Doxey Andrew C, Abu Mazen Nooran, Homm Max, Chu Vivian, Hunjan Manjot, Lobb Briallen, Lee Sojin, Kurs-Lasky Marcia, Williams John V, MacDonald William, Johnson Monika, Hirota Jeremy A, Shaikh Nader
Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
Genome Med. 2025 Mar 17;17(1):22. doi: 10.1186/s13073-025-01447-3.
Acute sinusitis (AS) is a frequent cause of antibiotic prescriptions in children. Distinguishing bacterial AS from common viral upper respiratory infections (URIs) is crucial to prevent unnecessary antibiotic use but is challenging with current diagnostic methods. Despite its speed and cost, untargeted RNA sequencing of clinical samples from children with suspected AS has the potential to overcome several limitations of other methods. In addition, RNA-seq may reveal novel host-response biomarkers for development of future diagnostic assays that distinguish bacterial from viral infections. There are however no available RNA-seq datasets of pediatric AS that provide a comprehensive view of both pathogen etiology and host immune response.
Here, we performed untargeted RNA-seq (metatranscriptomics) of nasopharyngeal samples from 221 children with AS and performed a comprehensive analysis of pathogen etiology and the impact of bacterial and viral infections on host immune responses. Accuracy of RNA-seq-based pathogen detection was evaluated by comparison with culture tests for three common bacterial pathogens and qRT-PCR tests for 12 respiratory viruses. Host gene expression patterns were explored to identify potential host responses that distinguish bacterial from viral infections.
RNA-seq-based pathogen detection showed high concordance with culture or qRT-PCR, showing 87%/81% sensitivity (sens) / specificity (spec) for detecting three AS-associated bacterial pathogens, and 86%/92% (sens/spec) for detecting 12 URI-associated viruses, respectively. RNA-seq also detected an additional 22 pathogens not tested for clinically and identified plausible pathogens in 11/19 (58%) of cases where no organism was detected by culture or qRT-PCR. We reconstructed genomes of 196 viruses across the samples including novel strains of coronaviruses, respiratory syncytial virus, and enterovirus D68, which provide useful genomic data for ongoing pathogen surveillance programs. By analyzing host gene expression, we identified host-response signatures that differentiate bacterial and viral infections, revealing hundreds of candidate gene biomarkers for future diagnostic assays.
Our study provides a one-of-kind dataset that profiles the interplay between pathogen infection and host responses in pediatric AS and URI. It reveals bacterial and viral-specific host responses that could enable new diagnostic approaches and demonstrates the potential of untargeted RNA-seq in diagnostic analysis of AS and URI.
急性鼻窦炎（AS）是儿童抗生素处方的常见原因。区分细菌性AS与常见的病毒性上呼吸道感染（URI）对于防止不必要的抗生素使用至关重要，但目前的诊断方法具有挑战性。尽管存在速度和成本问题，但对疑似AS儿童的临床样本进行非靶向RNA测序有可能克服其他方法的几个局限性。此外，RNA测序可能会揭示新的宿主反应生物标志物，用于开发未来区分细菌感染和病毒感染的诊断检测方法。然而，目前尚无可用的儿科AS的RNA测序数据集能全面呈现病原体病因和宿主免疫反应。
在此，我们对221例AS患儿的鼻咽样本进行了非靶向RNA测序（宏转录组学），并对病原体病因以及细菌和病毒感染对宿主免疫反应的影响进行了全面分析。通过与三种常见细菌病原体的培养试验以及12种呼吸道病毒的qRT-PCR试验进行比较，评估了基于RNA测序的病原体检测准确性。探索宿主基因表达模式，以识别区分细菌感染和病毒感染的潜在宿主反应。
基于RNA测序的病原体检测与培养或qRT-PCR显示出高度一致性，检测三种与AS相关的细菌病原体的灵敏度/特异性分别为87%/81%，检测12种与URI相关病毒的灵敏度/特异性分别为86%/92%。RNA测序还检测到另外22种未进行临床检测的病原体，并在11/19（58%）的培养或qRT-PCR未检测到病原体的病例中鉴定出可能的病原体。我们在样本中重建了196种病毒的基因组，包括新型冠状病毒、呼吸道合胞病毒和肠道病毒D68毒株，为正在进行的病原体监测计划提供了有用的基因组数据。通过分析宿主基因表达，我们确定了区分细菌感染和病毒感染的宿主反应特征，揭示了数百种未来诊断检测的候选基因生物标志物。
我们的研究提供了一个独一无二的数据集，描绘了儿科AS和URI中病原体感染与宿主反应之间的相互作用。它揭示了细菌和病毒特异性的宿主反应，这可能促成新的诊断方法，并证明了非靶向RNA测序在AS和URI诊断分析中的潜力。
