The viral and atypical bacterial causes of acute respiratory infection in children in Recife, Brazil

Introduction: Acute respiratory infections (ARI) are the commonest cause of mortality in childre

Diagnostic accuracy of blood tests of inflammation in paediatric appendicitis: a systematic review and meta-analysis

Objective: Possible childhood appendicitis is a common emergency presentation. The exact value of blood tests is debated. This study sought to determine the diagnostic accuracy of four blood tests (white cell count (WCC), neutrophil(count or percentage), C reactive protein (CRP) and/or procalcitonin) for childhood appendicitis. Design: A systematic review and diagnostic meta-analysis. Data sources included MEDLINE, EMBASE, Central, Web of Science searched from inception-March 2022 with reference searching and authors contacted for missing/unclear data. Eligibility criteria was studies reporting the diagnostic accuracy of the four blood tests compared to the reference standard (histology or follow-up). Risk of bias was assessed (QUADAS-2), pooled sensitivity and specificity were generated for each test and commonly presented cut-offs. To provide insight into clinical impact, we present strategies using a hypothetical cohort. Results: 67 studies were included (34 839 children, 13 342 with appendicitis), all in the hospital setting. The most sensitive tests were WCC (≥10 000 cells/µL, 53 studies sensitivity 0.85 (95% CI 0.80 to 0.89)) and absolute neutrophil count (ANC) (≥7500 cells/µL, five studies sensitivity 0.90 (95% CI 0.85 to 0.94)). Combination of WCC or CRP increased sensitivity further(≥10 000 cells/µL or ≥10 mg/L, individual patient data (IPD) of 6 studies, 0.97 (95% CI 0.93 to 0.99)). Applying results to a hypothetical cohort(1000 children with appendicitis symptoms, of whom 400 have appendicitis) 60 and 40 children would be wrongly discharged based solely on WCC and ANC, respectively, 12 with combination of WCC or CRP. The most specific tests were CRP alone (≥50 mg/L, 38 studies, specificity 0.87 (95% CI 0.80 to 0.91)) or combined with WCC (≥10 000 cells/µL and ≥50 mg/L, IPD of six studies, 0.93 (95% CI 0.91 to 0.95)). Conclusions: The best performing single blood tests for ruling-out paediatric appendicitis are WCC or ANC; with accuracy improved combining WCC and CRP. These tests could be used at the point of care in combination with clinical prediction rules. We provide insight into the best cut-offs for clinical application. PROSPERO registration number: CRD4201708003

Unbiased molecular definition of epithelial barrier formation and defects driving inflammatory bowel disease

The intestinal epithelial barrier is one of the body’s largest mucosal surfaces. The cells involved reflect the numerous functions the epithelium must perform. The barrier requires time critical co-ordination with other intestinal cell compartments in utero for normal development. In maturity, dysregulation of the barrier or cross-talk can lead to disease such as inflammatory bowel disease (IBD). Despite the importance of the intestinal epithelium in development and health, characterisation of the origins of dysregulation are lacking. Questions also remain about the full spectrum of epithelial cell diversity and its mutualistic relationship with other intestinal compartments. This project characterises the development of the epithelial and mesenchymal cross talk in utero, in health and in IBD at high resolution using single cell RNA-sequencing (scRNAseq). Studying intestinal epithelial diversity in health and disease, isolating epithelial cells from IBD and controls and mapping over 11,000 cells from health and UC inflammation, mapped cell diversity through the maturation of epithelium. This identified a hitherto unappreciated BEST4/OTOP2 cell that sensed pH and was dysregulated in inflammation and cancer. Furthermore, a second project mapped human intestinal development from 8-22 post conceptual weeks. This charted 101 cell types across developmental time and through spatial transcriptomics (ST) could map these to tissue revealing origins of diverse cellular compartments along with fibroblast and intestinal stem cells across space and time. These results provide a platform that maps the human intestinal epithelium and previously unappreciated resolution and from which the normal developmental cues can be established and allow identification of the drivers of dysregulation in IBD

