Development of a magnetic separation method to capture sepsis associated bacteria in blood

Advances in Host Depletion and Pathogen Enrichment Methods for Rapid Sequencing-Based Diagnosis of Bloodstream Infection

Bloodstream infection is a major cause of morbidity and death worldwide. Timely and appropriate treatment can reduce mortality among critically ill patients. Current diagnostic methods are too slow to inform precise antibiotic choice, leading to the prescription of empirical antibiotics, which may fail to cover the resistance profile of the pathogen, risking poor patient outcomes. Additionally, overuse of broad-spectrum antibiotics may lead to more resistant organisms, putting further pressure on the dwindling pipeline of antibiotics, and risk transmission of these resistant organisms in the health care environment. Therefore, rapid diagnostics are urgently required to better inform antibiotic choice early in the course of treatment. Sequencing offers great promise in reducing time to microbiological diagnosis; however, the amount of host DNA compared with the pathogen in patient samples presents a significant obstacle. Various host-depletion and bacterial-enrichment strategies have been used in samples, such as saliva, urine, or tissue. However, these methods have yet to be collectively integrated and/or extensively explored for rapid bloodstream infection diagnosis. Although most of these workflows possess individual strengths, their lack of analytical/clinical sensitivity and/or comprehensiveness demands additional improvements or synergistic application. This review provides a distinctive classification system for various methods based on their working principles to guide future research, and discusses their strengths and limitations and explores potential avenues for improvement to assist the reader in workflow selection.

Quantitative real-time PCR and magnetic separation strategy for specific detection of group B streptococcus in perinatal Women's urine

Introduction

Group B streptococcus(GBS)often causes adverse outcomes such as urinary system infection, intrauterine infection, premature birth, and stillbirth in perinatal women. Perinatal screening of GBS is conducive to guiding clinical scientific intervention and improving delivery outcomes.This study quantitative real-time PCR (RT-qPCR) combined with magnetic separation was used for GBS detection.

Materials and methods

Sample pre-treatment in this study involved the utilization of magnetic separation (MS) technology, aiming to expedite the detection process and enhance detection sensitivity, and the cfb gene of group B streptococcus was used as the target gene to establish quantitative real-time PCR (RT-qPCR) to detect group B streptococcus.

Results

It was found that penicillin-functionalized magnetic beads had a good ability to enrich and capture group B Streptococcus.The findings revealed an exceptional detection sensitivity, with the ability to detect B streptococcus in urine samples at levels as low as 102 CFU/mL.

Conclusions

The utilization of MS technology in conjunction with the RT-qPCR (MS-RT-qPCR) assay, as demonstrated in this study, offers a viable approach for prenatal screening of group B streptococcus among perinatal women.

Magnetic blood purification-based soluble fms-like tyrosine kinase-1 removal in comparison with dextran sulfate apheresis and therapeutic plasma exchange

BACKGROUND

Preeclampsia remains one of the most serious complications of pregnancy. Effective therapies are yet to be developed. Recent research has identified an imbalance of angiogenic and antiangiogenic factors as a root cause of preeclampsia. In particular, soluble fms-like tyrosine kinase-1 (sFlt-1) has been shown to bind the angiogenic factors vascular endothelial growth factor (VEGF) and placental growth factor (PlGF), reducing blood vessel growth. Increasing preclinical and clinical evidence suggests that removal of the sFlt-1 protein may benefit patients with early onset preeclampsia. sFlt-1 may be removed by conventional blood purification techniques, such as therapeutic plasma exchange (TPE) and dextran sulfate apheresis (DSA), or emerging technologies, including extracorporeal magnetic blood purification (MBP).

METHODS

We compare the performance and selectivity of TPE, DSA, and MBP for the therapeutic removal of sFlt-1. For MPB, we employ magnetic nanoparticles functionalized with either sFlt-1 antibodies or the sFlt-1-binding partner, vascular endothelial growth factor (VEGF).

