Structure-Functional Activity of Pyrone Derivatives for Inhibition of Barnacle Settlement and Biofilm Formation

Naturally occurring 6-pentyl-2H-pyran-2-one and its synthetic analogues greatly inhibit the settlement of Amphibalanus amphitrite cyprids and the growth and biofilm formation of marine bacteria. To optimize the antifouling activities of pyrone derivatives, this study designed pyrone analogues by modifying functional groups, such as the benzyl group, cyclopentane, and halides, substituted on both sides of a pyrone. The antifouling effects of the synthesized pyrone derivatives were subsequently evaluated against five marine biofilm-forming bacteria, Loktanella hongkongensis, Staphylococcus cohnii, S. saprophyticus, Photobacterium angustum, and Alteromonas macleodii, along with barnacle cyprids of Amphibalanus amphitrite. Substituting nonpolar parts-such as the aliphatic, cyclopentyl, or phenyl moieties on C-5 or the furan moieties on C-3-not only increased antibacterial activity and inhibited biofilm formation but also inhibited barnacle cyprid settlement when compared to 6-pentyl-2H-pyran-2-one.

Rapid and Simple Morphological Assay for Determination of Susceptibility/Resistance to Combined Ciprofloxacin and Ampicillin, Independently, in Escherichia coli

Current antibiograms cannot discern the particular effect of a specific antibiotic when the bacteria are incubated with a mixture of antibiotics. To prove that this task is achievable, Escherichia coli strains were treated with ciprofloxacin for 45 min, immobilized on a slide and stained with SYBR Gold. In susceptible strains, the nucleoid relative surface started to decrease near the MIC, being progressively condensed as the dose increased. The shrinkage level correlated with the DNA fragmentation degree. Ciprofloxacin-resistant bacilli showed no change. Additionally, E. coli strains were incubated with ampicillin for 45 min and processed similarly. The ampicillin-susceptible strain revealed intercellular DNA fragments that increased with dose, unlike the resistant strain. Co-incubation with both antibiotics revealed that ampicillin did not modify the nucleoid condensation effect of ciprofloxacin, whereas the quinolone partially decreased the background of DNA fragments induced by ampicillin. Sixty clinical isolates, with different combinations of susceptibility-resistance to each antibiotic, were co-incubated with the EUCAST breakpoints of susceptibility of ciprofloxacin and ampicillin. The morphological assay correctly categorized all the strains for each antibiotic in 60 min, demonstrating the feasible independent evaluation of a mixture of quinolone and beta-lactam. The rapid phenotypic assay may shorten the incubation times and necessary microbial mass currently required for evaluation.

Rapid, Ultrasensitive, and Visual Detection of Pathogens Based on Cation Dye-Triggered Gold Nanoparticle Electrokinetic Agglutination Analysis

Rapid prescribing of the right antibiotic is the key to treat infectious diseases and decelerate the challenge of bacterial antibiotic resistance. Herein, by targeting the 16S rRNA of bacteria, we developed a cation dye-triggered electrokinetic gold nanoparticle (AuNP) agglutination (CD-TEAA) method, which is rapid, visual, ultrasensitive, culture-independent, and low in cost. The limit of detection (LOD) is as low as 1 CFU mL-1 Escherichia coli. The infection identifications of aseptic fluid samples (n = 11) and urine samples with a clinically suspected urinary tract infection (UTI, n = 78) were accomplished within 50 and 30 min for each sample, respectively. The antimicrobial susceptibility testing (AST) of UTI urine samples was achieved within 2.5 h. In ROC analysis of urine, the sensitivity and specificity were 100 and 96% for infection identification, and 100 and 98% for AST, respectively. Moreover, the overall cost of materials for each test is about US$0.69. Therefore, the CD-TEAA method is a superior approach to existing, time-consuming, and expensive methods, especially in less developed areas.

Current and Future Flow Cytometry Applications Contributing to Antimicrobial Resistance Control

Antimicrobial resistance is a global threat to human health and welfare, food safety, and environmental health. The rapid detection and quantification of antimicrobial resistance are important for both infectious disease control and public health threat assessment. Technologies such as flow cytometry can provide clinicians with the early information, they need for appropriate antibiotic treatment. At the same time, cytometry platforms facilitate the measurement of antibiotic-resistant bacteria in environments impacted by human activities, enabling assessment of their impact on watersheds and soils. This review focuses on the latest applications of flow cytometry for the detection of pathogens and antibiotic-resistant bacteria in both clinical and environmental samples. Novel antimicrobial susceptibility testing frameworks embedding flow cytometry assays can contribute to the implementation of global antimicrobial resistance surveillance systems that are needed for science-based decisions and actions.

Handyfuge Microfluidic for On-Site Antibiotic Susceptibility Testing

Low-cost, rapid, and accurate acquisition of minimum inhibitory concentrations (MICs) is key to limiting the development of antimicrobial resistance (AMR). Until now, conventional antibiotic susceptibility testing (AST) methods are typically time-consuming, high-cost, and labor-intensive, making them difficult to accomplish this task. Herein, an electricity-free, portable, and robust handyfuge microfluidic chip was developed for on-site AST, termed handyfuge-AST. With simply handheld centrifugation, the bacterial-antibiotic mixtures with accurate antibiotic concentration gradients could be generated in less than 5 min. The accurate MIC values of single antibiotics (including ampicillin, kanamycin, and chloramphenicol) or their combinations against Escherichia coli could be obtained within 5 h. To further meet the growing demands of point-of-care testing, we upgraded our handyfuge-AST with a pH-based colorimetric strategy, enabling naked eye recognition or intelligent recognition with a homemade mobile app. Through a comparative study of 60 clinical data (10 clinical samples corresponding to six commonly used antibiotics), the accurate MICs by handyfuge-AST with 100% categorical agreements were achieved compared to clinical standard methods (area under curves, AUCs = 1.00). The handyfuge-AST could be used as a low-cost, portable, and robust point-of-care device to rapidly obtain accurate MIC values, which significantly limit the progress of AMR.

Rapid antimicrobial susceptibility testing for low bacterial concentrations integrating a centrifuge based bacterial cell concentrator

Antibiotic resistance threatens human health worldwide. Patients infected with antibiotic-resistant bacteria require appropriate antibiotic prescriptions based on a rapid antibiotic susceptibility test (AST). Various rapid AST methods have been developed to replace the conventional AST method, which requires a long testing time. However, in most cases, these methods require a high density of bacterial samples, which leads to an additional incubation or concentration process. In this study, we introduce a rapid AST platform that allows the use of low-density bacterial samples by concentrating bacterial cells and performing AST on a single microfluidic chip. In addition, the outlet-free loading process enables the platform to load the sample and concentrate bacteria into a small field of view for single-cell detection. Using this method, rapid AST determined antibiotic resistance in three hours from a standard strain of 10³ colony-forming unit (CFU) per ml bacterial concentration. This technique can be used for the cell-based drug testing of various low-concentration bacterial samples.

