Performance of the Rapidec®Carba NP assay for the detection of different carbapenemases in Klebsiella pneumoniae and Escherichia coli strains

PurposeThe spread of infections caused by Enterobacterales strains resistant to carbapenems is a global public health problem, and early detection of carbapenemases is very important to prevent their spread. The rapid detection of carbapenemase production with the new commercial assay Rapidec® Carba NP test is based on the biochemical detection of imipenem hydrolysis. Our study aims to evaluate the performance of the Rapidec® Carba NP test in OXA-48 positive isolates highly prevalent in our country and also in isolates with more than one carbapenemase gene that have an increased prevalence and to examine whether it can be used for confirmation of carbapenemase positivity in the routine laboratory.MethodsA total of 97 strains of 94 carbapenem-resistant Klebsiella pneumoniae and three carbapenem-resistant Escherichia coli isolated from various clinical specimens were included in the study. The results of the Rapidec® Carba NP assay were compared with those obtained by the multiplex PCR test.ResultsThe sensitivity of the Rapidec® Carba NP test was 97.8% for all carbapenemase-positive isolates. Of 90 PCR positive isolates, one OXA-48 and one OXA-48 ?+ ?NDM positive isolates were negative with Rapidec® Carba NP test.ConclusionsThe positive results detected by the Rapidec® Carba NP test make an important contribution to the early detection of carbapenemase production and infection control practices. Since two carbapenemase positive isolates were found to be negative with the Rapidec® Carba NP test in our study, it was concluded that negative results of carbapenem-resistant isolates obtained with this assay should be confirmed with an additional carbapenemase detection method to exclude false-negative results.     

Analysis of AcrB in Klebsiella pneumoniae reveals natural variants promoting enhanced multidrug resistance

Infections caused by Klebsiella pneumoniae are often difficult to manage due to the high frequency of multidrug resistance, often conferred by efflux pumps. In this study, we analyzed sequence variations of the major RND family multidrug efflux pump AcrB from 387 assembled K. pneumoniae genomes. We confirm that AcrB is a highly-conserved efflux pump in K. pneumoniae, and identified several variants that were prevalent in clinical isolates. Molecular dynamics analyses on two of these variants (L118M and S966A) suggested conformational changes that may correlate with increased drug efflux capabilities. The L118M change resulted in enhanced protein rigidity while the flexibility of drug binding pockets was stable or increased, and the interactions between the proximal pockets and water molecules were stronger. For S966A, the significantly enlarged proximal pocket suggested higher drug accommodation ability. Consistent with these predictions, the L118M and S966A variants conferred a slightly increased ability to grow in the presence of tetracycline and to survive cefoxitin exposure when overexpressed. In summary, our results suggest that the emergence of enhanced-function AcrB variants may be a potential risk for increased antibiotic resistance in clinical K. pneumoniae isolates.     

Effects of short-term continuous and pulse cadmium exposure on gut histology and microbiota of adult male frogs (Pelophylax nigromaculatus) during pre-hibernation

Cadmium (Cd) is an environmental endocrine-disrupting pollutant which mainly occurs in pulsed manner in natural waters, while traditional toxicology experiments have less examined the effects of pulsed exposure. Here, we studied the effects of short-term (7 days) continuous and pulse exposure to 100 μg/L Cd on gut morphology and microbiota of frogs (Pelophylax nigromaculatus) during pre-hibernation. Compared to continuous exposure, Cd pulse exposure significantly increased individual mortality and decreased the villi height and the ratio of villi height to crypt depth of the gut. Cd continuous and pulse exposure both changed the community structure and relative abundance of intestinal microbiota. Compared to continuous exposure, Cd pulse exposure significantly decreased the relative abundance of beneficial bacteria (e.g., Cetobacterium and Aeromonas genus), and significantly increased the relative abundance of harmful bacteria (e.g., Parabacteroides, Odoribacter, and Acinetobacter genus). This study shows that the gut histology and microbiota of amphibians during pre-hibernation are more susceptible to Cd pulse exposure than continuous exposure.     

