Biology subjects

Samuelsen, O.

Publications and source records attributed to Samuelsen, O..

14 recordsLinked to original sources

bioRxiv2025

Mapping the evolutionary path towards multi-drug resistance in the pandemic Escherichia coli ST131 lineage

Escherichia coli sequence type (ST) 131 is the most widely studied genetic lineage of the species to date, originally identified in the early 2000s as an increasingly common cause of human urinary tract and bloodstream infections worldwide. This lineage is subdivided into four extant main subclades A, B, C1 and C2 that exhibit distinct features in terms of invasiveness, antibiotic resistance and transmissibility. However, the evolutionary pathway from the generally susceptible ST131-B to the drug-resistant ST131-C clades remains poorly mapped. To fill this knowledge gap, we analysed in detail human clinical isolates obtained in Vietnam, designated as belonging to the generally neglected minor clade ST131-B0. We sequenced them using both short- and long-read technology, and combined these data with a recently published high-resolution genomic collection to provide further insight into the evolutionary process and its timeline. Extensive genomic analyses established ST131-B0 as an intermediary progenitor in the evolutionary path leading from ST131-B to the ST131-C clades, associated with multiple type I pili switches, as well as the loss and gain of specific chromosomal genes representing diverse core functions such as metabolism, transcription, DNA binding and type II toxin-antitoxin systems. Furthermore, all Vietnamese isolates of ST131-B0 unprecedentedly harboured blaCTX-M genes encoding extended-spectrum {beta}-lactamases, a trait dominant in ST131-C clades and not previously observed in ST131-B0. Our study supports the hypothesis that the ST131-C clades have gradually evolved from ST131-B by reducing the host range with better adaptation to colonising humans under selective conditions.

evolutionary biology↗

bioRxiv2025

Machine learning based lineage prediction from AMR phenotypes for Escherichia coli ST131 clade C surveillance across infection types

2.Rising antimicrobial resistance (AMR) in Escherichia coli bloodstream infections (BSIs) in high-income settings has typically been dominated by one clone, the sequence type (ST) 131. More specifically, ST131 clade C (ST131-C) is associated with fluoroquinolone resistance and extended-spectrum {beta}-lactamases (ESBLs). Even though urinary tract infections (UTIs) are a known common precursor to BSIs, there is currently limited knowledge on the longitudinal prevalence of ST131-C in UTIs and, therefore, the temporal link between the two infection types. Leveraging available genomic and antimicrobial susceptibility test (AST) data for ciprofloxacin, gentamicin, and ceftazidime in 2790 E. coli BSI isolates, we trained random forest and Extreme Gradient Boosting (XGBoost) classifiers to predict if an E. coli isolate belongs to ST131-C using only AST data. These models were used to predict the yearly prevalence of ST131-C in 22942 UTI and 24866 BSI isolates from Norway. The XGBoost classifier achieved a prediction F1-score of over 70% on a highly unbalanced dataset where only 4.3% of the genomic BSI isolates belonged to ST131-C. The predicted prevalence of ST131-C in UTIs exhibited a similar annual trend to that of BSIs, with a stable infection burden for eight years after its rapid expansion, confirming that the persistence of ST131-C in BSIs is largely driven by ST131-C UTIs. However, a higher prevalence of ST131-C in BSIs ([~]7%) compared to UTIs ([~]4%) suggests a subsequent enrichment of ST131-C. Our study highlights how existing epidemiological knowledge can be supplemented by utilising extensive data from AMR surveillance efforts without genomic markers. 3. Impact statementThis study proposes a potential analysis method that leverages AST data, which is already regularly collected for AMR surveillance purposes. Using such data to approximate the population-wide prevalence of MDR clones, such as ST131-C, could allow for larger-scale, retrospective studies of its prevalence in a population than genomic-based methods at a significantly lower cost. Such a method could supplement existing knowledge and epidemiology study practices. We use the proposed method to find relationships between the prevalence of the important MDR E. coli clone ST131-C in UTIs and BSIs in Norway. These results suggest that monitoring and reducing MDR in UTIs could reduce the burden of this invasive clone in hard-to-treat BSIs. 4. Data summaryAll AST data, clonal information for isolates with genomic data, and code used in this study can be found in the following repository: https://github.com/theodorross/EColi-UTI-Predictions. Only the clone and published metadata information is shown for the UTI data shared by Handal, Kaspersen et al.

