[Study of the resistome of human microbial communities using a targeted panel of antibiotic resistance genes in COVID-19 patients].

IF 0.3 4区医学 Q3 MEDICINE, GENERAL & INTERNAL

Terapevticheskii Arkhiv Pub Date : 2023-12-28 DOI:10.26442/00403660.2023.12.202490

O O Yanushevich, I V Maev, N I Krikheli, O V Levchenko, J S Galeeva, E V Starikova, D N Andreev, P S Sokolov, A K Fomenko, M K Devkota, N G Andreev, A V Zaborovsky, V V Evdokimov, S V Tsaregorodtsev, E N Ilina, V M Govorun, P A Bely, E A Sabelnikova, A A Solodov, S V Cheremushkin, R I Shaburov, A L Kebina

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引用次数: 0

Abstract

Aim: To study overall drug resistance genes (resistome) in the human gut microbiome and the changes in these genes during COVID-19 in-hospital therapy.

Materials and methods: A single-center retrospective cohort study was conducted. Only cases with laboratory-confirmed SARS-CoV-2 RNA using polymerase chain reaction in oro-/nasopharyngeal swab samples were subject to analysis. The patients with a documented history of or current comorbidities of the hepatobiliary system, malignant neoplasms of any localization, systemic and autoimmune diseases, as well as pregnant women were excluded. Feces were collected from all study subjects for subsequent metagenomic sequencing. The final cohort was divided into two groups depending on the disease severity: mild (group 1) and severe (group 2). Within group 2, five subgroups were formed, depending on the use of antibacterial drugs (ABD): group 2A (receiving ABD), group 2AC (receiving ABD before hospitalization), group 2AD (receiving ABD during hospitalization), group 2AE (receiving ABD during and before hospitalization), group 2B (not receiving ABD).

Results: The median number of antibiotic resistance (ABR) genes (cumulative at all time points) was significantly higher in the group of patients treated with ABD: 81.0 (95% CI 73.8-84.5) vs. 51.0 (95% CI 31.1-68.4). In the group of patients treated with ABD (2A), the average number of multidrug resistance genes (efflux systems) was significantly higher than in controls (group 2B): 47.0 (95% CI 46.0-51.2) vs. 21.5 (95% CI 7.0-43.9). Patients with severe coronavirus infection tended to have a higher median number of ABR genes but without statistical significance. Patients in the severe COVID-19 group who did not receive ABD before and during hospitalization also had more resistance genes than the patients in the comparison group.

Conclusion: This study demonstrated that fewer ABR genes were identified in the group with a milder disease than in the group with a more severe disease associated with more ABR genes, with the following five being the most common: SULI, MSRC, ACRE, EFMA, SAT.

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[利用 COVID-19 患者的抗生素耐药基因靶向面板研究人类微生物群落的耐药基因组]。

目的：研究人类肠道微生物组中的总体耐药基因（耐药基因组）以及这些基因在 COVID-19 住院治疗期间的变化：进行了一项单中心回顾性队列研究。仅对口腔/鼻咽拭子样本中经聚合酶链反应实验室确诊的 SARS-CoV-2 RNA 病例进行分析。有记录显示患有肝胆系统疾病、任何部位的恶性肿瘤、全身性疾病和自身免疫性疾病的患者以及孕妇不在分析范围内。所有研究对象的粪便都被收集起来，以便随后进行元基因组测序。根据疾病的严重程度，最终的研究对象分为两组：轻度组（第 1 组）和重度组（第 2 组）。在第 2 组中，根据抗菌药物（ABD）的使用情况分为 5 个亚组：第 2A 组（接受 ABD）、第 2AC 组（住院前接受 ABD）、第 2AD 组（住院期间接受 ABD）、第 2AE 组（住院期间和住院前接受 ABD）、第 2B 组（未接受 ABD）：结果：接受ABD治疗的患者抗生素耐药性（ABR）基因中位数（所有时间点的累积）明显高于接受ABD治疗的患者：81.0（95% CI 73.8-84.5）对51.0（95% CI 31.1-68.4）。在接受 ABD 治疗的患者组（2A）中，多药耐药基因（外流系统）的平均数量明显高于对照组（2B 组）：47.0（95% CI 46.0-51.2）对 21.5（95% CI 7.0-43.9）。严重冠状病毒感染患者的 ABR 基因中位数往往较高，但无统计学意义。在住院前和住院期间未接受ABD治疗的严重COVID-19组患者的耐药基因也比对比组患者多：这项研究表明，病情较轻的组别中发现的 ABR 基因少于病情较重的组别，而病情较重的组别中发现的 ABR 基因较多，其中以下五种基因最为常见：SULI、MSRC、ACRE、EFMA、SAT。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Terapevticheskii Arkhiv 医学-医学：内科

CiteScore

1.40

自引率

33.30%

发文量

171

审稿时长

3-8 weeks

期刊介绍： Терапевтический архив The journal was founded by the prominent Russian therapists M.P. Konchalovsky and G.F. Lang in 1923. Then its editors-in-chief were Professors V.N. Vinogradov and A.G. Gukasyan. Since 1972, E.I. Chazov, Academician of the Russian Academy of Sciences, has been heading the editorial board of the journal. Over 90 years, there have been more than 1000 issues where the authors and editorial staff have done their best for readers to keep abreast of current advances in medical science and practice and for physicians to master the advanced principles of recognition and treatment of a wide spectrum of visceral diseases. The papers published in the journal (editorials, original articles, lectures, reviews, etc.) cover both current scientific achievements and practical experience in diagnosing, treating, and preventing visceral diseases. The authors of publications are not only Russian, but also foreign scientists and physicians. All papers are peer-reviewed by highly qualified Russian specialists. The journal is published monthly. Traditionally, each issue has predominantly certain thematic areas covering individual therapy specializations. Every year, one of the issues is devoted to related problems in practical medicine (allergology and immunology, neurology and psychiatry, obstetrics, oncology, etc.). This all draws the attention of the reading public to the journal. The journal is indexed in RSCI (Russian Science Citation Index), PubMed/Medline, Index Medicus, Scopus/EMBASE, Web of Science Core Collection (Science Citation Index Expanded), Web of Science (Russian Science Citation Index - RSCI, Current Contents Connect, BIOSIS Previews), Google Scholar, Ulrich''s Periodicals Directory. The journal is included in the list of periodicals recommended by the Higher Attestation Committee for publishing the papers containing the basic materials of doctoral and candidate dissertations. By the decision of the Presidium of the Russian Academy of Medical Sciences, the “Therapevticheskiy Arkhiv” was awarded the Botkin medal. It was admitted to the European Association of Sciences Editors (EASE). The journal was honored with the Golden Press Fund decoration at the 13th International Press Professional Exhibition.