High-throughput functional trait testing for bacterial pathogens

Functional traits are characteristics that affect the fitness and metabolic function of a microorganism. There is growing interest in using high-throughput methods to characterize bacterial pathogens based on functional virulence traits. Traditional methods that phenotype a single organism for a single virulence trait can be time consuming and labor intensive. Alternatively, machine learning of whole-genome sequences (WGS) has shown some success in predicting virulence. However, relying solely on WGS can miss functional traits, particularly for organisms lacking classical virulence factors. We propose that high-throughput assays for functional virulence trait identification should become a prominent method of characterizing bacterial pathogens on a population scale. This work is critical as we move from compiling lists of bacterial species associated with disease to pathogen-agnostic approaches capable of detecting novel microbes. We discuss six key areas of functional trait testing and how advancing high-throughput methods could provide a greater understanding of pathogens.

Insights from a workplace SARS-CoV-2 specimen collection program, with genomes placed into global sequence phylogeny

In 2020, the Department of Energy established the National Virtual Biotechnology Laboratory (NVBL) to address key challenges associated with COVID-19. As part of that effort, Pacific Northwest National Laboratory (PNNL) established a capability to collect and analyze specimens from employees who self-reported symptoms consistent with the disease. During the spring and fall of 2021, 688 specimens were screened for SARS-CoV-2, with 64 (9.3%) testing positive using reverse-transcriptase quantitative PCR (RT-qPCR). Of these, 36 samples were released for research. All 36 positive samples released for research were sequenced and genotyped. Here, the relationship between patient age and viral load as measured by Ct values was measured and determined to be only weakly significant. Consensus sequences for each sample were placed into a global phylogeny and transmission dynamics were investigated, revealing that the closest relative for many samples was from outside of Washington state, indicating mixing of viral pools within geographic regions.

The Promise of Emergent Nanobiotechnologies for In Vivo Applications and Implications for Safety and Security

Nanotechnology, the multidisciplinary field based on the exploitation of the unique physicochemical properties of nanoparticles (NPs) and nanoscale materials, has opened a new realm of possibilities for biological research and biomedical applications. The development and deployment of mRNA-NP vaccines for COVID-19, for example, may revolutionize vaccines and therapeutics. However, regulatory and ethical frameworks that protect the health and safety of the global community and environment are lagging, particularly for nanotechnology geared toward biological applications (ie, bionanotechnology). In this article, while not comprehensive, we attempt to illustrate the breadth and promise of bionanotechnology developments, and how they may present future safety and security challenges. Specifically, we address current advancements to streamline the development of engineered NPs for in vivo applications and provide discussion on nano–bio interactions, NP in vivo delivery, nanoenhancement of human performance, nanomedicine, and the impacts of NPs on human health and the environment.

Polysaccharide-based liquid storage and transport media for non-refrigerated preservation of bacterial pathogens

The preservation of biological samples for an extended time period of days to weeks after initial collection is important for the identification, screening, and characterization of bacterial pathogens. Traditionally, preservation relies on cold-chain infrastructure; however, in many situations this is impractical or not possible. Thus, our goal was to develop alternative bacterial sample preservation and transport media that are effective without refrigeration or external instrumentation. The viability, nucleic acid stability, and protein stability of Bacillus anthracis Sterne 34F2, Francisella novicida U112, Staphylococcus aureus ATCC 43300, and Yersinia pestis KIM D27 (pgm-) was assessed for up to 28 days. Xanthan gum (XG) prepared in PBS with L-cysteine maintained more viable F. novicida U112 cells at elevated temperature (40°C) compared to commercial reagents and buffers. Viability was maintained for all four bacteria in XG with 0.9 mM L-cysteine across a temperature range of 22-40°C. Interestingly, increasing the concentration to 9 mM L-cysteine resulted in the rapid death of S. aureus. This could be advantageous when collecting samples in the built environment where there is the potential for Staphylococcus collection and stabilization rather than other organisms of interest. F. novicida and S. aureus DNA were stable for up to 45 days upon storage at 22°C or 40°C, and direct analysis by real-time qPCR, without DNA extraction, was possible in the XG formulations. XG was not compatible with proteomic analysis via LC-MS/MS due to the high amount of residual Xanthomonas campestris proteins present in XG. Our results demonstrate that polysaccharide-based formulations, specifically XG with L-cysteine, maintain bacterial viability and nucleic acid integrity for an array of both Gram-negative and Gram-positive bacteria across ambient and elevated temperatures.

