Imperial College London


Faculty of MedicineDepartment of Infectious Disease

Research Fellow



+44 (0)20 7594 3577v.wright




PaediatricsMedical SchoolSt Mary's Campus





Publication Type

87 results found

Moradi Marjaneh M, Challenger J, salas A, Gómez-Carballa A, Sivananthan A, Rivero-Calle I, Barbeito-Castiñeiras G, Foo C, Wu Y, Liew F, Jackson H, Habgood-Coote D, D'Souza G, Nichols S, Wright V, Levin M, Kaforou M, Thwaites R, Okell L, Martinon-Torres F, Cunnington A, PERFORM Consortium, GEN-COVID Study Groupet al., 2023, Analysis of blood and nasal epithelial transcriptomes to identify mechanisms associated with control of SARS-CoV-2 viral load in the upper respiratory tract, Journal of Infection, Vol: 87, Pages: 538-550, ISSN: 0163-4453

Objectives:The amount of SARS-CoV-2 detected in the upper respiratory tract (URT viral load) is a key driver of transmission of infection. Current evidence suggests that mechanisms constraining URT viral load are different from those controlling lower respiratory tract viral load and disease severity. Understanding such mechanisms may help to develop treatments and vaccine strategies to reduce transmission. Combining mathematical modelling of URT viral load dynamics with transcriptome analyses we aimed to identify mechanisms controlling URT viral load.Methods:COVID-19 patients were recruited in Spain during the first wave of the pandemic. RNA sequencing of peripheral blood and targeted NanoString nCounter transcriptome analysis of nasal epithelium were performed and gene expression analysed in relation to paired URT viral load samples collected within 15 days of symptom onset. Proportions of major immune cells in blood were estimated from transcriptional data using computational differential estimation. Weighted correlation network analysis (adjusted for cell proportions) and fixed transcriptional repertoire analysis were used to identify associations with URT viral load, quantified as standard deviations (z-scores) from an expected trajectory over time.ResultsEighty-two subjects (50% female, median age 54 years (range 3–73)) with COVID-19 were recruited. Paired URT viral load samples were available for 16 blood transcriptome samples, and 17 respiratory epithelial transcriptome samples. Natural Killer (NK) cells were the only blood cell type significantly correlated with URT viral load z-scores (r = −0.62, P = 0.010). Twenty-four blood gene expression modules were significantly correlated with URT viral load z-score, the most significant being a module of genes connected around IFNA14 (Interferon Alpha-14) expression (r = −0.60, P = 1e-10). In fixed repertoire analysis, prostanoid-related gene expression was significantly associated with higher vir

Journal article

Jackson HR, Zandstra J, Menikou S, Hamilton MS, McArdle AJ, Fischer R, Thorne AM, Huang H, Tanck MW, Jansen MH, De T, Agyeman PKA, Von Both U, Carrol ED, Emonts M, Eleftheriou I, Van der Flier M, Fink C, Gloerich J, De Groot R, Moll HA, Pokorn M, Pollard AJ, Schlapbach LJ, Tsolia MN, Usuf E, Wright VJ, Yeung S, Zavadska D, Zenz W, Coin LJM, Casals-Pascual C, Cunnington AJ, Martinon-Torres F, Herberg JA, de Jonge MI, Levin M, Kuijpers TW, Kaforou M, PERFORM consortiumet al., 2023, A multi-platform approach to identify a blood-based host protein signature for distinguishing between bacterial and viral infections in febrile children (PERFORM): a multi-cohort machine learning study, The Lancet: Digital Health, Vol: 5, Pages: e774-e785, ISSN: 2589-7500

BACKGROUND: Differentiating between self-resolving viral infections and bacterial infections in children who are febrile is a common challenge, causing difficulties in identifying which individuals require antibiotics. Studying the host response to infection can provide useful insights and can lead to the identification of biomarkers of infection with diagnostic potential. This study aimed to identify host protein biomarkers for future development into an accurate, rapid point-of-care test that can distinguish between bacterial and viral infections, by recruiting children presenting to health-care settings with fever or a history of fever in the previous 72 h. METHODS: In this multi-cohort machine learning study, patient data were taken from EUCLIDS, the Swiss Pediatric Sepsis study, the GENDRES study, and the PERFORM study, which were all based in Europe. We generated three high-dimensional proteomic datasets (SomaScan and two via liquid chromatography tandem mass spectrometry, referred to as MS-A and MS-B) using targeted and untargeted platforms (SomaScan and liquid chromatography mass spectrometry). Protein biomarkers were then shortlisted using differential abundance analysis, feature selection using forward selection-partial least squares (FS-PLS; 100 iterations), along with a literature search. Identified proteins were tested with Luminex and ELISA and iterative FS-PLS was done again (25 iterations) on the Luminex results alone, and the Luminex and ELISA results together. A sparse protein signature for distinguishing between bacterial and viral infections was identified from the selected proteins. The performance of this signature was finally tested using Luminex assays and by calculating disease risk scores. FINDINGS: 376 children provided serum or plasma samples for use in the discovery of protein biomarkers. 79 serum samples were collected for the generation of the SomaScan dataset, 147 plasma samples for the MS-A dataset, and 150 plasma samples for the MS-

Journal article

Kolberg L, Khanijau A, van der Velden F, Herberg J, De T, Galassini R, Cunnington A, Wright V, Shah P, Kaforou M, Wilson C, Kuijpers T, Martinón-Torres F, Rivero-Calle I, Moll H, Vermont C, Pokorn M, Kolnik M, Pollard A, Agyeman P, Schlapbach L, Tsolia M, Yeung S, Zavadska D, Zenz W, Schweintzger N, Van Der Flier M, de Groot R, Usuf E, Voice M, Calvo-Bado L, Mallet F, Fidler K, Levin M, Carrol E, Emonts M, von Both U, The PERFORM Consortiumet al., 2023, AWaRe-ness of antimicrobial stewardship challenges in pediatric emergency care: results from the PERFORM study assessing consistency and appropriateness of antibiotic prescribing across Europe, Clinical Infectious Diseases, ISSN: 1058-4838

ObjectivesOptimization of antimicrobial stewardship (AMS) is key to tackling antimicrobial resistance (AMR), which is exacerbated by over-prescription of antibiotics in pediatric Emergency Departments (EDs). We described patterns of empiric antibiotic use in European EDs, and characterized appropriateness and consistency of prescribing.MethodsBetween August 2016 and December 2019 febrile children attending the ED in nine European countries with suspected infection were recruited into the PERFORM (Personalised Risk assessment in Febrile illness to Optimise Real-life Management) study. Empiric systemic antibiotic use was determined in view of assigned final ‘bacterial’ or ‘viral’ phenotype. Antibiotics were classified according to WHO AWaRe.ResultsOf 2130 febrile episodes (excluding children with non-bacterial/non-viral phenotypes), 1549 (72.7%) were assigned a ‘bacterial’ and 581 (27.3%) a ‘viral’ phenotype. A total of 1318/1549 (85.1%) episodes with a ‘bacterial’ and 269/581 (46.3%) with a ‘viral’ phenotype received empiric systemic antibiotics (first two days of admission). Of those, the majority (87.8% in ‘bacterial’ and 87.0% in ‘viral’ group) received parenteral antibiotics. The top three antibiotics prescribed were third-generation cephalosporins, penicillins and penicillin/beta-lactamase inhibitor combinations. Of those treated with empiric systemic antibiotics in the ‘viral’ group 216/269 (80.3%) received ≥ one Watch antibiotic.ConclusionsDifferentiating bacterial from viral etiology in febrile illness on initial ED presentation remains challenging, resulting in a substantial over-prescription of antibiotics. A significant proportion of patients with a ‘viral’ phenotype received systemic antibiotics, predominantly classified as WHO Watch. Rapid and accurate point-of-care tests in the ED differentiating between bacterial and viral etiology

