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• Journal article
  Larrouy-Maumus G, Dortet L, Filloux A, bonnin, le hello, bonnet, kostrzewaet al., 2020,

  Detection of colistin resistance in Salmonella enterica using MALDIxin test on the routine MALDI Biotyper Sirius mass spectrometer

  , Frontiers in Microbiology, Vol: 11, Pages: 1-6, ISSN: 1664-302X

  Resistance to polymyxins in most Gram-negative bacteria arises from chemical modifications to the lipid A portion of their lipopolysaccharide (LPS) mediated by chromosomally-encoded mutations or the recently discovered plasmid-encoded mcr genes that have further complicated the landscape of colistin resistance. Currently, minimal inhibitory concentration (MIC) determination by broth microdilution, the gold standard for the detection of polymyxin resistance, is time consuming (24 hours) and challenging to perform in clinical and veterinatryveterinary laboratories. Here we present the use of the MALDIxin to detect colistin resistant Salmonella enterica using the MALDxin test on the routine matrix-assisted laser desorption ionization (MALDI) Biotyper Sirius system.

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• Journal article
  Zeden MS, Kviatkovski I, Schuster CF, Thomas VC, Fey PD, Grundling Aet al., 2020,

  Identification of the main glutamine and glutamate transporters in Staphylococcus aureus and their impact on c-di-AMP production

  , Molecular Microbiology, Vol: 113, Pages: 1085-1100, ISSN: 0950-382X

  A Staphylococcus aureus strain deleted for the c‐di‐AMP cyclase gene dacA is unable to survive in rich medium unless it acquires compensatory mutations. Previously identified mutations were in opuD, encoding the main glycine‐betaine transporter, and alsT, encoding a predicted amino acid transporter. Here, we show that inactivation of OpuD restores the cell size of a dacA mutant to near wild‐type (WT) size, while inactivation of AlsT does not. AlsT was identified as an efficient glutamine transporter, indicating that preventing glutamine uptake in rich medium rescues the growth of the S. aureus dacA mutant. In addition, GltS was identified as a glutamate transporter. By performing growth curves with WT, alsT and gltS mutant strains in defined medium supplemented with ammonium, glutamine or glutamate, we revealed that ammonium and glutamine, but not glutamate promote the growth of S. aureus. This suggests that besides ammonium also glutamine can serve as a nitrogen source under these conditions. Ammonium and uptake of glutamine via AlsT and hence likely a higher intracellular glutamine concentration inhibited c‐di‐AMP production, while glutamate uptake had no effect. These findings provide, besides the previously reported link between potassium and osmolyte uptake, a connection between nitrogen metabolism and c‐di‐AMP signalling in S. aureus.

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• Journal article
  Mathioudakis AG, Janssens W, Sivapalan P, Singanayagam A, Dransfield MT, Jensen J-US, Vestbo Jet al., 2020,

  Acute exacerbations of chronic obstructive pulmonary disease: in search of diagnostic biomarkers and treatable traits

  , THORAX, Vol: 75, Pages: 520-527, ISSN: 0040-6376
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  • Citations: 82
• Journal article
  Kumar K, Hinks TSC, Singanayagam A, 2020,

  Treatment of COVID-19-exacerbated asthma: should systemic corticosteroids be used?

  , AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY, Vol: 318, Pages: L1244-L1247, ISSN: 1040-0605
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  • Citations: 22
• Journal article
  Lewis Marffy A, McCarthy A, 2020,

  Leukocyte immunoglobulin-like receptors (LILRs) on human neutrophils: modulators of infection and immunity

  , Frontiers in Immunology, Vol: 11, ISSN: 1664-3224

  Neutrophils have a crucial role in defense against microbes. Immune receptors allow neutrophils to sense their environment, with many receptors functioning to recognize signs of infection and to promote antimicrobial effector functions. However, the neutrophil response must be tightly regulated to prevent excessive inflammation and tissue damage, and regulation is achieved by expression of inhibitory receptors that can raise activation thresholds. The leukocyte immunoglobulin-like receptor (LILR) family contain activating and inhibitory members that can up- or down-regulate immune cell activity. New ligands and functions for LILR continue to emerge. Understanding the role of LILR in neutrophil biology is of general interest as they can activate and suppress antimicrobial responses of neutrophils and because several human pathogens exploit these receptors for immune evasion. This review focuses on the role of LILR in neutrophil biology. We focus on the current knowledge of LILR expression on neutrophils, the known functions of LILR on neutrophils, and how these receptors may contribute to shaping neutrophil responses during infection.

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• Journal article
  Sewell L, Stylianou F, Xu Y, Taylor J, Sefer L, Matthews Set al., 2020,

  NMR insights into the pre-amyloid ensemble and secretion targeting of the curli subunit CsgA

  , Scientific Reports, Vol: 10, ISSN: 2045-2322

  The biofilms of Enterobacteriaceae are fortified by assembly of curli amyloid fibres on the cell surface. Curli not only provides structural reinforcement, but also facilitates surface adhesion. To prevent toxic intracellular accumulation of amyloid precipitate, secretion of the major curli subunit, CsgA, is tightly regulated. In this work, we have employed solution state NMR spectroscopy to characterise the structural ensemble of the pre-fibrillar state of CsgA within the bacterial periplasm, and upon recruitment to the curli pore, CsgG, and the secretion chaperone, CsgE. We show that the N-terminal targeting sequence (N) of CsgA binds specifically to CsgG and that its subsequent sequestration induces a marked transition in the conformational ensemble, which is coupled to a preference for CsgE binding. These observations lead us to suggest a sequential model for binding and structural rearrangement of CsgA at the periplasmic face of the secretion machinery.

