Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana.
Present address Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, 3086, Australia.
BMC Infect Dis. 2024 Sep 20;24(1):1020. doi: 10.1186/s12879-024-09948-z.
The association of the oral microbiome with SARS-CoV-2 infections and disease progression has been documented in European, Asian, and American populations but not in Africa.
We conducted a study in Ghana to evaluate and compare the naso-oropharyngeal microbiome in SARS-CoV-2-infected and uninfected persons before (pre-vaccine) and after vaccine availability (post-vaccine) in the country. 16S rRNA V3-V4 variable region was sequenced and analysed from DNA extracted from naso-oropharyngeal swabs.
Considering only the infection status, infected and uninfected groups had no difference in their within-group diversity and was evident in the study population pre- and post-vaccine availability. The introduction of vaccines reduced the diversity of the naso-oropharyngeal microbiome particularly among SARS-CoV-2 positive persons and, vaccinated individuals (both infected and uninfected) had higher microbial diversity compared to their unvaccinated counterparts. SARS-CoV-2-positive and -negative individuals were largely compositionally similar varying by 4-7% but considering vaccination*infection statuses, the genetic distance increased to 12% (P = 0.003) and was mainly influenced by vaccination. Common among the pre- and post-vaccine samples, Atopobium and Finegoldia were abundant in infected and uninfected individuals, respectively. Bacteria belonging to major butyrate-producing phyla, Bacillota (particularly class Clostridia) and Bacteroidota showed increased abundance more strikingly in infected individuals before vaccines were available. They reduced significantly after vaccines were introduced into the country with Fusobacterium and Lachnoanaerobaculum being the only common bacteria between pre-vaccine infected persons and vaccinated individuals, suggesting that natural infection and vaccination correlate with high abundance of short-chain fatty acids.
Our results show, in an African cohort, the abundance of bacteria taxa known for their protective pathophysiological processes, especially during infection, suggesting that this population is protected against severe COVID-19. The immune-related roles of the members of Bacillota and Bacteroidota that were found associated with infection and vaccination require further studies, and how these may be linked to ethnicity, diet and age. We also recommend expansion of microbiome-disease association studies across Africa to identify possible bacterial-mediated therapeutics for emerging infections.
欧洲、亚洲和美洲人群的口腔微生物组与 SARS-CoV-2 感染和疾病进展有关，但在非洲人群中尚未有相关研究。
我们在加纳开展了一项研究，评估和比较了该国在疫苗可及之前（疫苗前）和之后（疫苗后），SARS-CoV-2 感染和未感染人群的鼻咽微生物组。从鼻咽拭子中提取 DNA，对 16S rRNA V3-V4 可变区进行测序和分析。
仅考虑感染状态，感染组和未感染组在组内的多样性没有差异，这在研究人群中疫苗可及之前和之后都很明显。疫苗的引入降低了鼻咽微生物组的多样性，特别是在 SARS-CoV-2 阳性人群中，并且接种疫苗的个体（感染和未感染）的微生物多样性高于未接种疫苗的个体。SARS-CoV-2 阳性和阴性个体在很大程度上具有相似的组成，差异在 4-7%之间，但考虑到接种*感染状态，遗传距离增加到 12%（P=0.003），主要受接种影响。在疫苗前和疫苗后样本中都很常见的是，共生菌 Atopobium 和 Finegoldia 分别在感染和未感染个体中丰富。属于主要丁酸盐产生菌门的细菌，厚壁菌门（特别是梭菌纲）和拟杆菌门，在感染个体中，在疫苗可用之前就表现出更显著的增加，在疫苗引入该国后，它们显著减少。在疫苗前感染个体和接种个体之间，只有 Fusobacterium 和 Lachnoanaerobaculum 是共同的细菌，这表明自然感染和接种与短链脂肪酸的高丰度有关。
我们的研究结果表明，在非洲队列中，已知具有保护病理生理过程的细菌分类群的丰度很高，尤其是在感染期间，这表明该人群对严重 COVID-19 具有保护作用。在感染和接种过程中发现与 Bacillota 和 Bacteroidota 相关的成员的免疫相关作用需要进一步研究，以及它们如何与种族、饮食和年龄相关。我们还建议在非洲扩大微生物组-疾病关联研究，以确定针对新发感染的可能的细菌介导的治疗方法。
