Rapid discrimination of four Salmonella enterica serovars: A performance comparison between benchtop and handheld Raman spectrometers.

Foodborne illnesses, particularly those caused by Salmonella enterica with its extensive array of over 2600 serovars, present a significant public health challenge. Therefore, prompt and precise identification of S. enterica serovars is essential for clinical relevance, which facilitates the understanding of S. enterica transmission routes and the determination of outbreak sources. Classical serotyping methods via molecular subtyping and genomic markers currently suffer from various limitations, such as labour intensiveness, time consumption, etc. Therefore, there is a pressing need to develop new diagnostic techniques. Surface-enhanced Raman spectroscopy (SERS) is a non-invasive diagnostic technique that can generate Raman spectra, based on which rapid and accurate discrimination of bacterial pathogens could be achieved. To generate SERS spectra, a Raman spectrometer is needed to detect and collect signals, which are divided into two types: the expensive benchtop spectrometer and the inexpensive handheld spectrometer. In this study, we compared the performance of two Raman spectrometers to discriminate four closely associated S. enterica serovars, that is, S. enterica subsp. enterica serovar dublin, enteritidis, typhi and typhimurium. Six machine learning algorithms were applied to analyse these SERS spectra. The support vector machine (SVM) model showed the highest accuracy for both handheld (99.97%) and benchtop (99.38%) Raman spectrometers. This study demonstrated that handheld Raman spectrometers achieved similar prediction accuracy as benchtop spectrometers when combined with machine learning models, providing an effective solution for rapid, accurate and cost-effective identification of closely associated S. enterica serovars.

Detection of Helicobacter pylori Infection in Human Gastric Fluid Through Surface-Enhanced Raman Spectroscopy Coupled With Machine Learning Algorithms.

Diagnostic methods for Helicobacter pylori infection include, but are not limited to, urea breath test, serum antibody test, fecal antigen test, and rapid urease test. However, these methods suffer drawbacks such as low accuracy, high false-positive rate, complex operations, invasiveness, etc. Therefore, there is a need to develop simple, rapid, and noninvasive detection methods for H. pylori diagnosis. In this study, we propose a novel technique for accurately detecting H. pylori infection through machine learning analysis of surface-enhanced Raman scattering (SERS) spectra of gastric fluid samples that were noninvasively collected from human stomachs via the string test. One hundred participants were recruited to collect gastric fluid samples noninvasively. Therefore, 12,000 SERS spectra (n = 120 spectra/participant) were generated for building machine learning models evaluated by standard metrics in model performance assessment. According to the results, the Light Gradient Boosting Machine algorithm exhibited the best prediction capacity and time efficiency (accuracy = 99.54% and time = 2.61 seconds). Moreover, the Light Gradient Boosting Machine model was blindly tested on 2,000 SERS spectra collected from 100 participants with unknown H. pylori infection status, achieving a prediction accuracy of 82.15% compared with qPCR results. This novel technique is simple and rapid in diagnosing H. pylori infection, potentially complementing current H. pylori diagnostic methods.

Rapid diagnosis and precision treatment of Helicobacter pylori infection in clinical settings.

Helicobacter pylori is a gram-negative bacterium that colonizes the stomach of approximately half of the worldwide population, with higher prevalence in densely populated areas like Asia, the Caribbean, Latin America, and Africa. H. pylori infections range from asymptomatic cases to potentially fatal diseases, including peptic ulcers, chronic gastritis, and stomach adenocarcinoma. The management of these conditions has become more difficult due to the rising prevalence of drug-resistant H. pylori infections, which ultimately lead to gastric cancer and mucosa-associated lymphoid tissue (MALT) lymphoma. In 1994, the International Agency for Research on Cancer (IARC) categorized H. pylori as a Group I carcinogen, contributing to approximately 780,000 cancer cases annually. Antibiotic resistance against drugs used to treat H. pylori infections ranges between 15% and 50% worldwide, with Asian countries having exceptionally high rates. This review systematically examines the impacts of H. pylori infection, the increasing prevalence of antibiotic resistance, and the urgent need for accurate diagnosis and precision treatment. The present status of precision treatment strategies and prospective approaches for eradicating infections caused by antibiotic-resistant H. pylori will also be evaluated.