Journal article

Habgood-Coote D, Wilson C, Shimizu C, Barendregt AM, Philipsen R, Galassini R, Calle IR, Workman L, Agyeman PKA, Ferwerda G, Anderson ST, van den Berg JM, Emonts M, Carrol ED, Fink CG, de Groot R, Hibberd ML, Kanegaye J, Nicol MP, Paulus S, Pollard AJ, Salas A, Secka F, Schlapbach LJ, Tremoulet AH, Walther M, Zenz W, Pediatric Emergency Medicine Kawasaki Disease Research Group PEMKDRG, UK Kawasaki Genetics consortium, GENDRES consortium, EUCLIDS consortium, PERFORM consortium, Van der Flier M, Zar HJ, Kuijpers T, Burns JC, Martinón-Torres F, Wright VJ, Coin LJM, Cunnington AJ, Herberg JA, Levin M, Kaforou Met al., 2023, Diagnosis of childhood febrile illness using a multi-class blood RNA molecular signature, Med, Vol: 4, Pages: 635-654.e5, ISSN: 2666-6340

BACKGROUND: Appropriate treatment and management of children presenting with fever depend on accurate and timely diagnosis, but current diagnostic tests lack sensitivity and specificity and are frequently too slow to inform initial treatment. As an alternative to pathogen detection, host gene expression signatures in blood have shown promise in discriminating several infectious and inflammatory diseases in a dichotomous manner. However, differential diagnosis requires simultaneous consideration of multiple diseases. Here, we show that diverse infectious and inflammatory diseases can be discriminated by the expression levels of a single panel of genes in blood. METHODS: A multi-class supervised machine-learning approach, incorporating clinical consequence of misdiagnosis as a "cost" weighting, was applied to a whole-blood transcriptomic microarray dataset, incorporating 12 publicly available datasets, including 1,212 children with 18 infectious or inflammatory diseases. The transcriptional panel identified was further validated in a new RNA sequencing dataset comprising 411 febrile children. FINDINGS: We identified 161 transcripts that classified patients into 18 disease categories, reflecting individual causative pathogen and specific disease, as well as reliable prediction of broad classes comprising bacterial infection, viral infection, malaria, tuberculosis, or inflammatory disease. The transcriptional panel was validated in an independent cohort and benchmarked against existing dichotomous RNA signatures. CONCLUSIONS: Our data suggest that classification of febrile illness can be achieved with a single blood sample and opens the way for a new approach for clinical diagnosis. FUNDING: European Union's Seventh Framework no. 279185; Horizon2020 no. 668303 PERFORM; Wellcome Trust (206508/Z/17/Z); Medical Research Foundation (MRF-160-0008-ELP-KAFO-C0801); NIHR Imperial BRC.

Journal article

Shah P, Voice M, Calvo-Bado L, Rivero-Calle I, Morris S, Nijman R, Broderick C, De T, Eleftheriou I, Galassini R, Khanijau A, Kolberg L, Kolnik M, Rudzate A, Sagmeister MG, Schweintzger NA, Secka F, Thakker C, van der Velden F, Vermont C, Vincek K, Agyeman PKA, Cunnington AJ, De Groot R, Emonts M, Fidler K, Kuijpers TW, Mommert-Tripon M, Brengel-Pesce K, Mallet F, Moll H, Paulus S, Pokorn M, Pollard A, Schlapbach LJ, Shen C-F, Tsolia M, Usuf E, van der Flier M, von Both U, Yeung S, Zavadska D, Zenz W, Wright V, Carrol ED, Kaforou M, Martinon-Torres F, Fink C, Levin M, Herberg Jet al., 2023, Relationship between molecular pathogen detection and clinical disease in febrile children across Europe: a multicentre, prospective observational study, LANCET REGIONAL HEALTH-EUROPE, Vol: 32, ISSN: 2666-7762

Journal article

Tan CD, Vermont CL, Zachariasse JM, von Both U, Eleftheriou I, Emonts M, van der Flier M, Herberg J, Kohlmaier B, Levin M, Lim E, Maconochie IK, Martinon-Torres F, Nijman RG, Pokorn M, Rivero-Calle I, Tsolia M, Zenz W, Zavadska D, Moll HA, Carrol ED, PERFORM consortium Personalised Risk assessment in febrile children tooptimize Real-life Management across the European Unionet al., 2023, Emergency medical services utilisation among febrile children attending emergency departments across Europe: an observational multicentre study, European Journal of Pediatrics, Vol: 182, Pages: 3939-3947, ISSN: 0340-6199

Children constitute 6-10% of all patients attending the emergency department (ED) by emergency medical services (EMS). However, discordant EMS use in children occurs in 37-61% with fever as an important risk factor. We aimed to describe EMS utilisation among febrile children attending European EDs. This study is part of an observational multicentre study assessing management and outcome in febrile children up to 18 years (MOFICHE) attending twelve EDs in eight European countries. Discordant EMS use was defined as the absence of markers of urgency including intermediate/high triage urgency, advanced diagnostics, treatment, and admission in children transferred by EMS. Multivariable logistic regression analyses were performed for the association between (1) EMS use and markers of urgency, and (2) patient characteristics and discordant EMS use after adjusting all analyses for the covariates age, gender, visiting hours, presenting symptoms, and ED setting. A total of 5464 (15%, range 0.1-42%) children attended the ED by EMS. Markers of urgency were more frequently present in the EMS group compared with the non-EMS group. Discordant EMS use occurred in 1601 children (29%, range 1-59%). Age and gender were not associated with discordant EMS use, whereas neurological symptoms were associated with less discordant EMS use (aOR 0.2, 95%CI 0.1-0.2), and attendance out of office hours was associated with more discordant EMS use (aOR 1.6, 95%CI 1.4-1.9). Settings with higher percentage of self-referrals to the ED had more discordant EMS use (p < 0.05).  Conclusion: There is large practice variation in EMS use in febrile children attending European EDs. Markers of urgency were more frequently present in children in the EMS group. However, discordant EMS use occurred in 29%. Further research is needed on non-medical factors influencing discordant EMS use in febrile children across Europe, so that pre-emptive strategies can be implemented. What is Known:

Journal article

Herberg J, Shah P, Voice M, Calvo-Bado L, Rivero Calle I, Morris S, Nijman R, Broderick C, De T, Eleftheriou I, Galassini R, Khanijau A, Kolberg L, Kolnik M, Rudzate A, Sagmeister M, Schweintzger N, Secka F, Thakker C, van der Velden F, Vermont C, Vincek K, Agyeman P, Cunnington A, de Groot R, Emonts M, Fidler K, Kuijpers T, Mommert-Tripon M, Brengel-Pesce K, Mallet F, Moll H, Paulus S, Pokorn M, Pollard A, Schlapbach L, Shen C-F, Tsolia M, Usuf E, Van Der Flier M, von Both U, Yeung S, Zavadska D, Zenz W, Wright V, Carrol E, Kaforou M, Martinon-Torres F, Fink C, Levin M, PERFORM consortiumet al., 2023, Relationship between molecular pathogen detection and clinical disease in febrile children across Europe: a multicentre, prospective observational study, The Lancet Regional Health. Europe, Vol: 32, Pages: 1-17, ISSN: 2666-7762

