Integration and validation of host transcript signatures, including a novel 3-transcript tuberculosis signature, to enable one-step multiclass diagnosis of childhood febrile disease.

BACKGROUND: Whole blood host transcript signatures show great potential for diagnosis of infectious and inflammatory illness, with most published signatures performing binary classification tasks. Barriers to clinical implementation include validation studies, and development of strategies that enable simultaneous, multiclass diagnosis of febrile illness based on gene expression. METHODS: We validated five distinct diagnostic signatures for paediatric infectious diseases in parallel using a single NanoString nCounter® experiment. We included a novel 3-transcript signature for childhood tuberculosis, and four published signatures which differentiate bacterial infection, viral infection, or Kawasaki disease from other febrile illnesses. Signature performance was assessed using receiver operating characteristic curve statistics. We also explored conceptual frameworks for multiclass diagnostic signatures, including additional transcripts found to be significantly differentially expressed in previous studies. Relaxed, regularised logistic regression models were used to derive two novel multiclass signatures: a mixed One-vs-All model (MOVA), running multiple binomial models in parallel, and a full-multiclass model. In-sample performance of these models was compared using radar-plots and confusion matrix statistics. RESULTS: Samples from 91 children were included in the study: 23 bacterial infections (DB), 20 viral infections (DV), 14 Kawasaki disease (KD), 18 tuberculosis disease (TB), and 16 healthy controls. The five signatures tested demonstrated cross-platform performance similar to their primary discovery-validation cohorts. The signatures could differentiate: KD from other diseases with area under ROC curve (AUC) of 0.897 [95% confidence interval: 0.822-0.972]; DB from DV with AUC of 0.825 [0.691-0.959] (signature-1) and 0.867 [0.753-0.982] (signature-2); TB from other diseases with AUC of 0.882 [0.787-0.977] (novel signature); TB from healthy children with AUC of 0.910 [0.808-1.000]. Application of signatures outside of their designed context reduced performance. In-sample error rates for the multiclass models were 13.3% for the MOVA model and 0.0% for the full-multiclass model. The MOVA model misclassified DB cases most frequently (18.7%) and TB cases least (2.7%). CONCLUSIONS: Our study demonstrates the feasibility of NanoString technology for cross-platform validation of multiple transcriptomic signatures in parallel. This external cohort validated performance of all five signatures, including a novel sparse TB signature. Two exploratory multi-class models showed high potential accuracy across four distinct diagnostic groups.

National point-prevalence survey of healthcare-associated infections and antimicrobial use: UK-PAS/UKHSA joint call to action for all paediatric services.

The negative impact of high antimicrobial use (AMU), antimicrobial resistance and healthcare-associated infections (HCAIs) on children is concerning. However, a lack of available paediatric data makes it challenging to design and implement interventions that would improve health outcomes in this population, and impedes efforts to secure additional resources. The upcoming 2023 national point-prevalence survey of HCAIs and AMU in hospitals, led by the UK Health Security Agency, is an opportunity to collect valuable information, which will enable healthcare providers and policy makers to optimize antimicrobial stewardship and infection prevention practices in all populations, including children. These data will facilitate benchmarking and sharing of best practice, internally, nationally and internationally. This is a joint call to action asking all healthcare professionals-particularly in paediatrics-to nominate a lead for their institution and participate in this survey, to ensure appropriate paediatric representation, and help protect children from these growing threats.

Gene expression profiling reveals insights into infant immunological and febrile responses to group B meningococcal vaccine.

Neisseria meningitidis is a major cause of meningitis and septicaemia. A MenB vaccine (4CMenB) was licensed by the European Medicines Agency in January 2013. Here we describe the blood transcriptome and proteome following infant immunisations with or without concomitant 4CMenB, to gain insight into the molecular mechanisms underlying post-vaccination reactogenicity and immunogenicity. Infants were randomised to receive control immunisations (PCV13 and DTaP-IPV-Hib) with or without 4CMenB at 2 and 4 months of age. Blood gene expression and plasma proteins were measured prior to, then 4 h, 24 h, 3 days or 7 days post-vaccination. 4CMenB vaccination was associated with increased expression of ENTPD7 and increased concentrations of 4 plasma proteins: CRP, G-CSF, IL-1RA and IL-6. Post-vaccination fever was associated with increased expression of SELL, involved in neutrophil recruitment. A murine model dissecting the vaccine components found the concomitant regimen to be associated with increased gene perturbation compared with 4CMenB vaccine alone with enhancement of pathways such as interleukin-3, -5 and GM-CSF signalling. Finally, we present transcriptomic profiles predictive of immunological and febrile responses following 4CMenB vaccine.