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• Journal article
  Ibarra-Chávez R, Haag AF, Dorado-Morales P, Lasa I, Penadés JRet al., 2020,

  Rebooting synthetic phage-inducible chromosomal islands: one method to forge them all

  , BioDesign Research, Vol: 2020, Pages: 1-14

  Phage-inducible chromosomal islands (PICIs) are a widespread family of mobile genetic elements, which have an important role in bacterial pathogenesis. These elements mobilize among bacterial species at extremely high frequencies, representing an attractive tool for the delivery of synthetic genes. However, tools for their genetic manipulation are limited and timing consuming. Here, we have adapted a synthetic biology approach for rapidly editing of PICIs in Saccharomyces cerevisiae based on their ability to excise and integrate into the bacterial chromosome of their cognate host species. As proof of concept, we engineered several PICIs from Staphylococcus aureus and Escherichia coli and validated this methodology for the study of the biology of these elements by generating multiple and simultaneous mutations in different PICI genes. For biotechnological purposes, we also synthetically constructed PICIs as Trojan horses to deliver different CRISPR-Cas9 systems designed to either cure plasmids or eliminate cells carrying the targeted genes. Our results demonstrate that the strategy developed here can be employed universally to study PICIs and enable new approaches for diagnosis and treatment of bacterial diseases.

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• Journal article
  Sheppard D, Berry J-L, Denise R, Rocha EPC, Matthews S, Pelicic Vet al., 2020,

  The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold

  , Journal of Biological Chemistry, Vol: 295, Pages: 6594-6604, ISSN: 0021-9258

  <jats:p>Type IV filaments (T4F), which are helical assemblies of type IV pilins, constitute a superfamily of filamentous nanomachines virtually ubiquitous in prokaryotes that mediate a wide variety of functions. The competence (Com) pilus is a widespread T4F, mediating DNA uptake (the first step in natural transformation) in bacteria with one membrane (monoderms), an important mechanism of horizontal gene transfer. Here, we report the results of genomic, phylogenetic, and structural analyses of ComGC, the major pilin subunit of Com pili. By performing a global comparative analysis, we show that Com pili genes are virtually ubiquitous in Bacilli, a major monoderm class of Firmicutes. This also revealed that ComGC displays extensive sequence conservation, defining a monophyletic group among type IV pilins. We further report ComGC solution structures from two naturally competent human pathogens, <jats:italic>Streptococcus sanguinis</jats:italic> (ComGC<jats:sub>SS</jats:sub>) and <jats:italic>Streptococcus pneumoniae</jats:italic> (ComGC<jats:sub>SP</jats:sub>), revealing that this pilin displays extensive structural conservation. Strikingly, ComGC<jats:sub>SS</jats:sub> and ComGC<jats:sub>SP</jats:sub> exhibit a novel type IV pilin fold that is purely helical. Results from homology modeling analyses suggest that the unusual structure of ComGC is compatible with helical filament assembly. Because ComGC displays such a widespread distribution, these results have implications for hundreds of monoderm species.</jats:p>

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• Journal article
  Giraud-Gatineau A, Coya JM, Maure A, Biton A, Thomson M, Bernard EM, Marrec J, Gutierrez MG, Larrouy-Maumus G, Brosch R, Gicquel B, Tailleux Let al., 2020,

  The antibiotic bedaquiline activates host macrophage innate immune resistance to bacterial infection

  , eLife, Vol: 9, ISSN: 2050-084X

  Antibiotics are widely used in the treatment of bacterial infections. Although known for their microbicidal activity, antibiotics may also interfere with the host's immune system. Here, we analyzed the effects of bedaquiline (BDQ), an inhibitor of the mycobacterial ATP synthase, on human macrophages. Genome-wide gene expression analysis revealed that BDQ reprogramed cells into potent bactericidal phagocytes. We found that 579 and 1,495 genes were respectively differentially expressed in naive- and M. tuberculosis-infected macrophages incubated with the drug, with an over-representation of lysosome-associated genes. BDQ treatment triggered a variety of antimicrobial defense mechanisms, including phagosome-lysosome fusion, and autophagy. These effects were associated with activation of transcription factor EB, involved in the transcription of lysosomal genes, resulting in enhanced intracellular killing of different bacterial species that were naturally insensitive to BDQ. Thus, BDQ could be used as a host-directed therapy against a wide range of bacterial infections.

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• Journal article
  Chua F, Armstrong-James D, Desai SR, Barnett J, Kouranos V, Kon OM, Jose R, Vancheeswaran R, Loebinger MR, Wong J, Cutino-Moguel MT, Morgan C, Ledot S, Lams B, Yip WH, Li L, Lee YC, Draper A, Kho SS, Renzoni E, Ward K, Periselneris J, Grubnic S, Lipman M, Wells AU, Devaraj Aet al., 2020,

  The role of CT in case ascertainment and management of COVID-19 pneumonia in the UK: insights from high-incidence regions

  , The Lancet Respiratory Medicine, Vol: 8, Pages: 438-440, ISSN: 2213-2600
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