Sensitive Detection of Salmonella Based on CRISPR-Cas12a and the Tetrahedral DNA Nanostructure-Mediated Hyperbranched Hybridization Chain Reaction

Salmonella severely threatens global human health and causes financial burden. The ability to sensitively detect Salmonella in food samples is highly valuable but remains a challenge. Herein, a sensitive detection method for Salmonella was developed by coupling immunomagnetic separation with the CRISPR-Cas12a system and the tetrahedral DNA nanostructure-mediated hyperbranched hybridization chain reaction (TDN-hHCR). In the detection system, the target Salmonella was immunomagnetically separated and labeled with bio-barcode DNA-modified gold nanoparticles (AuNPs), which could transfer and magnify the signal of a bacterial cell into numerous bio-barcode DNA molecules. Afterward, the bio-barcode DNA can trigger the trans-cleavage activity of CRISPR-Cas12a to inhibit the process of the TDN-hHCR to generate a fluorescence readout. Due to the high immunomagnetic separation efficiency and the effective signal amplification of CRISPR-Cas12a and the TDN-hHCR, Salmonella as low as 8 CFU/mL could be easily detected. Meanwhile, this has been applied for practical use and showed the capability to detect 17 and 25 CFU/mL in spiked milk and egg white, respectively, indicating its potential application in real samples.

All-In-One Escherichia coli Viability Assay for Multi-dimensional Detection of Uncomplicated Urinary Tract Infections

The urinary tract infections by antibiotic-resistant bacteria have been a serious public health problem and increase the healthcare costs. The conventional technologies of diagnosis and antimicrobial susceptibility testing (AST) relying on multiple culture-based assays are time-consuming and labor-intensive and thus compel the empirical antimicrobial therapies to be prescribed, fueling the prevalence of antimicrobial resistance. Herein, we propose an all-in-one Escherichia coli viability assay in an enclosed 3D microwell array chip, termed digital β-d-glucuronidase (GUS)-AST assay. It employs GUS, a specific metabolism-related enzyme, to convert the presence of E. coli into bright fluorescence. The random distribution of single bacteria in microwell array enables to quantify the E. coli concentrations by counting the positive microwells. We incorporate the most probable number with digital quantification to lower the limit of detection and expand the dynamic range to 7 orders. The digital GUS-AST assay is able to indicate the potency of antibiotics and determine the minimum inhibitory concentrations. A streamlined procedure of urine removal, bacterial separation, and digital GUS-AST is established to perform the direct analysis of bacteria population in urine. The sample-to-result workflow can be finished in 4.5 h with a limit of detection of 39 CFU/mL. With further development for additional pathogens and multiple antibiotic conditions, the digital GUS-AST assay could help physicians to prescribe timely targeted therapies for better patient outcomes and the minimum emergence of resistant bacteria.

eMIC-AntiKP: Estimating minimum inhibitory concentrations of antibiotics towards Klebsiella pneumoniae using deep learning

Nowadays, antibiotic resistance has become one of the most concerning problems that directly affects the recovery process of patients. For years, numerous efforts have been made to efficiently use antimicrobial drugs with appropriate doses not only to exterminate microbes but also stringently constrain any chances for bacterial evolution. However, choosing proper antibiotics is not a straightforward and time-effective process because well-defined drugs can only be given to patients after determining microbic taxonomy and evaluating minimum inhibitory concentrations (MICs). Besides conventional methods, numerous computer-aided frameworks have been recently developed using computational advances and public data sources of clinical antimicrobial resistance. In this study, we introduce eMIC-AntiKP, a computational framework specifically designed to predict the MIC values of 20 antibiotics towards Klebsiella pneumoniae. Our prediction models were constructed using convolutional neural networks and k-mer counting-based features. The model for cefepime has the most limited performance with a test 1-tier accuracy of 0.49, while the model for ampicillin has the highest performance with a test 1-tier accuracy of 1.00. Most models have satisfactory performance, with test accuracies ranging from about 0.70-0.90. The significance of eMIC-AntiKP is the effective utilization of computing resources to make it a compact and portable tool for most moderately configured computers. We provide users with two options, including an online web server for basic analysis and an offline package for deeper analysis and technical modification.

Rolling Circle Amplification Tailored for Plasmonic Biosensors: From Ensemble to Single-Molecule Detection

We report on the tailoring of rolling circle amplification (RCA) for affinity biosensors relying on the optical probing of their surface with confined surface plasmon field. Affinity capture of the target analyte at the metallic sensor surface (e.g., by using immunoassays) is followed by the RCA step for subsequent readout based on increased refractive index (surface plasmon resonance, SPR) or RCA-incorporated high number of fluorophores (in surface plasmon-enhanced fluorescence, PEF). By combining SPR and PEF methods, this work investigates the impact of the conformation of long RCA-generated single-stranded DNA (ssDNA) chains to the plasmonic sensor response enhancement. In order to confine the RCA reaction within the evanescent surface plasmon field and hence maximize the sensor response, an interface carrying analyte-capturing molecules and additional guiding ssDNA strands (complementary to the repeating segments of RCA-generated chains) is developed. When using the circular padlock probe as a model target analyte, the PEF readout shows that the reported RCA implementation improves the limit of detection (LOD) from 13 pM to high femtomolar concentration when compared to direct labeling. The respective enhancement factor is of about 2 orders of magnitude, which agrees with the maximum number of fluorophore emitters attached to the RCA chain that is folded in the evanescent surface plasmon field by the developed biointerface. Moreover, the RCA allows facile visualizing of individual binding events by fluorescence microscopy, which enables direct counting of captured molecules. This approach offers a versatile route toward a fast digital readout format of single-molecule detection with further reduced LOD.

Investigating the origins of bacterial SERS responses to antibiotics observed in the extracellular matrix liquid

Surface-enhanced Raman spectroscopy (SERS) has been applied to analyze bacterial cells and their responses to antibiotic exposure. However, significant knowledge gaps remain regarding the origins of specific antibiotic response patterns and the necessary experimental steps required to see them clearly in the SERS spectra, particularly involving SERS responses observed in the extracellular matrix liquid of bacterial samples. In this study, a variety of experimental parameters were tested to assess the antibiotic response patterns seen in liquid samples from E. coli under different conditions. These include testing the impact of washing the cells with water after incubating them with antibiotics, as well as the effect of using different types of liquids with varying characteristics for incubating the bacteria with the antibiotics. It was found that the experimental procedure has a significant impact on the resulting SERS signals, and the target patterns could only be observed in specific conditions. In particular, the step of washing the bacteria with water is necessary for observing the antibiotic response patterns, and incubating the bacteria and antibiotics in a nutrient-rich growth medium is preferable to incubating the cells in a buffer or in distilled water. These findings can be used to improve existing methods for testing antibiotic responses with SERS, and could potentially help to further develop and optimize SERS-based procedures for assessing antibiotic sensitivity.

Ultrasensitive and rapid identification of ESRI developer- and piperacillin/tazobactam-resistant Escherichia coli by the MALDIpiptaz test

Background

The excessive use of piperacillin/tazobactam (P/T) has promoted the emergence of P/T-resistant Enterobacterales. We reported that in Escherichia coli, P/T contributes to the development of extended-spectrum resistance to β-lactam/β-lactamase inhibitor (BL/BLI) (ESRI) in isolates that are P/T susceptible but have low-level resistance to BL/BLI. Currently, the detection of P/T resistance relying on conventional methods is time-consuming. To overcome this issue, we developed a cost-effective test based on MALDI-MS technology, called MALDIpiptaz, which aims to detect P/T resistance and ESRI developers in E. coli.