Differentiation of closely-related species within Acinetobacter baumannii-calcoaceticus complex via Raman spectroscopy: a comparative machine learning analysis.

Bacterial species within the Acinetobacter baumannii-calcoaceticus (Acb) complex are very similar and are difficult to discriminate. Misidentification of these species in human infection may lead to severe consequences in clinical settings. Therefore, it is important to accurately discriminate these pathogens within the Acb complex. Raman spectroscopy is a simple method that has been widely studied for bacterial identification with high similarities. In this study, we combined surfaced-enhanced Raman spectroscopy (SERS) with a set of machine learning algorithms for identifying species within the Acb complex. According to the results, the support vector machine (SVM) model achieved the best prediction accuracy at 98.33% with a fivefold cross-validation rate of 96.73%. Taken together, this study confirms that the SERS-SVM method provides a convenient way to discriminate between A. baumannii, Acinetobacter pittii, and Acinetobacter nosocomialis in the Acb complex, which shows an application potential for species identification of Acinetobacter baumannii-calcoaceticus complex in clinical settings in near future.

[Evidence mapping of Chinese patent medicines in treatment of premature ventricular contractions].

This study employed evidence mapping to systematically sort out the clinical studies about the treatment of premature ventricular contractions with Chinese patent medicines and to reveal the distribution of evidence in this field. The articles about the treatment of premature ventricular contractions with Chinese patent medicines were searched against PubMed, Cochrane Library, Web of Science, CNKI, Wanfang, and VIP with the time interval from January 2016 to December 2022. Evidence was analyzed and presented by charts and graphs combined with text. According to the inclusion and exclusion criteria, 164 papers were included, including 147 interventional studies, 4 observational studies, and 13 systematic reviews. A total of 27 Chinese patent medicines were involved, in which Shensong Yangxin Capsules and Wenxin Granules had high frequency. There were off-label uses in clinical practice. In recent years, the number of articles published in this field showed a decreasing trend. Eight types of outcome indicators were used in interventional studies. Ambulatory electrocardiography, clinical response rate, safety, and echocardiography had high frequency, while the rate of ß-blocker decompensation, major cardiovascular events, and pharmaceutical economic indicators were rarely reported. The evaluation was one-sided. The low quality of the included articles reduced the reliability of the findings. In the future, the clinical use of medicines should be standardized, and the quality of clinical studies should be improved. Comprehensive clinical evaluation should be carried out to provide a sound scientific basis for the treatment of premature ventricular contractions with Chinese patent medicines.

Medial meniscus posterior root tears and partial meniscectomy significantly increase stress in the knee joint during dynamic gait.

PURPOSE: As a simple and invasive treatment, arthroscopic medial meniscal posterior horn resections (MMPHRs) can relieve the obstructive symptoms of medial meniscus posterior root tears (MMPRTs) but with the risk of aggravating biomechanical changes of the joint. The aim of this study was to analyze dynamic simulation of the knee joint after medial meniscus posterior root tear and posterior horn resection. METHODS: This study established static and dynamic models of MMPRTs and MMPHRs on the basis of the intact medial meniscus model (IMM). In the finite element analysis, the three models were subjected to 1000 N axial static load and the human walking gait load defined by the ISO14243-1 standard to evaluate the influence of MMPRTs and MMPHRs on knee joint mechanics during static standing and dynamic walking. RESULTS: In the static state, the load ratio of the medial and lateral compartments remained nearly constant (2:1), while in the dynamic state, the load ratio varied with the gait cycle. After MMPHRs, at 30% of the gait cycle, compared with the MMPRTs condition, the maximum von Mises stress of the lateral meniscus (LM) and the lateral tibial cartilage (LTC) were increased by 166.0% and 50.0%, respectively, while they changed by less than 5% during static analysis. The maximum von Mises stress of the medial meniscus (MM) decreased by 55.7%, and that of the medial femoral cartilage (MFC) increased by 53.5%. CONCLUSION: After MMPHRs, compared with MMPRTs, there was no significant stress increase in articular cartilage in static analysis, but there was a stress increase and concentration in both medial and lateral compartments in dynamic analysis, which may aggravate joint degeneration. Therefore, in clinical treatments, restoring the natural structure of MMPRTs is first recommended, especially for physically active patients.

