全国基因组流行病学调查揭示了耐碳青霉烯类大肠杆菌在健康人群中的传播及其对公共卫生的影响

IF 10.4 1区 生物学 Q1 GENETICS & HEREDITY
Yan Li, Yanyan Zhang, Xinran Sun, Yuchen Wu, Zelin Yan, Xiaoyang Ju, Yonglu Huang, Hongwei Zhou, Zhiqiang Wang, Shaolin Wang, Rong Zhang, Ruichao Li
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引用次数: 0

摘要

耐碳青霉烯类大肠埃希菌(CREC)已被视为世界卫生组织重点关注的病原体,在全球范围内引起了极大的公共卫生关注。虽然对患者的 CREC 进行了深入研究,但却忽视了 CREC 在健康人群中的流行情况和潜在风险。我们在此对健康人群中 CREC 的流行情况进行了系统研究。我们旨在描述 2020 年至 2022 年期间从中国健康人群中收集的 CREC 的特征,并比较从健康人群和临床患者中分离的 CREC 分离物的基因组。我们采用可靠的分子和基因组分析方法,对中国健康人群中分离出的 CREC 进行了一次全国范围的调查。我们利用抗菌药敏感性测试、全基因组测序和生物信息学分析了从 5064 名健康人粪便样本中分离出的 CREC 病毒群(n = 113)。提取代表性质粒用于第三代纳米孔测序。我们之前从中国 15 个省市的 ICU 患者中收集了 113 个非重复的 CREC 分离物(2018 年 59 个,2020 年 54 个),这些临床分离物被用来与本研究中的分离物进行比较。此外,我们还采用比较基因组学方法来阐明临床和非临床CREC分离株之间的分子变异和潜在相关性。从中国 11 个省采集的 5064 份样本中,共鉴定出 147 株 CREC 分离物。这些分离株被分为 64 个已知序列类型(ST),但没有观察到占优势的 ST。共检测到 7 个碳青霉烯酶基因,其中 blaNDM-5 (n = 116)是最常见的基因。blaNDM 的遗传环境和质粒骨架在从健康人体内分离出的 CREC 中保持一致。此外,我们比较了临床和健康人来源的CREC,发现23个抗性基因存在显著差异,包括blaNDM-1、blaNDM-5和blaKPC(χ2检验,P<0.05)。与健康人相比,临床分离株含有更多与铁吸收、粘附和侵袭相关的毒力因子。值得注意的是,一般在健康人身上发现的 CREC 分离物在住院病人身上也能检测到。我们的发现强调了健康人群中的 CRECs 作为抗生素耐药基因(ARGs)重要储存库的重要性。这突出表明有必要对健康人群中的 CREC 分离物进行持续监测,以准确评估临床 CREC 分离物带来的潜在风险。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
National genomic epidemiology investigation revealed the spread of carbapenem-resistant Escherichia coli in healthy populations and the impact on public health
Carbapenem-resistant Escherichia coli (CREC) has been considered as WHO priority pathogens, causing a great public health concern globally. While CREC from patients has been thoroughly investigated, the prevalence and underlying risks of CREC in healthy populations have been overlooked. Systematic research on the prevalence of CREC in healthy individuals was conducted here. We aimed to characterize CREC collected from healthy populations in China between 2020 and 2022 and to compare the genomes of CREC isolates isolated from healthy individuals and clinical patients. We present a nationwide investigation of CREC isolates among healthy populations in China, employing robust molecular and genomic analyses. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatics were utilized to analyze a cohort of CREC isolates (n = 113) obtained from fecal samples of 5 064 healthy individuals. Representative plasmids were extracted for third-generation nanopore sequencing. We previously collected 113 non-duplicate CREC isolates (59 in 2018, 54 in 2020) collected from ICU patients in 15 provinces and municipalities in China, and these clinical isolates were used to compare with the isolates in this study. Furthermore, we employ comparative genomics approaches to elucidate molecular variations and potential correlations between clinical and non-clinical CREC isolates. A total of 147 CREC isolates were identified from 5 064 samples collected across 11 provinces in China. These isolates were classified into 64 known sequence types (STs), but no dominant STs were observed. In total, seven carbapenemase genes were detected with blaNDM-5 (n = 116) being the most prevalent one. Genetic environments and plasmid backbones of blaNDM were conserved in CREC isolated from healthy individuals. Furthermore, we compared clinical and healthy human-originated CRECs, revealing noteworthy distinctions in 23 resistance genes, including blaNDM-1, blaNDM-5, and blaKPC (χ2 test, p < 0.05). Clinical isolates contained more virulence factors associated with iron uptake, adhesion, and invasion than those obtained from healthy individuals. Notably, CREC isolates generally found healthy people are detected in hospitalized patients. Our findings underscore the significance of healthy populations-derived CRECs as a crucial reservoir of antibiotic resistance genes (ARGs). This highlights the need for ongoing monitoring of CREC isolates in healthy populations to accurately assess the potential risks posed by clinical CREC isolates.
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来源期刊
Genome Medicine
Genome Medicine GENETICS & HEREDITY-
CiteScore
20.80
自引率
0.80%
发文量
128
审稿时长
6-12 weeks
期刊介绍: Genome Medicine is an open access journal that publishes outstanding research applying genetics, genomics, and multi-omics to understand, diagnose, and treat disease. Bridging basic science and clinical research, it covers areas such as cancer genomics, immuno-oncology, immunogenomics, infectious disease, microbiome, neurogenomics, systems medicine, clinical genomics, gene therapies, precision medicine, and clinical trials. The journal publishes original research, methods, software, and reviews to serve authors and promote broad interest and importance in the field.
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