Silica particles with encapsulated DNA as trophic tracers

Outbreak simulation on the neonatal ward using silica nanoparticles with encapsulated DNA - unmasking of key spread areas

PURPOSE

Nosocomial infections pose a serious threat. In neonatal intensive care units (NICUs) in particular, there are repeated outbreaks caused by microorganisms without the sources or dynamics being conclusively determined. This study aims to use amorphous silica nanoparticles with encapsulated DNA (SPED) to simulate outbreak events and to visualize dissemination patterns in a NICU to gain a better understanding of these dynamics.

METHODS

Three types of SPED were strategically placed on the ward to mimic three different dissemination dynamics among real-life conditions and employee activities. SPED DNA, resistant to disinfectants, was sampled at 22 predefined points across the ward for four days and qPCR analysis was conducted.

RESULTS

Starting from staff areas, a rapid ward-wide SPED dissemination including numerous patient rooms was demonstrated. In contrast, a primary deployment in a patient room only led to the spread in the staff area, with no distribution in the patient area.

CONCLUSION

This study pioneers SPED utilization in simulating outbreak dynamics. By unmasking staff areas as potential key trigger spots for ward-wide dissemination the revealed patterns could contribute to a more comprehensive view of outbreak events leading to rethinking of hygiene measures and training to reduce the rate of nosocomial infections in hospitals.

Scalable Combinatorial Assembly of Synthetic DNA for Tracking Applications

Synthetic DNA barcodes are double-stranded DNA molecules designed to carry recoverable information, information that can be used to represent and track objects and organisms. DNA barcodes offer robust, sensitive detection using standard amplification and sequencing techniques. While numerous research groups have promoted DNA as an information storage medium, less attention has been devoted to the design of economical, scalable DNA barcode libraries. Here, we present an alternative modular approach to sequence design. Barcode sequences were constructed from smaller, interchangeable blocks, allowing for the combinatorial assembly of numerous distinct tags. We demonstrated the design and construction of first-generation (N = 256) and second-generation (N = 512) modular barcode libraries, from fewer than 50 total single-stranded oligonucleotides for each library. To avoid contamination during experimental validation, a liquid-handling robot was employed for oligonucleotide mixing. Generating barcode sequences in-house reduces dependency upon external entities for unique tag generation, increasing flexibility in barcode generation and deployment. Next generation sequencing (NGS) detection of 256 different samples in parallel highlights the multiplexing afforded by the modular barcode design coupled with high-throughput sequencing. Deletion variant analysis of the first-generation library informed sequence design for enhancing barcode assembly specificity in the second-generation library.

An Accurate and Rapid Way for Identifying Food Geographical Origin and Authenticity: Editable DNA-Traceable Barcode

DNA offers significant advantages in information density, durability, and replication efficiency compared with information labeling solutions using electronic, magnetic, or optical devices. Synthetic DNA containing specific information via gene editing techniques is a promising identifying approach. We developed a new traceability approach to convert traditional digitized information into DNA sequence information. We used encapsulation to make it stable for storage and to enable reading and detection by DNA sequencing and PCR-capillary electrophoresis (PCR-CE). The synthesized fragment consisted of a short fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene from the Holothuria fuscogilva (ID: LC593268.1), inserted geographical origin information (18 bp), and authenticity information from Citrus sinensis (20 bp). The obtained DNA-traceable barcodes were cloned into vector PMD19-T. Sanger sequencing of the DNA-traceable barcode vector was 100% accurate and provided a complete readout of the traceability information. Using selected recognition primers CAI-B, DNA-traceable barcodes were identified rapidly by PCR amplification. We encapsulated the DNA-traceable barcodes into amorphous silica spheres and improved the encapsulation procedure to ensure the durability of the DNA-traceable barcodes. To demonstrate the applicability of DNA-traceable barcodes as product labels, we selected Citrus sinensis as an example. We found that the recovered and purified DNA-traceable barcode can be analyzed by standard techniques (PCR-CE for DNA-traceable barcode identification and DNA sequencing for readout). This study provides an accurate and rapid approach to identifying and certifying products' authenticity and traceability.

Silica nanoparticles with encapsulated DNA (SPED) to trace the spread of pathogens in healthcare

Background

To establish effective infection control protocols, understanding pathogen transmission pathways is essential. Non-infectious surrogate tracers may safely explore these pathways and challenge pre-existing assumptions. We used silica nanoparticles with encapsulated DNA (SPED) for the first time in a real-life hospital setting to investigate potential transmission routes of vancomycin-resistant enterococci in the context of a prolonged outbreak.

