利用长线程纳米孔测序技术对大肠埃希菌和肺炎克雷伯菌尿路感染进行基因组分析

IF 3.9 3区 生物学 Q2 MICROBIOLOGY MicrobiologyOpen Pub Date : 2024-01-17 DOI:10.1002/mbo3.1396
Stephen Mark Edward Fordham, Magdalena Barrow, Anna Mantzouratou, Elizabeth Sheridan
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引用次数: 0

摘要

从同一导尿管尿液样本(CSU)中分离出的大肠埃希菌和肺炎克雷伯菌具有相同的抗菌药敏感性。这两种菌株都是从一名长期留置导尿管的患者体内分离出来的。每个分离株在培养后都提取了 DNA。利用纳米孔长读数测序技术构建了每株菌株的质粒和染色体,以确定抗性编码质粒的潜在水平传播以及抗性基因与插入序列之间的关系。从泌尿微生物群中的抗性菌株中提取的质粒仍然特征不清。在每个菌株的质粒中都发现了相同的 11 个抗菌素耐药性(AMR)基因。来自肺炎克氏菌菌株的 185,239-bp FIB(K) pKBM1 还编码了五个 AMR 基因:Sul2、strA、strB、blaTEM-1B 和 blaCTX-M-15。在两个分离株的质粒中都发现了多聚 AMR 基因阵列和 IS26 插入序列。每个分离物的两个质粒都很相似。质粒的水平转移和随后的质粒重排很可能发生在感染过程中。此外,质粒中的抗性区域与国际流行的质粒 pKPN3-307_typeA(通常在肺炎双球菌 ST307 中发现)具有相似性。导管病人体内生物膜的形成可能使菌株之间的细胞密切接触。耐药基因可能会发生水平传播,导致多微生物感染。
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Genomic analyses of an Escherichia coli and Klebsiella pneumoniae urinary tract co-infection using long-read nanopore sequencing

Escherichia coli and Klebsiella pneumoniae isolates presenting with the same antimicrobial susceptibility profile were recovered from the same catheter sample of urine (CSU). Both strains were recovered from a patient with a long-standing indwelling urinary catheter. Each isolate had its DNA extracted following culture. Nanopore long-read sequencing was used to build the plasmids and chromosomes from each strain to closure to discern the potential horizontal propagation of resistance-encoding plasmids and the relationship between resistance genes and insertion sequences. Plasmids derived from resistance strains in the urinary microbiota remain poorly characterized. The same 11 antimicrobial resistance (AMR) genes were found in plasmids from each strain. The 185,239-bp FIB(K) pKBM1, from the K. pneumoniae strain, additionally encoded the five AMR genes: sul2, strA, strB, blaTEM-1B, and blaCTX-M-15. A multimeric array of AMR genes and IS26 insertion sequences were found in the plasmids from both isolates. Both plasmids from each isolate were similar. Horizontal transfer of plasmids, followed by subsequent plasmid rearrangement, is likely to have occurred during infection. Furthermore, the resistance region in the plasmids shared similarity against the internationally prevalent plasmid, pKPN3-307_typeA, commonly identified in K. pneumoniae ST307. Biofilm formation in catheterized patients may allow close cell contact between strains. Horizontal propagation of resistance genes may occur, leading to polymicrobial infections.

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来源期刊
MicrobiologyOpen
MicrobiologyOpen MICROBIOLOGY-
CiteScore
8.00
自引率
0.00%
发文量
78
审稿时长
20 weeks
期刊介绍: MicrobiologyOpen is a peer reviewed, fully open access, broad-scope, and interdisciplinary journal delivering rapid decisions and fast publication of microbial science, a field which is undergoing a profound and exciting evolution in this post-genomic era. The journal aims to serve the research community by providing a vehicle for authors wishing to publish quality research in both fundamental and applied microbiology. Our goal is to publish articles that stimulate discussion and debate, as well as add to our knowledge base and further the understanding of microbial interactions and microbial processes. MicrobiologyOpen gives prompt and equal consideration to articles reporting theoretical, experimental, applied, and descriptive work in all aspects of bacteriology, virology, mycology and protistology, including, but not limited to: - agriculture - antimicrobial resistance - astrobiology - biochemistry - biotechnology - cell and molecular biology - clinical microbiology - computational, systems, and synthetic microbiology - environmental science - evolutionary biology, ecology, and systematics - food science and technology - genetics and genomics - geobiology and earth science - host-microbe interactions - infectious diseases - natural products discovery - pharmaceutical and medicinal chemistry - physiology - plant pathology - veterinary microbiology We will consider submissions across unicellular and cell-cluster organisms: prokaryotes (bacteria, archaea) and eukaryotes (fungi, protists, microalgae, lichens), as well as viruses and prions infecting or interacting with microorganisms, plants and animals, including genetic, biochemical, biophysical, bioinformatic and structural analyses. The journal features Original Articles (including full Research articles, Method articles, and Short Communications), Commentaries, Reviews, and Editorials. Original papers must report well-conducted research with conclusions supported by the data presented in the article. We also support confirmatory research and aim to work with authors to meet reviewer expectations. MicrobiologyOpen publishes articles submitted directly to the journal and those referred from other Wiley journals.
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