Unbiased molecular definition of epithelial barrier formation and defects driving inflammatory bowel disease

The intestinal epithelial barrier is one of the body’s largest mucosal surfaces. The cells involved reflect the numerous functions the epithelium must perform. The barrier requires time critical co-ordination with other intestinal cell compartments in utero for normal development. In maturity, dysregulation of the barrier or cross-talk can lead to disease such as inflammatory bowel disease (IBD). Despite the importance of the intestinal epithelium in development and health, characterisation of the origins of dysregulation are lacking. Questions also remain about the full spectrum of epithelial cell diversity and its mutualistic relationship with other intestinal compartments. This project characterises the development of the epithelial and mesenchymal cross talk in utero, in health and in IBD at high resolution using single cell RNA-sequencing (scRNAseq). Studying intestinal epithelial diversity in health and disease, isolating epithelial cells from IBD and controls and mapping over 11,000 cells from health and UC inflammation, mapped cell diversity through the maturation of epithelium. This identified a hitherto unappreciated BEST4/OTOP2 cell that sensed pH and was dysregulated in inflammation and cancer. Furthermore, a second project mapped human intestinal development from 8-22 post conceptual weeks. This charted 101 cell types across developmental time and through spatial transcriptomics (ST) could map these to tissue revealing origins of diverse cellular compartments along with fibroblast and intestinal stem cells across space and time. These results provide a platform that maps the human intestinal epithelium and previously unappreciated resolution and from which the normal developmental cues can be established and allow identification of the drivers of dysregulation in IBD.</p

Spatiotemporal Analysis of Human Intestinal Development at Single Cell Resolution: Supplementary Data

Supplementary data for the study "Spatiotemporal Analysis of Human Intestinal Development at Single Cell Resolution" which utilises single cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST) to characterise the origins of human intestinal development between 8 and 22 post conceptual weeks. This supplementary data contains analysed sequencing data that was too large for main publications and details data that was used for comparisons of: cell type marker genes; ST varying genes; Transcription factor (TF) module nodes; Human Phenotype Ontology (HPO) disease comparisons across time and cell clusters; cell cluster comparisons and Gene Ontology Analysis. Specific content: A) An excel file with tabs of supplementary data (overview in first tab) including: 1 Sample overview 2 Endothelial Markers 3 Epithelial Markers 4 Fibroblast Markers 5 Immune Markers 6 Muscle Markers 7 Myofibroblast & Mesothelium markers 8 Neural markers 9 Pericyte Markers 10 Secretory epithelium markers 11 Compartment Markers 12 ST Distance varying genes 13 TF Tree Node Markers 14 TF Location Time Compartment 15 HPO Genes Time Varying 16 HPO Genes Cluster Specific 17 S2 Colon vs TI 18 S2 Time Course 19 Stem Cells TI vs Colon 20 Stem cells vs Stem progenitor 21 Stromal 4 differences 22 CITE-Seq Antibody Sequences 23 Neural GO BP 24 Morphogen modules 25 GO Terms ST dist genes B)Images of ST segments (n=8 tissue segments with low resolution and high resolution images of each

Microbiome, pattern recognition receptor function in health and inflammation

The innate immune system plays an important role in shaping the microbiota into configurations that are tolerated and beneficial to the host, thereby playing a crucial role in human health. Innate immunity is based on the fundamental principle that Pattern Recognition Receptors (PRRs) recognise pathogen associated molecular patterns as non-self-entities and trigger intracellular signalling pathways that lead to the induction of numerous cytokines and chemokines that help maintain host resistance to infections. Dysregulation of this interaction has been identified as the core defect that leads to chronic intestinal inflammation allowing certain microbiota to be harmful to host health. This dysbiosis of the microbiome is found associated with numerous chronic diseases. A logical explanation would be that genetic defects in the recognition and response pathways that the host uses to identify these microbial pathogens could lead to altered microbial colonisation or mis-recognition of normal bacteria leading to diseases. The interaction between pattern recognition receptors, microbial traits and human health with respect to the gut are now rapidly resolved and will be the subject of this review