Methods

The two study experiments took place in the 900-bed University Hospital Zurich, Switzerland. A three-run ‘Patient experiment’ investigated pathogen transmission via toilet seats in a two-patient room with shared bathroom. First, various predetermined body and fomite sites in a two-bed patient room were probed at baseline. Then, after the first patient was contaminated with SPED at the subgluteal region, both patients sequentially performed a toilet routine. All sites were consequently swabbed again for SPED contamination. Eight hours later, further spread was tested at predefined sites in the patient room and throughout the ward. A two-run ‘Mobile device experiment’ explored the potential transmission by mobile phones and stethoscopes in a quasi-realistic setting. All SPED contamination statuses and levels were determined by real-time qPCR.

Results

Over all three runs, the ‘Patient experiment’ yielded SPED in 59 of 73 (80.8%) predefined body and environmental sites. Specifically, positivity rates were 100% on subgluteal skin, toilet seats, tap handles, and entertainment devices, the initially contaminated patients’ hands; 83.3% on patient phones and bed controls; 80% on intravenous pumps; 75% on toilet flush plates and door handles, and 0% on the initially not contaminated patients’ hands. SPED spread as far as doctor’s keyboards (66.6%), staff mobile phones (33.3%) and nurses’ keyboards (33.3%) after eight hours. The ‘Mobile device experiment’ resulted in 16 of 22 (72.7%) positive follow-up samples, and transmission to the second patient occurred in one of the two runs.

Conclusions

For the first time SPED were used to investigate potential transmission pathways in a real hospital setting. The results suggest that, in the absence of targeted cleaning, toilet seats and mobile devices may result in widespread transmission of pathogens departing from one contaminated patient skin region.

Mosquito tagging using DNA-barcoded nanoporous protein microcrystals

Conventional mosquito marking technology for mark-release-recapture (MRR) is quite limited in terms of information capacity and efficacy. To overcome both challenges, we have engineered, lab-tested, and field-evaluated a new class of marker particles, in which synthetic, short DNA oligonucleotides (DNA barcodes) are adsorbed and protected within tough, crosslinked porous protein microcrystals. Mosquitoes self-mark through ingestion of microcrystals in their larval habitat. Barcoded microcrystals persist trans-stadially through mosquito development if ingested by larvae, do not significantly affect adult mosquito survivorship, and individual barcoded mosquitoes are detectable in pools of up to at least 20 mosquitoes. We have also demonstrated crystal persistence following adult mosquito ingestion. Barcode sequences can be recovered by qPCR and next-generation sequencing (NGS) without detectable amplification of native mosquito DNA. These DNA-laden protein microcrystals have the potential to radically increase the amount of information obtained from future MRR studies compared to previous studies employing conventional mosquito marking materials.

Transport characteristics of DNA-tagged silica colloids as a colloidal tracer in saturated sand columns; role of solution chemistry, flow velocity, and sand grain size

In recent years, DNA-tagged silica colloids have been used as an environmental tracer. A major advantage of this technique is that the DNA-coding provides an unlimited number of unique tracers without a background concentration. However, little is known about the effects of physio-chemical subsurface properties on the transport behavior of DNA-tagged silica tracers. We are the first to explore the deposition kinetics of this new DNA-tagged silica tracer for different pore water chemistries, flow rates, and sand grain size distributions in a series of saturated sand column experiments in order to predict environmental conditions for which the DNA-tagged silica tracer can best be employed. Our results indicated that the transport of DNA-tagged silica tracer can be well described by first order kinetic attachment and detachment. Because of massive re-entrainment under transient chemistry conditions, we inferred that attachment was primarily in the secondary energy minimum. Based on calculated sticking efficiencies of the DNA-tagged silica tracer to the sand grains, we concluded that a large fraction of the DNA-tagged silica tracer colliding with the sand grain surface did also stick to that surface, when the ionic strength of the system was higher. The experimental results revealed the sensitivity of DNA-tagged silica tracer to both physical and chemical factors. This reduces its applicability as a conservative hydrological tracer for studying subsurface flow paths. Based on our experiments, the DNA-tagged silica tracer is best applicable for studying flow routes and travel times in coarse grained aquifers, with a relatively high flow rate. DNA-tagged silica tracers may also be applied for simulating the transport of engineered or biological colloidal pollution, such as microplastics and pathogens.

Silica-encapsulated DNA tracers for measuring aerosol distribution dynamics in real-world settings

Aerosolized particles play a significant role in human health and environmental risk management. The global importance of aerosol-related hazards, such as the circulation of pathogens and high levels of air pollutants, have led to a surging demand for suitable surrogate tracers to investigate the complex dynamics of airborne particles in real-world scenarios. In this study, we propose a novel approach using silica particles with encapsulated DNA (SPED) as a tracing agent for measuring aerosol distribution indoors. In a series of experiments with a portable setup, SPED were successfully aerosolized, recaptured, and quantified using quantitative polymerase chain reaction (qPCR). Position dependency and ventilation effects within a confined space could be shown in a quantitative fashion achieving detection limits below 0.1 ng particles per m³ of sampled air. In conclusion, SPED show promise for a flexible, cost-effective, and low-impact characterization of aerosol dynamics in a wide range of settings.