Methods

We used automated Clover MS Data Analysis software to analyse the protein profile spectra obtained by MALDI-MS from a collection of 248 E. coli isolates (91 P/T-resistant, 81 ESRI developers and 76 P/T-susceptible). This software allowed to preprocess all the spectra to build different peak matrices that were analysed by machine learning algorithms.

Results

We demonstrated that MALDIpiptaz can efficiently and rapidly (15 min) discriminate between P/T-resistant, ESRI developer and P/T-susceptible isolates and allowed the correct classification between ESRI developers from their isogenic resistance to P/T.

Conclusion

The combination of excellent performance and cost-effectiveness are all desirable attributes, allowing the MALDIpiptaz test to be a useful tool for the rapid determination of P/T resistance in clinically relevant E. coli isolates.

Microtoxicology by microfluidic instrumentation: a review

Microtoxicology is concerned with the toxic effects of small amounts of substances. This review paper discusses the application of small amounts of noxious substances for toxicological investigation in small volumes. The vigorous development of miniaturized methods in microfluidics over the last two decades involves chip-based devices, micro droplet-based procedures, and the use of micro-segmented flow for microtoxicological studies. The studies have shown that the microfluidic approach is particularly valuable for highly parallelized and combinatorial dose-response screenings. Accurate dosing and mixing of effector substances in large numbers of microcompartments supplies detailed data of dose-response functions by highly concentration-resolved assays and allows evaluation of stochastic responses in case of small separated cell ensembles and single cell experiments. The investigations demonstrate that very different biological targets can be studied using miniaturized approaches, among them bacteria, eukaryotic microorganisms, cell cultures from tissues of multicellular organisms, stem cells, and early embryonic states. Cultivation and effector exposure tests can be performed in small volumes over weeks and months, confirming that the microfluicial strategy is also applicable for slow-growing organisms. Here, the state of the art of miniaturized toxicology, particularly for studying antibiotic susceptibility, drug toxicity testing in the miniaturized system like organ-on-chip, environmental toxicology, and the characterization of combinatorial effects by two and multi-dimensional screenings, is discussed. Additionally, this review points out the practical limitations of the microtoxicology platform and discusses perspectives on future opportunities and challenges.

Rapid Identification and Classification of Pathogens That Produce Carbapenemases and Cephalosporinases with a Colorimetric Paper-Based Multisensor

Infections caused by bacteria that produce β-lactamases (BLs) are a major problem in hospital settings. The phenotypic detection of these bacterial strains requires culturing samples prior to analysis. This procedure may take up to 72 h, and therefore it cannot be used to guide the administration of the first antibiotic regimen. Here, we propose a multisensor for identifying pathogens bearing different types of β-lactamases above the infectious dose threshold within 90 min that does not require culturing samples. Instead, bacterial cells are preconcentrated in the cellulose scaffold of a paper-based multisensor. Then, 12 assays are performed in parallel to identify whether the pathogens produce carbapenemases and/or cephalosporinases, including metallo-β-lactamases, extended-spectrum β-lactamases (ESBLs), and AmpC enzymes. The multisensor generates an array of colored spots that can be quantified with image processing software and whose interpretation leads to the detection of the different enzymes depending on their specificity toward the hydrolysis of certain antibiotics, and/or their pattern of inhibition or cofactor activation. The test was validated for the diagnosis of urinary tract infections. The inexpensive paper platform along with the uncomplicated colorimetric readout makes the proposed prototypes promising for developing fully automated platforms for streamlined clinical diagnosis.

Rapid Detection of MCR-Mediated Colistin Resistance in Escherichia coli

Colistin is one of the last-resort antibiotics for infections caused by multidrug-resistant Gram-negative bacteria. However, the wide spread of novel plasmid-carrying colistin resistance genes mcr-1 and its variants substantially compromise colistin's therapeutic effectiveness and pose a severe danger to public health. To detect colistin-resistant microorganisms induced by mcr genes, rapid and reliable antibiotic susceptibility testing (AST) is imminently needed. In this study, we identified an RNA-based AST (RBAST) to discriminate between colistin-susceptible and mcr-1-mediated colistin-resistant bacteria. After short-time colistin treatment, RBAST can detect differentially expressed RNA biomarkers in bacteria. Those candidate mRNA biomarkers were successfully verified within colistin exposure temporal shifts, concentration shifts, and other mcr-1 variants. Furthermore, a group of clinical strains were effectively distinguished by using the RBAST approach during the 3-h test duration with over 93% accuracy. Taken together, our findings imply that certain mRNA transcripts produced in response to colistin treatment might be useful indicators for the development of fast AST for mcr-positive bacteria.

IMPORTANCE The emergence and prevalence of mcr-1 and its variants in humans, animals, and the environment pose a global public health threat. There is a pressing urgency to develop rapid and accurate methods to identify MCR-positive colistin-resistant bacteria in the clinical samples, providing a basis for subsequent effective antibiotic treatment. Using the specific mRNA signatures, we develop an RNA-based antibiotic susceptibility testing (RBAST) for effectively distinguishing colistin-susceptible and mcr-1-mediated colistin-resistant strains. Meanwhile, the detection efficiency of these RNA biomarkers was evidenced in other mcr variants-carrying strains. By comparing with the traditional AST method, the RBAST method was verified to successfully characterize a set of clinical isolates during 3 h assay time with over 93% accuracy. Our study provides a feasible method for the rapid detection of colistin-resistant strains in clinical practice.

Dynamic insights into increasing antibiotic resistance in Staphylococcus aureus by label-free SERS using a portable Raman spectrometer

Rapid and quantitative detection of bacterial antibiotic resistance is of great significance for the prevention and treatment of infections and understanding drug-resistant mechanism. In this study, label-free surface-enhanced Raman spectroscopy (SERS) technology was applied to dynamically explore oxacillin/cefazolin-derived resistance in Staphylococcus aureus using a portable Raman spectrometer. The results showed that S. aureus rapidly responded to oxacillin/cefazolin stimulation and gradually developed different degrees of drug resistance during the 21 days of exposure. The molecular changes that accumulated in the drug-resistant strains were sensitively recorded by SERS in a whole-cell manner. Principal components-linear discriminant analysis correctly distinguished various degrees of drug-resistant strains. The typical Raman peak intensities of I₇₃₄/I₈₆₇ showed a negative and non-linear correlation with the minimum inhibitory concentration (MIC). The correlation coefficient reached above 0.9. The target sites of oxacillin/cefazolin on S. aureus clearly reflected on SERS profiles. The results collected by SERS were further verified by other biological methods including the antibiotic susceptibility test, MIC determination, and PCR results. This study indicates that SERS technology provides a rapid and flexible alternative to current drug susceptibility testing, laying a foundation for qualitative and quantitative evaluation of drug resistance in clinical detection.

Characteristics changes on Applications of Antibiotics and Current Approaches to Enhance Productivity with Soil Microbiome

The contamination of environmental sully with antibiotics is regarded as a major problem today and predictable to attain more recognition in near future. However, human intervention resulting in antibiotic consumption is being enhancing all around the world. Our review of literature revealed the role of microbiome in sully and how antibiotic resistant genes raised. The structure of antibiotics basically influenced by natural components such as biotic and abiotic push which shifts based on different soils. Therefore, management of microbiome in soil and their expression studies were distinctively revealed. The assessment of antibiotic resistance genes with help of next generation sequencing provided a clear comprehension on genome and transcriptome of the bacterial genes. Thus, interaction of microbiome with soil can also be well understood. The current findings in our study will guide every researcher to follow logical protocol in analyzing microbiota composition is covered as well and also to understand its metagenomic and sequenced with next-generation sequencer which helps to comprehend the diverse micro-flora present in soil and its operation. Finally, later progresses in bioinformatics computer program, flow of work, and applications for analyzing metagenomic information are put in a nutshell.

