THE GENOMIC POPULATION STUDY OF BLOODSTREAM ASSOCIATED ESCHERICHIA COLI IN 2020 IN SOUTHWEST, UK
THE GENOMIC POPULATION STUDY OF BLOODSTREAM ASSOCIATED ESCHERICHIA COLI IN 2020 IN SOUTHWEST, UK
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2020 年英国西南部血流相关大肠杆菌基因组群体研究
DOI：
10.1016/j.ijid.2023.04.013
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发表时间：
2023
影响因子：
8.4
通讯作者：
Lee W
中科院分区：
文献类型：
--
作者：
Lee W
主要由大肠杆菌引起的血流内感染（BSI）是日益增加的临床挑战。快速经验性抗菌治疗是至关重要的管理BSI，因此了解耐药的基因型基础，可以有助于提高empiric choice. MethodsThis study investigated the molecular epidemiology of 669 deduplicated，sequentialE. 2020年1月至12月期间，一个区域诊断实验室从BSI中分离出的大肠杆菌为150万人提供服务。在Illumina-HiSeq-2500上测序。询问测序数据以了解AMR决定簇和系统发育关系。结果表明，ST131是携带β-内酰胺类、氨基糖苷类和磺胺类耐药基因的主要序列类型（20%）。阿莫西林-克拉维汀和头孢噻肟的基因型-表型一致性分别最低和最高。系统发育关系表明，抗性菌株分布较分散，不同类群的菌株相互混杂。所代表的系统群为：A（5%）、B1（6%）、B2（66%）和D（16%）。χ 2分析表明，B2组与A组和B1组之间携带的"农场动物特异性耐药基因"--编码对链霉素、新霉素和氟苯尼考耐药的基因--在英国仅用于治疗农场动物，有很强的相关性（p <0.0001）。阿莫西林-克拉维霉素耐药通常涉及基因表达的变化，而环丙沙星耐药涉及点突变，生物信息学工具仅考虑移动的耐药基因的存在，未考虑这两种情况。χ 2分析表明，A群和B1群的BSI分离株可能来源于家畜。coliBSI。在专门用于监测研究之前，基于WGS的AMR预测仍需进一步优化。
IntroBloodstream infections (BSIs), predominantly caused byEscherichia coli, are an increasing clinical challenge. Rapid empiric antimicrobial therapy is vital for management for BSIs, therefore understanding the genotypic basis of resistance can contribute to improving empiric choice.MethodsThis study investigates the molecular epidemiology of 669 deduplicated, sequentialE. coliisolated from BSI by a regional diagnostic laboratory serving a population of 1.5 million people between January and December 2020.E. coliwere sequenced on the Illumina-HiSeq-2500. Sequencing data were interrogated for AMR determinants and phylogenetic relationships. Using a combination of antimicrobial susceptibility and sequencing data, the concordance of antimicrobial resistance prediction based on detection of resistant determinants and resistance was evaluated.FindingsST131 was the predominantly identified sequence type (20%) harbouring resistance genes associated with ß-lactams, aminoglycosides and sulphonamides. Genotypic-phenotypic concordance across the antimicrobial panel was lowest and highest for amoxicillin-clavulanate and cefotaxime respectively. Phylogenetic relationships showed resistance was dispersed and intermixed with isolates from different phylogroups. Phylogroups represented were: A (5%), B1 (6%), B2 (66%) and D (16%). χ2 analysis of phylogroup B2 versus A and B1 revealed there was a strong association (p<0.0001) between carriage of “farm-animal specific resistance genes” – those encoding resistance to streptomycin, neomycin and florfenicol, used in the UK only to treat farmanimals.DiscussionDisconcordance was observed with amoxicillin-clavulanate and ciprofloxacin. Amoxicillin-clavulanate resistance often involves changes in gene expression and ciprofloxicin resistance involves point mutations, both of which are not factored with bioinformatics tools that only consider presence of mobile resistance genes. χ2 analysis suggests that BSI isolates from phylogroups A and B1 have a farm-animal origin.ConclusionOverall, this study reveals that commonly human associated phylogroups B2 and D were most predominant groups inE. coliBSI. WGS-based prediction of AMR still requires further optimisation before implementing this exclusively for surveillance studies.