bioinformatics↗

bioRxiv2024

A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs

Members of the Klebsiella pneumoniae species complex (KpSC) are opportunistic pathogens that cause severe and difficult-to-treat infections. KpSC are common in non-human niches, but the clinical relevance of these populations is disputed. Utilising 3,255 whole-genome sequenced isolates from human, animal and marine sources collected during 2001-2020 in Norway, we showed the KpSC populations in different niches were distinct but overlapping. Notably, human infection isolates showed greatest connectivity with each other, followed by isolates from human carriage, pigs, and bivalves. Nearly 5% of human infection isolates had close relatives ([≤]22 substitutions) amongst animal and marine isolates, despite temporally and geographically distant sampling of these sources. Infection prevention measures are essential to limit transmission within human clinical settings and reduce disease burden. However, as colonisation often precedes infection, preventing transmission that leads to colonisation, e.g. transmission between animals and humans in the community, and in the food chain, could also be beneficial.

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↗

bioRxiv2022

Consistent typing of plasmids with the mge-cluster pipeline

Extrachromosomal elements of bacterial cells such as plasmids are notorious for their importance in evolution and adaptation to changing ecology. However, high-resolution population-wide analysis of plasmids has only become accessible recently with the advent of scalable long-read sequencing technology. Current typing methods for the classification of plasmids remain limited in their scope which motivated us to develop a computationally efficient approach to simultaneously recognize novel types and classify plasmids into previously identified groups. Our method can easily handle thousands of input sequences which are compressed using a unitig representation in a de Bruijn graph. We provide an intuitive visualization, classification and clustering scheme that users can explore interactively. This provides a framework that can be easily distributed and replicated, enabling a consistent labelling of plasmids across past, present, and future sequence collections. We illustrate the attractive features of our approach by the analysis of population-wide plasmid data from the opportunistic pathogen Escherichia coli and the distribution of the colistin resistance gene mcr-1.1 in the plasmid population.

bioinformatics↗

bioRxiv2022

Strong pathogen competition in neonatal gut colonisation

Bacterial pathogen species and their strains that colonise the human gut are generally understood to compete against both each other and the commensal species colonising this ecosystem. However, currently we are lacking a population-wide quantification of strain-level colonisation dynamics for many common bacterial pathogens and the relationship of colonisation potential to prevalence in disease is unknown. In addition, it is unclear how ecological factors might be modulating the dynamics. Here, using a combination of latest high-resolution metagenomics and strain-level genomic epidemiology methods leveraging large genomic reference libraries of key pathogens, we performed a characterisation of the competition (co-exclusion and co-presence) and colonisation dynamics for a longitudinal cohort of neonatal gut microbiomes. We found a strong inter- and intra-species competition dynamic in the gut colonisation process, but also a number of synergistic relationships among several species belonging to genus Klebsiella, which includes the prominent human pathogen Klebsiella pneumoniae. Additionally, we find no evidence of preferential colonisation by hospital-adapted pathogen lineages in either vaginal or caesarean section birth groups. Our analysis also enables the first unbiased assessment of the strain-level colonisation potential of extra-intestinal pathogenic Escherichia coli (ExPEC) in comparison with their potential to cause bloodstream infections. We determined that the established common ExPEC clones ST73 and ST95 are overall significantly more pathogenic than the more recent, globally circulating multi-drug resistant clone ST131, where only a single subclone (ST131-C2) exhibited excess pathogenic potential. Our study highlights the importance of systematic surveillance of bacterial gut pathogens, not only from disease but also from carriage state, to better inform therapies and preventive medicine in the future.