A New Colorimetric Method for Rapid Detection of Antibiotic Resistance in Escherichia coli Isolates

Background: The quick diagnosis and early initiation of antibiotic therapy in bacteria-induced infections is of paramount importance. Accordingly, the rapid identification of the causative agent, the short-term results of antibiotic sensitivity, the selection and use of right antibiotics for treatment further highlights the significance of this issue. Objectives: This study aimed to develop a new susceptibility testing method to provide rapid results in Escherichia coli clinical isolates and report the antibiotic susceptibility test results to clinicians in a short period. Methods: In the study, one hundred and ten E. coli clinical isolates were tested. In this regard, antibiotics recommended by the "Clinical and Laboratory Standards Institute (CLSI)" for testing the sensitivity of E. coli isolates, including amoxicillin-clavulanate, cefixime, ceftriaxone, ertapenem, ciprofloxacin, gentamicin, trimethoprim-sulfamethoxazole, and nitrofurantoin were tested. For quality control, E. coli ATCC25922, E. coli ATCC35218, Staphylococcus aureus ATCC29213, and E. coli 13846NTCC strains were used. The broth microdilution method recommended by CLSI was used as the reference method. Minimum inhibitory concentration values were determined, and antimicrobial susceptibilities were then determined according to the “European Committee on Antimicrobial Susceptibility Testing (EUCAST)” criteria. In the next phase, the results of the resazurin microplate method (RMM) were compared. Results: The comparison of the RMM developed in the present study with the reference method revealed that the calculated essential agreement ratios for eight antibiotics varied from 82.72 to 100%, and the categorical agreement values ranged from 95.45 to100%. Conclusions: According to the findings, the RMM results were highly in agreement with the results of the reference method. RMM allows the detection of antibiotic susceptibility quickly (e.g., within 5 hours) as such it is preferred, especially for laboratories with limited facilities. However, further multi-center studies are recommended to use this method in routine laboratories.

Miniaturised broth microdilution for simplified antibiotic susceptibility testing of Gram negative clinical isolates using microcapillary devices

Miniaturised antibiotic susceptibility testing: 100 times smaller microcapillary broth microdilution gives equivalent result to standard microplate broth microdilution.

Droplet-based microfluidics platform for antifungal analysis against filamentous fungi

Fungicides are extensively used in agriculture to control fungal pathogens which are responsible for significant economic impact on plant yield and quality. The conventional antifungal screening techniques, such as water agar and 96-well plates, are based on laborious protocols and bulk analysis, restricting the analysis at the single spore level and are time consuming. In this study, we present a droplet-based microfluidic platform that enables antifungal analysis of single spores of filamentous fungus Alternaria alternata. A droplet-based viability assay was developed, allowing the germination and hyphal growth of single A. alternata spores within droplets. The viability was demonstrated over a period of 24 h and the antifungal screening was achieved using Kunshi/Tezuma as antifungal agent. The efficacy results of the droplet-based antifungal analysis were compared and validated with the results obtained from conventional protocols. The percentage inhibitions assessed by the droplet-based platform were equivalent with those obtained by the other two methods, and the Pearson correlation analysis showed high correlation between the three assays. Taken together, this droplet-based microfluidic platform provides a wide range of potential applications for the analysis of fungicide resistance development as well as combinatorial screening of other antimicrobial agents and even antagonistic fungi.

Rapid Electrochemical-Based PCR-Less Microbial Quantification and Antimicrobial Susceptibility Profiling Directly From Blood and Urine With Unknown Microbial Load or Species

Novel molecular platforms are available for identifying (ID) the causative agents of microbial infections and generating antimicrobial susceptibility testing (AST) profiles, which can inform the suitable course of treatment. Many methods claim to perform AST in minutes or hours, often ignoring the need for time-consuming steps such as enrichment cultures and isolation of pure cultures. In clinical microbiology laboratories, an infectious microbial must first be cultured (overnight to days) and identified at the species level, followed by a subsequent AST with an additional turnaround time of 12-48 h due to the need for regrowth of the organism in the absence and presence of relevant antibiotics. Here, we present an electrochemical-based direct-from-specimen ID/AST method for reporting directly from unprocessed urine and blood in hours. In a limit of detection study of 0.5-ml whole blood samples for point-of-care and pediatric applications, 16.7% (4/24) of samples contrived at 2 CFU/ml and 100% (24/24) of samples contrived at 6 CFU/ml were reported positive in 6.5 h, indicating a limit of detection of 6 CFU/ml. In a separate direct-from-specimen AST study, the categorical susceptibility was reported correctly for blinded susceptible, intermediate, resistant, and polymicrobial contrived specimens in 4 h.

Antibiotic susceptibility test under a linear concentration gradient using travelling surface acoustic waves

An efficient and accurate antibiotic susceptibility test (AST) is indispensable for measuring the antimicrobial resistance of pathogenic bacteria. A minimal inhibitory concentration (MIC) can be obtained without performing repeated dilutions of the antibiotic by forming a linear antibiotic concentration gradient in a microfluidic channel. We demonstrated a device designed to use travelling surface acoustic waves (TSAWs) to enable a rapid formation of an antibiotic gradient in a few seconds. The TSAWs produced by a focused interdigital transducer deposited on the surface of a piezoelectric (LiNbO₃) substrate generated an acoustic streaming flow inside a microfluidic channel, which mixed confluent streams of antibiotics in a controlled fashion. The growth of bacteria exposed to the antibiotic gradient was determined by measuring the MIC, which was used as an indicator of the effectiveness of the AST. The concentration gradient produced using our device was linear, a feature that enhanced the reliability of measurements throughout the microchannel. Two ASTs, namely Pseudomonas aeruginosa against gentamicin and levofloxacin were chosen for the case of slowly proliferating bacteria, and one AST, namely Escherichia coli against gentamicin, were chosen for the rapidly proliferating case. Appropriate antibiotic doses for Pseudomonas aeruginosa and Escherichia coli were each obtained in an efficient manner.

