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  1. Article ; Online: Selective whole-genome sequencing of

    De Meulenaere, Katlijn / Cuypers, Wim L / Gauglitz, Julia M / Guetens, Pieter / Rosanas-Urgell, Anna / Laukens, Kris / Cuypers, Bart

    mBio

    2023  Volume 15, Issue 1, Page(s) e0196723

    Abstract: Importance: Malaria is caused by parasites of the ... ...

    Abstract Importance: Malaria is caused by parasites of the genus
    MeSH term(s) Animals ; Humans ; Parasites/genetics ; Nanopores ; Plasmodium/genetics ; Whole Genome Sequencing/methods ; DNA, Protozoan/genetics ; Plasmodium falciparum/genetics
    Chemical Substances DNA, Protozoan
    Language English
    Publishing date 2023-12-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.01967-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Highlights from the 16th International Society for Computational Biology Student Council Symposium 2020.

    Cuypers, Wim L / Dönertaş, Handan Melike / Grewal, Jasleen K / Fatima, Nazeefa / Donnelly, Chase / Mer, Arvind Singh / Krieger, Spencer / Cuypers, Bart / Rahman, Farzana

    F1000Research

    2021  Volume 10

    Abstract: In this meeting overview, we summarise the scientific program and organisation of the 16th International Society for Computational Biology Student Council Symposium in 2020 (ISCB SCS2020). This symposium was the first virtual edition in an uninterrupted ... ...

    Abstract In this meeting overview, we summarise the scientific program and organisation of the 16th International Society for Computational Biology Student Council Symposium in 2020 (ISCB SCS2020). This symposium was the first virtual edition in an uninterrupted series of symposia that has been going on for 15 years, aiming to unite computational biology students and early career researchers across the globe.
    Language English
    Publishing date 2021-06-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.53408.1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58.

    Rutanga, Jean Pierre / de Block, Tessa / Cuypers, Wim L / Cafmeyer, Josephine / Peeters, Marjan / Umumararungu, Esperance / Ngabonziza, Jean Claude S / Rucogoza, Aniceth / Vandenberg, Olivier / Martiny, Delphine / Dusabe, Angélique / Nkubana, Théoneste / Dougan, Gordon / Muvunyi, Claude Mambo / Mwikarago, Ivan Emil / Jacobs, Jan / Deborggraeve, Stijn / Van Puyvelde, Sandra

    PLoS neglected tropical diseases

    2023  Volume 17, Issue 6, Page(s) e0011285

    Abstract: Salmonella enterica serovar Typhi (S. Typhi) is the cause of typhoid fever, presenting high rates of morbidity and mortality in low- and middle-income countries. The H58 haplotype shows high levels of antimicrobial resistance (AMR) and is the dominant S. ...

    Abstract Salmonella enterica serovar Typhi (S. Typhi) is the cause of typhoid fever, presenting high rates of morbidity and mortality in low- and middle-income countries. The H58 haplotype shows high levels of antimicrobial resistance (AMR) and is the dominant S. Typhi haplotype in endemic areas of Asia and East sub-Saharan Africa. The situation in Rwanda is currently unknown and therefore to reveal the genetic diversity and AMR of S. Typhi in Rwanda, 25 historical (1984-1985) and 26 recent (2010-2018) isolates from Rwanda were analysed using whole genome sequencing (WGS). WGS was locally implemented using Illumina MiniSeq and web-based analysis tools, thereafter complemented with bioinformatic approaches for more in-depth analyses. Whereas historical S. Typhi isolates were found to be fully susceptible to antimicrobials and show a diversity of genotypes, i.e 2.2.2, 2.5, 3.3.1 and 4.1; the recent isolates showed high AMR rates and were predominantly associated with genotype 4.3.1.2 (H58, 22/26; 84,6%), possibly resulting from a single introduction in Rwanda from South Asia before 2010. We identified practical challenges for the use of WGS in endemic regions, including a high cost for shipment of molecular reagents and lack of high-end computational infrastructure for the analyses, but also identified WGS to be feasible in the studied setting and giving opportunity for synergy with other programs.
    MeSH term(s) Humans ; Salmonella typhi/genetics ; Haplotypes ; Anti-Bacterial Agents/therapeutic use ; Rwanda ; Typhoid Fever/epidemiology ; Whole Genome Sequencing ; Microbial Sensitivity Tests
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2023-06-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2429704-5
    ISSN 1935-2735 ; 1935-2735
    ISSN (online) 1935-2735
    ISSN 1935-2735
    DOI 10.1371/journal.pntd.0011285
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing.

