基于全基因组测序的产 NDM-5 尿路致病性大肠埃希菌 EC1390 的特征分析。
Whole-genome-sequence-based characterization of an NDM-5-producing uropathogenic Escherichia coli EC1390.
机构信息
Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan.
Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.
出版信息
BMC Microbiol. 2022 Jun 6;22(1):150. doi: 10.1186/s12866-022-02562-6.
BACKGROUND
Urinary tract infection (UTI) is one of the most common outpatient bacterial infections. In this study, we isolated and characterized an extensively-drug resistant (XDR) NDM-5-producing Escherichia coli EC1390 from a UTI patient by using whole-genome sequencing (WGS) in combination with phenotypic assays.
METHODS
Antimicrobial susceptibility to 23 drugs was determined by disk diffusion method. The genome sequence of EC1390 was determined by Nanopore MinION MK1C platform. Conjugation assays were performed to test the transferability of EC1390 plasmids to E. coli recipient C600. Phenotypic assays, including growth curve, biofilm formation, iron acquisition ability, and cell adhesion, were performed to characterize the function of EC1390 plasmids.
RESULTS
Our results showed that EC1390 was only susceptible to tigecycline and colistin, and thus was classified as XDR E. coli. A de novo genome assembly was generated using Nanopore 73,050 reads with an N value of 20,936 bp and an N value of 7,624 bp. WGS analysis showed that EC1390 belonged to the O101-H10 serotype and phylogenetic group A E. coli. Moreover, EC1390 contained 2 conjugative plasmids with a replicon IncFIA (pEC1390-1 with 156,286 bp) and IncFII (pEC1390-2 with 71,840 bp), respectively. No significant difference was observed in the bacterial growth rate in LB broth and iron acquisition ability between C600, C600 containing pEC1390-1, C600 containing pEC1390-2, and C600 containing pEC1390-1 and pEC1390-2. However, the bacterial growth rate in nutrition-limited M9 broth was increased in C600 containing pEC1390-2, and the cell adhesion ability was increased in C600 containing both pEC1390-1 and pEC1390-2. Moreover, these plasmids modulated the biofilm formation under different conditions.
CONCLUSIONS
In summary, we characterized the genome of XDR-E. coli EC1390 and identified two plasmids contributing to the antimicrobial resistance, growth of bacteria in a nutrition-limited medium, biofilm formation, and cell adhesion.
背景
尿路感染（UTI）是最常见的门诊细菌性感染之一。在这项研究中，我们通过全基因组测序（WGS）结合表型检测，从一名 UTI 患者中分离并鉴定了一株广泛耐药（XDR）产 NDM-5 型大肠埃希菌 EC1390。
方法
采用纸片扩散法测定 23 种药物的药敏性。使用 Nanopore MinION MK1C 平台测定 EC1390 的基因组序列。通过接合试验检测 EC1390 质粒向大肠杆菌受体 C600 的转移能力。通过生长曲线、生物膜形成、铁获取能力和细胞黏附等表型试验，对 EC1390 质粒的功能进行了表征。
结果
结果表明，EC1390 仅对替加环素和黏菌素敏感，因此被归类为 XDR 型大肠埃希菌。使用 Nanopore 73050 个读数进行从头基因组组装，N 值为 20936bp，N 值为 7624bp。WGS 分析显示，EC1390 属于 O101-H10 血清型和 A 型大肠埃希菌。此外，EC1390 含有 2 个可接合的质粒，分别为 IncFIA（pEC1390-1，长 156286bp）和 IncFII（pEC1390-2，长 71840bp）。在 LB 肉汤和铁获取能力方面，C600、含 pEC1390-1 的 C600、含 pEC1390-2 的 C600 和含 pEC1390-1 和 pEC1390-2 的 C600 之间，细菌的生长速率没有显著差异。然而，在营养受限的 M9 肉汤中，含 pEC1390-2 的 C600 细菌的生长速率增加，且含 pEC1390-1 和 pEC1390-2 的 C600 细胞黏附能力增加。此外，这些质粒在不同条件下调节生物膜的形成。
结论
综上所述，我们对 XDR-E. coli EC1390 的基因组进行了表征，并鉴定了两个有助于抗菌药物耐药性、细菌在营养受限培养基中生长、生物膜形成和细胞黏附的质粒。
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