1.Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long-and Short-read Multi-metagenomic Sequencing Studies
Rehner JACQUELINE ; Schmartz Pierre GEORGES ; Groeger LAURA ; Dastbaz JAN ; Ludwig NICOLE ; Hannig MATTHIAS ; Rupf STEFAN ; Seitz BERTHOLD ; Flockerzi ELIAS ; Berger TIM ; Reichert Christian MATTHIAS ; Krawczyk MARCIN ; Meese ECKART ; Herr CHRISTIAN ; Bals ROBERT ; L.Becker S?REN ; Keller ANDREAS ; Müller ROLF
Genomics, Proteomics & Bioinformatics 2022;20(2):405-417
High-quality DNA extraction is a crucial step in metagenomic studies.Bias by different isolation kits impairs the comparison across datasets.A trending topic is,however,the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases.We thus collected bile,stool,saliva,plaque,sputum,and conjunctival swab samples and performed DNA extraction with three commercial kits.For each combination of the specimen type and DNA extraction kit,20-gigabase(Gb)metagenomic data were generated using short-read sequencing.While profiles of the specimen types showed close proximity to each other,we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kits.No kit outperformed all selected kits on every specimen.We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit.Depending on the specimen,our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution,but DNA-based identification is superior to identification by mass spectrometry.Finally,long-read nanopore sequencing confirmed the results(correlation coefficient>0.98).Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.
2.Silent Intracerebral Hemorrhage in Patients Randomized to Stenting or Endarterectomy for Symptomatic Carotid Stenosis
Mandy D MÜLLER ; Lisa M JONGEN ; Aysun ALTINBAS ; Kristine A BLACKHAM ; Paul J NEDERKOORN ; Sumaira MACDONALD ; Rolf JÄGER ; Thomas WOLFF ; Philippe A LYRER ; L Jaap KAPPELLE ; Stephan G WETZEL ; Toby RICHARDS ; Jeroen HENDRIKSE ; Gert J DE BORST ; H Bart VAN DER WORP ; Stefan T ENGELTER ; David J WERRING ; Martin M BROWN ; Leo H BONATI
Journal of Stroke 2019;21(1):116-119
No abstract available.
Carotid Stenosis
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Cerebral Hemorrhage
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Endarterectomy
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Humans
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Stents
3.Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates.
Valentina GALATA ; Cédric C LACZNY ; Christina BACKES ; Georg HEMMRICH-STANISAK ; Susanne SCHMOLKE ; Andre FRANKE ; Eckart MEESE ; Mathias HERRMANN ; Lutz VON MÜLLER ; Achim PLUM ; Rolf MÜLLER ; Cord STÄHLER ; Andreas E POSCH ; Andreas KELLER
Genomics, Proteomics & Bioinformatics 2019;17(2):169-182
Emerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly-sequenced whole genomes) and culture-based resistance profiles (10,991 out of the 11,087 isolates comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns were observed including increased resistance rates for Acinetobacter baumannii to carbapenems and for Escherichia coli to fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species, including conserved essential genes and known resistance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene-drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into GEAR-base, a resource available for academic research use free of charge at https://gear-base.com.
Acinetobacter baumannii
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genetics
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isolation & purification
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Bacteria
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genetics
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isolation & purification
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Cell Culture Techniques
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methods
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Drug Resistance, Microbial
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genetics
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Escherichia coli
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genetics
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isolation & purification
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Genome, Bacterial
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Genotype
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Humans
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Internet
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Microbial Sensitivity Tests
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Phenotype
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Whole Genome Sequencing