Population-level impacts of antibiotic usage on the human gut microbiome.
Population-level impacts of antibiotic usage on the human gut microbiome.
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DOI：
10.1038/s41467-023-36633-7
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发表时间：
2023-03-02
影响因子：
16.6
通讯作者：
Quince, Christopher
中科院分区：
文献类型：
--
作者：
Lee, Kihyun;Raguideau, Sebastien;Siren, Kimmo;Asnicar, Francesco;Cumbo, Fabio;Hildebrand, Falk;Segata, Nicola;Cha, Chang-Jun;Quince, Christopher
抗菌素的广泛使用推动了病原微生物耐药性的进化，既增加了抗菌素耐药基因（ARGs）的流行，又通过水平基因转移（HGT）在物种间传播。然而，对与人体相关的更广泛的共生微生物群落（微生物组）的影响尚不清楚。小规模研究已经确定了抗生素消费的短暂影响，但我们对8972个宏基因组的ARGs进行了广泛调查，以确定人群水平的影响。通过研究未服用抗生素的健康个体的3096个肠道微生物组，我们发现在三大洲的十个国家中，总ARG丰度和多样性与人均抗生素使用率之间存在高度显著的相关性。来自中国的样本是显著的异常值。我们使用154,723个人类相关的宏基因组组装基因组（MAGs）将这些ARGs与分类群联系起来，并检测HGT。这表明，ARG丰度的相关性是由病原体和共生体之间共享的多物种移动ARG驱动的，在mag和ARG网络的高度连接的中心组成部分内。我们还观察到，个体人类肠道ARG谱可分为两种类型或抗性类型。较不常见的抗性型具有较高的ARG总体丰度，与某些类型的抗性有关，并且与ARG网络外围变形杆菌中的物种特异性基因有关。在此，作者研究了抗菌素耐药基因（ARGs）在人群水平上的影响。通过分析未服用抗生素的健康个体的8972个宏基因组和3096个肠道微生物组，他们发现在三大洲的十个国家中，总ARG丰度和多样性与人均抗生素使用率之间存在显著相关性。利用154,723个人类相关宏基因组组装基因组（MAGs），他们将这些ARGs与微生物分类群和水平基因转移联系起来。
The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network. Here, the authors study the population-level impact of antimicrobial resistance genes (ARGs). By analyzing 8972 metagenomes and 3,096 gut microbiomes from healthy individuals not taking antibiotics, they demonstrate significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Using a collection of 154,723 human-associated metagenome assembled genomes (MAGs) they link these ARGs to microbial taxa and horizontal gene transfer.
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DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
64.8
作者：
Arumugam, Manimozhiyan;Raes, Jeroen;Pelletier, Eric;Le Paslier, Denis;Yamada, Takuji;Mende, Daniel R.;Fernandes, Gabriel R.;Tap, Julien;Bruls, Thomas;Batto, Jean-Michel;Bertalan, Marcelo;Borruel, Natalia;Casellas, Francesc;Fernandez, Leyden;Gautier, Laurent;Hansen, Torben;Hattori, Masahira;Hayashi, Tetsuya;Kleerebezem, Michiel;Kurokawa, Ken;Leclerc, Marion;Levenez, Florence;Manichanh, Chaysavanh;Nielsen, H. Bjorn;Nielsen, Trine;Pons, Nicolas;Poulain, Julie;Qin, Junjie;Sicheritz-Ponten, Thomas;Tims, Sebastian;Torrents, David;Ugarte, Edgardo;Zoetendal, Erwin G.;Wang, Jun;Guarner, Francisco;Pedersen, Oluf;de Vos, Willem M.;Brunak, Soren;Dore, Joel;Weissenbach, Jean;Ehrlich, S. Dusko;Bork, Peer
通讯作者：
Bork, Peer
影响因子：
16.6
作者：
Ellabaan MMH;Munck C;Porse A;Imamovic L;Sommer MOA
通讯作者：
Sommer MOA
影响因子：
15.8
作者：
de Kraker ME;Stewardson AJ;Harbarth S
通讯作者：
Harbarth S
DOI：
10.1098/rstb.2016.0424
发表时间：
2017-12-05
影响因子：
6.3
作者：
Hall, James P. J.;Brockhurst, Michael A.;Harrison, Ellie
通讯作者：
Harrison, Ellie