Hamza Yunas Panikkaveettil, Kacem Mohamed Ali Ben Hadj, Al Molawi Naema Hassan, Yassine Hadi Mohamad, AlKhatib Hebah Atef Mohammad, Benslimane Fatiha, Al-Remaihi Hanan Ibrahim Kh B, Awni El Kahlout Reham, Ahmed El Kahlout Basema Ibrahim, Al Khalili Hajar, Al Khalili Makiyeh Ahmed, Doiphode Sanjay H, Elmagboul Emad Bashier Ibrahim, Akhter Javed, Al Kuwari Einas A/Aziz Eid, Coyle Peter V
Hamad Medical Corporation, Doha, Qatar.
Rajah Muthiah Medical College, Annamalai University, Chidambaram, India.
J Med Microbiol. 2025 Jul;74(7). doi: 10.1099/jmm.0.001996.
Respiratory viruses are seen as cofactors in bacterial airway infection, often leading to bacterial pneumonia. This study addressed their role in hospitalized patients with bacterial infection confirmed by culture, 16S real-time PCR (16S RT-PCR) and 16S rRNA sequencing (16S Sequencing). The potential for using 16S RT-PCR and 16S Sequencing as diagnostic tools was also addressed. The significance of virus infections on the lung microbiome and on bacterial superinfection in hospitalized patients needs additional evidence from real-world studies. The primary objective was to assess the impact of respiratory viruses on bacterial airway infection, with the secondary objective to see if 16S Sequencing had potential as a faster diagnostic tool that could augment culture. A total of 83 lower airway samples - 36 bronchoalveolar lavage fluids, 39 bronchial washes, 5 sputa and 3 endotracheal aspirates - were tested for respiratory virus and bacterial co-infection. Bacteria were tested by (a) culture, (b) 16S RT-PCR and (c) 16S Sequencing. The performance of culture-independent assays against culture was assessed, and the impact of confirmed viral infections on the airway bacterial load was determined. Virus infections reflected those co-circulating in the community and were significantly associated with culture and 16S Sequencing-confirmed bacterial infections [1-tailed mid P exact test (χ: =0.04; =0.05)]. There was substantive agreement of culture and 16S RT-PCR and 16S Sequencing: kappa score: 0.66 (CI: 0.50-0.82); diagnostic accuracy 83.13% (73.32-90.46%). Virus infections were highly associated with increased bacterial load by 16S RT-PCR [2-tailed χ (χ: 2.4 =0.003)]. Altered microbial diversity by 16S Sequencing was seen for samples stratified by culture but not by virus detection. Acute respiratory viral infections were significantly associated with bacterial airway infections confirmed by culture and 16S Sequencing. Airway dysbiosis was seen with bacterial-confirmed but not viral-confirmed infections, even though the latter were highly associated with increased bacterial loads using 16S RT-PCR. This suggests that virus infections induce changes in lung bacteria missed by culture and sequencing. The study supported a potential role for 16S Sequencing and 16S RT-PCR alongside culture.
呼吸道病毒被视为细菌性气道感染的辅助因素，常导致细菌性肺炎。本研究探讨了它们在经培养、16S实时聚合酶链反应（16S RT-PCR）和16S核糖体RNA测序（16S测序）确诊为细菌感染的住院患者中的作用。还探讨了将16S RT-PCR和16S测序用作诊断工具的可能性。病毒感染对住院患者肺部微生物群和细菌二重感染的影响需要来自实际研究的更多证据。主要目的是评估呼吸道病毒对细菌性气道感染的影响，次要目的是观察16S测序是否有潜力作为一种能辅助培养的更快诊断工具。共对83份下呼吸道样本——36份支气管肺泡灌洗液、39份支气管冲洗液、5份痰液和3份气管内吸出物——进行了呼吸道病毒和细菌合并感染检测。通过（a）培养、（b）16S RT-PCR和（c）16S测序对细菌进行检测。评估了非培养检测方法相对于培养的性能，并确定了确诊病毒感染对气道细菌载量的影响。病毒感染反映了社区中共同流行的情况，且与培养及16S测序确诊的细菌感染显著相关[单尾中P确切概率检验（χ：=0.04；=0.05）]。培养与16S RT-PCR及16S测序之间存在实质性一致性：kappa值为0.66（可信区间：0.50 - 0.82）；诊断准确率为83.13%（73.32 - 90.46%）。病毒感染与16S RT-PCR检测到的细菌载量增加高度相关[双尾χ（χ：2.4 =0.003）]。对于按培养分层而非按病毒检测分层的样本，通过16S测序观察到微生物多样性发生了改变。急性呼吸道病毒感染与培养及16S测序确诊的细菌性气道感染显著相关。在细菌确诊的感染中观察到气道生态失调，而在病毒确诊的感染中未观察到，尽管后者与16S RT-PCR检测到的细菌载量增加高度相关。这表明病毒感染会引起培养和测序遗漏的肺部细菌变化。该研究支持了16S测序和16S RT-PCR与培养一起发挥潜在作用。
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