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Fast Automated Multiplex Analysis of Neonatal Sepsis Markers on a Centrifugal Microfluidic Platform

Final Report Summary - ASCMICROPLAT (Fast Automated Multiplex Analysis of Neonatal Sepsis Markers on a Centrifugal Microfluidic Platform)

Executive Summary:
Neonatal sepsis is caused by bacterial pathogens that enter the blood stream and the disease remains among the major causes of infant death worldwide. Amongst other, the high rates of morbidity and mortality are also associated with short-comings in current diagnostics management of patient sepsis.
The project ASCMicroPlat aimed at developing new test methods for rapid diagnosis of neonatal sepsis, which would provide clinicians with vital information at earlier stages to reduce mortality and morbidity. Therefore a novel Polymerase-Chain-Reaction (PCR) assay including sample preparation (DNA extraction) was developed that enables identification of a whole panel of neonatal sepsis pathogens in human serum samples within 4 hours. The assay (denominated nucleic acid assay) was successfully tested for sensitivity and specificity to enable detection of low bacterial-loads and prevent unspecific signal generation in clinically relevant samples. The nucleic acid assay was successfully integrated on LabDisk test carriers to automate the entire process flow thereby massively reducing hands-on time for testing. Hereby, microfluidic modules for each process step were developed that enable automation by simple means of a rotation frequency protocol. The only manual handling steps remained initial loading of the sample and DNA extraction reagents on the LabDisk before starting the rotational protocol. The development now enables a true `sample-to-result´ system with ease of handling that aims at processing by untrained personnel at the point-of-care. The LabDisk test proofed to be highly sensitive and demonstrated the detection of pathogens also for extremely low bacterial loads below 10 cfu / sample. For validation of the nucleic acid assay, neonatal patient samples were collected in clinics throughout the entire duration of the project. This enabled testing the LabDisk with neonatal sepsis positive and negative samples and comparison with the diagnostic gold standard of blood culture. The tests with these clinical samples yielded promising results and demonstrated the capability of the system to conduct panel analysis of a complete set of neonatal sepsis relevant pathogens. Although the LabDisk test showed perfect agreement with the blood culture in some cases, there were several cases where contamination of skin flora bacteria, likely on the test carrier, superimposed the clinical test results. The contamination issue was identified and strategies for prevention of contamination during production were derived.
In addition to the nucleic acid assay, manual immunoassay tests (ELISA, immuno-PCR) for quantification of biomarkers C-reactive protein (CRP) and Procalcitonin (PCT) were developed. These protein-based assays were integrated on separate LabDisk test carriers for automation with rotational protocols. Hereby an automated magnetic ELISA enabled quantification of the biomarker C-reactive protein in human serum within 25 minutes in the clinically relevant range. A proof-of-principle for an automated magnetic immuno-PCR was also demonstrated for the first time that in future could provide multiplexing for analysis of both biomarkers.
Besides the assay integration, ASCMicroPlat also implemented the production of the LabDisks based on an inventive foil-technology on industrial machines. The LabDisk test carriers are fabricated by micro-thermoforming of thin polymer foils and the technology was brought from prototyping to industrial scale machines towards mass fabrication. Also a new mobile device (LabDisk player) was developed featuring fluorescence detection, PCR-thermocycling and the possibility to run predefined centrifugal protocols. This enables processing of the LabDisk at the point-of-care.

