In clinical practice, infections caused by Aspergillus species are common and associated with high mortality rates. However, isolating Aspergillus from clinical samples and cultures is challenging, and serological tests cannot differentiate between strains. Furthermore, the complex cell wall structure in Aspergillus species hinders DNA extraction and subsequent nucleic acid detection. Aspergillus fumigatus, Aspergillus flavus, and Aspergillus niger are common and frequently encountered pathogenic species. This study aimed to establish an efficient and rapid method for detecting Aspergillus species in clinical samples. Fe3O4@PEI.NH2 nanoparticles with large particle sizes were employed to capture Aspergillus from the samples. Flexible silver nanowires (AgNWs) were prepared and used as the surface-enhanced Raman scattering (SERS) substrate for Aspergillus detection. Through SERS spectroscopy, the identification of captured Aspergillus species was confirmed. Furthermore, the SERS spectrum underwent principal component analysis employing orthogonal partial least-squares discrimination analysis (OPLS-DA) as a multivariate analysis technique to distinguish between the various Aspergillus species effectively. After 10-fold cross-validation, the trained model achieved a testing accuracy of 99.15%, indicating excellent classification performance. By utilizing pre-prepared Fe3O4@PEI.NH2 and AgNWs, the detection process was completed within 60 min without disrupting the cell wall of Aspergillus.
To understand the clinical characteristics of Staphylococcus aureus bloodstream infection and the main risk factors affecting clinical prognosis, providing a reference for clinical prevention and control of Staphylococcus aureus bloodstream infection. In this study, the clinical data of 152 patients with Staphylococcusaureus bloodstream infection admitted to Guangdong Provincial People's Hospital from January 2019 to December 2021 were retrospectively analyzed by reviewing the electronic medical record system, including underlying diseases, clinical characteristics, risk factors, and bacterial resistance. Statistical methods such as Chi-Squared Test and t Test were used to analyze the related risk factors that may affect the clinical characteristics and prognosis of patients with Staphylococcusaureus and methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infection, then the variables with P<0.05 in univariate analysis were included in the multivariate logistic regression model to analyze the independent risk factors of poor prognosis. The results showed among 152 patients with Staphylococcus aureus bloodstream infection, 50 patients (32.89%) were infected with MRSA. In comparison, 102 patients (67.11%) were infected with methicillin-sensitive Staphylococcus aureus (MSSA). Except for rifampicin, the resistance rate of MRSA to commonly used antibiotics was all higher than that of MSSA, and the difference was statistically significant (Chi-square values were 8.272, 11.972, 4.998, 4.776, respectively;all P-values are less than 0.05). Strains resistant to vancomycin, linezolid, and quinupristin/dalfopristin were not found. In the MRSA group, indwelling catheter and drainage tube, carbapenems, and β-lactamase inhibitor treatment were significantly higher than the MSSA group. The difference was statistically significant (P<0.05). The incidence of poor prognosis of bloodstream infection in the MRSA group was higher than that in the MSSA group (34.00% vs 13.73%), and the difference was statistically significant (χ2=8.495, P<0.05). No independent risk factors associated with poor prognosis were found in the included patients with MRSA bloodstream infection.Multivariate Logistic regression model analysis showed that solid malignant tumors (OR=13.576, 95%CI: 3.352-54.977, P<0.05), mechanical ventilation (OR=7.468, 95%CI: 1.398-39.884, P<0.05) were the most important independent risk factors for poor prognosis in patients with Staphylococcus aureus bloodstream infection. In summary, the poor prognosis rate of MRSA bloodstream infection is higher than that of MSSA. The clinical evaluation of related risk factors should be strengthened, targeted prevention and control interventions should be taken to improve the prognosis of patients with Staphylococcus aureus bloodstream infection, and the use of antibiotics should be rational and standardized, to control bacterial infection and drug resistance effectively.探讨金黄色葡萄球菌血流感染的临床特征及影响预后的主要危险因素，为临床预防和控制金黄色葡萄球菌血流感染提供参考依据。本研究回顾性分析广东省人民医院2019年1月至2021年12月诊治的152例金黄色葡萄球菌血流感染患者的临床资料，包括基础疾病、临床特点、危险因素、细菌耐药性、治疗药物及预后等临床因素，采用χ2检验、t检验等统计学方法对可能影响金黄色葡萄球菌和耐甲氧西林金黄色葡萄球菌（MRSA）血流感染患者临床特征及预后的相关危险因素进行单因素分析，然后将单变量分析中P<0.05的变量纳入多因素logistic回归模型分析其预后不良的独立危险因素。结果显示，152例金黄色葡萄球菌血流感染患者中，检出MRSA 50例（32.89%），甲氧西林敏感金黄色葡萄球菌（MSSA）检出102例（67.11%）。MRSA组留置导尿管、留置引流管、使用碳青霉烯类抗生素、使用β-内酰胺酶抑制剂比率明显高于MSSA组（χ2分别为8.272、11.972、4.998、4.776，P均<0.05）。MRSA组血流感染预后不良发生率高于MSSA组（34.00% vs 13.73%）（χ2=8.495，P<0.05）。在纳入研究的MRSA血流感染患者中尚未发现与预后不良相关的独立危险因素。除对利福平外，MRSA对常用抗菌药物的耐药率均高于MSSA（P<0.05），未发现对万古霉素、利奈唑胺和奎奴普丁/达福普汀耐药株。多因素logistic回归模型分析显示，恶性实体肿瘤（OR=13.576、95%CI：3.352~54.977、P<0.05）、机械通气（OR=7.468、95%CI：1.398~39.884、P<0.05）是金黄色葡萄球菌血流感染患者预后不良的独立危险因素。综上，MRSA血流感染的预后不良率高于MSSA。临床上应加强对相关危险因素的评估，采取有针对性的防控干预措施，以改善金黄色葡萄球菌血流感染患者的预后，合理规范抗菌药物的使用，有效控制细菌感染和耐药性的发生。.
