Host transcriptional signatures as predictive markers of infection in children

Human Conjunctival Transcriptome in Acanthamoeba Keratitis: An Exploratory Study

PURPOSE

The purpose of this study was to identify conjunctival transcriptome differences in patients with Acanthamoeba keratitis compared with keratitis with no known associated pathogen.

METHODS

The host conjunctival transcriptome of 9 patients with Acanthamoeba keratitis (AK) is compared with the host conjunctival transcriptome of 13 patients with pathogen-free keratitis. Culture and/or confocal confirmed Acanthamoeba in 8 of 9 participants with AK who underwent metagenomic RNA sequencing as the likely pathogen. Cultures were negative in all 13 cases where metagenomic RNA sequencing did not identify a pathogen.

RESULTS

Transcriptome analysis identified 36 genes differently expressed between patients with AK and patients with presumed sterile, or pathogen-free, keratitis. Gene enrichment analysis revealed that some of these genes participate in several biologic pathways important for cellular signaling, ion transport and homeostasis, glucose transport, and mitochondrial metabolism. Notable relatively differentially expressed genes with potential relevance to Acanthamoeba infection included CPS1 , SLC35B4 , STEAP2 , ATP2B2 , NMNAT3 , and AKAP12 .

CONCLUSIONS

This research suggests that the local transcriptome in Acanthamoeba keratitis may be sufficiently robust to be detected in the conjunctiva and that corneas infected with Acanthamoeba may be distinguished from the inflamed cornea where no pathogen was identified. Given the low sensitivity for corneal cultures, identification of differentially expressed genes may serve as a suggestive transcriptional signature allowing for a complementary diagnostic technique to identify this blinding parasite. Knowledge of differentially expressed genes may also direct investigation of disease pathophysiology and suggest novel pathways for therapeutic targets.

Community-Acquired Pneumonia in Children

ABSTRACT

Community-acquired pneumonia (CAP) is the most common cause of childhood mortality globally. In the United States, CAP is a leading cause of pediatric hospitalization and antibiotic use and is associated with substantial morbidity. There has been a dramatic shift in microbiological etiologies for CAP in children over time as pneumococcal pneumonia has become less common and viral etiologies have become predominant. There is no commonly agreed on approach to the diagnosis of CAP in children. When indicated, antimicrobial treatment should consist of narrow-spectrum antibiotics. In this article, we will describe the current understanding of the microbiological etiologies, clinical presentation, diagnostic approach, risk factors, treatment, and future directions in the diagnosis and management of pediatric CAP.

Leveraging transcriptomics for precision diagnosis: Lessons learned from cancer and sepsis

Diagnostics require precision and predictive ability to be clinically useful. Integration of multi-omic with clinical data is crucial to our understanding of disease pathogenesis and diagnosis. However, interpretation of overwhelming amounts of information at the individual level requires sophisticated computational tools for extraction of clinically meaningful outputs. Moreover, evolution of technical and analytical methods often outpaces standardisation strategies. RNA is the most dynamic component of all -omics technologies carrying an abundance of regulatory information that is least harnessed for use in clinical diagnostics. Gene expression-based tests capture genetic and non-genetic heterogeneity and have been implemented in certain diseases. For example patients with early breast cancer are spared toxic unnecessary treatments with scores based on the expression of a set of genes (e.g., Oncotype DX). The ability of transcriptomics to portray the transcriptional status at a moment in time has also been used in diagnosis of dynamic diseases such as sepsis. Gene expression profiles identify endotypes in sepsis patients with prognostic value and a potential to discriminate between viral and bacterial infection. The application of transcriptomics for patient stratification in clinical environments and clinical trials thus holds promise. In this review, we discuss the current clinical application in the fields of cancer and infection. We use these paradigms to highlight the impediments in identifying useful diagnostic and prognostic biomarkers and propose approaches to overcome them and aid efforts towards clinical implementation.

