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Jakobs, M. E.

Publications and source records attributed to Jakobs, M. E..

2 recordsLinked to original sources

A NINE-YEAR LONGITUDINAL STUDY IN THE BLOOD OF A SUPERCENTENARIAN REVEALS AN EXTENSIVE SUBCLONAL ARCHITECTURE AND ONGOING SUBCLONAL DYNAMICS

The aged hematopoietic system is characterized by decreased immuno-competence and by a reduced number of hematopoietic stem cells (HSCs) that actively generates new blood cell (age-related clonal hematopoiesis, ARCH). While both aspects are commonly associated with an increased risk of aging-related diseases, it is currently unknown to what extent these aspects co-occur during exceptional longevity. Here, we investigated these aspects in blood cells of an immuno-hematopoietically normal female who reached 111 years. Blood samples were collected across a 9-year period at ages 103, 110 and 111 years. We applied several genetic sequencing approaches to investigate clonality in peripheral blood samples and sorted cell subsets. Immuno-competence was characterized using flow cytometry, T-cell receptor excision circle (TREC) assays, and in vitro proliferation assays. We identified a single DNMT3A-mutated HSC clone with a complex subclonal architecture and observed ongoing subclonal dynamics within the 9-year timeframe of our sampling. The mutated HSC generated 78-87% myeloid cells, 6-7% of the B-cells, 6% of CD8+ T-cells, and notably 22% of the CD4+ T-cells. Intriguingly, we found that T-cells were capable of robust proliferation when challenged in vitro. Moreover, we observed a surprisingly high TREC content, indicative of recent generation of naive T-cells. Concluding, we observed long-term stability of extreme ARCH with ongoing clonal dynamics combined with functional T-cell immunity. Our results indicate that extreme ARCH does not compromise immuno-competence and that a clonally expanded CD4+ T-cell subset may serve as a potential hallmark of the supercentenarian immune system. Key pointsO_LILongitudinal blood sampling from a female aged 103-111 revealed a dynamic clonal hematopoiesis contributing to myeloid and lymphoid subsets C_LIO_LIDespite the highly advanced age and extreme clonal hematopoiesis we observed functional T-cell immunity C_LI

immunology↗

Metagenomic sequencing to replace semi-quantitative urine culture for detection of urinary tract infections: a proof of concept

ABSTRACTSemi-quantitative bacterial culture is the standard method to diagnose urinary tract infections (UTI), but bacterial growth rate limits diagnostic speed and it is unreliable when patients have been pre-treated with antibiotics. Metagenomics could increase diagnostic speed and accuracy by sequencing the microbiome and resistome directly from urine samples, bypassing culture. However, a semi-quantitative approach - as needed for diagnosing UTIs - has not been established.\n\nMetagenomics was deployed to identify and semi-quantify bacterial presence indicative of UTI, predict antimicrobial susceptibility (AMR), and results were compared to semi-quantitative culture. Whole genome sequencing of the corresponding uropathogens was done for comparison. Analysis time and cost were tracked.\n\nForty-one consecutive urine samples underwent metagenomic analysis. All culture positive samples contained >200ng of DNA, suggestive of a threshold below which UTI could be ruled out solely based on DNA quantity. A semi-quantitative Diagnostic Index (DI) was created by multiplying the total DNA quantity by the relative abundance of uropathogens per urine sample. The DI allowed discrimination of UTI from non-UTI samples in all but 1 case. Metagenomic detection of AMR determinants correctly predicted the phenotype of uropathogens in 20 of 32 cases. The metagenomic work-flow was 31h and cost {euro}116 per sample, but could be reduced to 4.5h and {euro}5 for low-DNA-yield non-UTI samples.\n\nThe genomic determinants of AMR and their distribution across uropathogens need to be better understood for prediction of AMR phenotypes by metagenomics. The introduction of the DI demonstrates the potential of semi-quantitative metagenomics to replace culture as rapid diagnostic method for UTI.

microbiology↗