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Zink, F.

Publications and source records attributed to Zink, F..

7 recordsLinked to original sources

Intubation and mechanical ventilation lead to an extensive expansion of VAP-associated bacterial species in respiratory secretions of ventilated pigs

Ventilator associated pneumonia (VAP) remains one of the most critical nosocomial infections in intensive care medicine. Between 20-50% of ventilated patients develop VAP during treatment, often leading to long term sequelae and death, despite successful therapy of their underlying disease. VAP is typically caused by Gram-negative bacteria that can previously be detected on the mucosal membranes of the oral and upper respiratory tract. To assess and quantify bacterial colonization of the respiratory tract following intubation and ventilation a well-established pig model was used. Methods: After induction of anaesthesia and endotracheal intubation pigs underwent mechanical ventilation continuously for up to three days. To assess bacterial colonization of the upper respiratory tract, samples of respiratory secretions were taken at day 0, 1 and 2 directly above the cuff outside of the endotracheal tube (ETT) and by aspiration of tracheal secretions through the ETT. Quantification of bacteria was carried out by serial dilutions and CFU/ml determinations on sheep blood agar and MacConkey agar plates. Species identification was achieved by 16S-RNA gene sequencing. Results: Respiratory samples of 19 pigs were analysed and showed a sharp increase of predominantly Gram-negative organisms in the respiratory material sampled above the cuff from day 0 to 1. Starting at a median of 7.3 x 103 immediately after intubation numbers increased to a median of 2.0 x 107 Gram-negative bacteria at day 1 and 3.2 x 107 at day 2. Gram-negative species that were detected included Pseudomonas aeruginosa, Acinetobacter baumanii, Enterobacter aerogenes, Klebsiella pneumoniae and other Enterobacteriaceae. Tracheal secretions contained much less bacteria. While no Gram-negative bacteria could be cultured at the beginning of the experiment in 18 of 19 animals, colonization with Gram-negative bacteria gradually increased and was found in 7 of 19 and 9 of 14 animals on day 1 and day 2 respectively. Interestingly, in the vast majority of colonized tracheal secretions the identical Gram-negative species had previously been detected in secretions collected > 24h earlier at the cuff. Conclusion: A massive increase of the concentration of Gram-negative bacteria occurred at 24h of ventilation in mucosal secretions above the cuff. Detected species were the same Gram-negative bacteria that are frequently responsible for human infections, suggesting that especially the accumulation of bacteria in secretions above the cuff may be crucial in the development of VAP.

microbiology↗

Bayesian 13C-metabolic flux analysis of parallel tracer experiments in granulocytes: A directional shift within the non-oxidative pentose phosphate pathway supports phagocytosis

The pentose phosphate pathway (PPP) plays a key role in the cellular regulation of immune cell function; however, little is known about the interplay of metabolic adjustments in granulocytes, especially regarding the non-oxidative PPP. For the determination of metabolic mechanisms within glucose metabolism, we propose a novel Bayesian 13C-Metabolic flux analysis based on ex-vivo parallel tracer experiments with [1,2-13C]glucose, [U-13C]glucose, and [4,5,6-13C]glucose and gas chromatography-mass spectrometry labeling measurements of metabolic fragments including sugar phosphates. With this approach we obtained precise flux distributions and their joint confidence regions, which showed that phagocytic stimulation reversed the direction of non-oxidative PPP net fluxes from ribose-5-phosphate biosynthesis towards glycolytic pathways. This process was closely associated with the up-regulation of the oxidative PPP to promote the oxidative burst. The estimated fluxes showed strong pairwise inter-relations forming a single line in several cases. This behavior could be explained with a three-dimensional permissible space derived from stoichiometric-flux-constraint analysis and enabled a principal component analysis detecting only three distinct axes of coordinated flux changes that were sufficient to explain all flux observations.

