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  1. AU="Lipworth, Samuel"
  2. AU="Killian, Michael O"
  3. AU=Smaldino Paul E.
  4. AU=Bi Hai
  5. AU="Pintore, Giorgio"
  6. AU="Signorini C."
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  8. AU="Yong-ming GAO"
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  1. Article ; Online: Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing.

    Sanderson, Nicholas D / Hopkins, Katie M V / Colpus, Matthew / Parker, Melody / Lipworth, Samuel / Crook, Derrick / Stoesser, Nicole

    Microbial genomics

    2024  Volume 10, Issue 5

    Abstract: Whole-genome reconstruction of bacterial pathogens has become an important tool for tracking transmission and antimicrobial resistance gene spread, but highly accurate and complete assemblies have largely only historically been achievable using hybrid ... ...

    Abstract Whole-genome reconstruction of bacterial pathogens has become an important tool for tracking transmission and antimicrobial resistance gene spread, but highly accurate and complete assemblies have largely only historically been achievable using hybrid long- and short-read sequencing. We previously found the Oxford Nanopore Technologies (ONT) R10.4/kit12 flowcell/chemistry produced improved assemblies over the R9.4.1/kit10 combination, however long-read only assemblies contained more errors compared to Illumina-ONT hybrid assemblies. ONT have since released an R10.4.1/kit14 flowcell/chemistry upgrade and recommended the use of Bovine Serum Albumin (BSA) during library preparation, both of which reportedly increase accuracy and yield. They have also released updated basecallers trained using native bacterial DNA containing methylation sites intended to fix systematic basecalling errors, including common adenosine (A) to guanine (G) and cytosine (C) to thymine (T) substitutions. To evaluate these improvements, we successfully sequenced four bacterial reference strains, namely
    MeSH term(s) Genome, Bacterial ; Nanopores ; High-Throughput Nucleotide Sequencing/methods ; Escherichia coli/genetics ; Staphylococcus aureus/genetics ; Sequence Analysis, DNA/methods ; Pseudomonas aeruginosa/genetics ; Nanopore Sequencing/methods ; DNA, Bacterial/genetics ; Klebsiella pneumoniae/genetics ; Whole Genome Sequencing/methods ; Bacteria/genetics ; Bacteria/classification ; Humans
    Chemical Substances DNA, Bacterial
    Language English
    Publishing date 2024-05-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Evaluation Study
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.001246
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction.

    Sanderson, Nicholas D / Kapel, Natalia / Rodger, Gillian / Webster, Hermione / Lipworth, Samuel / Street, Teresa L / Peto, Timothy / Crook, Derrick / Stoesser, Nicole

    Microbial genomics

    2023  Volume 9, Issue 1

    Abstract: Complete, accurate, cost-effective, and high-throughput reconstruction of bacterial genomes for large-scale genomic epidemiological studies is currently only possible with hybrid assembly, combining long- (typically using nanopore sequencing) and short- ... ...

    Abstract Complete, accurate, cost-effective, and high-throughput reconstruction of bacterial genomes for large-scale genomic epidemiological studies is currently only possible with hybrid assembly, combining long- (typically using nanopore sequencing) and short-read (Illumina) datasets. Being able to use nanopore-only data would be a significant advance. Oxford Nanopore Technologies (ONT) have recently released a new flowcell (R10.4) and chemistry (Kit12), which reportedly generate per-read accuracies rivalling those of Illumina data. To evaluate this, we sequenced DNA extracts from four commonly studied bacterial pathogens, namely
    MeSH term(s) Nanopores ; High-Throughput Nucleotide Sequencing/methods ; Genomics/methods ; Sequence Analysis, DNA/methods ; Genome, Bacterial/genetics
    Language English
    Publishing date 2023-02-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.000910
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Erratum: Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction.

    Sanderson, Nicholas D / Kapel, Natalia / Rodger, Gillian / Webster, Hermione / Lipworth, Samuel / Street, Teresa L / Peto, Timothy / Crook, Derrick / Stoesser, Nicole

    Microbial genomics

    2023  Volume 9, Issue 11

    Language English
    Publishing date 2023-12-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.001144
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Erratum to "Case Series of Triathletes with Takotsubo Cardiomyopathy Presenting with Swimming-Induced Pulmonary Edema".

    Rigler, Caitlin / Menon, Gautam / Lipworth, Samuel / Langrish, Jeremy P / Kipps, Courtney / Shanmuganathan, Mayooran / Smith, Ralph

    Translational sports medicine

    2023  Volume 2023, Page(s) 9858459

    Abstract: This corrects the article DOI: 10.1155/2022/3602505.]. ...

    Abstract [This corrects the article DOI: 10.1155/2022/3602505.].
    Language English
    Publishing date 2023-10-11
    Publishing country England
    Document type Published Erratum
    ISSN 2573-8488
    ISSN (online) 2573-8488
    DOI 10.1155/2023/9858459
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  5. Article ; Online: Inhaled Corticosteroids and COVID-19.