RESULTS

We demonstrate that sFlt-1 removal by MBP is feasible and significantly more selective than TPE and DSA at comparable sFlt-1 removal efficiencies (MBP 96%, TPE 92%, DSA 78%). During both TPE and DSA, complement factors (incl. C3c and C4) are depleted to a considerable extent (-90% for TPE, -55% for DSA), while in MBP, complement factor concentrations remain unaltered. We further demonstrate that the removal efficacy of sFlt-1 in the MBP approach is strongly dependent on the nanoparticle type and dose and can be optimized to reach clinically feasible throughputs.

CONCLUSIONS

Taken together, the highly selective removal of sFlt-1 and potential other disease-causing factors by extracorporeal magnetic blood purification may offer new prospects for preeclamptic patients.

A Phage Receptor-Binding Protein as a Promising Tool for the Detection of Escherichia coli in Human Specimens

Escherichia coli is a problematic pathogen that causes life-threatening diseases, being a frequent causative agent of several nosocomial infections such as urinary tract and bloodstream infections. Proper and rapid bacterial identification is critical for allowing prompt and targeted antimicrobial therapy. (Bacterio)phage receptor-binding proteins (RBPs) display high specificity for bacterial surface epitopes and, therefore, are particularly attractive as biorecognition elements, potentially conferring high sensitivity and specificity in bacterial detection. In this study, we elucidated, for the first time, the potential of a recombinant RBP (Gp17) to recognize E. coli at different viability states, such as viable but not culturable cells, which are not detected by conventional techniques. Moreover, by using a diagnostic method in which we combined magnetic and spectrofluorimetric approaches, we demonstrated the ability of Gp17 to specifically detect E. coli in various human specimens (e.g., whole blood, feces, urine, and saliva) in about 1.5 h, without requiring complex sample processing.

Biomolecules capturing live bacteria from clinical samples

Rapid phenotypic antimicrobial susceptibility testing (AST) requires the enrichment of live bacteria from patient samples, which is particularly challenging in the context of life-threatening bloodstream infections (BSIs) due to low bacterial titers. Over two decades, an extensive array of pathogen-specific biomolecules has been identified to capture live bacteria. The prevailing biomolecules are immune proteins of the complement system, antibodies, aptamers, phage proteins, and antimicrobial peptides. These biomolecules differ by their binder generation technologies and exhibit highly variable specificities, ranging from bacterial strains to most pathogenic bacteria. Here, we summarize how these diverse biomolecules were identified, list examples of successfully reported capture assays, and provide an outlook on the use of nanobodies raised against conserved surface-accessible proteins as promising biomolecules for pathogen capture.

Point-of-care diagnosis of invasive non-typhoidal Salmonella enterica in bloodstream infections using immunomagnetic capture and loop-mediated isothermal amplification

Invasive non-typhoidal salmonellosis is gaining worldwide attention as an emerging disease cluster among bloodstream infections. The disease has the highest burden among immunocompromised and malnourished children in resource-limited areas due to poor access to reliable and rapid diagnostics. Point-of-care (POC) diagnostics are promising for use in such low infrastructure laboratory settings. However, there still remains a major challenge for POC testing to deal with the complexity of blood matrices in rapid detection of an extremely low concentration of blood-borne pathogens. In this work, the challenges were addressed by combining magnetic bead based pathogen concentration and Loop Mediated Isothermal Amplification (LAMP) technology. Sensitivity and performance of the combined approach were determined and compared with a direct PCR method. A direct visual detection strategy, adapted using SYTO-24 DNA intercalating dye, resulted in a limit of detection (LoD) as low as 14 CFU/mL in blood samples with a total analysis time of less than 2 h, including sample preparation. This approach has the potential for wide application as a high-throughput POC testing method to analyze pathogens in clinical, food, feed and environmental samples.

