A multicentre study reveals dysbiosis in the microbial co-infection and antimicrobial resistance gene profile in the nasopharynx of COVID-19 patients.
A multicentre study reveals dysbiosis in the microbial co-infection and antimicrobial resistance gene profile in the nasopharynx of COVID-19 patients.
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DOI：
10.1038/s41598-023-30504-3
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发表时间：
2023-03-13
影响因子：
4.6
通讯作者：
Reynolds, Eric C.
中科院分区：
文献类型：
--
作者：
Mahmud, A. Sayeed. M.;Seers, Christine A.;Shaikh, Aftab Ali;Taznin, Tarannum;Uzzaman, Mohammad Samir;Osman, Eshrar;Habib, Md. Ahashan;Akter, Shahina;Banu, Tanjina Akhtar;Sarkar, Md. Murshed Hasan;Goswami, Barna;Jahan, Iffat;Okeoma, Chioma M.;Khan, Md. Salim;Reynolds, Eric C.
SARS-CoV-2感染对鼻咽微生物群的影响尚未得到很好的表征。我们对从无症状（n = 14）、轻度（n = 64）或重度症状（n = 11）的sars - cov -2阳性个体以及从未感染过（n = 5）或已从感染中恢复（n = 7）的sars - cov -2阴性个体的鼻咽拭子中提取的遗传物质进行了测序。使用鲁棒滤波器，我们确定了1345个分类群，读取丰度约为0.1%或更高。总体而言，重症队列微生物组的多样性最低。在所有队列中均发现细菌性病原体，但真菌种类鉴定罕见。少数分类群在队列之间是共同的，这表明有限的人类鼻咽部核心微生物组。共鉴定出10种抗菌素耐药机制基因（> 25%序列覆盖率，315个基因，63个非冗余基因），其中β-内酰胺耐药基因几乎普遍存在。感染SARS-CoV-2的患者（无症状和轻度）比SARS-CoV-2阴性个体具有更高的抗生素耐药基因发生率和更大的微生物负担。在决定如何治疗COVID-19相关细菌感染时，应考虑到这一点。
The impact of SARS-CoV-2 infection on the nasopharyngeal microbiome has not been well characterised. We sequenced genetic material extracted from nasopharyngeal swabs of SARS-CoV-2-positive individuals who were asymptomatic (n = 14), had mild (n = 64) or severe symptoms (n = 11), as well as from SARS-CoV-2-negative individuals who had never-been infected (n = 5) or had recovered from infection (n = 7). Using robust filters, we identified 1345 taxa with approximately 0.1% or greater read abundance. Overall, the severe cohort microbiome was least diverse. Bacterial pathogens were found in all cohorts, but fungal species identifications were rare. Few taxa were common between cohorts suggesting a limited human nasopharynx core microbiome. Genes encoding resistance mechanisms to 10 antimicrobial classes (> 25% sequence coverages, 315 genes, 63 non-redundant) were identified, with β-lactam resistance genes near ubiquitous. Patients infected with SARS-CoV-2 (asymptomatic and mild) had a greater incidence of antibiotic resistance genes and a greater microbial burden than the SARS-CoV-2-negative individuals. This should be considered when deciding how to treat COVID-19 related bacterial infections.
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影响因子：
3.7
作者：
Erb-Downward JR;Thompson DL;Han MK;Freeman CM;McCloskey L;Schmidt LA;Young VB;Toews GB;Curtis JL;Sundaram B;Martinez FJ;Huffnagle GB
通讯作者：
Huffnagle GB
影响因子：
8.4
作者：
Barnes, Carrie E.;MacIntyre, C. Raina
通讯作者：
MacIntyre, C. Raina
DOI：
10.1016/j.cmi.2020.07.041
发表时间：
2021-01
期刊：
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
影响因子：
--
作者：
Garcia-Vidal C;Sanjuan G;Moreno-García E;Puerta-Alcalde P;Garcia-Pouton N;Chumbita M;Fernandez-Pittol M;Pitart C;Inciarte A;Bodro M;Morata L;Ambrosioni J;Grafia I;Meira F;Macaya I;Cardozo C;Casals C;Tellez A;Castro P;Marco F;García F;Mensa J;Martínez JA;Soriano A;COVID-19 Researchers Group
通讯作者：
COVID-19 Researchers Group
影响因子：
11.8
作者：
Bhatt, Pinki J.;Shiau, Stephanie;Narayanan, Navaneeth
通讯作者：
Narayanan, Navaneeth
影响因子：
9.5
作者：
Gao, Zhancheng;Kang, Yu;Yu, Jun;Ren, Lufeng
通讯作者：
Ren, Lufeng