    Lipworth, Brian / Kuo, Chris RuiWen / Lipworth, Samuel / Chan, Rory

    American journal of respiratory and critical care medicine

    2020  Volume 202, Issue 6, Page(s) 899–900

    MeSH term(s) Adrenal Cortex Hormones ; Asthma ; Betacoronavirus ; COVID-19 ; Coronavirus Infections ; Humans ; Pandemics ; Pneumonia, Viral ; SARS-CoV-2
    Chemical Substances Adrenal Cortex Hormones
    Keywords covid19
    Language English
    Publishing date 2020-07-15
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.202005-2000LE
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Weathering the Cytokine Storm in Susceptible Patients with Severe SARS-CoV-2 Infection.

    Lipworth, Brian / Chan, Rory / Lipworth, Samuel / RuiWen Kuo, Chris

    The journal of allergy and clinical immunology. In practice

    2020  Volume 8, Issue 6, Page(s) 1798–1801

    MeSH term(s) Administration, Inhalation ; Adrenal Cortex Hormones/adverse effects ; Age Factors ; Angiotensin-Converting Enzyme Inhibitors/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; Antibodies, Monoclonal, Humanized/therapeutic use ; Antiviral Agents/therapeutic use ; Azithromycin/therapeutic use ; Bromhexine/therapeutic use ; COVID-19 ; Coronavirus Infections/complications ; Coronavirus Infections/drug therapy ; Coronavirus Infections/epidemiology ; Coronavirus Infections/immunology ; Cytokines/immunology ; Expectorants/therapeutic use ; Humans ; Hydroxychloroquine/therapeutic use ; Hypertension/epidemiology ; Inflammation ; Interferon beta-1a/immunology ; Interleukin-1/immunology ; Interleukin-12/immunology ; Interleukin-6/immunology ; Lymphohistiocytosis, Hemophagocytic/etiology ; Lymphohistiocytosis, Hemophagocytic/immunology ; Obesity/epidemiology ; Pandemics ; Pneumonia, Viral/complications ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/immunology ; Pulmonary Disease, Chronic Obstructive/drug therapy ; Pulmonary Disease, Chronic Obstructive/epidemiology ; Respiratory Distress Syndrome/etiology ; Respiratory Distress Syndrome/immunology ; Risk Factors ; Smoking/epidemiology ; Tumor Necrosis Factor-alpha/immunology
    Chemical Substances Adrenal Cortex Hormones ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents ; Antibodies, Monoclonal, Humanized ; Antiviral Agents ; Cytokines ; Expectorants ; Interleukin-1 ; Interleukin-6 ; Tumor Necrosis Factor-alpha ; Interleukin-12 (187348-17-0) ; Hydroxychloroquine (4QWG6N8QKH) ; Azithromycin (83905-01-5) ; tocilizumab (I031V2H011) ; sarilumab (NU90V55F8I) ; Bromhexine (Q1J152VB1P) ; Interferon beta-1a (XRO4566Q4R)
    Keywords covid19
    Language English
    Publishing date 2020-04-18
    Publishing country United States
    Document type Editorial
    ZDB-ID 2843237-X
    ISSN 2213-2201 ; 2213-2198
    ISSN (online) 2213-2201
    ISSN 2213-2198
    DOI 10.1016/j.jaip.2020.04.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 7086: Show issues Location:
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  7. Article ; Online: Case Series of Triathletes with Takotsubo Cardiomyopathy Presenting with Swimming-Induced Pulmonary Edema.

    Rigler, Caitlin / Menon, Gautam / Lipworth, Samuel / Langrish, Jeremy P / Kipps, Courtney / Shanmuganathan, Mayooran / Smith, Ralph

    Translational sports medicine

    2022  Volume 2022, Page(s) 3602505

    Abstract: Objectives: To report three cases of triathletes who presented with swimming-induced pulmonary edema (SIPE) following water immersion. They were subsequently diagnosed with Takotsubo cardiomyopathy (TCM).: Design: Retrospective case series.: Method! ...