The PERFORM study aimed to understand causes of febrile childhood illness by comparing molecular pathogen detection with current clinical practice. Methods. Febrile children and controls were recruited on presentation to hospital in 9 European countries 2016-2020. Each child was assigned a standardized diagnostic category based on retrospective review of local clinical and microbiological data. Subsequently, centralised molecular tests (CMTs) for 19 respiratory and 27 blood pathogens were performed.Findings. Of 4,611 febrile children, 643 (14%) were classified as definite bacterial infection (DB), 491 (11%) as definite viral infection (DV), and 3,477 (75%) had uncertain aetiology. 1,061 controls without infection were recruited. CMTs detected blood bacteria more frequently in DB than DV cases for N.meningitidis (OR: 3.37, 95% CI: 1.92 – 5.99), S.pneumoniae (OR: 3.89, 95% CI: 2.07 – 7.59), Group A streptococcus (OR 2.73, 95% CI 1.13 – 6.09) and E.coli (OR 2.7, 95% CI 1.02 – 6.71). Respiratory viruses were more common in febrile children than controls, but only influenza A (OR 0.24, 95% CI 0.11 – 0.46), Influenza B (OR 0.12, 95% CI 0.02 – 0.37) and RSV (OR 0.16, 95% CI: 0.06 – 0.36) were less common in DB than DV cases. Of 16 blood viruses, enterovirus (OR 0.43, 95% CI 0.23 – 0.72) and EBV (OR 0.71, 95% CI 0.56 – 0.90) were detected less often in DB than DV cases. Combined local diagnostics and CMTs respectively detected blood viruses and respiratory viruses in 360 (56%) and 161 (25%) of DB cases, and virus detection ruled-out bacterial infection poorly, with predictive values of 0.64 and 0.68 respectively. Interpretation. Most febrile children cannot be conclusively defined as having bacterial or viral infection when molecular tests supplement conventional approaches. Viruses are detected in most patients with bacterial infections, and the clinical value of individual pathogen detection in determining treatment is

Journal article

Willems E, Gloerich J, Suppers A, van der Flier M, van den Heuvel LP, van de Kar N, Philipsen RHLA, van Dael M, Kaforou M, Wright VJ, Herberg JA, Torres FM, Levin M, de Groot R, van Gool AJ, Lefeber DJ, Wessels HJCT, de Jonge MI, PERFORM consortiumet al., 2023, Impact of infection on proteome-wide glycosylation revealed by distinct signatures for bacterial and viral pathogens, iScience, Vol: 26, ISSN: 2589-0042

Mechanisms of infection and pathogenesis have predominantly been studied based on differential gene or protein expression. Less is known about posttranslational modifications, which are essential for protein functional diversity. We applied an innovative glycoproteomics method to study the systemic proteome-wide glycosylation in response to infection. The protein site-specific glycosylation was characterized in plasma derived from well-defined controls and patients. We found 3862 unique features, of which we identified 463 distinct intact glycopeptides, that could be mapped to more than 30 different proteins. Statistical analyses were used to derive a glycopeptide signature that enabled significant differentiation between patients with a bacterial or viral infection. Furthermore, supported by a machine learning algorithm, we demonstrated the ability to identify the causative pathogens based on the distinctive host blood plasma glycopeptide signatures. These results illustrate that glycoproteomics holds enormous potential as an innovative approach to improve the interpretation of relevant biological changes in response to infection.

Journal article

van der Velden FJS, Lim E, Gills L, Broadey J, Hayes L, Roberts E, Courtney J, Ball J, Herberg J, Galassini R, Emonts M, DIAMONDS consortiumet al., 2023, Biobanking and consenting to research: a qualitative thematic analysis of young people's perspectives in the North East of England, BMC Medical Ethics, Vol: 24, Pages: 1-11, ISSN: 1472-6939

BACKGROUND: Biobanking biospecimens and consent are common practice in paediatric research. We need to explore children and young people's (CYP) knowledge and perspectives around the use of and consent to biobanking. This will ensure meaningful informed consent can be obtained and improve current consent procedures. METHODS: We designed a survey, in co-production with CYP, collecting demographic data, views on biobanking, and consent using three scenarios: 1) prospective consent, 2) deferred consent, and 3) reconsent and assent at age of capacity. The survey was disseminated via the Young Person's Advisory Group North England (YPAGne) and participating CYP's secondary schools. Data were analysed using a qualitative thematic approach by three independent reviewers (including CYP) to identify common themes. Data triangulation occurred independently by a fourth reviewer. RESULTS: One hundred two CYP completed the survey. Most were between 16-18 years (63.7%, N = 65) and female (66.7%, N = 68). 72.3% had no prior knowledge of biobanking (N = 73). Acceptability of prospective consent for biobanking was high (91.2%, N = 93) with common themes: 'altruism', 'potential benefits outweigh individual risk', 'frugality', and '(in)convenience'. Deferred consent was also deemed acceptable in the large majority (84.3%, N = 86), with common themes: 'altruism', 'body integrity' and 'sample frugality'. 76.5% preferred to reconsent when cognitively mature enough to give assent (N = 78), even if parental consent was previously in place. 79.2% wanted to be informed if their biobanked biospecimen is reused (N = 80). CONCLUSION: Prospective and deferred consent acceptability for biobanking is high among CYP in the UK. Altruism, frugality, body integrity, and privacy are the most important themes. Clear communication and justification are paramount to obtain consent. Any CYP with capacity

Journal article

Jackson HR, Miglietta L, Habgood-Coote D, D'Souza G, Shah P, Nichols S, Vito O, Powell O, Davidson MS, Shimizu C, Agyeman PKA, Beudeker CR, Brengel-Pesce K, Carrol ED, Carter MJ, De T, Eleftheriou I, Emonts M, Epalza C, Georgiou P, De Groot R, Fidler K, Fink C, van Keulen D, Kuijpers T, Moll H, Papatheodorou I, Paulus S, Pokorn M, Pollard AJ, Rivero-Calle I, Rojo P, Secka F, Schlapbach LJ, Tremoulet AH, Tsolia M, Usuf E, Van Der Flier M, Von Both U, Vermont C, Yeung S, Zavadska D, Zenz W, Coin LJM, Cunnington A, Burns JC, Wright V, Martinon-Torres F, Herberg JA, Rodriguez-Manzano J, Kaforou M, Levin Met al., 2023, Diagnosis of multisystem inflammatory syndrome in children by a whole-blood transcriptional signature, Journal of the Pediatric Infectious Diseases Society, Vol: 12, Pages: 322-331, ISSN: 2048-7207