microbiology↗

bioRxiv2022

Evolution of β-lactamase mediated cefiderocol resistance

Cefiderocol is a novel siderophore {beta}-lactam with improved hydrolytic stability toward {beta}-lactamases, including carbapenemases, achieved by combining structural moieties of two clinically efficient cephalosporins, ceftazidime and cefepime. Consequently, cefiderocol represents a treatment alternative for infections caused by multi-drug resistant Gram-negatives. Using directed evolution on a wide variety of different {beta}-lactamases, such as KPC-2 and CTX-M-15 (Ambler class A), NDM-1 (class B), CMY-2 (class C) and OXA-48 (class D), we studied the role of cefiderocol during {beta}-lactamase-mediated resistance development. First, we investigated how the expression of different {beta}-lactamases causes changes in cefiderocol susceptibility. In a low-copy number vector, we found that OXA-48 and KPC-2 conferred non or marginal decreases in cefiderocol susceptibility, respectively. On the contrary, CMY-2, CTX-M-15 and NDM-1 substantially decreased cefiderocol susceptibility by 16-, 8- and 32-fold, respectively. Second, we determined the evolutionary potential of these enzymes to adapt to increasing concentrations of cefiderocol. Our data show that with the acquisition of only 1 to 2 mutations, all {beta}-lactamases were evolvable to further cefiderocol resistance by 2- (NDM-1, CTX-M-15), 4- (CMY-2), 8- (OXA-48) and 16-fold (KPC-2). Cefiderocol resistance development was often associated with collateral susceptibility changes including increased resistance to ceftazidime and ceftazidime-avibactam as well as functional trade-offs against different {beta}-lactam drugs. Taken together, contemporary {beta}-lactamases of all Ambler classes can potentially contribute to cefiderocol resistance development and can acquire mutations allowing them to adapt to increasing cefiderocol concentration. At the same time, resistance development caused clinically important cross-resistance, especially against ceftazidime combinations. SummaryDespite the reported higher stability of cefiderocol against {beta}-lactamase hydrolysis, we show that the expression of {beta}-lactamases from different Ambler classes significantly contributes to cefiderocol resistance and that these enzymes have the evolutionary potential to evolve towards increasing cefiderocol concentrations.

molecular biology↗

bioRxiv2021

Evolutionary instability of collateral susceptibility networks in ciprofloxacin resistant clinical Escherichia coli strains

Collateral sensitivity and resistance occur when resistance development towards one antimicrobial either potentiates or deteriorates the effect of others, respectively. Previous reports on collateral effects on susceptibility focus on newly acquired resistance determinants and propose that novel treatment guidelines informed by collateral networks may reduce the evolution, selection and spread of antimicrobial resistance. In this study, we investigate the evolutionary stability of collateral networks in five ciprofloxacin resistant, clinical Escherichia coli strains. After 300 generations of experimental evolution without antimicrobials, we show complete fitness restoration in four of five genetic backgrounds and demonstrate evolutionary instability in collateral networks of newly acquired resistance determinants. We show that compensatory mutations reducing efflux expression is the main driver destabilizing initial collateral networks and identify rpoS as a putative target for compensatory evolution. Our results add another layer of complexity to future predictions and clinical application of collateral networks.

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↗

bioRxiv2021

A high-throughput multiplexing and selection strategy to complete bacterial genomes

BackgroundBacterial whole-genome sequencing based on short-read sequencing data often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits to unambiguously bridge those contiguous sequences into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates that can be long-read sequenced. Here we evaluated the recently released 96 barcoding kit from Oxford Nanopore Technologies (ONT) to generate complete genomes on a high-throughput basis. In addition, we propose a long-read isolate selection strategy that optimizes a representative selection of isolates from large-scale bacterial collections. ResultsDespite an uneven distribution of long-reads per barcode, near-complete chromosomal sequences (assembly contiguity = 0.89) were generated for 96 Escherichia coli isolates with associated short-read sequencing data. The assembly contiguity of the plasmid replicons was even higher (0.98) which indicated the suitability of the multiplexing strategy for studies focused on resolving plasmid sequences. We benchmarked hybrid and ONT-only assemblies and showed that the combination of ONT sequencing data with short-read sequencing data is still highly desirable: (i) to perform an unbiased selection of isolates for long-read sequencing, (ii) to achieve an optimal genome accuracy and completeness, and (iii) to include small plasmids underrepresented in the ONT library. ConclusionsThe proposed long-read isolate selection ensures completing bacterial genomes of isolates that span the genome diversity inherent in large collections of bacterial isolates. We show the potential of using this multiplexing approach to close bacterial genomes on a high-throughput basis.