Metatranscriptome Reveals Specific Immune and Microbial Signatures of Respiratory Syncytial Virus Infection in Children

Respiratory syncytial virus (RSV) is the most frequently detected respiratory virus in children with acute lower respiratory tract infection. Previous transcriptome studies have focused on systemic transcriptional profiles in blood and have not compared the expression of multiple viral transcriptomes. Here, we sought to compare transcriptome responses to infection with four common respiratory viruses for children (respiratory syncytial virus, adenovirus, influenza virus, and human metapneumovirus) in respiratory samples. Transcriptomic analysis showed that cilium organization and assembly were common pathways related to viral infection. Compared with other virus infections, collagen generation pathways were distinctively enriched in RSV infection. We identified two interferon-stimulated genes (ISGs), CXCL11 and IDO1, which were upregulated to a greater extent in the RSV group. In addition, a deconvolution algorithm was used to analyze the composition of immune cells in respiratory tract samples. The proportions of dendritic cells and neutrophils in the RSV group were significantly higher than those in the other virus groups. The RSV group exhibited a higher richness of Streptococcus than the other virus groups. The concordant and discordant responses mapped out here provide a window to explore the pathophysiology of the host response to RSV. Last, according to host-microbe network interference, RSV may disrupt respiratory microbial composition by changing the immune microenvironment. IMPORTANCE In the present study, we demonstrated the comparative results of host responses to infection between RSV and other three common respiratory viruses for children. The comparative transcriptomics study of respiratory samples sheds light on the significant roles that ciliary organization and assembly, extracellular matrix changes, and microbial interactions play in the pathogenesis of RSV infection. Additionally, it was demonstrated that the recruitment of neutrophils and dendritic cells (DCs) in the respiratory tract is more substantial in RSV infection than in other viral infections. Finally, we discovered that RSV infection dramatically increased the expression of two ISGs (CXCL11 and IDO1) and the abundance of Streptococcus.

Availability and use of rapid diagnostic tests for the management of acute childhood infections in Europe: A cross-sectional survey of paediatricians

BACKGROUND

Point-of-care-tests (POCTs) have been advocated to optimise care in patients with infections but their actual use varies. This study aimed to estimate the variability in the adoption of current POCTs by paediatricians across Europe, and to explore the determinants of variability.

METHODS AND FINDINGS

A cross-sectional survey was conducted of hospital and primary care paediatricians, recruited through professional networks. Questions focused on the availability and use of currently available POCTs. Data were analysed descriptively and using Median Odds Ratio (MOR) to measure variation between countries. Multilevel regression modelling using changes in the area under the receiver operating characteristic curve of models were used to assess the contribution of individual or workplace versus country level factors, to the observed variation. The commonest POCT was urine dipsticks (UD) which were available to >80% of primary care and hospital paediatricians in 68% (13/19) and 79% (23/29) countries, respectively. Availability of all POCTs varied between countries. In primary care, the country (MOR) varied from 1.61 (95%CI: 1.04-2.58) for lactate to 7.28 (95%CI: 3.04-24.35) for UD. In hospitals, the country MOR varied from 1.37 (95%CI:1.04-1.80) for lactate to 11.93 (95%CI:3.35-72.23) for UD. Most paediatricians in primary care (69%, 795/1154) and hospital (81%, 962/1188) would use a diagnostic test in the case scenario of an infant with undifferentiated fever. Multilevel regression modelling showed that the country of work was more important in predicting both the availability and use of POCTs than individual or workplace characteristics.

CONCLUSION

There is substantial variability in the adoption of POCTs for the management of acute infections in children across Europe. To inform future implementation of both existing and innovative tests, further research is needed to understand what drives the variation between countries, the needs of frontline clinicians, and the role of diagnostic tests in the management of acute childhood infections.

Guideline adherence in febrile children below 3 months visiting European Emergency Departments: an observational multicenter study

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 guidelines and their usage and adherence.

WHAT IS NEW

• Full guideline adherence is limited, whereas partial guideline adherence is moderate in febrile children below 3 months across Europe. • Guideline revision including new biomarkers is needed to improve management in young febrile children.