Diagnostic roles of urinary kidney injury molecule 1 and soluble C5b-9 in acute tubulointerstitial nephritis.

Acute tubulointerstitial nephritis (ATIN) is a common cause of acute kidney injury characterized by inflammatory cells infiltrating in the interstitium. The present study aimed to explore noninvasive biomarkers that might indicate activity of pathological injuries and help direct treatment. Fifty-four patients with clinical-pathologically diagnosed ATIN from January 1, 2014, to June 30, 2016, at Peking University First Hospital were enrolled. Urine samples were collected on the morning of renal biopsy and assessed for urinary kidney injury molecule-1 (KIM-1) and urinary soluble C5b-9 (sC5b-9). Immunofluorescence staining for KIM-1 and C5b-9 was performed in biopsied kidney sections from ATIN cases. The clinical and pathological relevance of the two urinary biomarkers was analyzed. Both urinary KIM-1 and sC5b-9 values were significantly elevated in patients with ATIN compared with healthy controls. The urinary KIM-1 level positively correlated with urinary N-acetyl-ß-d-glucosaminidase (r = 0. 542, P = 0.001) and the pathological tubular injury score (r = 0.469, P < 0.001), whereas the urinary sC5b-9 level was related to pathological activity scores for tubular injury (r = 0.413, P = 0.002), interstitial inflammation (r = 0.388, P = 0.004), and treatment response (r = 0.564, P < 0.001). Urinary KIM-1 tended to have better diagnostic value for tubular injury than urinary sC5b-9, whereas only urinary sC5b-9 was able to demonstrate severe interstitial inflammation. A combination of urinary KIM-1 and sC5b-9 had an area under the receiver-operating characteristic curve of 0.864 (95% confidence interval: 0.766-0.963, P < 0.001, sensitivity: 75%, specificity: 88%) for acute tissue injury in ATIN. KIM-1 expression was markedly increased in renal tubular cells in both ATIN and acute tubular necrosis conditions, whereas a significant upregulation of C5b-9 was only detected in the tubular cells and interstitial cells in ATIN cases. Urinary KIM-1 is a specific biomarker for renal tubular injury in ATIN, whereas urinary sC5b-9 is valuable in demonstrating severe interstitial inflammation. The combination of these two biomarkers helps identify patients at an acute injury stage and, therefore, might facilitate clinical evaluation and guide immunosuppressive therapy.

Adaptive methylation regulation of p53 pathway in sympatric speciation of blind mole rats, Spalax.

Epigenetic modifications play significant roles in adaptive evolution. The tumor suppressor p53, well known for controlling cell fate and maintaining genomic stability, is much less known as a master gene in environmental adaptation involving methylation modifications. The blind subterranean mole rat Spalax eherenbergi superspecies in Israel consists of four species that speciated peripatrically. Remarkably, the northern Galilee species Spalax galili (2n = 52) underwent adaptive ecological sympatric speciation, caused by the sharply divergent chalk and basalt ecologies. This was demonstrated by mitochondrial and nuclear genomic evidence. Here we show that the expression patterns of the p53 regulatory pathway diversified between the abutting sympatric populations of S. galili in sharply divergent chalk-basalt ecologies. We identified higher methylation on several sites of the p53 promoter in the population living in chalk soil (chalk population). Site mutagenesis showed that methylation on these sites linked to the transcriptional repression of p53 involving Cut-Like Homeobox 1 (Cux1), paired box 4 (Pax 4), Pax 6, and activator protein 1 (AP-1). Diverse expression levels of p53 between the incipiently sympatrically speciating chalk-basalt abutting populations of S. galili selectively affected cell-cycle arrest but not apoptosis. We hypothesize that methylation modification of p53 has adaptively shifted in supervising its target genes during sympatric speciation of S. galili to cope with the contrasting environmental stresses of the abutting divergent chalk-basalt ecologies.