The use of routinely collected electronic prescribing data to benchmark intravenous antibiotic use between two tertiary paediatric haematology-oncology inpatient units: a retrospective study.

Background: High-quality systematic data on antimicrobial use in UK inpatient paediatric haematology-oncology services are lacking, despite this population being at high risk from antimicrobial exposure and resistance. Objectives: We conducted a retrospective study to demonstrate how routinely collected electronic prescribing data can address this issue. Patients and methods: This retrospective study describes and compares IV antibiotic consumption between two UK paediatric haematology-oncology inpatient units, between 2018 and 2022. Both sites provide similar services and receive proactive antimicrobial stewardship input. Data were extracted from each site's antimicrobial surveillance system, which report monthly days of therapy (DOT) per 100 patient-days (PD). Consumption was reported for specific and total antibiotics. Trends were modelled using linear regression and autoregressive moving average models. Results: Total IV antibiotic consumption at each site was similar. Median monthly DOT per 100 PD were 25.9 (IQR: 22.1-34.0) and 29.4 (24.2-34.9). Total antibiotic use declined at both sites, with estimated annual yearly reductions of 3.52 DOT per 100 PD (95% CI: 0.46-6.59) and 2.57 (1.30-3.85). Absolute consumption was similar for carbapenems, piperacillin/tazobactam and aminoglycosides, whilst ceftriaxone and teicoplanin demonstrated approximately 3-fold relative differences in median monthly consumption. Meropenem, piperacillin/tazobactam, teicoplanin, vancomycin and gentamicin all demonstrated statistically significant reductions in use over time at either one or both sites, although this was most marked for piperacillin/tazobactam and vancomycin. Conclusions: Routinely collected electronic prescribing data can aid benchmarking of antibiotic use in paediatric haematology-oncology inpatients, highlighting areas to target stewardship strategies, and evaluating their impact. This approach should be rolled out nationally, and to other high-risk groups.

Trends in Enterobacterales Bloodstream Infections in Children.

OBJECTIVES: Enterobacterales bloodstream infections (E-BSI) cause a significant burden of disease in children and are associated with antimicrobial resistance. We assessed temporal changes in the population-based incidence of E-BSI in children in Queensland, Australia. METHODS: We conducted a cohort study of incidents of E-BSI occurring in children in Queensland between 2000 and 2019, with a total population of 19.7 million child years. Infections were linked to clinical outcomes in hospital admissions and vital statistics databases. We estimated age- and sex-standardized E-BSI incidence rates over time. Secondary outcomes included the proportion of extended-spectrum ß-lactamase phenotypes per year, hospital length of stay, and mortality. RESULTS: We identified 1980 E-BSI in 1795 children. The overall age- and sex-standardized incidence rate was 9.9 cases per 100 000 child years, which increased from 7.3 to 12.9 over the period studied, an increase of 3.9% (95% confidence interval: 3.1-4.7) per year. There were 3.6 cases of E. coli bloodstream infection per 100 000 child years, increasing annually by 4.7% (3.5-5.9). The Salmonella sp. bloodstream infection incidence was 3.0 cases per 100 000 child years, which increased from 2013 by 13.7% (3.8-24.3) per year. The proportion of extended-spectrum ß-lactamase E. coli increased over time. Mortality and length of stay were higher among children with comorbidities than those without (4.0% vs 0.3%, and 14 vs 4 days, respectively, P < .001). CONCLUSIONS: The age- and sex-standardized incidence of E-BSI almost doubled in Queensland children over 2 decades, driven by increases in Salmonella sp. and E. coli. Increasing resistance of E. coli should prompt the inclusion of children in antimicrobial clinical trials.

Immunoglobulin, glucocorticoid, or combination therapy for multisystem inflammatory syndrome in children: a propensity-weighted cohort study.

