Sandra Julich

Automated microfluidically controlled electrochemical biosensor for the rapid and highly sensitive detection of Francisella tularensis.

Tularemia is a highly infectious zoonotic disease caused by a Gram-negative coccoid rod bacterium, Francisella tularensis. Tularemia is considered as a life-threatening potential biological warfare agent due to its high virulence, transmission, mortality and simplicity of cultivation. In the work reported here, different electrochemical immunosensor formats for the detection of whole F. tularensis bacteria were developed and their performance compared. An anti-Francisella antibody (FB11) was used for the detection that recognises the lipopolysaccharide found in the outer membrane of the bacteria. In the first approach, gold-supported self-assembled monolayers of a carboxyl terminated bipodal alkanethiol were used to covalently cross-link with the FB11 antibody. In an alternative second approach F(ab) fragments of the FB11 antibody were generated and directly chemisorbed onto the gold electrode surface. The second approach resulted in an increased capture efficiency and higher sensitivity. Detection limits of 4.5 ng/mL for the lipopolysaccharide antigen and 31 bacteria/mL for the F. tularensis bacteria were achieved. Having demonstrated the functionality of the immunosensor, an electrode array was functionalised with the antibody fragment and integrated with microfluidics and housed in a tester set-up that facilitated complete automation of the assay. The only end-user intervention is sample addition, requiring less than one-minute hands-on time. The use of the automated microfluidic set-up not only required much lower reagent volumes but also the required incubation time was considerably reduced and a notable increase of 3-fold in assay sensitivity was achieved with a total assay time from sample addition to read-out of less than 20 min.

Hare-to-Human Transmission of Francisella tularensis subsp. holarctica, Germany

In November 2012, a group of 7 persons who participated in a hare hunt in North Rhine-Westphalia, Germany, acquired tularemia. Two F. tularensis subsp. holarctica isolates were cultivated from human and hare biopsy material. Both isolates belonged to the FTN002–00 genetic subclade (derived for single nucleotide polymorphisms B.10 and B.18), thus indicating likely hare-to-human transmission.

A microfluidic platform with integrated arrays for immunologic assays for biological pathogen detection

The ability to integrate complete assays on a microfluidic chip helps to greatly simplify instrument requirements and allows the use of lab-on-a-chip technology in the field. A core application for such field-portable systems is the detection of pathogens in a CBRN scenario such as permanent monitoring of airborne pathogens, e.g. in subway stations or hospitals etc. An immunological assay was chosen as method for the pathogen identification. The conceptual approach was its realization as a lab-on-a-chip system, enabling an easy handling of the sample in an automated manner. The immunological detection takes place on an antibody array directly implemented in the microfluidic network. Different immobilization strategies will be presented showing the performance of the system. Central elements of the disposable microfluidic device like fluidic interface, turning valves, liquid introduction and waste storage, as well as the architecture of measurement and control fluidic network, will be introduced. Overall process times of about 30 minutes were achieved and assays for the detection of Francisella tularensis and Yersinia pestis are presented. An important feature of the integrated lab-on-a-chip approach is that all waste liquids remain on-chip and contamination risks can be avoided.

Standoff detection: distinction of bacteria by hyperspectral laser induced fluorescence

Sensitive detection and rapid identification of hazardous bioorganic material with high sensitivity and specificity are essential topics for defense and security. A single method can hardly cover these requirements. While point sensors allow a highly specific identification, they only provide localized information and are comparatively slow. Laser based standoff systems allow almost real-time detection and classification of potentially hazardous material in a wide area and can provide information on how the aerosol may spread. The coupling of both methods may be a promising solution to optimize the acquisition and identification of hazardous substances. The capability of the outdoor LIF system at DLR Lampoldshausen test facility as an online classification tool has already been demonstrated. Here, we present promising data for further differentiation among bacteria. Bacteria species can express unique fluorescence spectra after excitation at 280 nm and 355 nm. Upon deactivation, the spectral features change depending on the deactivation method.

Evaluation of a microfluidic chip system for preparation of bacterial DNA from swabs, air, and surface water samples

The detection of bacterial pathogens from complex sample matrices by PCR requires efficient DNA extraction. In this study, a protocol for extraction and purification of DNA from swabs, air, and water samples using a microfluidic chip system was established. The optimized protocol includes a combination of thermal, chemical and enzymatic lysis followed by chip-based DNA purification using magnetic particles. The procedure was tested using Gram-positive Bacillus thuringiensis Berliner var. kurstaki as a model organism for Bacillus anthracis and the attenuated live vaccine strain of Francisella tularensis subsp. holarctica as Gram-negative bacterium. The detection limits corresponded to 103 genome equivalents per milliliter (GE/ml) for surface water samples spiked with F. tularensis and 102 GE/ml for B. thuringiensis. In air, 10 GE of F. tularensis per 10 L and 1 GE of B. thuringiensis per 10 L were detectable. For swab samples obtained from artificially contaminated surfaces the detection limits were 4 × 103 GE/cm2 for F. tularensis and 4 × 102 GE/cm2 for B. thuringiensis. Suitability of the chip-assisted procedure for DNA preparation of real samples was demonstrated using livestock samples. The presence of thermophilic Campylobacter spp. DNA could be confirmed in air samples collected on pig and broiler farms.