Systemic pro-inflammatory response facilitates the development of cerebral edema during short hypoxia.

BACKGROUND: High-altitude cerebral edema (HACE) is the severe type of acute mountain sickness (AMS) and life threatening. A subclinical inflammation has been speculated, but the exact mechanisms underlying the HACE are not fully understood. METHODS: Human volunteers ascended to high altitude (3860 m, 2 days), and rats were exposed to hypoxia in a hypobaric chamber (5000 m, 2 days). Human acute mountain sickness was evaluated by the Lake Louise Score (LLS), and plasma corticotrophin-releasing hormone (CRH) and cytokines TNF-α, IL-1ß, and IL-6 were measured in rats and humans. Subsequently, rats were pre-treated with lipopolysaccharide (LPS, intraperitoneal (ip) 4 mg/kg, 11 h) to induce inflammation prior to 1 h hypoxia (7000 m elevation). TNF-α, IL-1ß, IL-6, nitric oxide (NO), CRH, and aquaporin-4 (AQP4) and their gene expression, Evans blue, Na(+)-K(+)-ATPase activity, p65 translocation, and cell swelling were measured in brain by ELISA, Western blotting, Q-PCR, RT-PCR, immunohistochemistry, and transmission electron micrography. MAPKs, NF-κB pathway, and water permeability of primary astrocytes were demonstrated. All measurements were performed with or without LPS challenge. The release of NO, TNF-α, and IL-6 in cultured primary microglia by CRH stimulation with or without PDTC (NF-κB inhibitor) or CP154,526 (CRHR1 antagonist) were measured. RESULTS: Hypobaric hypoxia enhanced plasma TNF-α, IL-1ß, and IL-6 and CRH levels in human and rats, which positively correlated with AMS. A single LPS injection (ip, 4 mg/kg, 12 h) into rats increased TNF-α and IL-1ß levels in the serum and cortex, and AQP4 and AQP4 mRNA expression in cortex and astrocytes, and astrocyte water permeability but did not cause brain edema. However, LPS treatment 11 h prior to 1 h hypoxia (elevation, 7000 m) challenge caused cerebral edema, which was associated with activation of NF-κB and MAPKs, hypoxia-reduced Na(+)-K(+)-ATPase activity and blood-brain barrier (BBB) disruption. Both LPS and CRH stimulated TNF-α, IL-6, and NO release in cultured rat microglia via NF-κB and cAMP/PKA. CONCLUSIONS: Preexisting systemic inflammation plus a short severe hypoxia elicits cerebral edema through upregulated AQP4 and water permeability by TLR4 and CRH/CRHR1 signaling. This study revealed that both infection and hypoxia can cause inflammatory response in the brain. Systemic inflammation can facilitate onset of hypoxic cerebral edema through interaction of astrocyte and microglia by activation of TLR4 and CRH/CRHR1 signaling. Anti-inflammatory agents and CRHR1 antagonist may be useful for prevention and treatment of AMS and HACE.

Rapid discrimination and ratio quantification of mixed antibiotics in aqueous solution through integrative analysis of SERS spectra via CNN combined with NN-EN model.