Evaluation of FASTinov® ultra-rapid flow cytometry antimicrobial susceptibility testing directly from positive blood cultures

The ultra-rapid antimicrobial susceptibility test FASTinov® flow cytometry kit was directly evaluated on positive blood cultures (BC) at two sites: i) FASTinov® in Porto (Portugal) using spiked BC with well-characterized bacteria and ii) Ramon y Cajal University hospital in Madrid (Spain) using patients positive BC. Two kits were evaluated, FASTgramneg (Enterobacterales, Pseudomonas, Acinetobacter) and FASTgrampos (Staphylococcus, Enterococcus). A dedicated software for cytometric data analysis and interpretative reporting, both using CLSI and EUCAST criteria, were used. The FASTgramneg kit also provides information about the presence of resistant mechanisms, including ESBLs and carbapenemases. After 1-h incubation at 37°C bacteria were analysed by CytoFLEX® cytometer (Beckman, CA). Disk diffusion was performed as reference susceptibility method. Overall, 447 positive BC were included, 100 from hospitalized patients. Categorical agreement for FASTgramneg panel was 96.8% for EUCAST and 96.4% for CLSI. For FASTgrampos panel it was 98.6% when using both criteria. Using EUCAST criteria the percentage of errors for FASTgramneg panel was 2.1% minor errors (mE), 1.3% major errors (ME) and 0.6% very major errors (VME). Concerning CLSI, 2.9% mE, 0.9% ME and 0.4% VME were found. VMEs were mainly observed with amoxicillin-clavulanate, cefotaxime, ceftazidime and gentamicin. FASTgrampos panel showed 0.3% mE, 1.4% ME and 0.4% VME using EUCAST criteria (VME regarded gentamicin and Staphylococcus) while 0.4% mE, 1.4% ME and no VME when using CLSI criteria. FASTinov® flow cytometry kits represent a rapid alternative for direct antimicrobial susceptibility testing from positive BC, showing time-to-results <2-h, which can be used to personalized antibiotics and stewardship practices.

Fast Antibiotic Susceptibility Testing via Raman Microspectrometry on Single Bacteria: An MRSA Case Study

Despite recent advances in molecular diagnostics, ultrafast determination of the antibiotic susceptibility phenotype of pathogenic microorganisms is still a major challenge of in vitro diagnostics (IVD) of infectious diseases. Raman microspectroscopy has been proposed as a means to achieve this goal. Previous studies have shown that susceptibility phenotyping could be done through Raman analysis of microbial cells, either in large clusters or down to the single-cell level in the case of Gram-negative rods. Gram-positive cocci such as Staphylococcus aureus pose several challenges due to their size and their different metabolic and chemical characteristics. Using a tailored automated single-cell Raman spectrometer and a previously proposed sample preparation protocol, we acquired and analyzed 9429 S. aureus single cells belonging to three cefoxitin-resistant strains and two susceptible strains during their incubation in the presence of various concentrations of cefoxitin. We observed an effect on S. aureus spectra that is weaker than what was detected on previous bacteria/drug combinations, with a higher cell-to-cell response variability and an important impact of incubation conditions on the phenotypic resistance of a given strain. Overall, the proposed protocol was able to correlate strains' phenotype with a specific modification of the spectra using majority votes. We, hence, confirm that our previous results on single-cell Raman antibiotic susceptibility testing can be extended to the S. aureus case and further clarify potential limitations and development requirements of this approach in the move toward industrial applications.

Hyaluronidase-responsive phototheranostic nanoagents for fluorescence imaging and photothermal/photodynamic therapy of methicillin-resistant Staphylococcus aureus infections

Infectious diseases associated with antibiotic-resistant bacteria are ever-growing threats to public health. Effective treatment and detection methods of bacterial infections are in urgent demand. Herein, novel phototheranostic nanoagents (MoS2@HA-Ce6 nanosheets, MHC NSs) with hyaluronidase (HAase)-responsive fluorescence imaging (FLI) and photothermal/photodynamic therapy (PTT/PDT) functions were prepared. In this design, Ce6 is used as both a photosensitizer and a fluorescent probe, while MoS2 nanosheets (MoS2 NSs) serve as both a fluorescence quencher and a photothermal agent. Hyaluronic acid conjugated with Ce6 (HA-Ce6) was assembled on the surface of MoS2 NSs to form MHC NSs. Without the HAase secreted by methicillin-resistant Staphylococcus aureus (MRSA), the fluorescence of Ce6 is quenched by MoS2 NSs, while in the presence of MRSA, HAase can degrade the HA and release Ce6, which restores the fluorescence and photodynamic activity of Ce6. The experimental results show that MHC NSs can fluorescently image the MRSA both in vitro and in vivo by HAase activation. Meanwhile, MHC NSs can serve as PTT/PDT dual-mode antibacterial agents for MRSA. In vitro antibacterial results show that MHC NSs can kill 99.97% MRSA under 635 nm and 785 nm laser irradiation. In vivo study further shows that MHC NSs can kill 99.9% of the bacteria in MRSA infected tissues in mice and prompt wound healing by combined PTT/PDT. This work provides novel HAase-responsive phototheranostic nanoagents for effective detection and treatment of bacterial infections.

Impact of Sepsis Flow Chip, a novelty fast microbiology method, in the treatment of bacteremia caused by Gram-negative bacilli

Objective

The aim of this study was to assess the impact of the information provided by the new Sepsis Chip Flow system (SFC) and other fast microbiological techniques on the selection of the appropriate antimicrobial treatment by the clinical researchers of an antimicrobial stewardship team.

Methods

Two experienced clinical researchers performed the theoretical exercise of independently selecting the treatment for patients diagnosed by bacteremia due to bacilli gram negative (BGN). At first, the clinicians had only available the clinical characteristics of 74 real patients. Sequentially, information regarding the Gram stain, MALDI-TOF, and SFC from Vitro were provided. Initially, the researchers prescribed an antimicrobial therapy based on the clinical data, later these data were complementing with information from microbiological techniques, and the clinicians made their decisions again.

Results

The data provided by the Gram stain reduced the number of patients prescribed with combined treatments (for clinician 1, from 23 to 7, and for clinician 2, from 28 to 12), but the use of carbapenems remained constant. In line with this, the data obtained by the MALDI-TOF also decreased the combined treatment, and the use of carbapenems remained unchanged. By contrast, the data on antimicrobial resistance provided by the SFC reduced the carbapenems treatment.

Conclusions

From the theoretical model the Gram stain and the MALDI-TOF results achieved a reduction in the combined treatment. However, the new system tested (SFC), due to the resistance mechanism data provided, not only reduced the combined treatment, it also decreased the prescription of the carbapenems.

Recent development in antimicrobial activity of biopolymer-inorganic nanoparticle composites with water disinfection potential: a comprehensive review

Nowadays, water-borne diseases including hepatitis remain the critical health challenge due to the inadequate supply of potable and safe water for human activities. The major cause is that the pathogenic microorganisms causing diseases have developed resistance against common techniques used by sewage water treatment plants for water disinfection. Therefore, there is a need to improve these conventional water treatment techniques by taking into consideration the application of nanotechnology for wastewater purification. The main aim of this paper is to provide a review on the synthesis of biopolymer-inorganic nanoparticle composites (BINCs), their used as antimicrobial compounds for water disinfection, as well as to elaborate on their antimicrobial mechanism of action. The microbial properties affecting the activity of antimicrobial compounds are also evaluated.

Evaluation of the "AMR Direct Flow Chip Kit" DNA microarray for detecting antimicrobial resistance genes directly from rectal and nasopharyngeal clinical samples upon ICU admission

INTRODUCTION

Prompt detection of antibiotic resistance genes in healthcare institutions is of utmost importance in tackling the spread of multi-drug resistant micro-organisms. We evaluated the Antimicrobial Resistance (AMR) Direct Flow Chip Kit versus phenotypic screening assays for rectal and nasopharyngeal specimens upon ICU admission.

METHODS

A total of 184 dual specimens (92 rectal and 92 nasopharyngeal swabs) from 92 patients were collected from 11/2017 to 8/2018. All swabs were subjected to both AMR and phenotypic tests according to their origin. The degree of agreement of the two methods was assessed by the kappa coefficient.