Project Context and Objectives:
Neonatal sepsis is a potentially fatal disease characterized by a whole body inflammatory state coupled with the presence of a known or suspected infection. Mortality rates range from 1.5% in term babies to 40% in very low birth-weight babies, to up to 70% in the developing world. Neonatal sepsis occurs when microorganism enter the bloodstream resulting in an irrepressible systemic cytokine mediated inflammatory response. This can lead to collapse of circulation and perfusion of vital organs and thus to patient death. The clinical signs of neonatal sepsis are in general nonspecific and are hard to distinguish from other medical condition such as respiratory distress syndrome or meningitis. The time until initiation of antimicrobial treatment is a strong indicator of mortality rates. Administration of antibiotics within the first hour of documented hypotension is associated with a survival rate of 79.9% in adult sepsis. Each hour of delay in the administration of antibiotics was associated with an average decrease in survival of 7.6% in the following 6 hours. The immune system of a neonate is relatively immature compared to adults and progression of neonatal sepsis disease can be very rapid. Sepsis is widely regarded as the most challenging problem in intensive care, where more than half of all severe cases are treated. This is a direct consequence of the complexity of the disease and its rapid progression. Current antibiotic management initiates therapy for neonates at high risk of developing sepsis. Also administration of antibiotics is initiated to all individuals that display infectious symptoms regardless if actually infected or not. This may lead to adverse drug effects as well as spreading of resistant bacterial strains.
The diagnosis of neonatal sepsis in clinics usually has two major purposes: Identification of the causative pathogenic microorganism and determination of the inflammatory immune response elicited in the patient in response to the respective microbial agent via biomarker quantification.
Quantification of diagnostic biomarkers such as C-reactive protein (CRP), interleukin-6 or tumor-necrosis-factor-alpha for determination of the inflammatory immune response is usually conducted with automated bulky, high complex workstations in the clinics or in central laboratories. CRP is an acute phase response protein and the most commonly used neonatal sepsis marker in Europe. In view of the complexity of sepsis, a combination of markers would be more effective for diagnostic purposes and the most promising of the additional markers is procalcitonin (PCT). Systemic PCT secretion is a component of the inflammatory response that appears to be relatively specific to systemic bacterial infections.
Current ´gold standard´ for investigation of sepsis and identification of pathogens is blood culture, a method that has been applied in clinics for several decades. Blood samples are cultured with specific media for growth of bacterial targets, taking 1-5 days for result reporting and identification of the causative agent. Relating to the rapidly progressing neonatal sepsis, the time to results remains one of the major drawbacks of blood culture. Also, blood culture is also associated with false negative (e.g. to previous antibiotic treatment) as well as false positive (e.g. due to contamination) results that can lead to misuse of antibiotics and can worsen the prognosis of patients. To overcome the limitations of blood culture, molecular diagnostics were developed for rapid detection of specific gene sequences and identification of pathogens from neonate samples, such as whole blood, or blood serum. However, conventional molecular diagnostic tests, e.g. polymerase chain reaction (PCR) based assays are time consuming and apply complex protocols that require significant hands-on time, especially once sample pre-treatment of the sample matrix is considered as well. Therefore, usually trained personnel and high-level laboratory equipment is needed.
It is imperative to detect and diagnose neonatal sepsis as early as possible to ensure the best outcome for patients. Besides improvements in clinical specificity and sensitivity of new test methods, the state-of-the art does not provide the neonatal intensivist with a fast and accurate test, in particular at the point-of-care.
Within this context, the project ASCMicroPlat aimed at realization and clinical validation of a fully integrated and automated platform for the detection of neonatal sepsis biomarkers and a panel of sepsis-causing bacteria from serum samples. Centrifugal microfluidics were applied to develop an easy-to-use diagnostic test that can be applied at the point-of-care. Biomarker quantification was conducted by a novel magnetic immuno-PCR approach or by automated enzyme-linked immunosorbent assay (ELISA). Pathogen identification was based on a PCR test method that includes samples preparation (DNA extraction). The tests were integrated on a rotating test carrier, the `LabDisk´ that can be processed on a portable processing device using a specific rotational protocol. The system provides several novelties:

1. Fully automated and integrated analysis from serum (“sample-to-answer”) where several unit operations are integrated on the LabDisk. Major reagents of the test are pre-stored on the LabDisk.

2. Multiplexed detection for a complete panel analysis of sepsis causing bacterial agents within process duration below 4 hours.

3. Scalable fabrication technology based on micro-thermoforming of polymer foils, in order to achieve low-cost and high-throughput production of diagnostic kits.

4. Processing in a mobile, point-of-care processing device `LabDisk player`, that provides full control of defined rotation, acceleration and temperature and conducts optical signal readout.

As part of the project a clinical study was performed using clinical samples to validate the microfluidic LabDisk technology and to investigate the interaction between presence of microbial pathogens and the host response with a view to planning patient management more appropriately. The novel system was benchmarked against the gold standards currently used in the clinical laboratories.
In the respect of providing an easy-to-use, fast and conclusive test method, the project could have significant impact and market potential in clinics and also in laboratories. In contrast to current state-of-the-art of neonatal sepsis diagnostics, the platform could very well establish timely and especially specific treatment for patients. In the long term this may also reduce the spread of multiresistant strains emerging from the unspecific use of broad-spectrum antibiotics, which is considered as one of the major clinical and public health problem within the lifetime of most people living today. In the future, possibly the LabDisk principle could be applied in other cases where timely diagnostics is of the essence (pandemics, hospital acquired infections, etc.).
The interdisciplinary consortium included a university hospital, a research institute and three industrial companies (all of which are SMEs), who have together extensive experience in all relevant fields ranging from neonatal sepsis diagnostics using PCR based assays to polymer micro fabrication techniques and microfluidics. Thus, the full supply and value chain was covered by the consortium.