Background: This study analyzed the antimicrobial resistance phenotypes and mechanisms of quinolone, cephalosporins, and colistin resistance in nontyphoidal Salmonella from patients with diarrhea in Jiangsu, China. Methods: A total of 741 nontyphoidal Salmonella isolates were collected from hospitals in major cities of Jiangsu Province, China between 2016 and 2017. Their susceptibility to commonly used antibiotics was evaluated by broth micro-dilution and sequencing analysis of resistance genes screened by a PCR method. For mcr-1 positive isolates, genetic relationship study was carried out by pulsed-field gel electrophoresis and multiloci sequence typing analysis. The transferability of these plasmids was measured with conjugation experiments and the genetic locations of mcr-1 were analyzed by pulsed-field gel electrophoresis profiles of S1-digested genomic DNA and subsequent Southern blot hybridization. Results: Among 741 nontyphoidal Salmonella isolates, the most common serotypes identified were S. Typhimurium ( n =257, 34.7%) and S. Enteritidis ( n =127, 17.1%), and the isolates showed 21.7, 20.6, and 5.0% resistance to cephalosporins, ciprofloxacin, and colistin, respectively. Among the 335 nalidixic acid-resistant Salmonella , 213 (63.6%) and 45 (13.4%) had at least one mutation in gyrA and parC . Among the plasmid-borne resistance, qnrS1 (85; 41.9%) and aac(6')-Ib-cr4 (75; 36.9%) were the most common quinolone resistance (PMQR) genes, while bla CTX-M-14 ( n =35) and bla CTX-M-55 ( n =46) were found to be dominant extended-spectrum beta-lactamase (ESBL) genes in nontyphoidal Salmonella . In addition, eight mcr-1 -harboring strains were detected since 2016 and they were predominate in children under the age of 7years. Conjugation assays showed the donor Salmonella strain has functional and transferable colistin resistance and Southern blot hybridization revealed that mcr-1 was located in a high molecular weight plasmid. Conclusion: In nontyphoidal Salmonella , there is a rapidly increasing trend of colistin resistance and this is the first report of patients harboring mcr-1 -positive Salmonella with a new ST type ST155 and new serotype S. Sinstorf. These findings demonstrate the necessity for cautious use and the continuous monitoring of colistin in clinical applications.