RESULTS

The kappa coefficient showed perfect agreement for MRSA, ESBLs, oxacillinases and vancomycin resistance genes (1.000, p<0.01) and very good agreement for mecA-positive CoNS, KPC-carbapenemases and metallo-beta-lactamases (0.870, p<0.01; 0.864, p<0.01; and 0.912, p<0.01, respectively).

CONCLUSION

The AMR Direct Flow Chip Kit is a useful alternative to phenotypic testing for rapid detection of resistance markers.

Specific and rapid reverse assaying protocol for detection and antimicrobial susceptibility testing of Pseudomonas aeruginosa based on dual molecular recognition

The worldwide emergence and spread of antimicrobial resistance is accelerated by irrational administration and use of empiric antibiotics. A key point to the crisis is a lack of rapid diagnostic protocols for antimicrobial susceptibility testing (AST), which is crucial for a timely and rational antibiotic prescription. Here, a recombinant bacteriophage tail fiber protein (TFP) was functionalized on magnetic particles to specifically capture Pseudomonas aeruginosa, while fluorescein isothiocyanate-labeled-magainin II was utilized as the indicator. For solving the magnetic particles' blocking effects, a reverse assaying protocol based on TFP recognition was developed to investigate the feasibility of detection and AST of P. aeruginosa. P. aeruginosa can be rapidly, sensitively and specifically detected within 1.5 h with a linear range of 1.0 × 102 to 1.0 × 106 colony forming units (CFU)⋅mL-1 and a detection limit of 3.3 × 10 CFU⋅mL-1. Subsequently, AST results, which were consistent with broth dilution results, can be obtained within 3.5 h. Due to the high specificity of the TFP, AST can actually be conducted without the need for bacterial isolation and identification. Based on the proof-of-principle work, the detection and AST of other pathogens can be extended by expressing the TFPs of their bacteriophages.

Nucleic acid amplification-based microfluidic approaches for antimicrobial susceptibility testing

Because of the global spread of antimicrobials, there is an urgent need to develop rapid and effective tools for antimicrobial susceptibility testing to help clinicians prescribe accurate and appropriate antibiotic doses sooner. The conventional methods for antimicrobial susceptibility testing are usually based on bacterial culture methods, which are time-consuming, complicated, and labor-intensive. Therefore, other approaches are needed to address these issues. Recently, microfluidic technology has gained significant attention in infection management due to its advantages including rapid detection, high sensitivity and specificity, highly automated assay, simplicity, low cost, and potential for point-of-care testing in low-resource areas. Microfluidic advances for antimicrobial susceptibility testing can be classified into phenotypic (usually culture-based) and genotypic tests. Genotypic antimicrobial susceptibility testing is the detection of resistant genes in a microorganism using methods such as nucleic acid amplification. This review (with 107 references) surveys the different forms of nucleic acid amplification-based microdevices used for genotypic antimicrobial susceptibility testing. The first section reviews the serious threat of antimicrobial-resistant microorganisms and the urgent need for fast check-ups. Next, several conventional antimicrobial susceptibility testing methods are discussed, and microfluidic technology as a promising candidate for rapid detection of antimicrobial-resistant microorganisms is briefly introduced. The next section highlights several advancements of microdevices, with an emphasis on their working principles and performance. The review concludes with the importance of fully integrated microdevices and a discussion on future perspectives.

Evaluation of a New Culture-Based AtbFinder Test-System Employing a Novel Nutrient Medium for the Selection of Optimal Antibiotics for Critically Ill Patients with Polymicrobial Infections within 4 h

Here, we describe the validation of a new phenotypic culture-based AtbFinder method for rapid selection of antibiotics in vitro using specimens with mono- and polybacterial infections. AtbFinder, which can be applied to any type of non-blood tissue, does not require isolation of pure bacterial cultures. The method uses a novel TGV medium that allows more rapid bacterial growth of Gram-positive and Gram-negative monoisolates compared with that achieved with conventional laboratory media, demonstrating overall sensitivity, specificity, PPV, NPV values of 99.6%, 98.1%, 98.5%, and 99.4%, respectively, after 4 h. For polymicrobial infections, AtbFinder utilized a novel paradigm of the population response to antibiotics, enabling bacterial growth in the form of a mixed microbial community and selecting antibiotics targeting not only the principal pathogen, but also those bacteria that support their growth. TGV medium allowed culturing of a more diverse set of bacteria from polymicrobial biospecimens, compared with that achieved with the standard media, and enabled, within 4 h, accurate selection of the antibiotics that completely eliminated all cultivatable bacteria from clinical samples. In conclusion, the AtbFinder system may be a valuable tool in improving antibiotic selection, and enabling targeted empirical therapy and accurate antibiotic replacement, which is especially important in high-risk patients.

Recent Development of Rapid Antimicrobial Susceptibility Testing Methods through Metabolic Profiling of Bacteria

Due to the inappropriate use and overuse of antibiotics, the emergence and spread of antibiotic-resistant bacteria are increasing and have become a major threat to human health. A key factor in the treatment of bacterial infections and slowing down the emergence of antibiotic resistance is to perform antimicrobial susceptibility testing (AST) of infecting bacteria rapidly to prescribe appropriate drugs and reduce the use of broad-spectrum antibiotics. Current phenotypic AST methods based on the detection of bacterial growth are generally reliable but are too slow. There is an urgent need for new methods that can perform AST rapidly. Bacterial metabolism is a fast process, as bacterial cells double about every 20 to 30 min for fast-growing species. Moreover, bacterial metabolism has shown to be related to drug resistance, so a comparison of differences in microbial metabolic processes in the presence or absence of antimicrobials provides an alternative approach to traditional culture for faster AST. In this review, we summarize recent developments in rapid AST methods through metabolic profiling of bacteria under antibiotic treatment.

Natural polyketide 6-pentyl-2H-pyrone-2-one and its synthetic analogues efficiently prevent marine biofouling

Biofouling is a widespread phenomenon in oceans worldwide. With increasing human development and activities in open and coastal waters, and due to the environmental impact of AF organotins and copper-based paint, the demand for nontoxic antifouling (AF) paints is increasing. Various bioassays for antimicrobial activity, anti-biofilm formation and anti-barnacle settlement were established to evaluate the possibility of using marine natural products as AF agents. A series of natural products, isolated from the marine-derived fungi Trichoderma atroviride and T. reesei, were evaluated for their AF activity. One pyrone-type compound (1) demonstrated significant inhibitory activities toward barnacle cyprid settlement. Furthermore, a series of pyrone analogues (S1-S6) were synthesized, and their bioactivities were evaluated in the established systems. The results showed that compounds S5 and S6 exhibited a broad spectrum of bioactivities, such as anti-barnacle settlement, anti-biofilm formation and antimicrobial activities.

Oxford nanopore sequencing in clinical microbiology and infection diagnostics

Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting. Issues of timeliness and cost could soon be circumvented, however, with the emergence of detection methods involving single molecule sequencing technology. In the context of bringing diagnostics closer to the point of care, we examine the current state of Oxford Nanopore Technologies (ONT) products and their interaction with third-party software/databases to assess their capabilities for ID and antimicrobial resistance (AMR) prediction. We outline and discuss a potential diagnostic workflow, enumerating (1) rapid sample prep kits, (2) ONT hardware/software and (3) third-party software and databases to improve the cost, accuracy and turnaround times for ID and AMR. Multiple studies across a range of infection types support that the speed and accuracy of ONT sequencing is now such that established ID and AMR prediction tools can be used on its outputs, and so it can be harnessed for near real time, close to the point-of-care diagnostics in common clinical circumstances.