INTRODUCTION: Abusing antibiotic residues in the natural environment has become a severe public health and ecological environmental problem. The side effects of its biochemical and physiological consequences are severe. To avoid antibiotic contamination in water, implementing universal and rapid antibiotic residue detection technology is critical to maintaining antibiotic safety in aquatic environments. Surface-enhanced Raman spectroscopy (SERS) provides a powerful tool for identifying small molecular components with high sensitivity and selectivity. However, it remains a challenge to identify pure antibiotics from SERS spectra due to coexisting components in the mixture. OBJECTIVES: In this study, an intelligent analysis model for the SERS spectrum based on a deep learning algorithm was proposed for rapid identification of the antibiotic components in the mixture and quantitative determination of the ratios of these components. METHODS: We established a water environment system containing three antibiotic residues of ciprofloxacin, doxycycline, and levofloxacin. To facilitate qualitative and quantitative analysis of the SERS spectra antibiotic mixture datasets, we developed a computational framework integrating a convolutional neural network (CNN) and a non-negative elastic network (NN-EN) method. RESULTS: The experimental results demonstrate that the CNN model has a recognition accuracy of 98.68%, and the interpretation analysis of Shapley Additive exPlanations (SHAP) shows that our model can specifically focus on the characteristic peak distribution. In contrast, the NN-EN model can accurately quantify each component's ratio in the mixture. CONCLUSION: Integrating the SERS technique assisted by the CNN combined with the NN-EN model exhibits great potential for rapid identification and high-precision quantification of antibiotic residues in aquatic environments.

Pseudo-Siamese network combined with label-free Raman spectroscopy for the quantification of mixed trace amounts of antibiotics in human milk: A feasibility study.

The utilization of antibiotics is prevalent among lactating mothers. Hence, the rapid determination of trace amounts of antibiotics in human milk is crucial for ensuring the healthy development of infants. In this study, we constructed a human milk system containing residual doxycycline (DXC) and/or tetracycline (TC). Machine learning models and clustering algorithms were applied to classify and predict deficient concentrations of single and mixed antibiotics via label-free SERS spectra. The experimental results demonstrate that the CNN model has a recognition accuracy of 98.85% across optimal hyperparameter combinations. Furthermore, we employed Independent Component Analysis (ICA) and the pseudo-Siamese Convolutional Neural Network (pSCNN) to quantify the ratios of individual antibiotics in mixed human milk samples. Integrating the SERS technique with machine learning algorithms shows significant potential for rapid discrimination and precise quantification of single and mixed antibiotics at deficient concentrations in human milk.

Rapid discrimination between wild and cultivated Ophiocordyceps sinensis through comparative analysis of label-free SERS technique and mass spectrometry.

Ophiocordyceps sinensis is a genus of ascomycete fungi that has been widely used as a valuable tonic or medicine. However, due to over-exploitation and the destruction of natural ecosystems, the shortage of wild O. sinensis resources has led to an increase in artificially cultivated O. sinensis. To rapidly and accurately identify the molecular differences between cultivated and wild O. sinensis, this study employs surface-enhanced Raman spectroscopy (SERS) combined with machine learning algorithms to distinguish the two O. sinensis categories. Specifically, we collected SERS spectra for wild and cultivated O. sinensis and validated the metabolic profiles of SERS spectra using Ultra-Performance Liquid Chromatography coupled with Orbitrap High-Resolution Mass Spectrometry (UPLC-Orbitrap-HRMS). Subsequently, we constructed machine learning classifiers to mine potential information from the spectral data, and the spectral feature importance map is determined through an optimized algorithm. The results indicate that the representative characteristic peaks in the SERS spectra are consistent with the metabolites identified through metabolomics analysis, confirming the feasibility of the SERS method. The optimized support vector machine (SVM) model achieved the most accurate and efficient capacity in discriminating between wild and cultivated O. sinensis (accuracy = 98.95%, 5-fold cross-validation = 98.38%, time = 0.89s). The spectral feature importance map revealed subtle compositional differences between wild and cultivated O. sinensis. Taken together, these results are expected to enable the application of SERS in the quality control of O. sinensis raw materials, providing a foundation for the efficient and rapid identification of their quality and origin.

Identification of hypermucoviscous Klebsiella pneumoniae strains via untargeted surface-enhanced Raman spectroscopy.

