Biology subjects

Simonsen, G. S.

Publications and source records attributed to Simonsen, G. S..

3 recordsLinked to original sources

bioRxiv2026

From culture to clarity in four hours: accelerating clinical management of bloodstream infections using metagenomics

BackgroundMetagenomic next-generation sequencing (mNGS) has the potential to transform clinical diagnostics for bloodstream infections (BSIs). However, its clinical utility is currently limited by several challenges, including the extraction of DNA from blood cultures. Our aim was to develop, evaluate, and optimize an in-house method for host depletion and bacterial DNA extraction from positive blood cultures to enable rapid mNGS-based pathogen detection and antimicrobial resistance profiling, informing clinical management of BSIs. Methods151 clinical blood cultures (115 positive and 36 negative) were processed for DNA extraction using an in-house-developed SEPSINN method for host depletion and bacterial DNA extraction. mNGS on the MinION was performed, and the results for pathogen identification and antimicrobial susceptibility predictions were compared with the routine clinical workflow. SEPSINN was also evaluated against a commercial DNA extraction method to assess its effectiveness in depleting host DNA and recovering bacterial DNA. ResultsThe SEPSINN method achieved up to 1000-fold depletion of host DNA and outperformed the commercial DNA extraction method. At the sample level, mNGS achieved 100% accuracy, specificity, and sensitivity, identifying at least one pathogen in all 115 positive blood cultures. At the pathogen level, mNGS showed 98% accuracy (120/123), specificity, and sensitivity. For antimicrobial susceptibility predictions, mNGS achieved an accuracy of 95% (1382/1451), a sensitivity of 88% (203/230), and a specificity of 97% (1179/1221). Moreover, the method also identified fungi, indicating a wider taxonomic range. mNGS resulted in an approximately 4-hour turnaround time for pathogen identification and resistance profiling. ConclusionsThe method can provide information on BSI clinical management within approximately 24 hours of receiving the sample, including the time required for culture positivity. This represents an important advancement in the clinical management of BSIs, with the potential to save lives and promote antibiotic stewardship.

microbiology↗

bioRxiv2023

Escherichia coli plasmidome maps the game of clones

Escherichia coli is the most widely studied microbe in history, but its extrachromosomal elements known as plasmids remain poorly delineated. Here we used long-read technology to high-resolution sequence the entire plasmidome and the corresponding host chromosomes from an unbiased longitudinal survey covering two decades and over 2,000 E. coli isolates. We find that some plasmids have persisted in lineages even for centuries, demonstrating strong plasmid-lineage associations. Our analysis provides a detailed map of recent vertical and horizontal evolutionary events involving plasmids with key antibiotic resistance, competition and virulence determinants. We present genomic evidence of both chromosomal and plasmid-driven success strategies that represent convergent phenotypic evolution in distant lineages, and use in vitro experiments to verify the importance of bacteriocin-producing plasmids for clone success. Our study has general implications for understanding plasmid biology and bacterial evolutionary strategies.

microbiology↗

bioRxiv2021

A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-2015: Introduction and spread of ESBL facilitated by CG15 and CG307

SynopsisO_ST_ABSObjectiveC_ST_ABSWe have used the nationwide Norwegian surveillance program on resistant microbes in humans (NORM) to address longitudinal changes in the population structure K. pneumoniae isolates during 2001-15, encompassing the emergence and spread of ESBL-producing Enterobacterales (ESBL-E) in Norway. Material and methodsAmong blood (n= 6124) and urinary tract (n=5496) surveillance isolates from 2001-15, we used Illumina technology to whole genome sequence 201 ESBL-producing isolates from blood (n=130) and urine (n=71), and 667 non-ESBL isolates from blood. Complete genomes for four isolates were resolved with Oxford Nanopore sequencing. ResultsIn a highly diverse collection, Klebsiella variicola ssp. variicola caused a quarter of Klebsiella pneumoniae species complex bacteraemias. ESBL-production was limited to K. pneumoniae sensu stricto (98.5 %). A diverse ESBL population of 57 clonal groups (CGs) were dominated by multidrug resistant CG307 (17%), CG15 (12%), CG70 (6%), CG258 (5%) and CG45 (5%) carrying blaCTX-M-15. Yersiniabactin was significantly more common in ESBL-positive (37.8%) compared to non-ESBL K. pneumoniae sensu stricto isolates (12.7%), indicating convergence of virulence and resistance determinants Moreover, we found a significant lower prevalence of yersinabactin (3.0 %, 37.8 % and 17.3 %), IncFIB (58.7 %, 87.9 % and 79.4 %) and IncFII plasmid replicons (40.5 %, 82.8 % and 54.2%) in K. variicola ssp. variicola compared to ESBL- and non-ESBL K. pneumoniae sensu stricto, respectively. ConclusionThe increase in Norwegian KpSC ESBLs during 2010-15 was driven by blaCTX-M-15 carrying CG307 and CG15. K. variicola ssp. variicola was a frequent cause of invasive KpSC infection, but rarely carried ESBL.

microbiology↗