Detection of Carbapenem-resistance in CRE by Comparative Assessment of RAPIDEC® CARBA NP and Xpert™Carba-R Assay

Modelling the rapid detection of Carbapenemase-resistant Klebsiella pneumoniae based on machine learning and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In this study, 80 carbapenem-resistant Klebsiella pneumoniae (CR-KP) and 160 carbapenem-susceptible Klebsiella pneumoniae (CS-KP) strains detected in the clinic were selected and their matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) peaks were collected. K-means clustering was performed on the MS peak data to obtain the best "feature peaks", and four different machine learning models were built to compare the area under the ROC curve, specificity, sensitivity, test set score, and ten-fold cross-validation score of the models. By adjusting the model parameters, the test efficacy of the model is increased on the basis of reducing model overfitting. The area under the ROC curve of the Random Forest, Support Vector Machine, Logistic Regression, and Xgboost models used in this study are 0.99, 0.97, 0.96, and 0.97, respectively; the model scores on the test set are 0.94, 0.91, 0.90, and 0.93, respectively; and the results of the ten-fold cross-validation are 0.84, 0.81, 0.81, and 0.85, respectively. Based on the machine learning algorithms and MALDI-TOF MS assay data can realize rapid detection of CR-KP, shorten the in-laboratory reporting time, and provide fast and reliable identification results of CR-KP and CS-KP.

Antibiotic Resistance Trends Among Enterobacteriaceae in Saudi Arabia: A Systematic Review

Antibiotic resistance is a global public health concern that poses a significant threat to the effective treatment of bacterial infections. Enterobacteriaceae, a family of gram-negative bacteria, are associated with a wide range of infections, including urinary tract infections, bloodstream infections, and respiratory tract infections. This systematic review aimed to examine the antibiotic resistance trend among Enterobacteriaceae in Saudi Arabia in the period between 2003 and 2023. Five databases (PubMed, Medline, Ovid, Scopus, and Cochrane) were searched using the keywords "Resistance AND Enterobacteriaceae AND Saudi Arabia" in the title and abstract. All papers assessing the prevalence of resistance among Enterobacteriaceae in Saudi Arabia were included in the systematic review. Out of 97 papers that were extracted through the database search, 22 articles were considered suitable for the systematic review. The articles included 17027 Enterobacteriaceae isolates, out of which 7592 isolates were identified as resistant bacteria. The studies included various resistant strains, such as Escherichia coli and Klebsiella pneumoniae, that were responsible for various clinical conditions, including urinary tract infections, blood infections, surgical site infections, and pneumonia. In addition, the review highlighted the dynamic nature of antibiotic resistance, with the identification of new resistant bacterial species and the emergence of resistance to newer antibiotic classes over the last decade. Continued surveillance, rational antibiotic use, and the development of alternative treatment options are crucial to address the evolving landscape of antibiotic resistance among Enterobacteriaceae bacteria in the country.

ANCA: artificial nucleic acid circuit with argonaute protein for one-step isothermal detection of antibiotic-resistant bacteria

Endonucleases have recently widely used in molecular diagnostics. Here, we report a strategy to exploit the properties of Argonaute (Ago) proteins for molecular diagnostics by introducing an artificial nucleic acid circuit with Ago protein (ANCA) method. The ANCA is designed to perform a continuous autocatalytic reaction through cross-catalytic cleavage of the Ago protein, enabling one-step, amplification-free, and isothermal DNA detection. Using the ANCA method, carbapenemase-producing Klebsiella pneumoniae (CPKP) are successfully detected without DNA extraction and amplification steps. In addition, we demonstrate the detection of carbapenem-resistant bacteria in human urine and blood samples using the method. We also demonstrate the direct identification of CPKP swabbed from surfaces using the ANCA method in conjunction with a three-dimensional nanopillar structure. Finally, the ANCA method is applied to detect CPKP in rectal swab specimens from infected patients, achieving sensitivity and specificity of 100% and 100%, respectively. The developed method can contribute to simple, rapid and accurate diagnosis of CPKP, which can help prevent nosocomial infections.

