Blar i forfatter Det helsevitenskapelige fakultet "Corander, Jukka"

Viser treff 1-9 av 9

    • Bacterial genomic epidemiology with mixed samples 

      Mäklin, Tommi; Kallonen, Teemu; Alanko, Jarno; Samuelsen, Ørjan; Hegstad, Kristin; Mäkinen, Veli; Corander, Jukka; Heinz, Eva; Honkela, Antti (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-11-15)
      Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, opening the possibility to sequence all colonies on selective plates with a single DNA extraction and sequencing step. The pipeline includes the novel mGEMS read binner for ...

    • The COVID-19 Pandemic Sparked off a Large-Scale Outbreak of Carbapenem-Resistant Acinetobacter baumannii from the Endemic Strains at an Italian Hospital 

      Petazzoni, Greta; Bellinzona, Greta; Merla, Cristina; Corbella, Marta; Monzillo, Vincenzina; Samuelsen, Ørjan; Corander, Jukka; Sassera, Davide; Gaiarsa, Stefano; Cambieri, Patrizia (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-03-23)
      Acinetobacter baumannii is a nosocomial pathogen that poses a serious threat due to the rise of incidence of multidrug-resistant (MDR) strains. During the COVID-19 pandemic, MDR A. baumannii clones have caused several outbreaks worldwide. Here, we describe a detailed investigation of an MDR A. baumannii outbreak that occurred at Policlinico San Matteo (Pavia, Italy). A total of 96 A. baumannii ...

    • Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study 

      Gladstone, Rebecca Ashley; McNally, Alan; Pöntinen, Anna Kaarina; Tonkin-Hill, Gerry; Lees, John A.; Skytén, Kusti Onni; Cléon, Francois Pierre Alexandre; Christensen, Martin Owczarek Korsner; Haldorsen, Bjørg; Bye, Kristina K.; Gammelsrud, Karianne Wiger; Hjetland, Reidar; Kümmel, Angela; Larsen, Hege; Lindemann, Paul Christoffer; Löhr, Iren Høyland; Marvik, Åshild; Nilsen, Einar; Noer, Marie Therese; Simonsen, Gunnar Skov; Steinbakk, Martin; Tofteland, Ståle; Vattøy, Marit; Bentley, Stephen D.; Croucher, Nicholas J.; Parkhill, Julian; Johnsen, Pål Jarle; Samuelsen, Ørjan; Corander, Jukka (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-05-10)
      Background - The clonal diversity underpinning trends in multidrug resistant Escherichia coli causing bloodstream infections remains uncertain. We aimed to determine the contribution of individual clones to resistance over time, using large-scale genomics-based molecular epidemiology.<p> <p>Methods - This was a longitudinal, E coli population, genomic, cohort study that sampled isolates from ...

    • Evolutionary and functional history of the Escherichia coli K1 capsule 

      Alonso, Sergio Arredondo; Blundell-Hunter, George; Fu, Zuyi; Gladstone, Rebecca Ashley; Fillol-Salom, Alfred; Loraine, Jessica; Cloutman-Green, Elaine; Johnsen, Pål Jarle; Samuelsen, Ørjan; Pöntinen, Anna Kaarina; Cleon, Francois Pierre Alexandre; Chavez-Bueno, Susana; De la Cruz, Miguel A.; Ares, Miguel A.; Vongsouvath, Manivanh; Chmielarczyk, Agnieszka; Horner, Carolyne; Klein, Nigel; McNally, Alan; Reis, Joice N.; Penadés, José R.; Thomson, Nicholas R.; Corander, Jukka; Taylor, Peter W.; McCarthy, Alex J. (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-06-15)
      Escherichia coli is a leading cause of invasive bacterial infections in humans. Capsule polysaccharide has an important role in bacterial pathogenesis, and the K1 capsule has been firmly established as one of the most potent capsule types in E. coli through its association with severe infections. However, little is known about its distribution, evolution and functions across the E. coli phylogeny, ...

    • The global dissemination of hospital clones of Enterococcus faecium 

      van Hal, Sebastiaan J.; Willems, Rob J.L.; Gouliouris, Theodore; Ballard, Susan A.; Coque, Teresa M.; Hammerum, Anette M.; Hegstad, Kristin; Westh, Henrik; Howden, Benjamin P.; Malhotra-Kumar, Surbhi; Werner, Guido; Yanagihara, Katsunori; Earl, Ashlee M.; Raven, Katherine E.; Corander, Jukka; Bowden, Rory (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-03-30)
      <i>Background</i> - The hospital-adapted A1 group of <i>Enterococcus faecium</i> remains an organism of significant concern in the context of drug-resistant hospital-associated infections. How this pathogen evolves and disseminates remains poorly understood.<br><br> <i>Methods</i> - A large, globally representative collection of short-read genomic data from the hospital-associated A1 group of ...

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

      Alonso, Sergio Arredondo; Pöntinen, Anna K.; Cleon, Francois Pierre Alexandre; Gladstone, Rebecca Ashley; Schürch, Anita C.; Johnsen, Pål Jarle; Samuelsen, Ørjan; Corander, Jukka (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-12-09)
      Background: Bacterial whole-genome sequencing based on short-read technologies often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits those contiguous sequences to be unambiguously bridged into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates ...

    • Mge-cluster: a reference-free approach for typing bacterial plasmids 

      Alonso, Sergio Arredondo; Gladstone, Rebecca Ashley; Pöntinen, Anna Kaarina; Gama, João Alves; Schürch, Anita C.; Lanza, Val F.; Johnsen, Pål Jarle; Samuelsen, Ørjan; Tonkin-Hill, Gerry; Corander, Jukka (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-07-10)
      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 ...

    • Population structure and antimicrobial resistance among Klebsiella isolates sampled from human, animal, and environmental sources in Ghana: a cross-sectional genomic One Health study 

      Calland, Jessica K; Haukka, Kaisa; Kpordze, Stephen W; Brusah, Atanyiwoen; Corbella, Marta; Merla, Cristina; Samuelsen, Ørjan; Feil, Edward J; Sassera, Davide; Karikari, Akosua B; Saba, Courage K S; Thorpe, Harry; Corander, Jukka (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-10-16)
      Background One Health approaches to address the increasing threat of antimicrobial resistance (AMR) are gaining attention. However, data on the distribution and movement of bacteria and their AMR-associated genes between clinical and non-clinical sources are scarce, especially from low-income and middle-income countries. We aimed to analyse Klebsiella isolates from various sources in Ghana and ...

    • Strong pathogen competition in neonatal gut colonisation 

      Mäklin, Tommi; Thorpe, Harry Arthur Frank Wright; Pöntinen, Anna Kaarina; Gladstone, Rebecca Ashley; Shao, Yan; Pesonen, Maiju; McNally, Alan; Johnsen, Pål Jarle; Samuelsen, Ørjan; Lawley, Trevor D.; Honkela, Antti; Corander, Jukka (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-12-01)
      Opportunistic 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. Currently we are lacking a population-wide quantification of strain-level colonisation dynamics and the relationship of colonisation potential to prevalence in disease, and how ecological factors ...