Systematic Analysis of Mobile Genetic Elements Mediating β-Lactamase Gene Amplification in Noncarbapenemase-Producing Carbapenem-Resistant Enterobacterales Bloodstream Infections.
Systematic Analysis of Mobile Genetic Elements Mediating β-Lactamase Gene Amplification in Noncarbapenemase-Producing Carbapenem-Resistant Enterobacterales Bloodstream Infections.
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DOI：
10.1128/msystems.00476-22
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发表时间：
2022-10-26
期刊：
影响因子：
6.4
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中科院分区：
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--
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非产碳青霉烯酶的碳青霉烯耐药肠杆菌（non-CP-CRE）越来越被认为是碳青霉烯耐药肠杆菌（CRE）感染的重要原因。然而，对非cp - cre引起侵袭性疾病的机制了解有限。在德克萨斯州休斯顿的MD安德森癌症中心，使用长、短读全基因组测序来阐明肠杆菌血液分离株中碳青霉烯类非敏感性决定因素。我们通过系统发育分析、抗微生物基因检测/拷贝数定量、孔蛋白评估和移动遗传元件（MGE）鉴定相结合，研究了碳青霉烯非敏感肠杆菌（CNSE）的机制（即具有碳青霉烯中间耐药表型或更高表型的分离株）。大多数CNSE分离株为非cp - cre(41/79; 51.9%), 25.3%（20/79）为碳青霉烯类中等敏感性肠杆菌（CIE）， 22.8%（18/79）为产碳青霉烯酶肠杆菌（CPE）。在非cp - cr大肠杆菌（中位CNV = 2.6×， n = 17）和肺炎克雷伯菌（中位CNV = 3.2×， n = 17）中均存在扩展谱β-内酰胺酶（ESBL）基因拷贝数变异（拷贝数变异）（Wilcoxon检验，p值< 0.001）。所有非cp - cr大肠杆菌和肺炎克雷伯菌均预测至少一种外膜孔蛋白基因（即ompC/ompF或ompK36/ompK35）的表达减少。完全解析的CNSE基因组显示，IS26和ISEcp1结构包含blaCTX-M变体以及其他抗微生物元件与基因扩增相关，主要发生在IncFIB/IncFII质粒环境中。mge介导的β-内酰胺酶基因扩增导致串联阵列（主要由IS26易位单元介导）或片段复制（通常由ISEcp1转位单元介导）。非cp -CRE菌株是CRE菌血症最常见的原因，由并发的孔蛋白丢失和mge介导的blaCTX-M基因扩增驱动碳青霉烯不敏感性。碳青霉烯耐药肠杆菌（CRE）被认为是紧急抗菌素耐药性（AMR）威胁。绝大多数CRE研究集中在产碳青霉烯酶肠杆菌（CPE）上，尽管在一些监测研究中，不产碳青霉烯酶的CRE （non-CP-CRE）占分离物的50%或更多。因此，非cp - cre的碳青霉烯耐药机制仍然不清楚。为了解决这个问题，我们对一组CRE菌血症分离物应用了短读和长读测序技术，并利用这些数据揭示了介导β-内酰胺酶基因扩增的复杂移动遗传元件结构。通过生成65个碳青霉烯非敏感肠杆菌（CNSE）的完整基因组，涵盖了遗传多样性的分离株，我们的发现既对非cp - cre如何克服碳青霉烯处理产生了新的见解，也为研究人员提供了表征他们自己的非cp - cre分离株的支架。提高对非cp - cre发展机制的认识，有助于设计和实施未来的战略，以减轻这些日益被认识到的抗菌素耐药性病原体的影响。
Noncarbapenemase-producing carbapenem-resistant Enterobacterales (non-CP-CRE) are increasingly recognized as important contributors to prevalent carbapenem-resistant Enterobacterales (CRE) infections. However, there is limited understanding of mechanisms underlying non-CP-CRE causing invasive disease. Long- and short-read whole-genome sequencing was used to elucidate carbapenem nonsusceptibility determinants in Enterobacterales bloodstream isolates at MD Anderson Cancer Center in Houston, Texas. We investigated carbapenem nonsusceptible Enterobacterales (CNSE) mechanisms (i.e., isolates with carbapenem intermediate resistance phenotypes or greater) through a combination of phylogenetic analysis, antimicrobial resistance gene detection/copy number quantification, porin assessment, and mobile genetic element (MGE) characterization. Most CNSE isolates sequenced were non-CP-CRE (41/79; 51.9%), whereas 25.3% (20/79) were Enterobacterales with intermediate susceptibility to carbapenems (CIE), and 22.8% (18/79) were carbapenemase-producing Enterobacterales (CPE). Statistically significant copy number variants (CNVs) of extended-spectrum β-lactamase (ESBL) genes (Wilcoxon Test; P-value < 0.001) were present in both non-CP-CR E. coli (median CNV = 2.6×; n = 17) and K. pneumoniae (median CNV = 3.2×, n = 17). All non-CP-CR E. coli and K. pneumoniae had predicted reduced expression of at least one outer membrane porin gene (i.e., ompC/ompF or ompK36/ompK35). Completely resolved CNSE genomes revealed that IS26 and ISEcp1 structures harboring blaCTX-M variants along with other antimicrobial resistance elements were associated with gene amplification, occurring in mostly IncFIB/IncFII plasmid contexts. MGE-mediated β-lactamase gene amplifications resulted in either tandem arrays, primarily mediated by IS26 translocatable units, or segmental duplication, typically due to ISEcp1 transposition units. Non-CP-CRE strains were the most common cause of CRE bacteremia with carbapenem nonsusceptibility driven by concurrent porin loss and MGE-mediated amplification of blaCTX-M genes. IMPORTANCE Carbapenem-resistant Enterobacterales (CRE) are considered urgent antimicrobial resistance (AMR) threats. The vast majority of CRE research has focused on carbapenemase-producing Enterobacterales (CPE) even though noncarbapenemase-producing CRE (non-CP-CRE) comprise 50% or more of isolates in some surveillance studies. Thus, carbapenem resistance mechanisms in non-CP-CRE remain poorly characterized. To address this problem, we applied a combination of short- and long-read sequencing technologies to a cohort of CRE bacteremia isolates and used these data to unravel complex mobile genetic element structures mediating β-lactamase gene amplification. By generating complete genomes of 65 carbapenem nonsusceptible Enterobacterales (CNSE) covering a genetically diverse array of isolates, our findings both generate novel insights into how non-CP-CRE overcome carbapenem treatments and provide researchers scaffolds for characterization of their own non-CP-CRE isolates. Improved recognition of mechanisms driving development of non-CP-CRE could assist with design and implementation of future strategies to mitigate the impact of these increasingly recognized AMR pathogens.
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影响因子：
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