Advances in the detection of β-lactamase: A review

β-lactamase, an enzyme secreted by bacteria, is the main resistant mechanism of Gram-negative bacteria to β-lactam antibiotics. The resistance of bacteria to β-lactam antibiotics can be evaluated by testing the activity of β-lactamase. Traditional phenotypic detection is a golden principle, but it is time-consuming. In recent years, many new methods have emerged, which improve the efficiency by virtue of their sensitivity, low cost, easy operation, and other advantages. In this paper, we systematically review these researches and emphasize their limits of detection, sample operation, and test duration. Noteworthily, some detection systems can identify the β-lactamase subtype conveniently. We mainly divide these tests into three categories to elaborate their characteristics and application status. Both advantages and disadvantages of these methods are discussed. Additionally, we analyze the recent 5 years published researches to predict the trend of development in this field.

An Overview of Antimicrobial Resistance in Saudi Arabia (2013-2023) and the Need for National Surveillance

Antimicrobial resistance (AMR) is a well-recognized global threat. The World Health Organization (WHO) issued a report ranking the critical types of bacterial resistance that need to be monitored. Several studies from individual institutions in Saudi Arabia have reported rates of antimicrobial resistance using automated methods. However, no national surveillance study has been conducted to date using gold standard methods for antimicrobial susceptibility testing. This review summarizes AMR rates for major bacterial pathogens in Saudi Arabia and provides a justification for the need for a national surveillance project. In Saudi Arabia, AMR rates for both Gram-positive and Gram-negative bacteria are on the rise. Surveillance studies help identify AMR trends and emergence of outbreaks. The WHO has started a program, the Global Antimicrobial Resistance Surveillance System (GLASS), encouraging its member states, including Saudi Arabia, to conduct antimicrobial surveillance studies to estimate AMR rates worldwide. Of the microbiological methods used to test antimicrobial susceptibility, only broth microdilution (BMD) is considered the "gold standard." As AMR studies in Saudi Arabia are sparse, mostly limited to single centers and were conducted using automated methods, a national AMR surveillance project is needed to evaluate the current status and to inform stewardship decisions.

A Review of Carbapenem Resistance in Enterobacterales and Its Detection Techniques

Infectious disease outbreaks have caused thousands of deaths and hospitalizations, along with severe negative global economic impacts. Among these, infections caused by antimicrobial-resistant microorganisms are a major growing concern. The misuse and overuse of antimicrobials have resulted in the emergence of antimicrobial resistance (AMR) worldwide. Carbapenem-resistant Enterobacterales (CRE) are among the bacteria that need urgent attention globally. The emergence and spread of carbapenem-resistant bacteria are mainly due to the rapid dissemination of genes that encode carbapenemases through horizontal gene transfer (HGT). The rapid dissemination enables the development of host colonization and infection cases in humans who do not use the antibiotic (carbapenem) or those who are hospitalized but interacting with environments and hosts colonized with carbapenemase-producing (CP) bacteria. There are continuing efforts to characterize and differentiate carbapenem-resistant bacteria from susceptible bacteria to allow for the appropriate diagnosis, treatment, prevention, and control of infections. This review presents an overview of the factors that cause the emergence of AMR, particularly CRE, where they have been reported, and then, it outlines carbapenemases and how they are disseminated through humans, the environment, and food systems. Then, current and emerging techniques for the detection and surveillance of AMR, primarily CRE, and gaps in detection technologies are presented. This review can assist in developing prevention and control measures to minimize the spread of carbapenem resistance in the human ecosystem, including hospitals, food supply chains, and water treatment facilities. Furthermore, the development of rapid and affordable detection techniques is helpful in controlling the negative impact of infections caused by AMR/CRE. Since delays in diagnostics and appropriate antibiotic treatment for such infections lead to increased mortality rates and hospital costs, it is, therefore, imperative that rapid tests be a priority.