Abstract: Scrub typhus is a vector-borne infectious disease caused by Orientia tsutsugamushi . Accurate and timely diagnosis at the early infection stage could save the patients’ lives. Traditional technologies were limited to rapidly and successfully detecting Orientia tsutsugamushi due to poor specificity, especially in the condition of atypical symptoms. The technology of Metagenomic next-generation sequencing (mNGS) is amenable to finding the real pathogen because it holds potential as a diagnostic platform for unbiased pathogen identification and precision medicine. Herein, we reported two clinical case reports relative to the Orientia tsutsugamushi infection diagnosed by mNGS. We hope these two cases will improve clinical diagnosis. Keywords: scrub typhus, metagenomic next-generation sequencing, Orientia tsutsugamushi
Pneumonia produced by coinfection with Pneumocystis jirovecii (PJ) and cytomegalovirus (CMV) in infants and young children without timely diagnosis and treatment is often fatal due to the limitations of traditional tests. More accurate and rapid diagnostic methods for multiple infections are urgently needed.Here, we report a case of a 2-month-old boy with pneumonia caused by Pneumocystis jirovecii (PJ) and cytomegalovirus (CMV) without HIV infection. Chest computed tomography (CT) showed massive exudative consolidation in both lungs. Microscopic examination of stained sputum and smear specimens and bacterial and fungal culture tests were all negative, and CMV nucleic acid and antibody tests were positive. After a period of antiviral and anti-infective therapy, pulmonary inflammation was not relieved. Subsequently, sputum and venous blood samples were analysed by metagenomic next-generation sequencing (mNGS), and the sequences of PJ and CMV were acquired. The patient was finally diagnosed with pneumonia caused by PJ and CMV coinfection. Anti-fungal combined with anti-viral therapy was given immediately. mNGS re-examination of bronchoalveolar lavage fluid (BALF) also revealed the same primary pathogen. Therapy was stopped due to the request of the patient's guardian. Hence, the child was discharged from the hospital and eventually died.This case emphasizes the combined use of mNGS and traditional tests in the clinical diagnosis of mixed lung infections in infants without HIV infection. mNGS is a new adjunctive diagnostic method that can rapidly discriminate multiple causes of pneumonia.
Rapid and sensitive RNA detection is of great value in diverse areas, ranging from biomedical research to clinical diagnostics. Existing methods for RNA detection often rely on reverse transcription (RT) and DNA amplification or involve a time-consuming procedure and poor sensitivity. Herein, we proposed a CRISPR/Cas12a-enabled amplification-free assay for rapid, specific, and sensitive RNA diagnostics. This assay, which we termed T7/G4-CRISPR, involved the use of a T7-powered nucleic acid circuit to convert a single RNA target into numerous DNA activators via toehold-mediated strand displacement reaction and T7 exonuclease-mediated target recycling amplification, followed by activating Cas12a trans-cleavage of the linker strands inhibiting split G-Quadruplex (G4) assembly, thereby inducing fluorescence attenuation proportion to the input RNA target. We first performed step-by-step validation of the entire assay process and optimized the reaction parameters. Using the optimal conditions, T7/G4-CRISPR was capable of detecting as low as 3.6 pM target RNA, obtaining ∼100-fold improvement in sensitivity compared with the most direct Cas12a assays. Meanwhile, its excellent specificity could discriminate single nucleotide variants adjacent to the toehold region and allow species-specific pathogen identification. Furthermore, we applied it for analyzing bacterial 16S rRNA in 40 clinical urine samples, exhibiting a sensitivity of 90% and a specificity of 100% when validated by RT-quantitative PCR. Therefore, we envision that T7/G4-CRISPR will serve as a promising RNA sensing approach to expand the toolbox of CRISPR-based diagnostics.
The Gram-negative non-motile Klebsiella pneuomoniae is currently a major cause of hospital-acquired (HA) and community-acquired (CA) infections, leading to great public health concern globally, while rapid identification and accurate tracing of the pathogenic bacterium is essential in facilitating monitoring and controlling of K. pneumoniae outbreak and dissemination. Multi-locus sequence typing (MLST) is a commonly used typing approach with low cost that is able to distinguish bacterial isolates based on the allelic profiles of several housekeeping genes, despite low resolution and labor intensity of the method. Core-genome MLST scheme (cgMLST) is recently proposed to sub-type and monitor outbreaks of bacterial strains with high resolution and reliability, which uses hundreds or thousands of genes conserved in all or most members of the species. However, the method is complex and requires whole genome sequencing of bacterial strains with high costs. Therefore, it is urgently needed to develop novel methods with high resolution and low cost for bacterial typing. Surface enhanced Raman spectroscopy (SERS) is a rapid, sensitive and cheap method for bacterial identification. Previous studies confirmed that classification and prediction of bacterial strains via SERS spectral analysis correlated well with MLST typing results. However, there is currently no similar comparative analysis in K. pneumoniae strains. In this pilot study, 16 K. pneumoniae strains with different sequencing typings (STs) were selected and a phylogenetic tree was constructed based on core genome analysis. SERS spectra (N=45/each strain) were generated for all the K. pneumoniae strains, which were then comparatively classified and predicted via six representative machine learning (ML) algorithms. According to the results, SERS technique coupled with the ML algorithm Support Vector Machine (SVM) could achieve the highest accuracy (5-Fold Cross Validation=100%) in terms of differentiating and predicting all the K. pneumoniae strains that were consistent to corresponding MLSTs. In sum, we show in this pilot study that the SERS-SVM based method is able to accurately predict K. pneumoniae MLST types, which has the application potential in clinical settings for tracing dissemination and controlling outbreak of K. pneumoniae in hospitals and communities with low costs and high rapidity.
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