Klebsiella pneumoniae is one of the most common causes of hospital-acquired infections, especially due to the emergence of the hypervirulent K. pneumoniae (hvKp) strains. Multiple methods have been developed to discriminate hvKp strains from classical K. pneumoniae (cKp) strains, such as the presence of candidate genes (e.g., peg-344, iroB, and iucA), high level of siderophore production, hypermucoviscosity phenotype, etc. Although the string test is commonly used to confirm the hypermucoviscosity of K. pneumoniae strains, it is a method lacking rigidity and accuracy. Surface-enhanced Raman spectroscopy (SERS) coupled with machine learning algorithms has been widely used in discriminating bacterial pathogens with different phenotypes. However, the technique has not be applied to identify hypermucoviscous K. pneumoniae (hmvKp) strains. In this study, we isolated a set of K. pneumoniae strains from clinical samples, among which hmvKp strains (N = 10) and cKP strains (N = 10) were randomly selected to collect SESR spectra. Eight machine learning algorithms were recruited for model construction and spectral prediction in this study, among which support vector machine (SVM) outperforms all other algorithms with the highest prediction accuracy of hmvKp strains (5-fold cross validation = 99.07%). Taken together, this pilot study confirms that SERS, combined with machine learning algorithms, can accurately identify hmvKp strains, which can facilitate the fast recognition of hvKP strains when combined with relevant methods and biomarkers in clinical settings in the near future.

Identification of chronic non-atrophic gastritis and intestinal metaplasia stages in the Correa's cascade through machine learning analyses of SERS spectral signature of non-invasively-collected human gastric fluid samples.

The progression of gastric cancer involves a complex multi-stage process, with gastroscopy and biopsy being the standard procedures for diagnosing gastric diseases. This study introduces an innovative non-invasive approach to differentiate gastric disease stage using gastric fluid samples through machine-learning-assisted surface-enhanced Raman spectroscopy (SERS). This method effectively identifies different stages of gastric lesions. The XGBoost algorithm demonstrates the highest accuracy of 96.88% and 91.67%, respectively, in distinguishing chronic non-atrophic gastritis from intestinal metaplasia and different subtypes of gastritis (mild, moderate, and severe). Through blinded testing validation, the model can achieve more than 80% accuracy. These findings offer new possibilities for rapid, cost-effective, and minimally invasive diagnosis of gastric diseases.

Recent advances in surface enhanced Raman spectroscopy for bacterial pathogen identifications.

BACKGROUND: The rapid and reliable detection of pathogenic bacteria at an early stage is a highly significant research field for public health. However, most traditional approaches for pathogen identification are time-consuming and labour-intensive, which may cause physicians making inappropriate treatment decisions based on an incomplete diagnosis of patients with unknown infections, leading to increased morbidity and mortality. Therefore, novel methods are constantly required to face the emerging challenges of bacterial detection and identification. In particular, Raman spectroscopy (RS) is becoming an attractive method for rapid and accurate detection of bacterial pathogens in recent years, among which the newly developed surface-enhanced Raman spectroscopy (SERS) shows the most promising potential. AIM OF REVIEW: Recent advances in pathogen detection and diagnosis of bacterial infections were discussed with focuses on the development of the SERS approaches and its applications in complex clinical settings. KEY SCIENTIFIC CONCEPTS OF REVIEW: The current review describes bacterial classification using surface enhanced Raman spectroscopy (SERS) for developing a rapid and more accurate method for the identification of bacterial pathogens in clinical diagnosis. The initial part of this review gives a brief overview of the mechanism of SERS technology and development of the SERS approach to detect bacterial pathogens in complex samples. The development of the label-based and label-free SERS strategies and several novel SERS-compatible technologies in clinical applications, as well as the analytical procedures and examples of chemometric methods for SERS, are introduced. The computational challenges of pre-processing spectra and the highlights of the limitations and perspectives of the SERS technique are also discussed.Taken together, this systematic review provides an overall summary of the SERS technique and its application potential for direct bacterial diagnosis in clinical samples such as blood, urine and sputum, etc.

Identification of geographic origins of Morus alba Linn. through surfaced enhanced Raman spectrometry and machine learning algorithms.