Background: Multisystem inflammatory syndrome in children (MIS-C), a hyperinflammatory condition associated with SARS-CoV-2 infection, has emerged as a serious illness in children worldwide. Immunoglobulin or glucocorticoids, or both, are currently recommended treatments. Methods: The Best Available Treatment Study evaluated immunomodulatory treatments for MIS-C in an international observational cohort. Analysis of the first 614 patients was previously reported. In this propensity-weighted cohort study, clinical and outcome data from children with suspected or proven MIS-C were collected onto a web-based Research Electronic Data Capture database. After excluding neonates and incomplete or duplicate records, inverse probability weighting was used to compare primary treatments with intravenous immunoglobulin, intravenous immunoglobulin plus glucocorticoids, or glucocorticoids alone, using intravenous immunoglobulin as the reference treatment. Primary outcomes were a composite of inotropic or ventilator support from the second day after treatment initiation, or death, and time to improvement on an ordinal clinical severity scale. Secondary outcomes included treatment escalation, clinical deterioration, fever, and coronary artery aneurysm occurrence and resolution. This study is registered with the ISRCTN registry, ISRCTN69546370. Findings: We enrolled 2101 children (aged 0 months to 19 years) with clinically diagnosed MIS-C from 39 countries between June 14, 2020, and April 25, 2022, and, following exclusions, 2009 patients were included for analysis (median age 8·0 years [IQR 4·2-11·4], 1191 [59·3%] male and 818 [40·7%] female, and 825 [41·1%] White). 680 (33·8%) patients received primary treatment with intravenous immunoglobulin, 698 (34·7%) with intravenous immunoglobulin plus glucocorticoids, 487 (24·2%) with glucocorticoids alone; 59 (2·9%) patients received other combinations, including biologicals, and 85 (4·2%) patients received no immunomodulators. There were no significant differences between treatments for primary outcomes for the 1586 patients with complete baseline and outcome data that were considered for primary analysis. Adjusted odds ratios for ventilation, inotropic support, or death were 1·09 (95% CI 0·75-1·58; corrected p value=1·00) for intravenous immunoglobulin plus glucocorticoids and 0·93 (0·58-1·47; corrected p value=1·00) for glucocorticoids alone, versus intravenous immunoglobulin alone. Adjusted average hazard ratios for time to improvement were 1·04 (95% CI 0·91-1·20; corrected p value=1·00) for intravenous immunoglobulin plus glucocorticoids, and 0·84 (0·70-1·00; corrected p value=0·22) for glucocorticoids alone, versus intravenous immunoglobulin alone. Treatment escalation was less frequent for intravenous immunoglobulin plus glucocorticoids (OR 0·15 [95% CI 0·11-0·20]; p<0·0001) and glucocorticoids alone (0·68 [0·50-0·93]; p=0·014) versus intravenous immunoglobulin alone. Persistent fever (from day 2 onward) was less common with intravenous immunoglobulin plus glucocorticoids compared with either intravenous immunoglobulin alone (OR 0·50 [95% CI 0·38-0·67]; p<0·0001) or glucocorticoids alone (0·63 [0·45-0·88]; p=0·0058). Coronary artery aneurysm occurrence and resolution did not differ significantly between treatment groups. Interpretation: Recovery rates, including occurrence and resolution of coronary artery aneurysms, were similar for primary treatment with intravenous immunoglobulin when compared to glucocorticoids or intravenous immunoglobulin plus glucocorticoids. Initial treatment with glucocorticoids appears to be a safe alternative to immunoglobulin or combined therapy, and might be advantageous in view of the cost and limited availability of intravenous immunoglobulin in many countries. Funding: Imperial College London, the European Union's Horizon 2020, Wellcome Trust, the Medical Research Foundation, UK National Institute for Health and Care Research, and National Institutes of Health.

Differentiating vaccine reactions from invasive bacterial infections in young infants presenting to the emergency department in the 4CMenB era: a retrospective observational comparison.