Lab-on-a-chip modules for detection of highly pathogenic bacteria: from sample preparation to detection

Lab-on-a-chip systems are innovative tools for the detection and identification of microbial pathogens in human and veterinary medicine. The major advantages are small sample volume and a compact design. Several fluidic modules have been developed to transform analytical procedures into miniaturized scale including sampling, sample preparation, target enrichment, and detection procedures. We present evaluation data for single modules that will be integrated in a chip system for the detection of pathogens. A microfluidic chip for purification of nucleic acids was established for cell lysis using magnetic beads. This assay was evaluated with spiked environmental aerosol and swab samples. Bacillus thuringiensis was used as simulant for Bacillus anthracis, which is closely related but non-pathogenic for humans. Stationary PCR and a flow-through PCR chip module were investigated for specific detection of six highly pathogenic bacteria. The conventional PCR assays could be transferred into miniaturized scale using the same temperature/time profile. We could demonstrate that the microfluidic chip modules are suitable for the respective purposes and are promising tools for the detection of bacterial pathogens. Future developments will focus on the integration of these separate modules to an entire lab-on-a-chip system.

Development of a versatile lab-on-a-chip enzyme assay platform for pathogen detection in CBRNE scenarios

The ability to integrate complete assays on a microfluidic chip helps to greatly simplify instrument requirements and allows the use of lab-on-a-chip technology in the field. A core application for such field-portable systems is the detection of pathogens in a CBRNE scenario such as permanent monitoring of airborne pathogens, e.g. in metro stations or hospitals etc. As one assay methodology for the pathogen identification, enzymatic assays were chosen. In order evaluate different detection strategies, the realized on-chip enzyme assay module has been designed as a general platform chip. In all application cases, the assays are based on immobilized probes located in microfluidic channels. Therefore a microfluidic chip was realized containing a set of three individually addressable channels, not only for detection of the sample itself also to have a set of references for a quantitative analysis. It furthermore includes two turning valves and a waste container for clear and sealed storage of potential pathogenic liquids to avoid contamination of the environment. All liquids remain in the chip and can be disposed of in proper way subsequently to the analysis. The chip design includes four inlet ports consisting of one sample port (Luer interface) and three mini Luer interfaces for fluidic support of e.g. washing buffer, substrate and enzyme solution. The sample can be applied via a special, sealable sampling vessel with integrated female Luer interface. Thereby also pre-anaytical contamination of the environment can be provided. Other reagents that are required for analysis will be stored off chip.

Sequential continuous flow PCR for detection of Bacillus anthracis, Brucella melitensis, Burkholderia mallei, Coxiella burnetii, Francisella tularensis and Yersinia pestis using a microfluidic chip system

In food and food-producing animals monitoring of antimicrobial resistant bacteria is mostly conducted on commensal E. coli. From 2015 on in the EU also the selective isolation and subsequent resistance testing on ESBL/AmpC-producing E. coli is mandatory (2013/652/EU).Question: Domestic pigs and Eurasian wild boar (Sus scrofa) share several important viral and bacterial pathogens. Therefore, direct and indirect contacts between domestic pigs and wild boar present a risk of pathogen spill-over and can lead to long-term perpetuation of infection. Biological indicators could be a powerful tool to understand and characterize contacts between wild boar and domestic pigs. Here, faecal E. coli were explored as potential biological indicator under experimental conditions. Methods: Within an animal trial domestic pigs (group 2, n=8) were brought into contact with faecal material of wild boar (group 1, n=8). Before and three to five weeks after transmission of faeces fecal samples of both groups were collected, coliforme bacteria isolated, and the bacteria tested by CHEF-PFGE for clonal relatedness. The study was meant as test and calibration phase for potential field studies. Results: Eighty-eight individual E. coli clones were detected by XbaI restriction and PFGE analysis. Selecting only one isolates representing a distinct clone from an individual faecal sample, 123 E. coli isolates were further analysed. Overall, 17 different clones were found in several animals of a group (1 or 2) or both samples from one animal. Additionally, five clones were detected in group 1 as well as in contact group 2. Conclusions: The data gained in our pilot study suggest that faecal E. coli can be used as biological indicator of contact between wild boar and domestic pig. Based on these promising results, future field studies will especially target the practicability of E. coli microbiome molecular typing as surrogate of contacts at the wildlife-livestock interface. This study is funded by the European Unions Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 311931 (ASFORCE).

Purification of Bacillus thuringiensis DNA with polymer-based, microfluidic lab-on-a-chip systems

Aim of the study was to establish and evaluate a “lab-on-a-chip” system for the detection of bacterial B-agents using Bacillus (B.) thuringiensis as simulant for B. anthracis. To enable reliable detection of target DNA using PCR assays it is crucial that purified DNA is extracted from the sample matrix. We established chip-based assays for cell lysis, sample concentration, and DNA purification using magnetic particles with special surface modifications and compared these assays with a commercial routine method. DNA yield was determined using quantitative real-time PCR assays with TaqMan probes targeting the cry1Ac gene. Lab-on-a-chip systems are applicable for point-of-care analysis and provide several advantages in comparison to conventional diagnostic techniques. Purification of DNA and subsequent PCR analysis can be integrated and the instrumentation can be miniaturized. Therefore, such tests can also be useful in medical and veterinary diagnostics.