The leaves of Morus alba Linn., which is also known as white mulberry, have been commonly used in many of traditional systems of medicine for centuries. In traditional Chinese medicine (TCM), mulberry leaf is mainly used for anti-diabetic purpose due to its enrichment in bioactive compounds such as alkaloids, flavonoids and polysaccharides. However, these components are variable due to the different habitats of the mulberry plant. Therefore, geographic origin is an important feature because it is closely associated with bioactive ingredient composition that further influences medicinal qualities and effects. As a low-cost and non-invasive method, surface enhanced Raman spectrometry (SERS) is able to generate the overall fingerprints of chemical compounds in medicinal plants, which holds the potential for the rapid identification of their geographic origins. In this study, we collected mulberry leaves from five representative provinces in China, namely, Anhui, Guangdong, Hebei, Henan and Jiangsu. SERS spectrometry was applied to characterize the fingerprints of both ethanol and water extracts of mulberry leaves, respectively. Through the combination of SERS spectra and machine learning algorithms, mulberry leaves were well discriminated with high accuracies in terms of their geographic origins, among which the deep learning algorithm convolutional neural network (CNN) showed the best performance. Taken together, our study established a novel method for predicting the geographic origins of mulberry leaves through the combination of SERS spectra with machine learning algorithms, which strengthened the application potential of the method in the quality evaluation, control and assurance of mulberry leaves.

Rapid discrimination of Shigella spp. and Escherichia coli via label-free surface enhanced Raman spectroscopy coupled with machine learning algorithms.

Shigella and enterotoxigenic Escherichia coli (ETEC) are major bacterial pathogens of diarrheal disease that is the second leading cause of childhood mortality globally. Currently, it is well known that Shigella spp., and E. coli are very closely related with many common characteristics. Evolutionarily speaking, Shigella spp., are positioned within the phylogenetic tree of E. coli. Therefore, discrimination of Shigella spp., from E. coli is very difficult. Many methods have been developed with the aim of differentiating the two species, which include but not limited to biochemical tests, nucleic acids amplification, and mass spectrometry, etc. However, these methods suffer from high false positive rates and complicated operation procedures, which requires the development of novel methods for accurate and rapid identification of Shigella spp., and E. coli. As a low-cost and non-invasive method, surface enhanced Raman spectroscopy (SERS) is currently under intensive study for its diagnostic potential in bacterial pathogens, which is worthy of further investigation for its application in bacterial discrimination. In this study, we focused on clinically isolated E. coli strains and Shigella species (spp.), that is, S. dysenteriae, S. boydii, S. flexneri, and S. sonnei, based on which SERS spectra were generated and characteristic peaks for Shigella spp., and E. coli were identified, revealing unique molecular components in the two bacterial groups. Further comparative analysis of machine learning algorithms showed that, the Convolutional Neural Network (CNN) achieved the best performance and robustness in bacterial discrimination capacity when compared with Random Forest (RF) and Support Vector Machine (SVM) algorithms. Taken together, this study confirmed that SERS paired with machine learning could achieve high accuracy in discriminating Shigella spp., from E. coli, which facilitated its application potential for diarrheal prevention and control in clinical settings. Graphical abstract.

Molecular mechanisms of glycogen particle assembly in Escherichia coli.

It has been reported that glycogen in Escherichia coli has two structural states, that is, fragility and stability, which alters dynamically. However, molecular mechanisms behind the structural alterations are not fully understood. In this study, we focused on the potential roles of two important glycogen degradation enzymes, glycogen phosphorylase (glgP) and glycogen debranching enzyme (glgX), in glycogen structural alterations. The fine molecular structure of glycogen particles in Escherichia coli and three mutants (ΔglgP, ΔglgX and ΔglgP/ΔglgX) were examined, which showed that glycogen in E. coli ΔglgP and E. coli ΔglgP/ΔglgX were consistently fragile while being consistently stable in E. coli ΔglgX, indicating the dominant role of GP in glycogen structural stability control. In sum, our study concludes that glycogen phosphorylase is essential in glycogen structural stability, leading to molecular insights into structural assembly of glycogen particles in E. coli.