Detection of the urban release of a bacillus anthracis simulant by air sampling

In 2005 and 2009, the Pentagon Force Protection Agency (PFPA) staged deliberate releases of a commercially available organic pesticide containing Bacillus amyloliquefaciens to evaluate PFPA's biothreat response protocols. In concert with, but independent of, these releases, the Department of Homeland Security sponsored experiments to evaluate the efficacy of commonly employed air and surface sampling techniques for detection of an aerosolized biological agent. High-volume air samplers were placed in the expected downwind plume, and samples were collected before, during, and after the releases. Environmental surface and personal air samples were collected in the vicinity of the high-volume air samplers hours after the plume had dispersed. The results indicate it is feasible to detect the release of a biological agent in an urban area both during and after the release of a biological agent using high-volume air and environmental sampling techniques.

Detecting laboratory DNA contamination using polyester-rayon wipes: a method validation study

Due to the high sensitivity of many PCR assays, extraneous target DNA in a laboratory setting can lead to false positive results. To assess the presence of extraneous DNA, many laboratories use gauze wipes to sample laboratory surfaces. The accuracy, precision, limits of detection, linearity, and robustness of a wipe test method and each associated wipe processing step were evaluated using E. coli genomic DNA. The method demonstrated a limit of detection of 108 copies of DNA, which equates to detectable surface concentration of 4.5×10(5) copies of DNA per area sampled. Recovery efficiency or accuracy is 22±10% resulting from a >58% loss of DNA occurring at the wipe wash step. The method is robust, performing consistently despite deliberate modifications of the protocol.

Detection and tracking of a novel genetically tagged biological simulant in the environment

A variant of Bacillus thuringiensis subsp. kurstaki containing a single, stable copy of a uniquely amplifiable DNA oligomer integrated into the genome for tracking the fate of biological agents in the environment was developed. The use of genetically tagged spores overcomes the ambiguity of discerning the test material from pre-existing environmental microflora or from previously released background material. In this study, we demonstrate the utility of the genetically "barcoded" simulant in a controlled indoor setting and in an outdoor release. In an ambient breeze tunnel test, spores deposited on tiles were reaerosolized and detected by real-time PCR at distances of 30 m from the point of deposition. Real-time PCR signals were inversely correlated with distance from the seeded tiles. An outdoor release of powdered spore simulant at Aberdeen Proving Ground, Edgewood, MD, was monitored from a distance by a light detection and ranging (LIDAR) laser. Over a 2-week period, an array of air sampling units collected samples were analyzed for the presence of viable spores and using barcode-specific real-time PCR assays. Barcoded B. thuringiensis subsp. kurstaki spores were unambiguously identified on the day of the release, and viable material was recovered in a pattern consistent with the cloud track predicted by prevailing winds and by data tracks provided by the LIDAR system. Finally, the real-time PCR assays successfully differentiated barcoded B. thuringiensis subsp. kurstaki spores from wild-type spores under field conditions.

Reaerosolization of Bacillus spp. in outdoor environments: a review of the experimental literature

Reaerosolization or resuspension-that is, the reintroduction of previously airborne particles into the atmosphere-is a complex phenomenon. Microbial reaerosolization is particularly poorly understood because few studies have been done in this area, and many of the studies that have been performed are not in the peer-reviewed literature. The reaerosolization of Bacillus anthracis in outdoor environments is of particular concern because of its stability and potential for use as a biological weapon. This review pulls together data from more than 30 publications, spanning field and laboratory experiments, to summarize the current state of our understanding of Bacillus spp. reaerosolization in outdoor environments.