早孕期监测子宫动脉多普勒参数在预测低危人群不良妊娠结局的价值

目的 建立妊娠11~13+6周子宫动脉多普勒参数在低危人群中的正常参考值，同时评估其对不良妊娠结局的预测价值。方法 收集2019年6月至2021年6月于我院行产前超声检查的妊娠11~13+6周孕妇，根据妊娠结局分组。收集两侧子宫动脉多普勒指标，包括搏动指数（PI）、阻力指数（RI）、舒张早期是否有切迹，以及孕妇基本临床资料和胎儿出生信息，将以上相关参数进行统计学分析。结果 最终纳入800例孕妇，包括正常妊娠结局组740例和不良妊娠结局组60例。两组孕妇体质量指数（BMI）、分娩孕周和胎儿出生体质量比较，差异均有统计学意义（均P＜0.05）。随着孕周的增加，子宫动脉两侧平均搏动指数（mPI）、平均阻力指数（mRI）和两侧舒张早期切迹检出率均呈逐渐下降的趋势。ROC曲线分析显示，mPI、mRI及两侧舒张早期切迹预测妊娠结局的曲线下面积（AUC）分别为0.542、0.574、0.521，三者联合预测妊娠结局的AUC为0.648；孕妇BMI、年龄mPI、mRI及两侧舒张早期切迹预测妊娠结局的AUC为0.751。结论 建立了低危人群在妊娠11~13+6周子宫动脉多普勒参数的正常参考值范围。在妊娠11~13+6周单纯应用子宫动脉多普勒参数预测妊娠结局的价值有限，将子宫动脉参数与临床相关指标结合可提高对不良妊娠结局的预测价值。     

Communicating regulatory high-throughput sequencing data using BioCompute Objects

This project demonstrates the use of the IEEE 2791–2020 Standard (BioCompute Objects [BCO]) to enable the complete and concise communication of results from next generation sequencing (NGS) analysis. One arm of a clinical trial was replicated using synthetically generated data made to resemble real biological data and then two independent analyses were performed. The first simulated a pharmaceutical regulatory submission to the US Food and Drug Administration (FDA) including analysis of results and a BCO. The second simulated an FDA review that included an independent analysis of the submitted data. Of the 118 simulated patient samples generated, 117 (99.15%) were in agreement in the two analyses. This process exemplifies how a template BCO (tBCO), including a verification kit, facilitates transparency and reproducibility, thereby reinforcing confidence in the regulatory submission process.     

Induction of tumor cell autosis by myxoma virus-infected CAR-T and TCR-T cells to overcome primary and acquired resistance

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Paradox of complex diversity: Challenges in the diagnosis and management of bacterial keratitis

Bacterial keratitis continues to be one of the leading causes of corneal blindness in the developed as well as the developing world, despite swift progress since the dawn of the “anti-biotic era”. Although, we have expeditiously developed our understanding about the different causative organisms and associated pathology leading to keratitis, extensive gaps in knowledge continue to dampen the efforts required for early and accurate diagnosis, and management in these patients, resulting in poor clinical outcomes. The ability of the causative bacteria to subdue the therapeutic challenge stems from their large genome encoding complex regulatory networks, variety of unique virulence factors, and rapid secretion of tissue damaging proteases and toxins.In this review article, we provide an overview of the established diagnostic techniques and therapeutics for keratitis caused by various bacteria. We extensively report the recent in-roads through novel tools for accurately diagnosing mono- and poly-bacterial corneal infections. Furthermore, we outline the recent progress by our groups and others in understanding the sub-cellular genomic changes that lead to antibiotic resistance in these organisms. Finally, we discuss in detail, the novel therapies and drug delivery systems in development for the efficacious management of bacterial keratitis.     

金黄色葡萄球菌异质性耐药机制及实验室检测技术

 异质性耐药是一种特殊的细菌耐药类型，常表现为同一克隆来源的不同细菌亚群对某种抗菌药物表现出不一致的耐药特征，大多数亚群对某种抗菌药物敏感，而少部分亚群对其耐药或高度耐药。异质性耐药分离株常会导致特定抗菌药物抗感染治疗失败。针对异质性耐药菌较为深入的研究主要集中于革兰阴性菌，革兰阳性球菌的相关报道较少。近年有研究报道万古霉素、利奈唑胺、苯唑西林等多种类型抗菌药物异质性耐药金黄色葡萄球菌分离株出现，但其实际临床意义尚待进一步评估。此文对金黄色葡萄球菌异质性耐药机制和检测技术最新进展进行综述，为细菌异质性耐药机制研究和新型检测技术研发提供新的思路。