BACKGROUND: To identify a diagnostic blood transcriptomic signature that distinguishes multisystem inflammatory syndrome in children (MIS-C) from Kawasaki disease (KD), bacterial infections, and viral infections. METHODS: Children presenting with MIS-C to participating hospitals in the United Kingdom and the European Union between April 2020 and April 2021 were prospectively recruited. Whole-blood RNA Sequencing was performed, contrasting the transcriptomes of children with MIS-C (n = 38) to those from children with KD (n = 136), definite bacterial (DB; n = 188) and viral infections (DV; n = 138). Genes significantly differentially expressed (SDE) between MIS-C and comparator groups were identified. Feature selection was used to identify genes that optimally distinguish MIS-C from other diseases, which were subsequently translated into RT-qPCR assays and evaluated in an independent validation set comprising MIS-C (n = 37), KD (n = 19), DB (n = 56), DV (n = 43), and COVID-19 (n = 39). RESULTS: In the discovery set, 5696 genes were SDE between MIS-C and combined comparator disease groups. Five genes were identified as potential MIS-C diagnostic biomarkers (HSPBAP1, VPS37C, TGFB1, MX2, and TRBV11-2), achieving an AUC of 96.8% (95% CI: 94.6%-98.9%) in the discovery set, and were translated into RT-qPCR assays. The RT-qPCR 5-gene signature achieved an AUC of 93.2% (95% CI: 88.3%-97.7%) in the independent validation set when distinguishing MIS-C from KD, DB, and DV. CONCLUSIONS: MIS-C can be distinguished from KD, DB, and DV groups using a 5-gene blood RNA expression signature. The small number of genes in the signature and good performance in both discovery and validation sets should enable the development of a diagnostic test for MIS-C.

Journal article

Morfopoulou S, Buddle S, Torres Montaguth OE, Atkinson L, Guerra-Assunção JA, Moradi Marjaneh M, Zennezini Chiozzi R, Storey N, Campos L, Hutchinson JC, Counsell JR, Pollara G, Roy S, Venturini C, Antinao Diaz JF, Siam A, Tappouni LJ, Asgarian Z, Ng J, Hanlon KS, Lennon A, McArdle A, Czap A, Rosenheim J, Andrade C, Anderson G, Lee JCD, Williams R, Williams CA, Tutill H, Bayzid N, Martin Bernal LM, Macpherson H, Montgomery K-A, Moore C, Templeton K, Neill C, Holden M, Gunson R, Shepherd SJ, Shah P, Cooray S, Voice M, Steele M, Fink C, Whittaker TE, Santilli G, Gissen P, Kaufer BB, Reich J, Andreani J, Simmonds P, Alrabiah DK, Castellano S, Chikowore P, Odam M, Rampling T, Houlihan C, Hoschler K, Talts T, Celma C, Gonzalez S, Gallagher E, Simmons R, Watson C, Mandal S, Zambon M, Chand M, Hatcher J, De S, Baillie K, Semple MG, DIAMONDS Consortium, PERFORM Consortium, ISARIC4C Investigators, Martin J, Ushiro-Lumb I, Noursadeghi M, Deheragoda M, Hadzic N, Grammatikopoulos T, Brown R, Kelgeri C, Thalassinos K, Waddington SN, Jacques TS, Thomson E, Levin M, Brown JR, Breuer Jet al., 2023, Genomic investigations of unexplained acute hepatitis in children, Nature, Vol: 617, Pages: 564-573, ISSN: 0028-0836

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children.

Journal article

Ho A, Orton R, Tayler R, Asamaphan P, Herder V, Davis C, Tong L, Smollett K, Manali M, Allan J, Rawlik K, McDonald SE, Vink E, Pollock L, Gannon L, Evans C, McMenamin J, Roy K, Marsh K, Divala T, Holden MTG, Lockhart M, Yirrell D, Currie S, O'Leary M, Henderson D, Shepherd SJ, Jackson C, Gunson R, MacLean A, McInnes N, Bradley-Stewart A, Battle R, Hollenbach JA, Henderson P, Odam M, Chikowore P, Oosthuyzen W, Chand M, Hamilton MS, Estrada-Rivadeneyra D, Levin M, Avramidis N, Pairo-Castineira E, Vitart V, Wilkie C, DIAMONDS Consortium, ISARIC4C Investigators, Palmarini M, Ray S, Robertson DL, da Silva Filipe A, Willett BJ, Breuer J, Semple MG, Turner D, Baillie JK, Thomson ECet al., 2023, Adeno-associated virus 2 infection in children with non-A-E hepatitis., Nature, Vol: 617, Pages: 555-563

An outbreak of acute hepatitis of unknown aetiology in children was reported in Scotland1 in April 2022 and has now been identified in 35 countries2. Several recent studies have suggested an association with human adenovirus with this outbreak, a virus not commonly associated with hepatitis. Here we report a detailed case-control investigation and find an association between adeno-associated virus 2 (AAV2) infection and host genetics in disease susceptibility. Using next-generation sequencing, PCR with reverse transcription, serology and in situ hybridization, we detected recent infection with AAV2 in plasma and liver samples in 26 out of 32 (81%) cases of hepatitis compared with 5 out of 74 (7%) of samples from unaffected individuals. Furthermore, AAV2 was detected within ballooned hepatocytes alongside a prominent T cell infiltrate in liver biopsy samples. In keeping with a CD4+ T-cell-mediated immune pathology, the human leukocyte antigen (HLA) class II HLA-DRB1*04:01 allele was identified in 25 out of 27 cases (93%) compared with a background frequency of 10 out of 64 (16%; P = 5.49 × 10-12). In summary, we report an outbreak of acute paediatric hepatitis associated with AAV2 infection (most likely acquired as a co-infection with human adenovirus that is usually required as a 'helper virus' to support AAV2 replication) and disease susceptibility related to HLA class II status.

Journal article

Moradi Marjaneh M, Challenger J, Salas A, Gómez-Carballa A, Sivananthan A, Rivero-Calle I, Barbeito-Castiñeiras G, Foo C, Wu Y, Liew F, Jackson H, Habgood-Coote D, DSouza G, Nichols S, Wright V, Levin M, Kaforou M, Thwaites R, Okell L, Martinón-Torres F, Cunnington A, GEN-COVID Study Group, PERFORM Consortiumet al., 2023, Analysis of blood and nasal epithelial transcriptomes to identify mechanisms associated with control of SARS-CoV-2 viral load in the upper respiratory tract

Working paper

Kuiper R, Wright VJ, Habgood-Coote D, Shimizu C, Huigh D, Tremoulet AH, van Keulen D, Hoggart CJ, Rodriguez-Manzano J, Herberg JA, Kaforou M, Tempel D, Burns JC, Levin Met al., 2023, Bridging a diagnostic Kawasaki disease classifier from a microarray platform to a qRT-PCR assay, Pediatric Research, Vol: 93, Pages: 559-569, ISSN: 0031-3998

BACKGROUND: Kawasaki disease (KD) is a systemic vasculitis that mainly affects children under 5 years of age. Up to 30% of patients develop coronary artery abnormalities, which are reduced with early treatment. Timely diagnosis of KD is challenging but may become more straightforward with the recent discovery of a whole-blood host response classifier that discriminates KD patients from patients with other febrile conditions. Here, we bridged this microarray-based classifier to a clinically applicable quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay: the Kawasaki Disease Gene Expression Profiling (KiDs-GEP) classifier. METHODS: We designed and optimized a qRT-PCR assay and applied it to a subset of samples previously used for the classifier discovery to reweight the original classifier. RESULTS: The performance of the KiDs-GEP classifier was comparable to the original classifier with a cross-validated area under the ROC curve of 0.964 [95% CI: 0.924-1.00] vs 0.992 [95% CI: 0.978-1.00], respectively. Both classifiers demonstrated similar trends over various disease conditions, with the clearest distinction between individuals diagnosed with KD vs viral infections. CONCLUSION: We successfully bridged the microarray-based classifier into the KiDs-GEP classifier, a more rapid and more cost-efficient qRT-PCR assay, bringing a diagnostic test for KD closer to the hospital clinical laboratory. IMPACT: A diagnostic test is needed for Kawasaki disease and is currently not available. We describe the development of a One-Step multiplex qRT-PCR assay and the subsequent modification (i.e., bridging) of the microarray-based host response classifier previously described by Wright et al. The bridged KiDs-GEP classifier performs well in discriminating Kawasaki disease patients from febrile controls. This host response clinical test for Kawasaki disease can be adapted to the hospital clinical laboratory.

