摘要
      随着新冠肺炎疫情在全球蔓延，抗生素的消费量增加。然而，没有研究评估抗生素使用对大流行期间新冠肺炎患者肠道菌群抗生素耐药性的影响。为了探讨这一问题，我们收集了15个无抗生素使用史的健康对照组（HC）粪便样本的宏基因组数据，23个接受经验性抗生素[新冠肺炎（abx+）]治疗的新冠肺炎患者粪便样本的元基因组数据，18个抗生物素新冠肺炎患者[新冠肺炎（abx-）]粪便样本的元数据数据，以及来自序列读取档案数据库的6份社区获得性肺炎患者粪便样本的宏基因组数据[PC（abx+）]。共发现18种ARG类型的513种抗生素抗性基因（ARG）亚型。抗生素治疗导致新冠肺炎患者肠道菌群中ARG丰度显著增加，并显著改变ARG成分。对Bray-Curtis不同值对的分组比较表明，HC与新冠肺炎（abx+）组的不同程度显著高于HC与新冠肺炎（abx-）组的差异程度。mexF、mexD、OXA_209、主要促进因子超家族转运体和EmrB_QacA家族主要促进因子转运体基因是新冠肺炎（abx+）组的区别性ARG亚型。新冠肺炎（abx+）组IS621、qacEdelta、转座酶和ISCR显著增加；它们在很大程度上有助于解释ARG类型相对丰度的变化。总的来说，我们的数据为新冠肺炎流行期间抗生素使用对新冠肺炎患者抗生素耐药性的影响提供了重要的见解。
Abstract
As the COVID-19 pandemic spread globally, the consumption of antibiotics increased. However, no studies exist evaluating the effect of antibiotics use on the antibiotic resistance of intestinal flora in COVID-19 patients during the pandemic. To explore this issue, we collected 15 metagenomic data of fecal samples from healthy controls (HCs) with no use history of antibiotics, 23 metagenomic data of fecal samples from COVID-19 patients who received empirical antibiotics [COVID-19 (abx+)], 18 metagenomic data of fecal samples from antibiotics-naïve COVID-19 patients [COVID-19 (abx-)], and six metagenomic data of fecal samples from patients with community-acquired pneumonia [PC (abx+)] from the Sequence Read Archive database. A total of 513 antibiotic-resistant gene (ARG) subtypes of 18 ARG types were found. Antibiotic treatment resulted in a significant increase in the abundance of ARGs in intestinal flora of COVID-19 patients and markedly altered the composition of ARG profiles. Grouped comparisons of pairs of Bray-Curtis dissimilarity values demonstrated that the dissimilarity of the HC versus the COVID-19 (abx+) group was significantly higher than the dissimilarity of the HC versus the COVID-19 (abx-) group. The mexF, mexD, OXA_209, major facilitator superfamily transporter, and EmrB_QacA family major facilitator transporter genes were the discriminative ARG subtypes for the COVID-19 (abx+) group. IS621, qacEdelta, transposase, and ISCR were significantly increased in COVID-19 (abx+) group; they greatly contributed toward explaining variation in the relative abundance of ARG types. Overall, our data provide important insights into the effect of antibiotics use on the antibiotic resistance of COVID-19 patients during the COVID-19 epidemic.

https://www.sciencedirect.com/science/article/pii/S1438463921001978