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  • Journal article
    Janssens J, Aibar S, Taskiran II, Ismail JN, Gomez AE, Aughey G, Spanier K, De Rop F, Gonzalez-Blas CB, Dionne M, Grimes K, Quan XJ, Papasokrati D, Hulselmans G, Makhzami S, De Waegeneer M, Christiaens V, Southall T, Aerts Set al., 2022,

    Decoding gene regulation in the fly brain

    , NATURE, Vol: 601, Pages: 630-+, ISSN: 0028-0836
  • Conference paper
    Martinez-Gili L, Gordon H, Blad W, McDonald JAK, Holmes E, Marchesi JR, Harbord Met al., 2022,

    Gut bacteria composition and familiality echo Inflammatory Bowel Disease type and pathological spectrum

    , 17th Congress of ECCO, Publisher: Oxford University Press, Pages: I601-I602, ISSN: 1873-9946

    BackgroundInflammatory bowel disease (IBD) aetiology encompasses genetic and environmental factors. Twin studies provide valuable insights to the familial degree (shared genetics and environment) of observed phenotypes. We characterised the gut bacterial composition of twins with IBD to find taxa associated with disease and estimate their familiality.MethodsFaecal samples were collected from 88 monozygotic (MZ) and dizygotic (DZ) twin pairs concordant or discordant for Crohn’s disease (CD; 26 MZ; 19 DZ) or ulcerative colitis (UC; 16 MZ; 27 DZ). The 16S rRNA gene was sequenced and amplicon sequence variants (ASV) generated. ANCOM software was used to assess differences in IBD vs. non-IBD, stratifying by disease type (CD/UC) and adjusting for age, gender and smoking. Twin pair and zygosity were added as random effects to estimate familiality, defined as percentage of variation due to common environment and genetics. IBD-affected twins were used for differences in disease location or treatment. Participants reporting antibiotic/probiotic treatment within the last 3 months or with a stoma/pouch were not included. In UC, surgery-naive patients were compared to an excluded subset who underwent ileostomy or pouch surgery without any recent antibiotic courses.ResultsDisease concordance in MZ twins was higher in CD (54%) than UC (19%). Alpha diversity was lower in CD, but not UC, and in ileostomy and pouch vs. surgery-naive UC. Principal component analysis showed that CD-affected twins clustered apart from non-IBD ones (Figure 1A). Familiality was lower in CD, with 5% of ASVs having familiality > 50%, compared to 17% in UC (Figure 1B). Two Lachnospirales order ASVs were less abundant in UC, while 15 ASVs from Clostridia, Bacteroidia, Bacilli and Coriobacteriia classes differentiated CD from non-IBD. Firmicutes were higher in CD (β= 0.95; 95%CI [0.34,1.56]), while no phyla changed in UC. Veillonella, Barnesiella, Faecalimonas and Holdemania genera had opposite t
  • Journal article
    Furniss RCD, Kaderabkova N, Barker D, Bernal P, Maslova E, Antwi AAA, McNeil HE, Pugh HL, Dortet L, Blair JMA, Larrouy-Maumus G, McCarthy RR, Gonzalez D, Mavridou DAet al., 2022,

    Breaking antimicrobial resistance by disrupting extracytoplasmic protein folding

    , ELIFE, Vol: 11, ISSN: 2050-084X
  • Journal article
    Nuh A, Ramadan N, Schelenz S, Armstrong-James Det al., 2022,

    Comparative Evaluation of MIRONAUT-AM and CLSI broth microdilution method for antifungal susceptibility testing of <i>Aspergillus species</i> against four commonly used antifungals (vol 81, myaa020, 2018)

    , MEDICAL MYCOLOGY, Vol: 60, ISSN: 1369-3786
  • Journal article
    McQuail J, Carpousis AJ, Wigneshweraraj S, 2022,

    The association between Hfq and RNase E in long-term nitrogen-starved <i>Escherichia coli</i>