Journal article

van der Velden FJS, de Vries G, Martin A, Lim E, von Both U, Kolberg L, Carrol ED, Khanijau A, Herberg JA, De T, Galassini R, Kuijpers TW, Martinón-Torres F, Rivero-Calle I, Vermont CL, Hagedoorn NN, Pokorn M, Pollard AJ, Schlapbach LJ, Tsolia M, Elefhteriou I, Yeung S, Zavadska D, Fink C, Voice M, Zenz W, Kohlmaier B, Agyeman PKA, Usuf E, Secka F, de Groot R, Levin M, van der Flier M, Emonts M, PERFORM consortiumet al., 2023, Correction to: Febrile illness in high-risk children: a prospective, international observational study., European Journal of Pediatrics, Vol: 182, Pages: 555-556, ISSN: 0340-6199

Journal article

Boeddha NP, Atkins L, de Groot R, Driessen G, Hazelzet J, Zenz W, Carrol ED, Anderson ST, Martinon-Torres F, Agyeman PKA, Galassini R, Herberg J, Levin M, Schlapbach LJ, Emonts Met al., 2023, Group A streptococcal disease in paediatric inpatients: a European perspective (Vol 182, pg 697, 2023), EUROPEAN JOURNAL OF PEDIATRICS, ISSN: 0340-6199

Journal article

Tan CD, van der Walle EEPL, Vermont CL, von Both U, Carrol ED, Eleftheriou I, Emonts M, van der Flier M, de Groot R, Herberg J, Kohlmaier B, Levin M, Lim E, Maconochie IK, Martinon-Torres F, Nijman RG, Pokorn M, Rivero-Calle I, Tsolia M, Yeung S, Zenz W, Zavadska D, Moll HA, PERFORM consortium Personalised Risk assessment in febrile children to optimize Real-life Management across the European Unionet al., 2022, Guideline adherence in febrile children below 3 months visiting European Emergency Departments: an observational multicenter study, European Journal of Pediatrics, Vol: 181, Pages: 4199-4209, ISSN: 0340-6199

Febrile children below 3 months have a higher risk of serious bacterial infections, which often leads to extensive diagnostics and treatment. There is practice variation in management due to differences in guidelines and their usage and adherence. We aimed to assess whether management in febrile children below 3 months attending European Emergency Departments (EDs) was according to the guidelines for fever. This study is part of the MOFICHE study, which is an observational multicenter study including routine data of febrile children (0-18 years) attending twelve EDs in eight European countries. In febrile children below 3 months (excluding bronchiolitis), we analyzed actual management compared to the guidelines for fever. Ten EDs applied the (adapted) NICE guideline, and two EDs applied local guidelines. Management included diagnostic tests, antibiotic treatment, and admission. We included 913 children with a median age of 1.7 months (IQR 1.0-2.3). Management per ED varied as follows: use of diagnostic tests 14-83%, antibiotic treatment 23-54%, admission 34-86%. Adherence to the guideline was 43% (374/868) for blood cultures, 29% (144/491) for lumbar punctures, 55% (270/492) for antibiotic prescriptions, and 67% (573/859) for admission. Full adherence to these four management components occurred in 15% (132/868, range 0-38%), partial adherence occurred in 56% (484/868, range 35-77%). CONCLUSION: There is large practice variation in management. The guideline adherence was limited, but highest for admission which implies a cautious approach. Future studies should focus on guideline revision including new biomarkers in order to optimize management in young febrile children. WHAT IS KNOWN: • Febrile children below 3 months have a higher risk of serious bacterial infections, which often leads to extensive diagnostics and treatment. • There is practice variation in management of young febrile children due to differences in guideline

Journal article

Kumar V, Pouw RB, Autio M, Sagmeister MG, Phua ZY, Borghini L, Wright VJ, Hoggart C, Pan B, Tan AKY, Binder A, Brouwer MC, Pinnock E, De Groot R, Hazelzet J, Emonts M, van der Flier M, Reiter K, Nothen MM, Hoffmann P, Schlapbach LJ, Bellos E, Anderson S, Secka F, Martinon-Torres F, Salas A, Fink C, Carrol ED, Pollard AJ, Coin LJ, Zenz W, Wouters D, Ang LT, Hibberd ML, Levin M, Kuijpers TW, Davila Set al., 2022, Variation in <i>CFHR3</i> determines susceptibility to meningococcal disease by controlling factor H concentrations, AMERICAN JOURNAL OF HUMAN GENETICS, Vol: 109, Pages: 1680-1691, ISSN: 0002-9297

Journal article

Jackson H, Calle IR, Broderick C, Habgood-Coote D, dSouza G, Nichols S, Gómez-Rial J, Rivero-Velasco C, Rodríguez-Núñez N, Barbeito-Castiñeiras G, Pérez-Freixo H, Acosta MB-D, Cunnington AJ, Herberg JA, Wright VJ, Gómez-Carballa A, Salas A, Levin M, Martinon-Torres F, Kaforou Met al., 2022, Characterisation of the blood RNA host response underpinning severity in COVID-19 patients, Scientific Reports, Vol: 12, ISSN: 2045-2322

Infection with SARS-CoV-2 has highly variable clinical manifestations, ranging from asymptomatic infection through to life-threatening disease. Host whole blood transcriptomics can offer unique insights into the biological processes underpinning infection and disease, as well as severity. We performed whole blood RNA Sequencing of individuals with varying degrees of COVID-19 severity. We used differential expression analysis and pathway enrichment analysis to explore how the blood transcriptome differs between individuals with mild, moderate, and severe COVID-19, performing pairwise comparisons between groups. Increasing COVID-19 severity was characterised by an abundance of inflammatory immune response genes and pathways, including many related to neutrophils and macrophages, in addition to an upregulation of immunoglobulin genes. Our insights into COVID-19 severity reveal the role of immune dysregulation in the progression to severe disease and highlight the need for further research exploring the interplay between SARS-CoV-2 and the inflammatory immune response.