Microfluidic Technology for Antibacterial Resistance Study and Antibiotic Susceptibility Testing: Review and Perspective

A review on microfluidic technology for antibacterial resistance study and antibiotic susceptibility testing (AST) is presented here. Antibiotic resistance has become a global health crisis in recent decades, severely threatening public health, patient care, economic growth, and even national security. It is extremely urgent that antibiotic resistance be well looked into and aggressively combated in order for us to survive this crisis. AST has been routinely utilized in determining bacterial susceptibility to antibiotics and identifying potential resistance. Yet conventional methods for AST are increasingly incompetent due to unsatisfactory test speed, high cost, and deficient reliability. Microfluidics has emerged as a powerful and very promising platform technology that has proven capable of addressing the limitation of conventional methods and advancing AST to a new level. Besides, potential technical challenges that are likely to hinder the development of microfluidic technology aimed at AST are observed and discussed. To conclude, it is noted that (1) the translation of microfluidic innovations from laboratories to be ready AST platforms remains a lengthy journey and (2) ensuring all relevant parties engaged in a collaborative and unified mode is foundational to the successful incubation of commercial microfluidic platforms for AST.

Deep Learning Analysis of Vibrational Spectra of Bacterial Lysate for Rapid Antimicrobial Susceptibility Testing

Rapid antimicrobial susceptibility testing (AST) is an integral tool to mitigate the unnecessary use of powerful and broad-spectrum antibiotics that leads to the proliferation of multi-drug-resistant bacteria. Using a sensor platform composed of surface-enhanced Raman scattering (SERS) sensors with control of nanogap chemistry and machine learning algorithms for analysis of complex spectral data, bacteria metabolic profiles post antibiotic exposure are correlated with susceptibility. Deep neural network models are able to discriminate the responses of Escherichia coli and Pseudomonas aeruginosa to antibiotics from untreated cells in SERS data in 10 min after antibiotic exposure with greater than 99% accuracy. Deep learning analysis is also able to differentiate responses from untreated cells with antibiotic dosages up to 10-fold lower than the minimum inhibitory concentration observed in conventional growth assays. In addition, analysis of SERS data using a generative model, a variational autoencoder, identifies spectral features in the P. aeruginosa lysate data associated with antibiotic efficacy. From this insight, a combinatorial dataset of metabolites is selected to extend the latent space of the variational autoencoder. This culture-free dataset dramatically improves classification accuracy to select effective antibiotic treatment in 30 min. Unsupervised Bayesian Gaussian mixture analysis achieves 99.3% accuracy in discriminating between susceptible versus resistant to antibiotic cultures in SERS using the extended latent space. Discriminative and generative models rapidly provide high classification accuracy with small sets of labeled data, which enormously reduces the amount of time needed to validate phenotypic AST with conventional growth assays. Thus, this work outlines a promising approach toward practical rapid AST.

Rapid Detection and Antibiotic Susceptibility of Uropathogenic Escherichia coli by Flow Cytometry

Background: Early preliminary data on antibiotic resistance patterns available before starting the empiric therapy of urinary tract infections (UTIs) in patients with risk factors for acquiring antibiotic resistance could improve both clinical and epidemiological outcomes. The aim of the present study was two-fold: (i) to assess the antibiotic susceptibility of uropathogenic Escherichia coli isolates, exhibiting different antibiotic resistance phenotypes, directly in artificially contaminated urine samples using a flow cytometry (FC) based protocol; (ii) to optimize the protocol on urine samples deliberately contaminated with bacterial suspensions prepared from uropathogenic E. coli strains. Results: The results of the FC based antimicrobial susceptibility testing (AST) protocol were compared with the reference AST methods results (disk diffusion and broth microdilution) for establishing the sensitivity and specificity. The proposed FC protocol allowed the detection and quantification of uropathogenic E. coli strains susceptibility to nitrofurantoin, trimethoprim–sulfamethoxazole, ciprofloxacin, and ceftriaxone within 4 h after the inoculation of urine specimens. The early availability of preliminary antibiotic susceptibility results provided by direct analysis of clinical specimens could essentially contribute to a more targeted emergency therapy of UTIs in the anticipation of AST results obtained by reference methodology. Conclusions: This method will increase the therapeutic success rate and help to prevent the emergence and dissemination of drug resistant pathogens.

Automated and rapid identification of multidrug resistant Escherichia coli against the lead drugs of acylureidopenicillins, cephalosporins, and fluoroquinolones using specific Raman marker bands

A Raman-based, strain-independent, semi-automated method is presented that allows the rapid (<3 hours) determination of antibiotic susceptibility of bacterial pathogens isolated from clinical samples. Applying a priori knowledge about the mode of action of the respective antibiotic, we identified characteristic Raman marker bands in the spectrum and calculated batch-wise weighted sum scores from standardized Raman intensity differences between spectra of antibiotic exposed and nonexposed samples of the same strains. The lead substances for three relevant antibiotic classes (fluoroquinolone ciprofloxacin, third-generation cephalosporin cefotaxime, ureidopenicillin piperacillin) against multidrug-resistant Gram-negative bacteria (MRGN) revealed a high sensitivity and specificity for the susceptibility testing of two Escherichia coli laboratory strains and 12 clinical isolates. The method benefits from the parallel incubation of control and treated samples, which reduces the variance due to alterations in cultivation conditions and the standardization of differences between batches leading to long-term comparability of Raman measurements.

Capillary-Driven Flow Microfluidics Combined with Smartphone Detection: An Emerging Tool for Point-of-Care Diagnostics

Point-of-care (POC) or near-patient testing allows clinicians to accurately achieve real-time diagnostic results performed at or near to the patient site. The outlook of POC devices is to provide quicker analyses that can lead to well-informed clinical decisions and hence improve the health of patients at the point-of-need. Microfluidics plays an important role in the development of POC devices. However, requirements of handling expertise, pumping systems and complex fluidic controls make the technology unaffordable to the current healthcare systems in the world. In recent years, capillary-driven flow microfluidics has emerged as an attractive microfluidic-based technology to overcome these limitations by offering robust, cost-effective and simple-to-operate devices. The internal wall of the microchannels can be pre-coated with reagents, and by merely dipping the device into the patient sample, the sample can be loaded into the microchannel driven by capillary forces and can be detected via handheld or smartphone-based detectors. The capabilities of capillary-driven flow devices have not been fully exploited in developing POC diagnostics, especially for antimicrobial resistance studies in clinical settings. The purpose of this review is to open up this field of microfluidics to the ever-expanding microfluidic-based scientific community.

Direct detection of intact Klebsiella pneumoniae carbapenemase variants from cell lysates: Identification, characterization and clinical implications

Introduction

Carbapenemase-producing organisms (CPOs) are a growing threat to human health. Among the enzymes conferring antibiotic resistance produced by these organisms, Klebsiella pneumoniae carbapenemase (KPC) is considered to be a growing global health threat. Reliable and specific detection of this antibiotic resistance-causing enzyme is critical both for effective therapy and to mitigate further spread.

