Taboada Blanca, Espinoza Marco A, Isa Pavel, Aponte Fernando E, Arias-Ortiz María A, Monge-Martínez Jesús, Rodríguez-Vázquez Rubén, Díaz-Hernández Fidel, Zárate-Vidal Fernando, Wong-Chew Rosa María, Firo-Reyes Verónica, del Río-Almendárez Carlos N, Gaitán-Meza Jesús, Villaseñor-Sierra Alberto, Martínez-Aguilar Gerardo, Salas-Mier Ma del Carmen, Noyola Daniel E, Pérez-Gónzalez Luis F, López Susana, Santos-Preciado José I, Arias Carlos F
Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
Colegio de Pediatría del Estado de Veracruz, Veracruz, Mexico.
PLoS One. 2014 Nov 20;9(11):e113570. doi: 10.1371/journal.pone.0113570. eCollection 2014.
Viruses are the most frequent cause of respiratory disease in children. However, despite the advanced diagnostic methods currently in use, in 20 to 50% of respiratory samples a specific pathogen cannot be detected. In this work, we used a metagenomic approach and deep sequencing to examine respiratory samples from children with lower and upper respiratory tract infections that had been previously found negative for 6 bacteria and 15 respiratory viruses by PCR. Nasal washings from 25 children (out of 250) hospitalized with a diagnosis of pneumonia and nasopharyngeal swabs from 46 outpatient children (out of 526) were studied. DNA reads for at least one virus commonly associated to respiratory infections was found in 20 of 25 hospitalized patients, while reads for pathogenic respiratory bacteria were detected in the remaining 5 children. For outpatients, all the samples were pooled into 25 DNA libraries for sequencing. In this case, in 22 of the 25 sequenced libraries at least one respiratory virus was identified, while in all other, but one, pathogenic bacteria were detected. In both patient groups reads for respiratory syncytial virus, coronavirus-OC43, and rhinovirus were identified. In addition, viruses less frequently associated to respiratory infections were also found. Saffold virus was detected in outpatient but not in hospitalized children. Anellovirus, rotavirus, and astrovirus, as well as several animal and plant viruses were detected in both groups. No novel viruses were identified. Adding up the deep sequencing results to the PCR data, 79.2% of 250 hospitalized and 76.6% of 526 ambulatory patients were positive for viruses, and all other children, but one, had pathogenic respiratory bacteria identified. These results suggest that at least in the type of populations studied and with the sampling methods used the odds of finding novel, clinically relevant viruses, in pediatric respiratory infections are low.
病毒是儿童呼吸道疾病最常见的病因。然而，尽管目前使用了先进的诊断方法，但在20%至50%的呼吸道样本中仍无法检测到特定病原体。在本研究中，我们采用宏基因组学方法和深度测序技术，对先前经PCR检测6种细菌和15种呼吸道病毒均呈阴性的上下呼吸道感染儿童的呼吸道样本进行检测。研究了250名住院诊断为肺炎的儿童中的25名（鼻洗液样本）以及526名门诊儿童中的46名（鼻咽拭子样本）。在25名住院患者中，20名患者的DNA测序结果显示至少有一种与呼吸道感染常见相关的病毒，其余5名儿童检测到致病性呼吸道细菌的序列。对于门诊患者，所有样本合并到25个DNA文库中进行测序。在这种情况下，25个测序文库中有22个鉴定出至少一种呼吸道病毒，而在所有其他文库（除一个外）中检测到致病性细菌。在两组患者中均鉴定出呼吸道合胞病毒、冠状病毒OC43和鼻病毒的序列。此外，还发现了与呼吸道感染相关性较低的病毒。门诊儿童中检测到萨福尔德病毒，住院儿童中未检测到。两组均检测到指环病毒、轮状病毒和星状病毒，以及几种动植物病毒。未鉴定出新病毒。将深度测序结果与PCR数据相加，250名住院患者中有79.2%、526名门诊患者中有76.6%病毒检测呈阳性，其余所有儿童（除一名外）均鉴定出致病性呼吸道细菌。这些结果表明，至少在所研究的人群类型和所采用的采样方法下，在儿科呼吸道感染中发现新的、具有临床相关性病毒的几率较低。