Journal article

van Beek AE, Pouw RB, Wright VJ, Sallah N, Inwald D, Hoggart C, Brouwer MC, Galassini R, Thomas J, Calvo-Bado L, Fink CG, Jongerius I, Hibberd M, Wouters D, Levin M, Kuijpers TWet al., 2022, Low levels of factor H family proteins during meningococcal disease indicate systemic processes rather than specific depletion by neisseria meningitidis, Frontiers in Immunology, Vol: 13, ISSN: 1664-3224

Neisseria meningitidis, the causative agent of meningococcal disease (MD), evades complement-mediated clearance upon infection by ‘hijacking’ the human complement regulator factor H (FH). The FH protein family also comprises the homologous FH-related (FHR) proteins, hypothesized to act as antagonists of FH, and FHR-3 has recently been implicated to play a major role in MD susceptibility. Here, we show that the circulating levels of all FH family proteins, not only FH and FHR-3, are equally decreased during the acute illness. We did neither observe specific consumption of FH or FHR-3 by N. meningitidis, nor of any of the other FH family proteins, suggesting that the globally reduced levels are due to systemic processes including dilution by fluid administration upon admission and vascular leakage. MD severity associated predominantly with a loss of FH rather than FHRs. Additionally, low FH levels associated with renal failure, suggesting insufficient protection of host tissue by the active protection by the FH protein family, which is reminiscent of reduced FH activity in hemolytic uremic syndrome. Retaining higher levels of FH may thus limit tissue injury during MD.

Journal article

Channon-Wells S, Coote D, Wright V, Levin M, Kaforou M, Herberg Jet al., 2022, VALIDATION OF TRANSCRIPTOMIC SIGNATURES FOR FEBRILE CHILDREN USING NANOSTRING TECHNOLOGY AND EXPLORATION OF MULTI-CLASS PREDICTION MODELS, The European Society For Paediatric Infectious Diseases Conference 2022

Backgrounds: Many host transcript signatures for paediatric inflammatory and infectious diseases are in development, but require validation in independent cohorts; their translation to clinically useful test platforms lags behind discovery. We used NanoString technology to efficiently validate multiple signatures in parallel and explore the potential for more sophisticated multi-class classification models. Methods: We validated five transcriptomic diagnostic signatures using prospectively recruited patients from multiple paediatric cohorts. Final phenotypes were assigned using pre-agreed definitions after review of clinical and laboratory data. We quantified 69 transcripts on a custom NanoString nCounter cartridge, normalising expression values using reference genes. Signature performance was assessed using Area Under ROC Curve (AUC) statistics. We explored two approaches to multiclassification diagnostics to develop proof-of-concept methods: a mixed test combining four independent one-vs-all models, and a multinomial model. Results: Our cohort of 92 paediatric patients included 23 definite bacterial and 20 definite viral infections, 15 Kawasaki disease, 18 with tuberculosis and 16 healthy controls. The signatures achieved AUCs above 0.82 (Table 1), with confidence intervals overlapping those of the respective discovery studies. However, performance declined in all signatures when tasked with differentiating additional groups. For example, the single-transcript BATF2 had AUC of 0.910 differentiating TB from healthy individuals, reducing to 0.745 when differentiating TB from other febrile diseases. In comparison, the multinomial approach identified a 24-transcript model that correctly classified all 76 non-control patients (0% in-sample error), outperforming the mixed-model (19 transcripts, 19.8% in-sample error).

Conference paper

Hoggart C, Shimizu C, Galassini R, Wright VJ, Shailes H, Bellos E, Herberg JA, Pollard AJ, O'Connor D, Choi SW, Seaby EG, Menikou S, Hibberd M, Sallah N, Burgner D, Brogan P, Patel H, Kim J, Tremoulet AH, Salo E, van Stijn D, Kuijpers T, Burns JC, Levin Met al., 2021, Identification of novel locus associated with coronary artery aneurysms and validation of loci for susceptibility to Kawasaki disease, European Journal of Human Genetics, Vol: 29, Pages: 1734-1744, ISSN: 1018-4813

Kawasaki disease (KD) is a paediatric vasculitis associated with coronary artery aneurysms (CAA). Genetic variants influencing susceptibility to KD have been previously identified, but no risk alleles have been validated that influence CAA formation. We conducted a genome-wide association study (GWAS) for CAA in KD patients of European descent with 200 cases and 276 controls. A second GWAS for susceptibility pooled KD cases with healthy paediatric controls from vaccine trials in the UK (n = 1609). Logistic regression mixed models were used for both GWASs. The susceptibility GWAS was meta-analysed with 400 KD cases and 6101 controls from a previous European GWAS, these results were further meta-analysed with Japanese GWASs at two putative loci. The CAA GWAS identified an intergenic region of chromosome 20q13 with multiple SNVs showing genome-wide significance. The risk allele of the most associated SNV (rs6017006) was present in 13% of cases and 4% of controls; in East Asian 1000 Genomes data, the allele was absent or rare. Susceptibility GWAS with meta-analysis with previously published European data identified two previously associated loci (ITPKC and FCGR2A). Further meta-analysis with Japanese GWAS summary data from the CASP3 and FAM167A genomic regions validated these loci in Europeans showing consistent effects of the top SNVs in both populations. We identified a novel locus for CAA in KD patients of European descent. The results suggest that different genes determine susceptibility to KD and development of CAA and future work should focus on the function of the intergenic region on chromosome 20q13.

Journal article

Li HK, Kaforou M, Rodriguez-Manzano J, Channon-Wells S, Monir A, Habgood-Coote D, Gupta RK, Mills EA, Lin J, Chiu Y-H, Pennisi I, Miglietta L, Mehta R, Obaray N, Herberg JA, Wright VJ, Georgiou P, Shallcross LJ, Mentzer AJ, Levin M, Cooke GS, Noursadeghi M, Sriskandan Set al., 2021, Discovery and validation of a 3-gene signature to distinguish COVID-19 and other viral infections in emergency infectious disease presentations; a case-control then observational cohort study, The Lancet Microbe, Vol: 2, Pages: 594-603, ISSN: 2666-5247

Background: Emergency admissions for infection often lack initial diagnostic certainty. COVID-19 has highlighted a need for novel diagnostic approaches to indicate likelihood of viral infection in a pandemic setting. We sought to derive and validate a blood transcriptional signature to detect viral infections including COVID-19 among adults with suspected infection presenting to the Emergency Department (ED).Methods: Blood RNA sequencing was performed on a discovery cohort of adults attending the ED with suspected infection who had subsequently-confirmed viral, bacterial, or no infection diagnoses. Differentially expressed host genes were subjected to feature selection to derive the most parsimonious discriminating signature. RT-qPCR validation of the signature was then performed in a prospective cohort of ED patients presenting with undifferentiated fever, and a second case-control cohort of ED patients with COVID-19 or bacterial infection. Signature performance was assessed by calculating area under receiver-operating characteristic curves (AUC-ROCs), sensitivities, and specificities.Findings: A 3-gene transcript signature was derived from the discovery cohort of 56 bacterial and 27 viral infection cases. In the validation cohort of 200 cases, the signature differentiated bacterial from viral infections with an AUC-ROC of 0.976 (95% CI: 0.919-1.000), sensitivity 97.3% and specificity of 100%. The AUC-ROC for C-reactive protein (CRP) and leucocyte count (WCC) was 0.833 (95% CI: 0.694-0.944) and 0.938 (95% CI: 0.840-0.986) respectively. The signature achieved higher net benefit in decision curve analysis than either CRP or WCC for discriminating viral infections from all other cases. In the second validation analysis the signature discriminated 35 bacterial infections from 34 SARS-CoV-2 positive COVID-19 infections with AUC-ROC of 0.953 (95% CI: 0.893-0.992), sensitivity 88.6% and specificity of 94.1%.Interpretation: This novel 3-gene signature discriminates viral i