Transport of Bacillus thuringiensis var. kurstaki via fomites

The intentional and controlled release of an aerosolized bacterium provides an opportunity to investigate the implications of a biological attack. Since 2006, Los Alamos National Laboratory has worked with several urban areas, including Fairfax County, VA, to design experiments to evaluate biodefense concepts of operations using routine spraying of Bacillus thuringiensis var. kurstaki (Btk). Btk is dispersed in large quantities as a slurry to control the gypsy moth, Lymantria dispar. Understanding whether personnel and equipment pick up residual contamination during sampling activities and transport it to other areas is critical for the formulation of appropriate response and recovery plans. While there is a growing body of literature surrounding the transmission of viral diseases via fomites, there is limited information on the transport of Bacillus species via this route. In 2008, LANL investigated whether field sampling activities conducted near sprayed areas, post-spray, resulted in measurable cross-contamination of sampling personnel, equipment, vehicles, and hotel rooms. Viable Btk was detected in all sample types, indicating transport of the agent occurred via fomites.

Persistence of Bacillus thuringiensis subsp. kurstaki in Urban Environments following Spraying

Bacillus thuringiensis subsp. kurstaki is applied extensively in North America to control the gypsy moth, Lymantria dispar. Since B. thuringiensis subsp. kurstaki shares many physical and biological properties with Bacillus anthracis, it is a reasonable surrogate for biodefense studies. A key question in biodefense is how long a biothreat agent will persist in the environment. There is some information in the literature on the persistence of Bacillus anthracis in laboratories and historical testing areas and for Bacillus thuringiensis in agricultural settings, but there is no information on the persistence of Bacillus spp. in the type of environment that would be encountered in a city or on a military installation. Since it is not feasible to release B. anthracis in a developed area, the controlled release of B. thuringiensis subsp. kurstaki for pest control was used to gain insight into the potential persistence of Bacillus spp. in outdoor urban environments. Persistence was evaluated in two locations: Fairfax County, VA, and Seattle, WA. Environmental samples were collected from multiple matrices and evaluated for the presence of viable B. thuringiensis subsp. kurstaki at times ranging from less than 1 day to 4 years after spraying. Real-time PCR and culture were used for analysis. B. thuringiensis subsp. kurstaki was found to persist in urban environments for at least 4 years. It was most frequently detected in soils and less frequently detected in wipes, grass, foliage, and water. The collective results indicate that certain species of Bacillus may persist for years following their dispersal in urban environments.

Application of time-resolved infrared spectroscopy to electronic structure in metal-to-ligand charge-transfer excited states

Infrared data in the nu(CO) region (1800-2150 cm(-1), in acetonitrile at 298 K) are reported for the ground (nu(gs)) and polypyridyl-based, metal-to-ligand charge-transfer (MLCT) excited (nu(es)) states of cis-[Os(pp)2(CO)(L)](n)(+) (pp = 1,10-phenanthroline (phen) or 2,2'-bipyridine (bpy); L = PPh3, CH(3)CN, pyridine, Cl, or H) and fac-[Re(pp)(CO)3(4-Etpy)](+) (pp = phen, bpy, 4,4'-(CH3)2bpy, 4,4'-(CH3O)2bpy, or 4,4'-(CO2Et)2bpy; 4-Etpy = 4-ethylpyridine). Systematic variations in nu(gs), nu(es), and Delta(nu) (Delta(nu) = nu(es) - nu(gs)) are observed with the excited-to-ground-state energy gap (E(0)) derived by a Franck-Condon analysis of emission spectra. These variations can be explained qualitatively by invoking a series of electronic interactions. Variations in dpi(M)-pi(CO) back-bonding are important in the ground state. In the excited state, the important interactions are (1) loss of back-bonding and sigma(M-CO) bond polarization, (2) pi(pp*-)-pi(CO) mixing, which provides the orbital basis for mixing pi(CO)- and pi(4,4'-X(2)bpy)-based MLCT excited states, and (3) dpi(M)-pi(pp) mixing, which provides the orbital basis for mixing pipi- and pi(4,4'-X(2)bpy*-)-based MLCT states. The results of density functional theory (DFT) calculations on the ground and excited states of fac-[Re(I)(bpy)(CO)3(4-Etpy)](+) provide assignments for the nu(CO) modes in the MLCT excited state. They also support the importance of pi(4,4'-X2bpy*-)-pi(CO) mixing, provide an explanation for the relative intensities of the A'(2) and A' ' excited-state bands, and provide an explanation for the large excited-to-ground-state nu(CO) shift for the A'(2) mode and its relative insensitivity to variations in X.