    Cuypers, Wim L / Jacobs, Jan / Wong, Vanessa / Klemm, Elizabeth J / Deborggraeve, Stijn / Van Puyvelde, Sandra

    Microbial genomics

    2018  Volume 4, Issue 7

    Abstract: Fluoroquinolone (FQ)-resistant Salmonella spp. were listed by the WHO in 2017 as priority pathogens for which new antibiotics were urgently needed. The overall global burden of Salmonella infections is high, but differs per region. Whereas typhoid fever ... ...

    Abstract Fluoroquinolone (FQ)-resistant Salmonella spp. were listed by the WHO in 2017 as priority pathogens for which new antibiotics were urgently needed. The overall global burden of Salmonella infections is high, but differs per region. Whereas typhoid fever is most prevalent in South and South-East Asia, non-typhoidal salmonellosis is prevalent across the globe and associated with a mild gastroenteritis. By contrast, invasive non-typhoidal Salmonella cause bloodstream infections associated with high mortality, particularly in sub-Saharan Africa. Most Salmonella strains from clinical sources are resistant to first-line antibiotics, with FQs now being the antibiotic of choice for treatment of invasive Salmonella infections. However, FQ resistance is increasingly being reported in Salmonella, and multiple molecular mechanisms are already described. Whole-genome sequencing (WGS) is becoming more frequently used to analyse bacterial genomes for antibiotic-resistance markers, and to understand the phylogeny of bacteria in relation to their antibiotic-resistance profiles. This mini-review provides an overview of FQ resistance in Salmonella, guided by WGS studies that demonstrate that WGS is a valuable tool for global surveillance.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Ciprofloxacin/therapeutic use ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Fluoroquinolones/pharmacology ; Fluoroquinolones/therapeutic use ; Genetic Markers ; Genome, Bacterial ; Humans ; Phylogeny ; Salmonella/classification ; Salmonella/drug effects ; Salmonella/genetics ; Salmonella Infections/drug therapy ; Salmonella Infections/microbiology ; Typhoid Fever/microbiology ; Whole Genome Sequencing
    Chemical Substances Anti-Bacterial Agents ; Fluoroquinolones ; Genetic Markers ; Ciprofloxacin (5E8K9I0O4U)
    Language English
    Publishing date 2018-07-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.000195
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia.

    Cuypers, Wim L / Meysman, Pieter / Weill, François-Xavier / Hendriksen, Rene S / Beyene, Getenet / Wain, John / Nair, Satheesh / Chattaway, Marie A / Perez-Sepulveda, Blanca M / Ceyssens, Pieter-Jan / de Block, Tessa / Lee, Winnie W Y / Pardos de la Gandara, Maria / Kornschober, Christian / Moran-Gilad, Jacob / Veldman, Kees T / Cormican, Martin / Torpdahl, Mia / Fields, Patricia I /
    Černý, Tomáš / Hardy, Liselotte / Tack, Bieke / Mellor, Kate C / Thomson, Nicholas / Dougan, Gordon / Deborggraeve, Stijn / Jacobs, Jan / Laukens, Kris / Van Puyvelde, Sandra

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 3517

    Abstract: Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other ... ...

    Abstract Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance.
    MeSH term(s) Humans ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Ethiopia/epidemiology ; Genomics ; Salmonella/genetics
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2023-06-14
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-38902-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A genomic appraisal of invasive Salmonella Typhimurium and associated antibiotic resistance in sub-Saharan Africa.