    Abstract Objectives: To report three cases of triathletes who presented with swimming-induced pulmonary edema (SIPE) following water immersion. They were subsequently diagnosed with Takotsubo cardiomyopathy (TCM).
    Design: Retrospective case series.
    Method: All cases were recreational athletes competing in mass participation triathlons between June 2018 and 2019. They were initially managed by the event medical team and subsequently at the local tertiary level hospital. Written consent was gained from all the subjects.
    Results: The three triathletes were aged between 50 and 60 years, two were females, and all presented with acute dyspnoea on exiting the water. Two also presented with chest pain and haemoptysis. A diagnosis of SIPE was suspected by the medical event team on initial presentation of low oxygen saturations and clinical signs of pulmonary oedema. All were transferred to the local emergency department and had signs of pulmonary oedema on chest radiographs. Further investigations led to a diagnosis of TCM with findings of
    Conclusions: This case series presents triathletes diagnosed with SIPE and TCM following the open water swim phase. It is unclear whether the myocardial dysfunction contributed to causation of SIPE or was the result of SIPE. Mass participation race organizers must be prepared that both SIPE and TCM can present in this population. Those presenting with an episode of SIPE require prompt evaluation of their cardiac and pulmonary physiology. Further research is required to ascertain the exact nature of the relationship between TCM and SIPE.
    Language English
    Publishing date 2022-10-26
    Publishing country England
    Document type Journal Article
    ISSN 2573-8488
    ISSN (online) 2573-8488
    DOI 10.1155/2022/3602505
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Author Correction: The plasmidome associated with Gram-negative bloodstream infections: a large-scale observational study using complete plasmid assemblies.

    Lipworth, Samuel / Matlock, William / Shaw, Liam / Vihta, Karina-Doris / Rodger, Gillian / Chau, Kevin / Barker, Leanne / George, Sophie / Kavanagh, James / Davies, Timothy / Vaughan, Alison / Andersson, Monique / Jeffery, Katie / Oakley, Sarah / Morgan, Marcus / Hopkins, Susan / Peto, Timothy / Crook, Derrick / Walker, A Sarah /
    Stoesser, Nicole

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 3060

    Language English
    Publishing date 2024-04-09
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-47494-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies.

    Lipworth, Samuel / Matlock, William / Shaw, Liam / Vihta, Karina-Doris / Rodger, Gillian / Chau, Kevin / Barker, Leanne / George, Sophie / Kavanagh, James / Davies, Timothy / Vaughan, Alison / Andersson, Monique / Jeffery, Katie / Oakley, Sarah / Morgan, Marcus / Hopkins, Susan / Peto, Timothy / Crook, Derrick / Walker, A Sarah /
    Stoesser, Nicole

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 1612

    Abstract: Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have ... ...

    Abstract Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative 'backbone' of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes.
    MeSH term(s) Anti-Bacterial Agents ; Plasmids/genetics ; Bacteria/genetics
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2024-02-22
    Publishing country England
    Document type Observational Study ; Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-45761-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK.

    Matlock, William / Lipworth, Samuel / Chau, Kevin K / AbuOun, Manal / Barker, Leanne / Kavanagh, James / Andersson, Monique / Oakley, Sarah / Morgan, Marcus / Crook, Derrick W / Read, Daniel S / Anjum, Muna / Shaw, Liam P / Stoesser, Nicole

    eLife

    2023  Volume 12

    Abstract: Plasmids enable the dissemination of antimicrobial resistance (AMR) in common Enterobacterales pathogens, representing a major public health challenge. However, the extent of plasmid sharing and evolution between Enterobacterales causing human infections ...

    Abstract Plasmids enable the dissemination of antimicrobial resistance (AMR) in common Enterobacterales pathogens, representing a major public health challenge. However, the extent of plasmid sharing and evolution between Enterobacterales causing human infections and other niches remains unclear, including the emergence of resistance plasmids. Dense, unselected sampling is essential to developing our understanding of plasmid epidemiology and designing appropriate interventions to limit the emergence and dissemination of plasmid-associated AMR. We established a geographically and temporally restricted collection of human bloodstream infection (BSI)-associated, livestock-associated (cattle, pig, poultry, and sheep faeces, farm soils) and wastewater treatment work (WwTW)-associated (influent, effluent, waterways upstream/downstream of effluent outlets) Enterobacterales. Isolates were collected between 2008 and 2020 from sites <60 km apart in Oxfordshire, UK. Pangenome analysis of plasmid clusters revealed shared 'backbones', with phylogenies suggesting an intertwined ecology where well-conserved plasmid backbones carry diverse accessory functions, including AMR genes. Many plasmid 'backbones' were seen across species and niches, raising the possibility that plasmid movement between these followed by rapid accessory gene change could be relatively common. Overall, the signature of identical plasmid sharing is likely to be a highly transient one, implying that plasmid movement might be occurring at greater rates than previously estimated, raising a challenge for future genomic One Health studies.
    MeSH term(s) Humans ; Animals ; Cattle ; Swine ; Sheep/genetics ; Escherichia coli/genetics ; Livestock/genetics ; Wastewater ; Plasmids/genetics ; Klebsiella pneumoniae/genetics ; Gammaproteobacteria ; Sepsis ; United Kingdom ; Anti-Bacterial Agents ; beta-Lactamases/genetics ; Microbial Sensitivity Tests
    Chemical Substances Wastewater ; Anti-Bacterial Agents ; beta-Lactamases (EC 3.5.2.6)
    Language English
    Publishing date 2023-03-24
    Publishing country England
    Document type Journal Article
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.85302
    Database MEDical Literature Analysis and Retrieval System OnLINE

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