BSA Hydrogel Beads Functionalized with a Specific Aptamer Library for Capturing Pseudomonas aeruginosa in Serum and Blood

Systemic blood stream infections are a major threat to human health and are dramatically increasing worldwide. Pseudomonas aeruginosa is a WHO-alerted multi-resistant pathogen of extreme importance as a cause of sepsis. Septicemia patients have significantly increased survival chances if sepsis is diagnosed in the early stages. Affinity materials can not only represent attractive tools for specific diagnostics of pathogens in the blood but can prospectively also serve as the technical foundation of therapeutic filtration devices. Based on the recently developed aptamers directed against P. aeruginosa, we here present aptamer-functionalized beads for specific binding of this pathogen in blood samples. These aptamer capture beads (ACBs) are manufactured by crosslinking bovine serum albumin (BSA) in an emulsion and subsequent functionalization with the amino-modified aptamers on the bead surface using the thiol- and amino-reactive bispecific crosslinker PEG₄-SPDP. Specific and quantitative binding of P. aeruginosa as the dedicated target of the ACBs was demonstrated in serum and blood. These initial but promising results may open new routes for the development of ACBs as a platform technology for fast and reliable diagnosis of bloodstream infections and, in the long term, blood filtration techniques in the fight against sepsis.

Rapid Detection of Escherichia coli Antibiotic Susceptibility Using Live/Dead Spectrometry for Lytic Agents

Antibiotic resistance is a serious threat to public health. The empiric use of the wrong antibiotic occurs due to urgency in treatment combined with slow, culture-based diagnostic techniques. Inappropriate antibiotic choice can promote the development of antibiotic resistance. We investigated live/dead spectrometry using a fluorimeter (Optrode) as a rapid alternative to culture-based techniques through application of the LIVE/DEAD® BacLightTM Bacterial Viability Kit. Killing was detected by the Optrode in near real-time when Escherichia coli was treated with lytic antibiotics-ampicillin and polymyxin B-and stained with SYTO 9 and/or propidium iodide. Antibiotic concentration, bacterial growth phase, and treatment time used affected the efficacy of this detection method. Quantification methods of the lethal action and inhibitory action of the non-lytic antibiotics, ciprofloxacin and chloramphenicol, respectively, remain to be elucidated.

Vancomycin-dendrimer based multivalent magnetic separation nanoplatforms combined with multiplex quantitative PCR assay for detecting pathogenic bacteria in human blood

Sepsis caused by bacteria has high morbidity and mortality, and it is neccerssay to establish a fast, convenient, and facility assays for detection of bacteria. In this study, we have developed established a simple, rapid, and ultrasensitive vancomycin (Van) and dendrimer nanoparticles-based method to isolate and detect bacteria in human blood using a multivalent binding strategy. The proposed Bio-den-Van multivalent capture nanoplatform combined with m-qPCR for simultaneous detection of two kinds of bacteria was demonstrated with rapid 2 min bacteria isolation with a linear range at 3.2 × 10¹-3.2 × 10⁶ CFU·mL^-1 for L. monocytogenes and 4.1 × 10¹-4.1 × 10⁶ CFU·mL^-1 for S. aureus, respectively. The limit of detection (LOD) for simultaneous detection of L. monocytogenes and S. aureus were 32 and 41 CFU·mL^-1 in spiked human blood samples, respectively. Other bacteria had an insignificant interference with the test results. This Bio-den-Van multivalent capture nanoplatform combined with m-qPCR detection exhibited rapid, high sensitivity and specificity in simultaneous detection of various bacteria. To our knowledge, this is the first time that Bio-den-Van multivalent capture nanoplatform was used with Van as a recognition molecule for the simultaneous capture and subsequent detection of two bacteria from spiked human blood sample. This method holds great potential for future clinical applications.

Functional BOD-Ad-Cmyc@BSA complex nanosensor for Cu(II) and the detection of live E. coli