    , MOLECULAR MICROBIOLOGY, Vol: 117, Pages: 54-66, ISSN: 0950-382X
  • Journal article
    Hughes DA, Archangelidi O, Coates M, Armstrong-James D, Elborn SJ, Carr SB, Davies JCet al., 2022,

    Clinical characteristics of Pseudomonas and Aspergillus co-infected cystic fibrosis patients: A UK registry study

    , JOURNAL OF CYSTIC FIBROSIS, Vol: 21, Pages: 129-135, ISSN: 1569-1993
  • Journal article
    McCarthy AJ, Taylor PW, 2022,

    Analysis of Escherichia coli K1 Virulence Genes by Transposon-Directed Sequencing.

    , Methods Mol Biol, Vol: 2377, Pages: 199-213

    Transposon-directed insertion site sequencing (TraDIS) combines random transposon mutagenesis and massively parallel sequencing to shed light on bacterial gene function on a genome-wide scale and in a high-throughput manner. The technique has proven to be successful in the determination of the fitness contribution of every gene under specific conditions both in vitro and in vivo. In this contribution, we describe the procedure used for the identification of Escherichia coli K1 genes essential for in vitro growth, survival in pooled human serum and gastrointestinal colonisation in a rodent model of neonatal invasive infection. TraDIS has broad application for systems-level analysis of a wide range of pathogenic, commensular and saprophytic bacteria.
  • Journal article
    Ha KP, Edwards AM, 2021,

    DNA repair in Staphylococcus aureus

    , Microbiology and Molecular Biology Reviews, Vol: 85, ISSN: 1092-2172

    Staphylococcus aureus is a common cause of both superficial and invasive infections of humans and animals. Despite a potent host response and apparently appropriate antibiotic therapy, staphylococcal infections frequently become chronic or recurrent, demonstrating a remarkable ability of S. aureus to withstand the hostile host environment. There is growing evidence that staphylococcal DNA repair makes important contributions to the survival of the pathogen in host tissues, as well as promoting the emergence of mutants that resist host defenses and antibiotics. While much of what we know about DNA repair in S. aureus is inferred from studies with model organisms, the roles of specific repair mechanisms in infection are becoming clear and differences with Bacillus subtilis and Escherichia coli have been identified. Furthermore, there is growing interest in staphylococcal DNA repair as a target for novel therapeutics that sensitize the pathogen to host defenses and antibiotics. In this review, we discuss what is known about staphylococcal DNA repair and its role in infection, examine how repair in S. aureus is similar to, or differs from, repair in well-characterized model organisms, and assess the potential of staphylococcal DNA repair as a novel therapeutic target.
  • Journal article
    Sanchez Garrido J, Alberdi L, Chatterjee S, Frankel G, Mullineaux-Sanders Cet al., 2021,

    Type III secretion system effector subnetworks elicit distinct host immune responses to infection

    , Current Opinion in Microbiology, Vol: 64, Pages: 19-26, ISSN: 1369-5274

    Citrobacter rodentium, a natural mouse pathogen which colonises the colon of immuno-competent mice, provides a robust model for interrogating host-pathogen-microbiota interactions in vivo. This model has been key to providing new insights into local host responses to enteric infection, including changes inintestinal epithelial cell immuno metabolism and mucosal immunity. C. rodent iuminjects 31 bacterial effectors into epithelial cells via a type III secretion system (T3SS). Recently, these effectors were shown to be able to form multiple intracellular subnetworks which can withstand significant contractions whilst maintaining virulence. Here we highlight recent advances in understanding gut mucosal responses to infection and effector biology, as well as potential uses for artificial intelligence (AI) in understanding infectious diseaseand speculate on the role of T3SS effector networks in host adaption.
  • Journal article
    Ronneau S, Hill PWS, Helaine S, 2021,

    Antibiotic persistence and tolerance: not just one and the same

    , CURRENT OPINION IN MICROBIOLOGY, Vol: 64, Pages: 76-81, ISSN: 1369-5274

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