Excited-State Electron Transfer in a Chromophore-Quencher Complex. Spectroscopic Identification of a Redox-Separated State

In the chromophore-quencher complex fac-[Re(Aqphen)(CO)(3)(py-PTZ)](+) (Aqphen is 12,17-dihydronaphtho[2,3-h]dipyrido[3,2-a:2',3'-c]-phenazine-12,17-dione; py-PTZ is 10-(4-picolyl)phenothiazine), Aqphen is a dppz derivative, containing a pendant quinone acceptor at the terminus of a rigid ligand framework. This introduces a third, low-lying, ligand-based pi acceptor level localized largely on the quinone fragment. Laser flash excitation of fac-[Re(Aqphen)(CO)(3)(py-PTZ)](+) (354.7 nm; in 1,2-dichloroethane) results in the appearance of a relatively long-lived transient that decays with tau(298K) = 300 ns (k = 3.3 x 10(6) s(-)(1)). Application of transient absorption, time-resolved resonance Raman, and time-resolved infrared spectroscopies proves that this transient is the redox-separated state fac-[Re(I)(Aqphen(*)(-)())(CO)(3)(py-PTZ(*)(+)())](+) in which the excited electron is localized largely on the quinone portion of the Aqphen ligand.

Excited-State Electronic Structure in Polypyridyl Complexes Containing Unsymmetrical Ligands

Step-scan Fourier transform infrared absorption difference time-resolved (S(2)FTIR DeltaA TRS) and time-resolved resonance Raman (TR(3)) spectroscopies have been applied to a series of questions related to excited-state structure in the metal-to-ligand charge transfer (MLCT) excited states of [Ru(bpy)(2)(4,4'-(CO(2)Et)(2)bpy)](2+), [Ru(bpy)(2)(4-CO(2)Et-4'-CH(3)bpy)](2+), [Ru(bpy)(4,4'-(CO(2)Et)(2)bpy)(2)](2+), [Ru(4,4'-(CO(2)Et)(2)bpy)(3)](2+), [Ru(bpy)(2)(4,4'-(CONEt(2))(2)bpy)](2+), [Ru(bpy)(2)(4-CONEt(2)-4'-CH(3)bpy)](2+), and [Ru(4-CONEt(2)-4'-CH(3)bpy)(3)](2+) (bpy is 2,2'-bipyridine). These complexes contain bpy ligands which are either symmetrically or unsymmetrically derivatized with electron-withdrawing ester or amide substituents. Analysis of the vibrational data, largely based on the magnitudes of the nu(CO) shifts of the amide and ester substituents (Deltanu(CO)), reveals that the ester- or amide-derivatized ligands are the ultimate acceptors and that the excited electron is localized on one acceptor ligand on the nanosecond time scale. In the unsymmetrically substituted acceptor ligands, the excited electron is largely polarized toward the ester- or amide-derivatized pyridine rings. In the MLCT excited states of [Ru(bpy)(2)(4,4'-(CO(2)Et)(2)bpy)](2+) and [Ru(bpy)(2)(4,4'-(CONEt(2))(2)bpy)](2+), Deltanu(CO) is only 60-70% of that observed upon complete ligand reduction due to a strong polarization interaction in the excited state between the dpi(5) Ru(III) core and the excited electron.

Mid-Infrared Spectrum of [Ru(phen)(3)](2+)

Time-resolved infrared spectra in the fingerprint region (1300-1700 cm(-)(1)) are reported for the metal-to-ligand charge-transfer (MLCT) excited state(s) of [Ru(phen)(3)](2+) and [Os(phen)(DAS)(2)](2+) (phen is 1,10-phenanthroline; DAS is 1,2-bis(diphenylarsino)ethane) in acetonitrile-d(3) at 298 K. The spectra are assigned by comparison to electrochemically generated [Ru(III)(phen)(3)](3+) and [Ru(II)(phen(*)(-)())(phen)(2)](+). The data provide clear evidence for the localized description [Ru(III)(phen(*)(-)())(phen)(2)](2+) on the approximately 100 ns time scale. They also give insight into electronic distribution in the excited state, aid in the interpretation of the time-resolved resonance Raman spectrum of [Ru(phen)(3)](2+), and suggest why measuring ground- and excited-state resonance Raman spectra of phen complexes is difficult.