Tomographic Reservoir Imaging with DNA-Labeled Silica Nanotracers: The First Field Validation

This study presents the first field validation of using DNA-labeled silica nanoparticles as tracers to image subsurface reservoirs by travel time based tomography. During a field campaign in Switzerland, we performed short-pulse tracer tests under a forced hydraulic head gradient to conduct a multisource-multireceiver tracer test and tomographic inversion, determining the two-dimensional hydraulic conductivity field between two vertical wells. Together with three traditional solute dye tracers, we injected spherical silica nanotracers, encoded with synthetic DNA molecules, which are protected by a silica layer against damage due to chemicals, microorganisms, and enzymes. Temporal moment analyses of the recorded tracer concentration breakthrough curves (BTCs) indicate higher mass recovery, less mean residence time, and smaller dispersion of the DNA-labeled nanotracers, compared to solute dye tracers. Importantly, travel time based tomography, using nanotracer BTCs, yields a satisfactory hydraulic conductivity tomogram, validated by the dye tracer results and previous field investigations. These advantages of DNA-labeled nanotracers, in comparison to traditional solute dye tracers, make them well-suited for tomographic reservoir characterizations in fields such as hydrogeology, petroleum engineering, and geothermal energy, particularly with respect to resolving preferential flow paths or the heterogeneity of contact surfaces or by enabling source zone characterizations of dense nonaqueous phase liquids.

A DNA Tracer System for Hydrological Environment Investigations

To monitor and manage hydrological pollution effectively, tracing sources of pollutants is of great importance and also is in urgent need. A variety of tracers have been developed such as isotopes, silica, bromide, and dyes; however, practical limitations of these traditional tracers still exist such as lack of multiplexed, multipoint tracing and interference of background noise. To overcome these limitations, a new tracing system based on DNA nanomaterials, namely DNA tracer, has already been developed. DNA tracers possess remarkable advantages including sufficient species, specificity, environmental friendly, stable migration, and high sensitivity as well as allowing for multipoints tracing. In this review article, we introduce the molecular design, synthesis, protection and signal readout strategies of DNA tracers, compare the advantages and disadvantages of DNA tracer with traditional tracers, and summarize the-state-of-art applications in hydrological environment investigations. In the end, we provide our perspective on the future development of DNA tracers.

Detecting and Number Counting of Single Engineered Nanoparticles by Digital Particle Polymerase Chain Reaction

The concentrations of nanoparticles present in colloidal dispersions are usually measured and given in mass concentration (e.g. mg/mL), and number concentrations can only be obtained by making assumptions about nanoparticle size and morphology. Additionally traditional nanoparticle concentration measures are not very sensitive, and only the presence/absence of millions/billions of particles occurring together can be obtained. Here, we describe a method, which not only intrinsically results in number concentrations, but is also sensitive enough to count individual nanoparticles, one by one. To make this possible, the sensitivity of the polymerase chain reaction (PCR) was combined with a binary (=0/1, yes/no) measurement arrangement, binomial statistics and DNA comprising monodisperse silica nanoparticles. With this method, individual tagged particles in the range of 60-250 nm could be detected and counted in drinking water in absolute number, utilizing a standard qPCR device within 1.5 h of measurement time. For comparison, the method was validated with single particle inductively coupled plasma mass spectrometry (sp-ICPMS).

Industrial applications of nanoparticles

This tutorial review analyses where nanoparticle research has left the laboratory and today contributes to valuable products.

Labeling milk along its production chain with DNA encapsulated in silica

The capability of tracing a food product along its production chain is important to ensure food safety and product authenticity. For this purpose and as an application example, recently developed Silica Particles with Encapsulated DNA (SPED) were added to milk at concentrations ranging from 0.1 to 100 ppb (μg per kg milk). Thereby the milk, as well as the milk-derived products yoghurt and cheese, could be uniquely labeled with a DNA tag. Procedures for the extraction of the DNA tags from the food matrixes were elaborated and allowed identification and quantification of previously marked products by quantitative polymerase chain reaction (qPCR) with detection limits below 1 ppb of added particles. The applicability of synthetic as well as naturally occurring DNA sequences was shown. The usage of approved food additives as DNA carrier (silica = E551) and the low cost of the technology (<0.1 USD per ton of milk labeled with 10 ppb of SPED) display the technical applicability of this food labeling technology.

DNA protection against ultraviolet irradiation by encapsulation in a multilayered SiO2/TiO2assembly

The here presented method allows to protect DNA against UV-induced damage by encapsulating it in a core–shell–shell particulate construct.