State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.
Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Centre, Shanghai, People's Republic of China.
Emerg Microbes Infect. 2020 Mar 17;9(1):605-615. doi: 10.1080/22221751.2020.1737578. eCollection 2020.
The source of secondary lower respiratory tract bacterial infections in influenza patients is not fully understood. A case-control study was conducted during the 2017-2018 influenza epidemic period in Beijing, China. Nasopharyngeal swabs were collected from 52 virologically confirmed influenza patients and 24 healthy medical staff. The nasopharyngeal microbiota taxonomic composition was analysed using high-throughput sequencing of the 16S rRNA gene V3-V4 regions. The super-dominant pathobiontic bacterial genus (SDPG) was defined as that accounting for >50% of sequences in a nasopharyngeal swab. We attempted to isolate bacteria of this genus from both nasopharyngeal swabs and lower-respiratory tract samples and analyse their genetic similarities. We observed a significantly lower taxonomy richness in influenza cases compared with healthy controls. A SDPG was detected in 61% of severe cases but in only 24% of mild cases and 29% of healthy controls. In 10 cases, the species isolated from lower-respiratory tract infection sites were identified as belonging to the nasopharyngeal microbiota SDPG. Genetically identical strains were isolated from both nasopharyngeal swabs and lower-respiratory tract infection sites, including 23 strains from six severe cases, six strains from two severe cases, five strains from one severe and one mild case, and four strains from two severe cases. The SDPG in the nasopharyngeal microbiota are the likely cause of subsequent infection in influenza patients.
流感患者继发性下呼吸道细菌感染的来源尚不完全清楚。本研究在北京地区进行了一项 2017-2018 年流感流行期间的病例对照研究。采集了 52 例经病毒学确诊的流感患者和 24 例健康医务人员的鼻咽拭子标本。采用高通量测序技术对 16S rRNA 基因 V3-V4 区进行检测，分析鼻咽部微生物群落的分类组成。将超级优势病原性细菌属（SDPG）定义为在一个鼻咽拭子中占序列的>50%的细菌属。我们试图从鼻咽拭子和下呼吸道样本中分离该属细菌，并分析其遗传相似性。与健康对照组相比，我们观察到流感患者的分类丰富度显著降低。61%的重症患者存在 SDPG，但轻症患者和健康对照组中分别为 24%和 29%。在 10 例患者中，从下呼吸道感染部位分离出的物种被鉴定为属于鼻咽部微生物 SDPG。从鼻咽拭子和下呼吸道感染部位均分离出遗传上相同的菌株，包括来自 6 例重症患者的 23 株、来自 2 例重症患者的 6 株、来自 1 例重症和 1 例轻症患者的 5 株、以及来自 2 例重症患者的 4 株。鼻咽部微生物群中的 SDPG 可能是流感患者继发感染的原因。