Rapid Prediction of Multidrug-Resistant Klebsiella pneumoniae through Deep Learning Analysis of SERS Spectra.

Klebsiella pneumoniae is listed by the WHO as a priority pathogen of extreme importance that can cause serious consequences in clinical settings. Due to its increasing multidrug resistance all over the world, K. pneumoniae has the potential to cause extremely difficult-to-treat infections. Therefore, rapid and accurate identification of multidrug-resistant K. pneumoniae in clinical diagnosis is important for its prevention and infection control. However, the limitations of conventional and molecular methods significantly hindered the timely diagnosis of the pathogen. As a label-free, noninvasive, and low-cost method, surface-enhanced Raman scattering (SERS) spectroscopy has been extensively studied for its application potentials in the diagnosis of microbial pathogens. In this study, we isolated and cultured 121 K. pneumoniae strains from clinical samples with different drug resistance profiles, which included polymyxin-resistant K. pneumoniae (PRKP; n = 21), carbapenem-resistant K. pneumoniae, (CRKP; n = 50), and carbapenem-sensitive K. pneumoniae (CSKP; n = 50). For each strain, a total of 64 SERS spectra were generated for the enhancement of data reproducibility, which were then computationally analyzed via the convolutional neural network (CNN). According to the results, the deep learning model CNN plus attention mechanism could achieve a prediction accuracy as high as 99.46%, with robustness score of 5-fold cross-validation at 98.87%. Taken together, our results confirmed the accuracy and robustness of SERS spectroscopy in the prediction of drug resistance of K. pneumoniae strains with the assistance of deep learning algorithms, which successfully discriminated and predicted PRKP, CRKP, and CSKP strains. IMPORTANCE This study focuses on the simultaneous discrimination and prediction of Klebsiella pneumoniae strains with carbapenem-sensitive, carbapenem-resistant, and polymyxin-resistant phenotypes. The implementation of CNN plus an attention mechanism makes the highest prediction accuracy at 99.46%, which confirms the diagnostic potential of the combination of SERS spectroscopy with the deep learning algorithm for antibacterial susceptibility testing in clinical settings.

Serum anti-CRP antibodies differentiate etiology and predict relapse in acute tubulointerstitial nephritis.

INTRODUCTION: Acute tubulointerstitial nephritis (ATIN) is a common cause of acute kidney injury with various etiologies. It has been shown that autoimmune-related ATIN (AI-ATIN) has a higher recurrence rate and a greater likelihood of developing into chronic kidney disease compared with drug-induced ATIN, yet misdiagnosis at renal biopsy is not uncommon. METHODS: Patients who were clinicopathologically diagnosed as ATIN from January 2006 to December 2015 in Peking University First Hospital were enrolled. Clinical, pathological and follow-up data were collected. Serum samples on the day of renal biopsy were collected and tested for anti-C-reactive protein (CRP) antibodies. CRP and its linear peptides were used as coating antigens to detect antibodies. Statistical analysis was used to assess the diagnostic value of the antibodies. RESULTS: Altogether 146 patients were enrolled. The receiver operating characteristic-area under the curve of the anti-CRP antibody for the identification of late-onset AI-ATIN was 0.750 (95% confidence interval 0.641-0.860, P < 0.001) and the positivity was associated with ATIN relapse (adjusted hazard ratio = 4.321, 95% confidence interval 2.402-7.775, P < 0.001). Antibodies detected by CRP linear peptide 6 (PT6) were superior with regard to differentiating patients with AI-ATIN, while antibodies detected by peptide 17 (PT17) could predict ATIN relapse. Antibodies detected by these two peptides were positively correlated with the severity of tubular dysfunction and pathological injury. CONCLUSIONS: Serum anti-CRP antibody could be used to differentiate late-onset AI-ATIN and predict relapse of ATIN at the time of renal biopsy. The CRP linear peptides PT6 and PT17 could be used as coating antigens to detect anti-CRP antibodies, which may provide more information for the clinical assessment of ATIN.