BACKGROUND: Differentiating infants with adverse events following immunisation (AEFIs) or invasive bacterial infection (IBI) is a significant clinical challenge. Young infants post vaccination are therefore often admitted to the hospital for parenteral antibiotics to avoid missing rare cases of IBI. METHODS: During a service evaluation project, we conducted a single-centre retrospective observational study of infants with IBI, urinary tract infection (UTI) or AEFI from two previously published cohorts. All patients presented to hospital in Oxfordshire, UK, between 2011 and 2018, spanning the introduction of the capsular group-B meningococcal vaccine (4CMenB) into routine immunisation schedules. Data collection from paper and electronic notes were unblinded. Clinical features, including National Institute for Health and Care Excellence (NICE) 'traffic light' risk of severe illness and laboratory tests performed on presentation, were described, and comparisons made using regression models, adjusting for age and sex. We also compared biochemical results on presentation to those of well infants post vaccination, with and without 4CMenB regimens. RESULTS: The study included 232 infants: 40 with IBI, 97 with probable AEFI, 24 with possible AEFI, 27 with UTI and 44 post vaccination 'well' infants. C-reactive protein (CRP) was the only discriminatory blood marker, with CRP values above 83 mg/L only observed in infants with IBI or UTI. NICE risk stratification was significantly different between groups but still missed cases of IBI, and classification as intermediate risk was non-differential. Fever was more common in probable AEFI cases, while seizures and rashes were equally frequent. Diarrhoea and clinician-reported irritability or rigours were all more common in IBI. CONCLUSIONS: Clinical features on presentation may aid risk stratification but cannot reliably differentiate IBI from AEFI in infants presenting to the emergency department. Blood results are generally unhelpful due to post vaccination inflammatory responses, particularly in children receiving 4CMenB vaccination. Improved biomarkers and clinical prediction tools are required to aid management in febrile infants post vaccination.

Discovery and validation of a three-gene signature to distinguish COVID-19 and other viral infections in emergency infectious disease presentations: a case-control and observational cohort study.

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 aimed to derive and validate a blood transcriptional signature to detect viral infections, including COVID-19, among adults with suspected infection who presented to the emergency department. METHODS: Individuals (aged ≥18 years) presenting with suspected infection to an emergency department at a major teaching hospital in the UK were prospectively recruited as part of the Bioresource in Adult Infectious Diseases (BioAID) discovery cohort. Whole-blood RNA sequencing was done on samples from participants with subsequently confirmed viral, bacterial, or no infection diagnoses. Differentially expressed host genes that met additional filtering criteria were subjected to feature selection to derive the most parsimonious discriminating signature. We validated the signature via RT-qPCR in a prospective validation cohort of participants who presented to an emergency department with undifferentiated fever, and a second case-control validation cohort of emergency department participants with PCR-positive COVID-19 or bacterial infection. We assessed signature performance by calculating the area under receiver operating characteristic curves (AUROCs), sensitivities, and specificities. FINDINGS: A three-gene transcript signature, comprising HERC6, IGF1R, and NAGK, was derived from the discovery cohort of 56 participants with bacterial infections and 27 with viral infections. In the validation cohort of 200 participants, the signature differentiated bacterial from viral infections with an AUROC of 0·976 (95% CI 0·919-1·000), sensitivity of 97·3% (85·8-99·9), and specificity of 100% (63·1-100). The AUROC for C-reactive protein (CRP) was 0·833 (0·694-0·944) and for leukocyte count was 0·938 (0·840-0·986). The signature achieved higher net benefit in decision curve analysis than either CRP or leukocyte count for discriminating viral infections from all other infections. In the second validation analysis, which included SARS-CoV-2-positive participants, the signature discriminated 35 bacterial infections from 34 SARS-CoV-2-positive COVID-19 infections with AUROC of 0·953 (0·893-0·992), sensitivity 88·6%, and specificity of 94·1%. INTERPRETATION: This novel three-gene signature discriminates viral infections, including COVID-19, from other emergency infection presentations in adults, outperforming both leukocyte count and CRP, thus potentially providing substantial clinical utility in managing acute presentations with infection. FUNDING: National Institute for Health Research, Medical Research Council, Wellcome Trust, and EU-FP7.

COVID-19 pneumonia and the masquerades.

During the COVID-19 pandemic, chest CT is frequently used to help with the diagnosis. The classic CT patterns of COVID-19 pneumonia are well-published and recognised among radiologists. However, when there are pre-existing conditions particularly in the elderly population that could mask or result in similar patterns of disease, then the diagnosis is more difficult. This imaging essay highlights the commonly encountered situations including patients with heart failure, other possible infections particularly in the immunodeficient, and when there is trauma to the thorax. We illustrate imaging clues available to the radiologist to either make the diagnosis or at least reduce the differential diagnosis.