Ecology and diversity in upper respiratory tract microbial population structures from a cross-sectional community swabbing study
Ecology and diversity in upper respiratory tract microbial population structures from a cross-sectional community swabbing study
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DOI：
10.1099/jmm.0.000773
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发表时间：
2018-08-01
影响因子：
3
通讯作者：
Clarke, Stuart C.
中科院分区：
文献类型：
--
作者：
Coughtrie, Abigail L.;Morris, Denise E.;Clarke, Stuart C.
目的。全世界每年有超过280万人死于呼吸道感染，而携带病原体是感染的必备先兆。作为一项基于人群的横断面携带研究的一部分，我们试图确定细菌和病毒呼吸道病原体的携带流行病学。在2012年5月至8月(春末/夏季)和2013年2月至4月(冬季/早春)这两个不同的时间点采集了鼻部自拭子样本。除呼吸道合胞病毒、流感病毒A和B、鼻病毒/肠道病毒、冠状病毒、副流感病毒1-3和腺病毒外，还检测出肺炎链球菌、流感嗜血杆菌、卡他分支杆菌、金黄色葡萄球菌、铜绿假单胞菌和脑膜炎奈瑟菌6种细菌。载量随年龄、近期RTI和其他物种的存在而变化。微生物群落的空间结构在0~4岁年龄组和近期RTI组中较为紊乱。在年轻个体中，物种的频率分布比随机预期的更平坦(X-2=20.42P=0.002)，表明物种的空间聚集符合促进关系。夏季和老年个体的生态位偏离中性模式，而冬季和年轻个体(0-4年)则没有，表明呼吸群落存在季节性和年龄相关的生态位过程。将流行病学方法和生态学理论应用于呼吸道样本，对驱动微生物群落组成的因素产生了新的见解。
Purpose. Respiratory tract infections (RTIs) are responsible for over 2.8 million deaths per year worldwide with pathobiont carriage a required precursor to infection. We sought to determine carriage epidemiology for both bacterial and viral respiratory pathogens as part of a large population-based cross-sectional carriage study.Methodology. Nose self-swab samples were collected in two separate time-points, May to August 2012 (late spring/summer) and February to April 2013 (winter/early spring). The presence of six bacterial species: S. pneumoniae, H. influenzae, M. catarrhalis, S. aureus, P. aeruginosa and N. meningitidis in addition to respiratory syncytial virus, influenza viruses A and B, rhinovirus/enterovirus, coronavirus, parainfluenza viruses 1-3 and adenovirus was determined using culture and PCR methods.Results/Key findings. Carriage was shown to vary with age, recent RTI and the presence of other species. Spatial structures of microbial communities were more disordered in the 0-4 age group and those with recent RTI. Species frequency distributions were flatter than random expectation in young individuals (X-2 = 20.42, P= 0.002), indicating spatial clumping of species consistent with facilitative relationships. Deviations from a neutral model of ecological niches were observed in summer samples and from older individuals but not in the winter or younger individuals (0-4 years), suggesting the presence of seasonal and age-dependent niche processes in respiratory community assembly.Conclusion. The application of epidemiological methods and ecological theory to respiratory tract samples has yielded novel insights into the factors that drive microbial community composition.