Journal article

Nijman R, Oostenbrink R, Moll HA, Casals-Pascual C, von Both U, Cunnington A, De T, Eleftheriou I, Emonts M, Fink C, Van Der Flier M, de Groot R, Kaforou M, Kohlmaier B, Kuijpers TW, Lim E, Maconochie I, Paulus S, Martinon-Torres F, Pokorn M, Romaine S, Rivero Calle I, Schlapbach L, Smit FJ, Tsolia M, Usuf E, Wright V, Yeung S, Zavadska D, Zenz W, Levin M, Herberg J, Carrol EDet al., 2021, A novel framework for phenotyping children with suspected or confirmed infection for future biomarker studies, Frontiers in Pediatrics, Vol: 9, Pages: 1-18, ISSN: 2296-2360

Background: The limited diagnostic accuracy of biomarkers in children at risk of a serious bacterial infection (SBI) might be due to the imperfect reference standard of SBI. We aimed to evaluate the diagnostic performance of a new classification algorithm for biomarker discovery in children at risk of SBI.Methods: We used data from five previously published, prospective observational biomarker discovery studies, which included patients aged 0– <16 years: the Alder Hey emergency department (n = 1,120), Alder Hey pediatric intensive care unit (n = 355), Erasmus emergency department (n = 1,993), Maasstad emergency department (n = 714) and St. Mary's hospital (n = 200) cohorts. Biomarkers including procalcitonin (PCT) (4 cohorts), neutrophil gelatinase-associated lipocalin-2 (NGAL) (3 cohorts) and resistin (2 cohorts) were compared for their ability to classify patients according to current standards (dichotomous classification of SBI vs. non-SBI), vs. a proposed PERFORM classification algorithm that assign patients to one of eleven categories. These categories were based on clinical phenotype, test outcomes and C-reactive protein level and accounted for the uncertainty of final diagnosis in many febrile children. The success of the biomarkers was measured by the Area under the receiver operating Curves (AUCs) when they were used individually or in combination.Results: Using the new PERFORM classification system, patients with clinically confident bacterial diagnosis (“definite bacterial” category) had significantly higher levels of PCT, NGAL and resistin compared with those with a clinically confident viral diagnosis (“definite viral” category). Patients with diagnostic uncertainty had biomarker concentrations that varied across the spectrum. AUCs were higher for classification of “definite bacterial” vs. “definite viral” following the PERFORM algorithm than using the “SBI” vs. “non-SBI” c

Journal article

Jackson H, Menikou S, Hamilton M, McArdle A, Shimizu C, Galassini R, Huang H, Kim J, Tremoulet A, de Jonge M, Kuijpers T, Wright V, Burns J, Casals-Pascual C, Herberg J, Levin M, Kaforou Met al., 2021, Kawasaki Disease patient stratification and pathway analysis based on host transcriptomic and proteomic profiles, International Journal of Molecular Sciences, Vol: 11, Pages: 1-24, ISSN: 1422-0067

The aetiology of Kawasaki Disease (KD), an acute inflammatory disorder of childhood, remains unknown despite various triggers of KD having been proposed. Host ‘omic profiles offer insights into the host response to infection and inflammation, with the interrogation of multiple ‘omic levels in parallel providing a more comprehensive picture. We used differential abundance analysis, pathway analysis, clustering and classification techniques to explore whether the host response in KD is more similar to the response to bacterial or viral infection at the transcriptomic and proteomic levels through comparison of ‘omic profiles from children with KD to those with bacterial and viral infections. Pathways activated in patients with KD included those involved in anti-viral and anti-bacterial responses. Unsupervised clustering showed that the majority of KD patients clustered with bacterial patients on both ‘omic levels, whilst application of diagnostic signatures specific for bacterial and viral infections revealed that many transcriptomic KD samples had low probabilities of having bacterial or viral infections, suggesting that KD may be triggered by a different process not typical of either common bacterial or viral infections. Clustering based on the transcriptomic and proteomic responses during KD revealed three clusters of KD patients on both ‘omic levels, suggesting heterogeneity within the inflammatory response during KD. The observed heterogeneity may reflect differences in the host response to a common trigger, or variation dependent on different triggers of the condition.

Journal article

Gliddon H, Kaforou M, Alikian M, Coote D, Zhou C, Oni T, Anderson ST, Brent AJ, Crampin AC, Eley B, Heyderman R, Langford PR, Kern F, Ottenhoff THM, Hibberd ML, French N, Wright V, Dockrell HM, Coin L, Wilkinson R, Levin Met al., 2021, Identification of reduced host transcriptomic signatures for tuberculosis disease and digital PCR-based validation and quantification, Frontiers in Immunology, Vol: 12, ISSN: 1664-3224

Recently, host whole blood gene expression signatures have been identified for diagnosis of tuberculosis (TB). Absolute quantification of the concentrations of signature transcripts in blood have not been reported, but would facilitate diagnostic test development. To identify minimal transcript signatures, we applied a transcript selection procedure to microarray data from African adults comprising 536 patients with TB, other diseases (OD) and latent TB (LTBI), divided into training and test sets. Signatures were further investigated using reverse transcriptase (RT)—digital PCR (dPCR). A four-transcript signature (GBP6, TMCC1, PRDM1, and ARG1) measured using RT-dPCR distinguished TB patients from those with OD (area under the curve (AUC) 93.8% (CI95% 82.2–100%). A three-transcript signature (FCGR1A, ZNF296, and C1QB) differentiated TB from LTBI (AUC 97.3%, CI95%: 93.3–100%), regardless of HIV. These signatures have been validated across platforms and across samples offering strong, quantitative support for their use as diagnostic biomarkers for TB.

Journal article

Borghesi A, Trück J, Asgari S, Sancho-Shimizu V, Agyeman PKA, Bellos E, Giannoni E, Stocker M, Posfay-Barbe KM, Heininger U, Bernhard-Stirnemann S, Niederer-Loher A, Kahlert CR, Natalucci G, Relly C, Riedel T, Kuehni CE, Thorball CW, Chaturvedi N, Martinon-Torres F, Kuijpers TW, Coin L, Wright V, Herberg J, Levin M, Aebi C, Berger C, Fellay J, Schlapbach LJ, EUCLIDS consortium and the Swiss Paediatric Sepsis Studyet al., 2020, Whole-exome sequencing for the identification of rare variants in primary immunodeficiency genes in children with sepsis - a prospective population-based cohort study., Clinical Infectious Diseases, Vol: 71, Pages: e614-e623, ISSN: 1058-4838

BACKGROUND: The role of primary immunodeficiencies (PID) in susceptibility to sepsis remains unknown. It is unclear whether children with sepsis benefit from genetic investigations. We hypothesized that sepsis may represent the first manifestation of underlying PID. We applied whole-exome sequencing (WES) to a national cohort of children with sepsis to identify rare, predicted pathogenic variants in PID genes. METHODS: Multicenter population-based prospective study including previously healthy children ≥28 days and <17 years admitted with blood culture-proven sepsis. Using a stringent variant filtering procedure, analysis of WES data was restricted to rare, predicted pathogenic variants in 240 PID genes for which increased susceptibility to bacterial infection has been reported. RESULTS: 176 children presenting with 185 sepsis episodes underwent WES (median age 52 months, IQR 15.4-126.4). 41 unique predicted pathogenic PID variants (1 homozygous, 5 hemizygous, and 35 heterozygous) were found in 35/176 (20%) patients, including 3/176 (2%) patients carrying variants which were previously reported to lead to PID. The variants occurred in PID genes across all 8 PID categories as defined by the International Union of Immunological Societies. We did not observe a significant correlation between clinical or laboratory characteristics of patients and the presence or absence of PID variants. CONCLUSIONS: Applying WES to a population-based cohort of previously healthy children with bacterial sepsis detected Variants of Uncertain Significance in PID genes in one out of five children. Future studies need to investigate the functional relevance of these variants to determine whether variants in PID genes contribute to pediatric sepsis susceptibility.