    Van Puyvelde, Sandra / de Block, Tessa / Sridhar, Sushmita / Bawn, Matt / Kingsley, Robert A / Ingelbeen, Brecht / Beale, Mathew A / Barbé, Barbara / Jeon, Hyon Jin / Mbuyi-Kalonji, Lisette / Phoba, Marie-France / Falay, Dadi / Martiny, Delphine / Vandenberg, Olivier / Affolabi, Dissou / Rutanga, Jean Pierre / Ceyssens, Pieter-Jan / Mattheus, Wesley / Cuypers, Wim L /
    van der Sande, Marianne A B / Park, Se Eun / Kariuki, Simon / Otieno, Kephas / Lusingu, John P A / Mbwana, Joyce R / Adjei, Samuel / Sarfo, Anima / Agyei, Seth O / Asante, Kwaku P / Otieno, Walter / Otieno, Lucas / Tahita, Marc C / Lompo, Palpouguini / Hoffman, Irving F / Mvalo, Tisungane / Msefula, Chisomo / Hassan-Hanga, Fatimah / Obaro, Stephen / Mackenzie, Grant / Deborggraeve, Stijn / Feasey, Nicholas / Marks, Florian / MacLennan, Calman A / Thomson, Nicholas R / Jacobs, Jan / Dougan, Gordon / Kariuki, Samuel / Lunguya, Octavie

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 6392

    Abstract: Invasive non-typhoidal Salmonella (iNTS) disease manifesting as bloodstream infection with high mortality is responsible for a huge public health burden in sub-Saharan Africa. Salmonella enterica serovar Typhimurium (S. Typhimurium) is the main cause of ... ...

    Abstract Invasive non-typhoidal Salmonella (iNTS) disease manifesting as bloodstream infection with high mortality is responsible for a huge public health burden in sub-Saharan Africa. Salmonella enterica serovar Typhimurium (S. Typhimurium) is the main cause of iNTS disease in Africa. By analysing whole genome sequence data from 1303 S. Typhimurium isolates originating from 19 African countries and isolated between 1979 and 2017, here we show a thorough scaled appraisal of the population structure of iNTS disease caused by S. Typhimurium across many of Africa's most impacted countries. At least six invasive S. Typhimurium clades have already emerged, with ST313 lineage 2 or ST313-L2 driving the current pandemic. ST313-L2 likely emerged in the Democratic Republic of Congo around 1980 and further spread in the mid 1990s. We observed plasmid-borne as well as chromosomally encoded fluoroquinolone resistance underlying emergences of extensive-drug and pan-drug resistance. Our work provides an overview of the evolution of invasive S. Typhimurium disease, and can be exploited to target control measures.
    MeSH term(s) Humans ; Africa South of the Sahara/epidemiology ; Drug Resistance, Microbial ; Genomics ; Salmonella Infections/epidemiology ; Salmonella typhimurium/genetics
    Language English
    Publishing date 2023-10-23
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-41152-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia

    Cuypers, Wim L. / Meysman, Pieter / Weill, François Xavier / Hendriksen, Rene S. / Beyene, Getenet / Wain, John / Nair, Satheesh / Chattaway, Marie A. / Perez-Sepulveda, Blanca M. / Ceyssens, Pieter Jan / de Block, Tessa / Lee, Winnie W.Y. / Pardos de la Gandara, Maria / Kornschober, Christian / Moran-Gilad, Jacob / Veldman, Kees T. / Cormican, Martin / Torpdahl, Mia / Fields, Patricia I. /
    Černý, Tomáš / Hardy, Liselotte / Tack, Bieke / Mellor, Kate C. / Thomson, Nicholas / Dougan, Gordon / Deborggraeve, Stijn / Jacobs, Jan / Laukens, Kris / Van Puyvelde, Sandra

    Nature Communications

    2023  Volume 14, Issue 1

    Abstract: Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other ... ...

    Abstract Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance.
    Keywords Life Science
    Language English
    Publishing country nl
    Document type Article ; Online
    ZDB-ID 2553671-0
    ISSN 2041-1723
    ISSN 2041-1723
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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