microbiology↗

bioRxiv2020

Cryptic β-lactamase evolution is driven by low β-lactam concentrations

Our current understanding of how low antibiotic concentrations shape the evolution of contemporary {beta}-lactamases is limited. Using the wide-spread carbapenemase OXA-48, we tested the long-standing hypothesis that selective compartments with low antibiotic concentrations cause standing genetic diversity that could act as a gateway to develop clinical resistance. Here, we subjected Escherichia coli expressing blaOXA-48, on a clinical plasmid, to experimental evolution at sub-minimum inhibitory concentrations (sub-MIC) of ceftazidime. We identified and characterized seven single variants of OXA-48. Susceptibility profiles and dose-response curves showed that they increased resistance only marginally. However, in competition experiments at sub-MIC of ceftazidime, they showed strong selectable fitness benefits. Increased resistance was also reflected in elevated catalytic efficiencies towards ceftazidime. These changes are likely caused by enhanced flexibility of the {Omega}- and {beta}5-{beta}6 loops. In conclusion, low-level concentrations of {beta}-lactams can drive the evolution of {beta}-lactamases through cryptic phenotypes which may act as stepping-stones towards clinical resistance.

evolutionary biology↗

bioRxiv2020

The chemotherapeutic drug methotrexate selects for antibiotic resistance

Understanding drivers of antibiotic resistance evolution is fundamental for designing optimal treatment strategies and interventions to reduce the spread of antibiotic resistance. Various cytotoxic drugs used in cancer chemotherapy have antibacterial properties, but how bacterial populations are affected by these selective pressures is unknown. Here we test the hypothesis that the widely used cytotoxic drug methotrexate affects the evolution and selection of antibiotic resistance through the same mechanisms as the antibiotic trimethoprim. We show that methotrexate can select for trimethoprim resistance determinants located on the chromosome or a plasmid in clinical strains of Escherichia coli. Additionally, methotrexate can co-select for virtually any antibiotic resistance determinant when present together with trimethoprim resistance on a multidrug-resistance clinical plasmid. These selective effects occur at concentrations 40- to >320-fold below the methotrexate minimal inhibitory concentration for E. coli, suggesting a selective role of methotrexate chemotherapy for antibiotic resistance in patients that strongly depend on effective antibiotic treatment. Significance statementThe presented data show that methotrexate has the potential to select for virtually any given antibiotic resistance gene when genetically linked to trimethoprim resistance. This study highlights the need for increased awareness of the presence of acquired antibiotic resistance determinants in the gut of patients with impaired immunity undergoing methotrexate treatment to preserve the effects of downstream antibiotic treatments.

microbiology↗

bioRxiv2020

Piggybacking on niche-adaptation reduces the cost of multidrug resistance plasmids

The persistence of plasmids in bacterial populations represents a puzzling evolutionary problem with serious clinical implications due to their role in the ongoing antibiotic resistance crisis. Recently, major advancements have been made towards resolving this "plasmid paradox" but mainly in a non-clinical context. Here we propose an additional explanation for the maintenance of multidrug resistance (MDR) plasmids in clinical Escherichia coli strains. After co-evolving two MDR plasmids encoding last resort carbapenem resistance with an extraintestinal pathogenic E. coli strain, we observed that chromosomal media adaptive mutations in the global regulatory systems CCR (Carbon Catabolite Repression) and ArcAB (Aerobic Respiration Control) pleiotropically mitigated the costs of both plasmids. Mechanistically, cost reductions were due to a net downregulation of plasmid gene expression. Our results suggest that global chromosomal transcriptional re-wiring during bacterial niche-adaptation may facilitate plasmid maintenance.

microbiology↗

bioRxiv2018

Conserved collateral susceptibility networks in diverse clinical strains of Escherichia coli.

There is urgent need to develop novel treatment strategies to reduce antimicrobial resistance. Collateral sensitivity (CS), where resistance to one antimicrobial increases susceptibility to other drugs, is a uniquely promising strategy that enables selection against resistance during treatment. However, using CS-informed therapy depends on conserved CS networks across genetically diverse bacterial strains. We examined CS conservation in 10 clinical strains of E. coli resistant to four clinically relevant antibiotics. Collateral susceptibilities of these 40 resistant mutants were then determined against a panel of 16 antibiotics. Multivariate statistical analyses demonstrate that resistance mechanisms, in particular efflux-related mutations, as well as relative fitness were principal contributors to collateral changes. Moreover, collateral responses shifted the mutant selection window suggesting that CS-informed therapies could affect evolutionary trajectories of antimicrobial resistance. Our data allow optimism for CS-informed therapy and further suggest that early detection of resistance mechanisms is important to accurately predict collateral antimicrobial responses.

microbiology↗