systems biology↗

The sequences of 150,119 genomes in the UK biobank

We describe the analysis of whole genome sequences (WGS) of 150,119 individuals from the UK biobank (UKB). This constitutes a set of high quality variants, including 585,040,410 SNPs, representing 7.0% of all possible human SNPs, and 58,707,036 indels. The large set of variants allows us to characterize selection based on sequence variation within a population through a Depletion Rank (DR) score for windows along the genome. DR analysis shows that coding exons represent a small fraction of regions in the genome subject to strong sequence conservation. We define three cohorts within the UKB, a large British Irish cohort (XBI) and smaller African (XAF) and South Asian (XSA) cohorts. A haplotype reference panel is provided that allows reliable imputation of most variants carried by three or more sequenced individuals. We identified 895,055 structural variants and 2,536,688 microsatellites, groups of variants typically excluded from large scale WGS studies. Using this formidable new resource, we provide several examples of trait associations for rare variants with large effects not found previously through studies based on exome sequencing and/or imputation.

genetics↗

Genetic predisposition to mosaic Y chromosome loss in blood is associated with genomic instability in other tissues and susceptibility to non-haematological cancers

Mosaic loss of chromosome Y (LOY) in circulating white blood cells is the most common form of clonal mosaicism, yet our knowledge of the causes and consequences of this is limited. Using a newly developed approach, we estimate that 20% of the UK Biobank male population (N=205,011) has detectable LOY. We identify 156 autosomal genetic determinants of LOY, which we replicate in 757,114 men of European and Japanese ancestry. These loci highlight genes involved in cell-cycle regulation, cancer susceptibility, somatic drivers of tumour growth and cancer therapy targets. Genetic susceptibility to LOY is associated with non-haematological health outcomes in both men and women, supporting the hypothesis that clonal haematopoiesis is a biomarker of genome instability in other tissues. Single-cell RNA sequencing identifies dysregulated autosomal gene expression in leukocytes with LOY, providing insights into how LOY may confer cellular growth advantage. Collectively, these data highlight the utility of studying clonal mosaicism to uncover fundamental mechanisms underlying cancer and other ageing-related diseases.

genetics↗

Recurrence of de novo mutations in families

De novo mutations (DNMs) cause a large fraction of severe rare diseases of childhood. DNMs that occur in early embryos may result in mosaicism of both somatic and germ cells. Such early mutations may be transmitted to more than one offspring and cause recurrence of serious disease. We scanned 1,007 sibling pairs from 251 families and identified 885 DNMs shared by siblings (ssDNMs) at 451 genomic sites. We estimated the probability of DNM recurrence based on presence in the blood of the parent, sharing by other siblings, parent-of-origin, mutation type, and genomic position. We detected 52.1% of ssDNMs in the parental blood. The probability of a DNM being shared goes down by 2.28% per year for paternal DNMs and 1.82% for maternal DNMs. Shared paternal DNMs are more likely to be T>C mutations than maternal ones, but less likely to be C>T mutations. Depending on DNM properties, the probability of recurrence in a younger sibling ranges from 0.013% to 29.6%. We have launched an online DNM recurrence probability calculator, to use in genetic counselling in cases of rare genetic diseases.

genomics↗

Graphtyper: Population-scale genotyping using pangenome graphs

A fundamental requisite for genetic studies is an accurate determination of sequence variation. While human genome sequence diversity is increasingly well characterized, there is a need for efficient ways to utilize this knowledge in sequence analysis. Here we present Graphtyper, a publicly available novel algorithm and software for discovering and genotyping sequence variants. Graphtyper realigns short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths. Our results show that Graphtyper is fast, highly scalable, and provides sensitive and accurate genotype calls. Graphtyper genotyped 89.4 million sequence variants in whole-genomes of 28,075 Icelanders using less than 100,000 CPU days, including detailed genotyping of six human leukocyte antigen (HLA) genes. We show that Graphtyper is a valuable tool in characterizing sequence variation in population-scale sequencing studies.

bioinformatics↗