Journal article

Channon-Wells S, O'Connor D, Valente-Pinto M, Kaforou M, Wright V, Coote D, Plested E, Thompson A, Robinson H, Levin M, Snape M, Pollard Aet al., 2020, RNA EXPRESSION RELIABLY DISTINGUISHES BACTERIAL INFECTION FROM TRANSIENT VACCINE REACTIONS IN YOUNG CHILDREN, The European Society For Paediatric Infectious Diseases Conference 2020

Background: Current diagnostics do not reliably differentiate serious bacterial infections from transient vaccine reactions in febrile young infants. We hypothesised that analysis of host RNA-expression could provide novel diagnostics for this specific common clinical setting. Methods: RNA-sequencing was used to compare whole-blood RNA expression in healthy postvaccination infants at 4-months of age with gene expression in young children under 5 years with definite bacterial infection from two distinct cohorts. Vaccinated infants received routine vaccinations according to the UK vaccination schedule, with half also receiving the 4CMenB vaccine. Batch correction was performed using the COCONUT R-package. Cases were split into training and test sets. To distinguish bacterial infection from vaccine reaction three minimal transcript signatures were selected using differential expression analysis and three separate machine learning tools on the training set. The performance of these signatures was evaluated on the test set. Results: On the training set of 86 children (42 infections, 44 post-vaccination) we identified three signatures with 3-, 6- and 11-transcripts. In the test set (52 children) all three signatures performed similarly, with AUCs all above 0.99 (Figure 1). The best performing signature (11-transcripts) distinguished bacterial infection from vaccine reaction with 97% sensitivity and 93% specificity in the test set, outperforming both CRP and WCC in the whole cohort (CRP: sensitivity 83%, specificity 90%). Conclusions: This preliminary work has identified novel transcript-sets that discriminate bacterial infection from vaccine reaction. Further testing is required to validate these findings. Our aim is to develop a quantitative PCR assay for clinical use, to help minimise admissions and antibiotic administrations in children suffering from a transient vaccine response. Clinical Trial Registration: Not applicable


Zandstra J, van de Geer A, Tanck MWT, Dimitriades DVS-B, Aarts CEM, Dietz SM, van Bruggen R, Schweintzger NA, Zenz W, Emonts M, Zavadska D, Pokorn M, Usuf E, Moll HA, Schlapbach LJ, Carrol ED, Paulus S, Tsolia M, Fink C, Yeung S, Shimizu C, Tremoulet A, Galassini R, Wright VJ, Martinon-Torres F, Herberg J, Burns J, Levin M, Kuijpers TWet al., 2020, Biomarkers for the discrimination of acute kawasaki disease from infections in childhood, Frontiers in Pediatrics, Vol: 8, ISSN: 2296-2360

Background: Kawasaki disease (KD) is a vasculitis of early childhood mimicking several infectious diseases. Differentiation between KD and infectious diseases is essential as KD's most important complication—the development of coronary artery aneurysms (CAA)—can be largely avoided by timely treatment with intravenous immunoglobulins (IVIG). Currently, KD diagnosis is only based on clinical criteria. The aim of this study was to evaluate whether routine C-reactive protein (CRP) and additional inflammatory parameters myeloid-related protein 8/14 (MRP8/14 or S100A8/9) and human neutrophil-derived elastase (HNE) could distinguish KD from infectious diseases.Methods and Results: The cross-sectional study included KD patients and children with proven infections as well as febrile controls. Patients were recruited between July 2006 and December 2018 in Europe and USA. MRP8/14, CRP, and HNE were assessed for their discriminatory ability by multiple logistic regression analysis with backward selection and receiver operator characteristic (ROC) curves. In the discovery cohort, the combination of MRP8/14+CRP discriminated KD patients (n = 48) from patients with infection (n = 105), with area under the ROC curve (AUC) of 0.88. The HNE values did not improve discrimination. The first validation cohort confirmed the predictive value of MRP8/14+CRP to discriminate acute KD patients (n = 26) from those with infections (n = 150), with an AUC of 0.78. The second validation cohort of acute KD patients (n = 25) and febrile controls (n = 50) showed an AUC of 0.72, which improved to 0.84 when HNE was included.Conclusion: When used in combination, the plasma markers MRP8/14, CRP, and HNE may assist in the discrimination of KD from both proven and suspected infection.

Journal article

Mashbat B, Bellos E, Hodeib S, Bidmos F, Thwaites RS, Lu Y, Wright VJ, Herberg JA, Klobassa DS, Zenz W, Hansel TT, Nadel S, Langford PR, Schlapbach LJ, Li M-S, Redinbo MR, Di YP, Levin M, Sancho-Shimizu Vet al., 2020, A rare mutation in SPLUNC1 underlies meningococcal disease affecting bacterial adherence and invasion, Clinical Infectious Diseases, Vol: 70, Pages: 2045-2053, ISSN: 1058-4838

BackgroundNeisseriameningitidis (Nm) is a nasopharyngeal commensal carried by healthy individuals. However, invasive infections occurs in a minority of individuals, with devastating consequences. There is evidence that common polymorphisms are associated with invasive meningococcal disease (IMD) but the contribution of rare variants other than complement has not been determined.MethodsWe identified familial cases of IMD in the UK meningococcal disease study and the European Union Life-threatening Infectious Disease Study. Candidate genetic variants were identified by whole exome sequencing of two patients with familial IMD. Candidate variants were further validated by in vitro assays.ResultsExomes of two siblings with IMD identified a novel heterozygous missense mutation in BPIFA1/SPLUNC1. Sequencing of 186 other non-familial cases identified another unrelated IMD patient with the same mutation. SPLUNC1 is an innate immune defence protein expressed in the nasopharyngeal epithelia, however, its role in invasive infections is unknown. In vitro assays demonstrated that recombinant SPLUNC1 inhibits biofilm formation by Nm, and impedes Nm adhesion and invasion of human airway cells. The dominant negative mutant rSPLUNC1 (p.G22E) showed reduced anti-biofilm activity, increased meningococcal adhesion and invasion of cells compared with wild type SPLUNC1.ConclusionsA mutation in SPLUNC1 affecting mucosal attachment, biofilm formation and invasion of mucosal epithelial cells is a new genetic cause of meningococcal disease.

Journal article

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