Bacteriophage populations mirror those of bacterial pathogens at sites of infection.
Bacteriophage populations mirror those of bacterial pathogens at sites of infection.
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DOI：
10.1128/msystems.00497-23
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发表时间：
2023-08-31
期刊：
影响因子：
6.4
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中科院分区：
文献类型：
--
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噬菌体，寄生于细菌的病毒，已知在细菌定植位点大量存在，但在感染位点噬菌体和细菌之间的关系尚不清楚。噬菌体对它们的细菌宿主物种是高度特异性的，因此我们假设噬菌体种群会反映受感染组织内的细菌病原体。为了验证这一点，在这里，我们研究了公开可用的无细胞DNA (cfDNA)，这些DNA是使用新一代感染体液测序产生的，包括尿液、关节液、腹膜液、支气管肺泡灌洗液、脑脊液和脓肿液，以及未感染的对照样本。这些分析使用计算管道鉴定噬菌体序列在cfDNA。我们发现噬菌体序列存在于感染和未感染的体液中，并代表了各种噬菌体形态和细菌宿主。此外，大肠杆菌、链球菌和金黄色葡萄球菌的噬菌体在感染这些病原体的液体中所占的比例和多样性都过高。这些数据表明，噬菌体反映了感染部位细菌宿主的相对丰度。噬菌体序列可能有助于未来利用无细胞DNA研究感染组织内微生物组的调查和诊断方法。噬菌体是微生物组研究的一个活跃领域，但大多数研究都集中在细菌定植部位的噬菌体群体上。对活动性感染部位的噬菌体生态学知之甚少。为了解决这方面的知识差距，我们利用公开可用的数据集来研究从感染部位收集的无细胞DNA中的噬菌体种群。我们发现噬菌体反映了感染部位细菌宿主的相对丰度。这些研究可能会导致未来的调查和诊断方法，包括噬菌体和细菌无细胞DNA。
Bacteriophages, viruses that parasitize bacteria, are known to be abundant at sites of bacterial colonization, but the relationship between phages and bacteria at sites of infection is unclear. Bacteriophages are highly specific to their bacterial host species, and so we hypothesize that phage populations would mirror those of bacterial pathogens within infected tissues. To test this, here we study publicly available cell-free DNA (cfDNA) generated using next-generation sequencing of infected bodily fluids, including urine, joint fluid, peritoneal fluid, bronchoalveolar lavage fluid, cerebrospinal fluid, and abscess fluid, as well as uninfected control samples. These were analyzed using a computational pipeline for identifying bacteriophage sequences in cfDNA. We find that bacteriophage sequences are present in both infected and uninfected bodily fluids and represent a variety of bacteriophage morphologies and bacterial hosts. Additionally, phages from Escherichia coli, Streptococcus, and Staphylococcus aureus are overrepresented both in terms of proportion and diversity in fluids infected with these same pathogens. These data indicate that phages reflect the relative abundance of their bacterial hosts at sites of infection. Bacteriophage sequences may help inform future investigative and diagnostic approaches that utilize cell-free DNA to study the microbiome within infected tissues. Bacteriophages are an active area of investigation in microbiome research, but most studies have focused on phage populations at sites of bacterial colonization. Little is known about bacteriophage ecology at sites of active infection. To address this gap in knowledge, we utilized a publicly available data set to study bacteriophage populations in cell-free DNA collected from sites of infection. We find that phages reflect the relative abundance of their bacterial hosts at sites of infection. These studies may lead to future investigative and diagnostic approaches that incorporate phages as well as bacterial cell-free DNA.
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影响因子：
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