Escherichia coli (E. coli) is abundantly present in nature. It is generally harmless to humans but some strains have been deemed very dangerous. Therefore, as an indicator of hygienic testing, the detection of E. coli is essential. In this work, a fluorescent assembly was synthesized and characterized by spectroscopic methods. It was found that the amantadine (Ad) conjugated dye (BOD-Ad) intercalated into Cmyc G4 (aptamer) forming a non-emission assembly (BOD-Ad-Cmyc), which could be lighted-up by BSA due to the formation of fluorescence nanoparticle BOD-Ad-Cmyc@BSA. Further, BOD-Ad-Cmyc@BSA can selectively bind Cu²⁺ forming non-emission species BOD-Ad-Cmyc@BSA-Cu²⁺. E. coli can turn-on the emission of BOD-Ad-Cmyc@BSA-Cu²⁺ system due to the copper accumulation or reduction by E. coli. Therefore, a fluorescence method for the determination of E. coli was built. The detection limit of BOD-Ad-Cmyc@BSA-Cu²⁺ of E. coli is 6.3 CFU/mL. Thus, this BOD-Ad-Cmyc@BSA-Cu²⁺ fluorescent assembly can be used for the detection of live E. coli in the environment.

A novel flow cytometry assay based on bacteriophage-derived proteins for Staphylococcus detection in blood

Bloodstream infections (BSIs) are considered a major cause of death worldwide. Staphylococcus spp. are one of the most BSIs prevalent bacteria, classified as high priority due to the increasing multidrug resistant strains. Thus, a fast, specific and sensitive method for detection of these pathogens is of extreme importance. In this study, we have designed a novel assay for detection of Staphylococcus in blood culture samples, which combines the advantages of a phage endolysin cell wall binding domain (CBD) as a specific probe with the accuracy and high-throughput of flow cytometry techniques. In order to select the biorecognition molecule, three different truncations of the C-terminus of Staphylococcus phage endolysin E-LM12, namely the amidase (AMI), SH3 and amidase+SH3 (AMI_SH3) were cloned fused with a green fluorescent protein. From these, a higher binding efficiency to Staphylococcus cells was observed for AMI_SH3, indicating that the amidase domain possibly contributes to a more efficient binding of the SH3 domain. The novel phage endolysin-based flow cytometry assay provided highly reliable and specific detection of 1-5 CFU of Staphylococcus in 10 mL of spiked blood, after 16 hours of enrichment culture. Overall, the method developed herein presents advantages over the standard BSIs diagnostic methods, potentially contributing to an early and effective treatment of BSIs.

Integrated microsystems for the in situ genetic detection of dengue virus in whole blood using direct sample preparation and isothermal amplification

Owing to the frequent outbreak of dengue fever worldwide, a highly sensitive but in situ simple process diagnostic device is required to detect the dengue virus. However, the current immune affinity-based methods have sensitivity issues and nucleic acid-based diagnostic devices have not been suitable for field diagnosis due to the complexity in sample preparation. Here, a simple and fast nucleic acid-based diagnostic tool to directly detect dengue viruses in whole blood is demonstrated using a microbead-assisted direct sample preparation buffer (MB-buffer) and isothermal amplification (loop-mediated isothermal amplification, LAMP). To maximize the performance of the sample preparation process in the microfluidic chip platform, the chemical composition of the sample preparation buffer is simplified and combined with physical tools (heating and bead beating). The entire serial processes consisted of only (1) sample (whole blood) loading, (2) stirring for 90 s, (3) heating at 70 °C for 10 min, and (4) LAMP amplification in the simply designed microfluidic chip cartridge. A single syringe was utilized for sample loading and microfluidic solution transfer. Consequently, dengue viruses were qualitatively detected and discriminated with high sensitivity (LOD: 10² PFU per 200 μL of whole blood) in less than 1 hour without the use of any sophisticated system.

Factors affecting sedimentational separation of bacteria from blood

Rapid diagnosis of blood infections requires fast and efficient separation of bacteria from blood. We have developed spinning hollow disks that separate bacteria from blood cells via the differences in sedimentation velocities of these particles. Factors affecting separation included the spinning speed and duration, and disk size. These factors were varied in dozens of experiments for which the volume of separated plasma, and the concentration of bacteria and red blood cells (RBCs) in separated plasma were measured. Data were correlated by a parameter of characteristic sedimentation length, which is the distance that an idealized RBC would travel during the entire spin. Results show that characteristic sedimentation length of 20 to 25 mm produces an optimal separation and collection of bacteria in plasma. This corresponds to spinning a 12-cm-diameter disk at 3,000 rpm for 13 s. Following the spin, a careful deceleration preserves the separation of cells from plasma and provides a bacterial recovery of about 61 ± 5%.

