Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Department of Statistics and Actuarial Science, Faculty of Economic and Management Sciences, Stellenbosch University, Stellenbosch, South Africa.
Microbiome. 2023 Jun 5;11(1):127. doi: 10.1186/s40168-023-01563-5.
Bacteria colonizing the nasopharynx play a key role as gatekeepers of respiratory health. Yet, dynamics of early life nasopharyngeal (NP) bacterial profiles remain understudied in low- and middle-income countries (LMICs), where children have a high prevalence of risk factors for lower respiratory tract infection. We investigated longitudinal changes in NP bacterial profiles, and associated exposures, among healthy infants from low-income households in South Africa.
We used short fragment (V4 region) 16S rRNA gene amplicon sequencing to characterize NP bacterial profiles from 103 infants in a South African birth cohort, at monthly intervals from birth through the first 12 months of life and six monthly thereafter until 30 months.
Corynebacterium and Staphylococcus were dominant colonizers at 1 month of life; however, these were rapidly replaced by Moraxella- or Haemophilus-dominated profiles by 4 months. This succession was almost universal and largely independent of a broad range of exposures. Warm weather (summer), lower gestational age, maternal smoking, no day-care attendance, antibiotic exposure, or low height-for-age z score at 12 months were associated with higher alpha and beta diversity. Summer was also associated with higher relative abundances of Staphylococcus, Streptococcus, Neisseria, or anaerobic gram-negative bacteria, whilst spring and winter were associated with higher relative abundances of Haemophilus or Corynebacterium, respectively. Maternal smoking was associated with higher relative abundances of Porphyromonas. Antibiotic therapy (or isoniazid prophylaxis for tuberculosis) was associated with higher relative abundance of anerobic taxa (Porphyromonas, Fusobacterium, and Prevotella) and with lower relative abundances of health associated-taxa Corynebacterium and Dolosigranulum. HIV-exposure was associated with higher relative abundances of Klebsiella or Veillonella and lower relative abundances of an unclassified genus within the family Lachnospiraceae.
In this intensively sampled cohort, there was rapid and predictable replacement of early profiles dominated by health-associated Corynebacterium and Dolosigranulum with those dominated by Moraxella and Haemophilus, independent of exposures. Season and antibiotic exposure were key determinants of NP bacterial profiles. Understudied but highly prevalent exposures prevalent in LMICs, including maternal smoking and HIV-exposure, were associated with NP bacterial profiles. Video Abstract.
定植于鼻咽部的细菌在呼吸道健康中起着关键作用。然而，在儿童存在下呼吸道感染风险因素高发的中低收入国家（LMICs），鼻咽部（NP）细菌谱的早期动态仍研究不足。我们研究了南非低收入家庭中健康婴儿 NP 细菌谱的纵向变化及其相关暴露因素。
我们使用短片段（V4 区）16S rRNA 基因扩增子测序，在南非出生队列中对 103 名婴儿从出生到 12 个月的每月和之后每 6 个月一次进行 NP 细菌谱特征分析，直至 30 个月。
在 1 个月时，棒状杆菌属和葡萄球菌属是主要定植菌；然而，到 4 个月时，它们迅速被莫拉菌属或嗜血杆菌属为主的谱取代。这种转变几乎是普遍的，并且在很大程度上独立于广泛的暴露因素。温暖的天气（夏季）、较低的胎龄、母亲吸烟、不参加日托、抗生素暴露或 12 个月时身高年龄 z 分数低与更高的α和β多样性相关。夏季还与葡萄球菌属、链球菌属、奈瑟菌属或厌氧菌革兰氏阴性细菌的相对丰度较高相关，而春季和冬季分别与嗜血杆菌属或棒状杆菌属的相对丰度较高相关。母亲吸烟与卟啉单胞菌属的相对丰度较高相关。抗生素治疗（或结核分枝杆菌异烟肼预防）与厌氧菌属（卟啉单胞菌属、梭杆菌属和普雷沃氏菌属）的相对丰度较高和与健康相关的梭菌属和 Dolosigranulum 属的相对丰度较低相关。HIV 暴露与克雷伯菌属或韦荣球菌属的相对丰度较高和未分类属 within the family Lachnospiraceae 的相对丰度较低相关。
在这个密集采样的队列中，早期由健康相关的棒状杆菌属和 Dolosigranulum 属主导的谱迅速且可预测地被莫拉菌属和嗜血杆菌属主导的谱取代，而与暴露无关。季节和抗生素暴露是 NP 细菌谱的关键决定因素。在 LMICs 中普遍存在但研究不足的暴露因素，包括母亲吸烟和 HIV 暴露，与 NP 细菌谱相关。
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