagenomic sequencing with Illumina® MiSeq system. Discover its benefits and learn about other helpful methods.

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Report on the 2nd Conference on Clinical Metagenomics

Metagenomic sequencing is used to recover information regarding clinically relevant infections. In their report, Ruppé & Schrenzel summarise last year’s 2nd International Conference on Clinical Metagenomics (ICCMg2). This post focusses on the current status, experiences, diagnostic use and clinical impact of sample treatment.

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Diagnosis of Culture-Negative Infective Endocarditis

Identification of aetiologies of infective endocarditis is crucial for initiation of targeted antibiotic treatment and patient outcome, but culture often fails. Marsch and his colleagues analysed 46 heart valves with negative or inconsistent culture results by 16S/18S rDNA PCR. In 7 patients, PCR results led to the change of the antibiotic regime.

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Visit Molzym at the AACC Annual Meeting in Chicago, IL

The 70th AACC Annual Scientific Meeting & Clinical Lab Expo is the largest global scientific conference in laboratory medicine. Molzym will be exhibiting their innovative products for rapid culture-independent molecular diagnosis of microbes focussing on unique solutions for microbial DNA enrichment from clinical specimens and DNA-free PCR assays.

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Unbiased PCR and Sequencing of Blood Stream Infections

Rapid diagnosis of sepsis pathogens is crucial for an early targeted antibiotic treatment and improved outcome of patients. Blood culture needs days until pathogen identification and often stays negative. Tkadlec et al. discuss the pros and cons of broad-range 16S rDNA PCR and sequencing on the basis of blood sample results of 330 patients.

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EU-Funded Project on Invasive Fungal Disease Detection

Invasive fungal disease is a major cause of morbidity and mortality in immuno-compromised patients. In a FP7 project of the European Commission, Molzym partners with 5 institutions from 4 countries to develop and evaluate in multi-centre clincial studies fast DNA, enzymatic and protein-based assays.

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SelectNA™plus - Robotic Pathogen DNA Extraction System

SelectNA™plus is the ‘Selective extraction of microbial Nucleic Acids’ from mixtures including host and microbial cells providing a ‘plus’ benefit by walk-away automated processing of clinical samples. This highly enriched microbial DNA guarantees highest analytical performance in research and routine diagnosis.

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Molzym - 15 Years Expertise in Molecular Diagnostics

Molzym turns 15 years this month. Over the years, Molzym won reputation as a specialist in the fast molecular diagnosis of microbial pathogens without the need of cultivation. Our expertise in unique DNA extraction solutions and the supply of DNA-free amplification reagents supports the standardisation of qPCR, gene clone library and NGS assaying.

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Molzym Partners EU-Funded Project on Fast Pathogen ID

Molzym partners EU Horizon 2020 project “Fast Assay for Pathogen Identification and Characterization” (FAPIC). Ten members from 7 countries joined to develop and clinically evaluate fast molecular assays for the identification of bacterial pathogens. Health system-relevant issues led to the prototyping of new automated diagnostic systems.

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Overview of MolYsis™ Applications in Research

Remove your host DNA for increased sensitivity for detection of microbes in a great variety of specimens, e.g body fluids and tissues. Here, we provide a collection of applications of MolYsis™ sample pre-treatment in combination with various analytical methods, including NGS, PCR and Real-time PCR, DNA arrays and amplicon cloning.

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One Protocol for Preparation of Bacterial and Fungal DNA

Efficient cell destruction is a key problem of microbial DNA isolation. As a component of Molzym's DNA extraction kits, the BugLysis reagent ensures degradation of the very different cell walls among prokaryotes and fungi. The high efficiency of BugLysis becomes obvious when considering that 1,330 species have been identified in studies and assaying so far.

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Thank You for Visiting US at ECCMID 2018

The Molzym-Team was delighted to participate and exhibit at the European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) that took place in Madrid, Spain, from 21st to 24th of April 2018. Here we want to share some impressions and highlights of this year’s ECCMID with you.

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Standardised Method for Infection Diagnosis with NGS

In a poster presentation at ECCMID 2018 congress, Edelmann et al. [1] compared 4 DNA extraction kits and the influence of human DNA removal for use in microbiome analysis. Additionally, two master mixes were tested for bacterial DNA contamination. An efficient workflow towards a standardised use of NGS in infection diagnosis was proposed.

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Automated Microbial DNA Enrichment in Clinical Routine

Micro-Dx™ combines automated pathogen enrich-ment and DNA extraction with broad-range PCR and sequencing ID of species. A multi-centre analysis of 409 routine samples of tissues, fluids and swabs indicated acceptable diagnostic performance in comparison to other molecular tests and culture. Additional pathogens could be identified by Micro-Dx™.

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Comparison of Microbial DNA Enrichment Tools for WGS

In most clinical samples, human DNA outnumbers the amount of pathogen DNA. Thus, pathogen analysis with metagenomic whole genome sequencing (MWGS) is often limited by unspecific primer binding to human sequences. Read a comparison study of two commercial kits with respect to their enrichment of microbial DNA and effect on MWGS.

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Special Edition on the Occasion of ECCMID 2018

In this special newsletter we highlight some noteworthy presentations on this year's ECCMID. Don't miss out the new developments in 16S metagenomics, diagnostic approaches in bacterial bloodstream infections and in innovations in molecular pathogen detection. Stop by our booth #159 and explore our portfolio of products.

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Vol 3/2018 - Diversity of Pathogens in 16S rDNA Routine Diagnosis

Two case reports address the added value of broad-range 16S rDNA PCR in pathogen diagnosis. In case 1, standard methods were negative while PCR identified a pathogen. In case 2, an unusual bacterial pathogen was identified by PCR. Read also an application note on the benefits of culture-independent diagnosis of pathogens in daily routine.

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Vol 2/2018 - Whole Genome Sequencing in Routine Infection Diagnosis

In this newsletter, we focus on the application of whole genome sequencing for pathogen detection in clinical routine and the challenges coming along with it. Three featured publications discuss, among others, the impact of DNA extraction, the problem of microbial contaminations of reagents and the need for improved resolution and standardisation.

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Vol 1/2018 - Micro-Dx™ Received CE IVD Marking

Our latest development, Micro-Dx™, received CE mark for in vitro diagnostics. Micro-Dx™ comprises automated pathogen DNA enrichment from clinical material on the SelectNA™plus robot together with 16S/18S rDNA amplification and sequencing analysis. Results of multi-sites evaluations by routine labs are summarised in an application note.

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Molzym Exhibits at ECCMID Congress in Madrid

The European Congress on Clinical Microbiology and Infectious Diseases is an important event that attracts specialists in the fields globally. Molzym will be exhibiting their innovative products for rapid culture-independent molecular pathogen diagnosis focussing on unique automation of microbial DNA enrichment from diverse clinical specimens.

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Automated Enrichment of Pathogen DNA from Heart Valves

The SelectNA™plus robot with DNA-free Micro-Dx™ kit reagents (SNP) enriches pathogens and isolates microbial DNA from specimens automatically. In this post, a 16S/18S PCR and sequencing analysis of heart valves and other biopsies from 52 infectious endocarditis patients is discussed. SNP found substantially more relevant pathogens than culture.

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