Project Results:
Development of nucleic acid assay and protein assay

During the ASCMicroPlat project a nucleic acid based pathogen detection assay was developed consisting of target pathogen lysis, nucleic acid purification, nucleic acid amplification and amplification detection by fluorescence. The sample material used in the nucleic acid assay was 200 µL of human serum extracted from whole blood.
Each of the bacterial targets were tested to have a sensitivity below 100 copies/PCR reaction in full laboratory scale, with some of the more sensitive targets repeatedly identified in as low concentrations as 10 copies/reaction. Sensitivities of only few copies per reaction were intentionally avoided in order to reduce the contamination vulnerability of the assay.
Development of immunoassays for quantification of C-reactive protein and Procalcitonin (WP3)
Besides the assay for pathogen detection on the basis of nucleic acids, immunoassays for quantification of C-reactive protein (CRP) and Procalcitonin (PCT) were developed for subsequent integration on LabDisk test carriers. The immunoassay format chosen was immuno-PCR, where signal generation is based on realtime-PCR amplification of marker-DNA that is conjugated to antibodies.

Disposable production technology

In summary, a couple of adjustments regarding the thermoforming technology and the machine components were necessary to thermoform the required microstructure of the LabDisks. In combination with the newly developed production process parameters stable dimensions of the LabDisks as well as a stable process could be established. Finally this results in sharp edges and corners of the cavities and channels which are essential for the microfluidic properties. The project therefore led successful modification of the conventional thermoforming process in order to produce micro-thermoformed LabDisks with much higher precision. Microfluidic tests proved the function of the LabDisks.

Development of processing device for LabDisk test carriers

In collaboration with HSG-IMIT and Qiagen the LabDisk player prototype was developed, that now enables processing of LabDisks for the developed assays featuring centrifugal rotation control, PCR thermocycling, signal readout and magnetic actuation.

Microfluidic integration of nucleic acid assay on LabDisk test carriers

The developed nucleic acid assay protocol was integrated on a microfluidic LabDisk test carrier. For each assay process step (Liquid handling, DNA extraction, PCR preamplification, Realtime PCR amplification) separate modules were developed that were finally combined and integrated.

Microfluidic integration of immunoassay on LabDisk test carriers

Both, an ELISA as well as an immuno-PCR assay were successfully automated on the LabDisk. For a proof-of-principle, human serum was spiked with known concentrations of CRP and the samples processed with the LabDisk test. The results showed a clear correlation of human serum concentration to the signal increase (thermocycles).

Clinical testing and validation

In summary, clinical testing of the bacterial LabDisk assay demonstrated the capability of the system to detect a range of pathogens in neonate serum including Escherichia coli, Klebsiella oxytoca, Klebsiella pneumonia, Staphylococcus capitis, Staphylococcus epidermidis. The immuno-PCR assays for CRP and PCT showed a good correlation with gold standard CRP detection and also for PCT at low concentrations.

Potential Impact:

The final adaptation of an integrated LabDisk test for bacteria and biomarkers will undoubtedly prove useful for diagnosis of neonatal sepsis, reducing reporting hold ups for identification of pathogens and abnormal immune responses, and improving patient outcomes in this potentially fatal disease.
The developed immuno-PCR assay for quantification of CRP and PCT (once fully validated for PCT), will offer an improvement on current gold standard biomarker detection, which typically only includes CRP.
The interdisciplinary ASCMicroPlat project integrated microfluidic technology, production technology, processing device technology and biochemistry into one diagnostic platform. In ASCMicroPlat, the complete value chain from development of production technologies and microfluidic design to clinical validation was covered. For production of the LabDisk test carriers, an existing blister packaging production technology was used as basis to develop a production technology for the microfluidic LabDisk disposables. The technology will be used in follow-up projects and may incorporate the production technology of choice for LabDisk products.

Exploitations of results

The technical project results could be a starting point for a commercial development of a point-of-care diagnostic system for neonatal sepsis. The proof-of-principle was generated. Currently, there are expert interviews with key opinion leaders in Germany ongoing to assess the potential of such a product. A market study by HSG-IMIT to assess the requirements for a potential product is currently ongoing. If the outcome shows a clear clinical and economic benefit, this could trigger the involvement of venture capital and a spin-off company.

List of Websites:

The project webpage can be accessed using the link www.ascmicroplat.eu

final1-publishable-summary.pdf