Objectives

The objective of this study is to develop an intact protein mass spectrometry-based method for detection and differentiation of clinically-relevant KPC variants directly from bacterial cell lysates. The method should be specific for any variant expressed in multiple bacterial species, limit false positive results and be rapid in nature to directly influence clinical outcomes.

Methods

Lysates obtained directly from bacterial colonies were used for intact protein detection using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Bottom-up and top-down proteomic methods were used to characterize the KPC protein targets of interest. Comparisons between KPC-producing and KPC-non-producing isolates from a wide variety of species were also performed.

Results

Characterization of the mature KPC protein revealed an unexpected signal peptide cleavage site preceding an AXA signal peptide motif, modifying the molecular weight (MW) of the mature protein. Taking the additional AXA residues into account allowed for direct detection of the intact protein using top-down proteomic methods. Further validation was performed by transforming a KPC-harboring plasmid into a negative control strain, followed by MS detection of the KPC variant from the transformed cell line. Application of this approach to clearly identify clinically-relevant variants among several species is presented for KPC-2, KPC-3, KPC-4 and KPC-5.

Conclusion

Direct detection of these enzymes contributes to the understanding of occurrence and spread of these antibiotic-resistant organisms. The ability to detect intact KPC variants via a simple LC-MS/MS approach could have a direct and positive impact on clinical therapy, by providing both direction for epidemiological tracking and appropriate therapy.

Modern Tools for Rapid Diagnostics of Antimicrobial Resistance

Fast, robust, and affordable antimicrobial susceptibility testing (AST) is required, as roughly 50% of antibiotic treatments are started with wrong antibiotics and without a proper diagnosis of the pathogen. Validated growth-based AST according to EUCAST or CLSI (European Committee on Antimicrobial Susceptibility Testing, Clinical Laboratory Standards Institute) recommendations is currently suggested to guide the antimicrobial therapy. Any new AST should be validated against these standard methods. Many rapid diagnostic techniques can already provide pathogen identification. Some of them can additionally detect the presence of resistance genes or resistance proteins, but usually isolated pure cultures are needed for AST. We discuss the value of the technologies applying nucleic acid amplification, whole genome sequencing, and hybridization as well as immunodiagnostic and mass spectrometry-based methods and biosensor-based AST. Additionally, we evaluate the potential of integrated systems applying microfluidics to integrate cultivation, lysis, purification, and signal reading steps. We discuss technologies and commercial products with potential for Point-of-Care Testing (POCT) and their capability to analyze polymicrobial samples without pre-purification steps. The purpose of this critical review is to present the needs and drivers for AST development, to show the benefits and limitations of AST methods, to introduce promising new POCT-compatible technologies, and to discuss AST technologies that are likely to thrive in the future.

Evaluation of the "AMR Direct Flow Chip Kit" DNA microarray for detecting antimicrobial resistance genes directly from rectal and nasopharyngeal clinical samples upon ICU admission

INTRODUCTION

Prompt detection of antibiotic resistance genes in healthcare institutions is of utmost importance in tackling the spread of multi-drug resistant micro-organisms. We evaluated the Antimicrobial Resistance (AMR) Direct Flow Chip Kit versus phenotypic screening assays for rectal and nasopharyngeal specimens upon ICU admission.

METHODS

A total of 184 dual specimens (92 rectal and 92 nasopharyngeal swabs) from 92 patients were collected from 11/2017 to 8/2018. All swabs were subjected to both AMR and phenotypic tests according to their origin. The degree of agreement of the two methods was assessed by the kappa coefficient.

RESULTS

The kappa coefficient showed perfect agreement for MRSA, ESBLs, oxacillinases and vancomycin resistance genes (1.000, p<0.01) and very good agreement for mecA-positive CoNS, KPC-carbapenemases and metallo-beta-lactamases (0.870, p<0.01; 0.864, p<0.01; and 0.912, p<0.01, respectively).

CONCLUSION

The AMR Direct Flow Chip Kit is a useful alternative to phenotypic testing for rapid detection of resistance markers.

Computational design of probes to detect bacterial genomes by multivalent binding

Rapid methods for diagnosis of bacterial infections are urgently needed to reduce inappropriate use of antibiotics, which contributes to antimicrobial resistance. In many rapid diagnostic methods, DNA oligonucleotide probes, attached to a surface, bind to specific nucleotide sequences in the DNA of a target pathogen. Typically, each probe binds to a single target sequence; i.e., target-probe binding is monovalent. Here we show using computer simulations that the detection sensitivity and specificity can be improved by designing probes that bind multivalently to the entire length of the pathogen genomic DNA, such that a given probe binds to multiple sites along the target DNA. Our results suggest that multivalent targeting of long pieces of genomic DNA can allow highly sensitive and selective binding of the target DNA, even if competing DNA in the sample also contains binding sites for the same probe sequences. Our results are robust to mild fragmentation of the bacterial genome. Our conclusions may also be relevant for DNA detection in other fields, such as disease diagnostics more broadly, environmental management, and food safety.

Microfluidic systems for rapid antibiotic susceptibility tests (ASTs) at the single-cell level

Infectious diseases caused by multidrug resistant (MDR) bacterial pathogens are impending threats to global health. Since delays in identifying drug resistance would significantly increase mortality, fast and accurate antibiotic susceptibility tests (ASTs) are critical for addressing the antibiotic resistance issue. However, the conventional methods for ASTs are always labor-intensive, imprecise, complex and slow (taking 2-3 days). To address these issues, some advanced microfluidic systems have been designed for rapid phenotypic and genotypic analysis of antibiotic resistance. This review highlights the recent development of microfluidics-based ASTs at the single-cell or single-molecule level for guiding antibiotic treatment decisions and predicting therapeutic outcomes.

A Multiplex Fluidic Chip for Rapid Phenotypic Antibiotic Susceptibility Testing

Prompt and effective antimicrobial therapy is crucial for the management of patients with severe bacterial infections but is becoming increasingly difficult to provide due to emerging antibiotic resistance. The traditional methods for antibiotic susceptibility testing (AST) used in most clinical laboratories are reliable but slow with turnaround times of 2 to 3 days, which necessitates the use of empirical therapy with broad-spectrum antibiotics. There is a great need for fast and reliable AST methods that enable starting targeted treatment within a few hours to improve patient outcome and reduce the overuse of broad-spectrum antibiotics. The multiplex fluidic chip for phenotypic AST described in the present study may enable data on antimicrobial resistance within 2 to 4 h, allowing for an early initiation of appropriate antibiotic therapy.

Many patients with severe infections receive inappropriate empirical treatment, and rapid detection of bacterial antibiotic susceptibility can improve clinical outcome and reduce mortality. To this end, we have developed a multiplex fluidic chip for rapid phenotypic antibiotic susceptibility testing of bacteria. A total of 21 clinical isolates of Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus were acquired from the EUCAST Development Laboratory and tested against amikacin, ceftazidime, and meropenem (Gram-negative bacteria) or gentamicin, ofloxacin, and tetracycline (Gram-positive bacteria). The bacterial samples were mixed with agarose and loaded in an array of growth chambers in the chip where bacterial microcolony growth was monitored over time using automated image analysis. MIC values were automatically obtained by tracking the growth rates of individual microcolonies in different regions of antibiotic gradients. Stable MIC values were obtained within 2 to 4 h, and the results showed categorical agreement with reference MIC values as determined by broth microdilution in 86% of the cases.