Point of care technologies for sepsis diagnosis and treatment

Sepsis is a rapidly progressing, life threatening immune response triggered by infection that affects millions worldwide each year. Current clinical diagnosis relies on broad physiological parameters and time consuming lab-based cell culture. If proper treatment is not provided, cases of sepsis can drastically increase in severity over the course of a few hours. Development of new point of care tools for sepsis has the potential to improve diagnostic speed and accuracy, leading to prompt administration of appropriate therapeutics, thereby reducing healthcare costs and improving patient outcomes. In this review we examine developing and commercially available technologies to assess the feasibility of rapid, accurate sepsis diagnosis, with emphasis on point of care.

A 3D-Printed Millifluidic Platform Enabling Bacterial Preconcentration and DNA Purification for Molecular Detection of Pathogens in Blood

Molecular detection of pathogens in clinical samples often requires pretreatment techniques, including immunomagnetic separation and magnetic silica-bead-based DNA purification to obtain the purified DNA of pathogens. These two techniques usually rely on handling small tubes containing a few millilitres of the sample and manual operation, implying that an automated system encompassing both techniques is needed for larger quantities of the samples. Here, we report a three-dimensional (3D)-printed millifluidic platform that enables bacterial preconcentration and genomic DNA (gDNA) purification for improving the molecular detection of target pathogens in blood samples. The device consists of two millichannels and one chamber, which can be used to preconcentrate pathogens bound to antibody-conjugated magnetic nanoparticles (Ab-MNPs) and subsequently extract gDNA using magnetic silica beads (MSBs) in a sequential manner. The platform was able to preconcentrate very low concentrations (1–1000 colony forming units (CFU)) of Escherichia coli O157:H7 and extract their genomic DNA in 10 mL of buffer and 10% blood within 30 min. The performance of the platform was verified by detecting as low as 1 CFU of E. coli O157:H7 in 10% blood using either polymerase chain reaction (PCR) with post gel electrophoresis or quantitative PCR. The results suggest that the 3D-printed millifluidic platform is highly useful for lowering the limitations on molecular detection in blood by preconcentrating the target pathogen and isolating its DNA in a large volume of the sample.

On the challenges of detecting whole Staphylococcus aureus cells with biosensors

Due to the increasing number of nosocomial infections and multidrug-resistant bacterial strains, Staphylococcus aureus is now a major worldwide concern. Rapid detection and characterization of this bacterium has become an important issue for biomedical applications. Biosensors are increasingly appearing as low-cost, easy-to-operate and fast alternatives for rapid detection. In this review, we will introduce the main characteristics of S. aureus and will focus on the interest of biosensors for a faster detection of whole S. aureus cells. In particular, we will review the most promising strategies in the choice of ligand for the design of selective and efficient biosensors. Their specific characteristics as well as their advantages and/or disadvantages will also be commented.

Rapid separation of bacteria from blood - Chemical aspects

To rapidly diagnose infectious organisms causing blood sepsis, bacteria must be rapidly separated from blood, a very difficult process considering that concentrations of bacteria are many orders of magnitude lower than concentrations of blood cells. We have successfully separated bacteria from red and white blood cells using a sedimentation process in which the separation is driven by differences in density and size. Seven mL of whole human blood spiked with bacteria is placed in a 12-cm hollow disk and spun at 3000rpm for 1min. The red and white cells sediment more than 30-fold faster than bacteria, leaving much of the bacteria in the plasma. When the disk is slowly decelerated, the plasma flows to a collection site and the red and white cells are trapped in the disk. Analysis of the recovered plasma shows that about 36% of the bacteria is recovered in the plasma. The plasma is not perfectly clear of red blood cells, but about 94% have been removed. This paper describes the effects of various chemical aspects of this process, including the influence of anticoagulant chemistry on the separation efficiency and the use of wetting agents and platelet aggregators that may influence the bacterial recovery. In a clinical scenario, the recovered bacteria can be subsequently analyzed to determine their species and resistance to various antibiotics.