Recovery of bacillus spore contaminants from rough surfaces: a challenge to space mission cleanliness control

Microbial Protocols for Spacecraft: 1. Effects of Surface Texture, Low Pressure, and UV Irradiation on Recovery of Microorganisms from Surfaces

Modeling risks for the forward contamination of planetary surfaces from endemic bioburdens on landed spacecraft requires precise data on the biocidal effects of space factors on microbial survival. Numerous studies have been published over the preceding 60 years on the survival of diverse microorganisms exposed to solar heating, solar ultraviolet (UV) irradiation, vacuum, ionizing radiation, desiccation, and many other planetary surface conditions. These data were generated with diverse protocols that can impair the interpretations of the results due to dynamic experimental errors inherent in all lab protocols. The current study (1) presents data on how metal surfaces can affect spore adhesion, (2) proposes doping and extraction protocols that can achieve very high recovery rates (close to 100%) from aluminum coupons with four Bacillus spp., (3) establishes a timeline in which dried spores on aluminum coupons should be used to minimize aging effects of spore monolayers, (4) confirms that vacuum alone does not dislodge spores dried on aluminum coupons, and (5) establishes that multiple UV irradiation sources yield similar results if properly cross-calibrated. The protocols are given to advance discussions in the planetary protection community on how to standardize lab protocols to align results from diverse labs into a coherent interpretation of how space conditions will degrade microbial survival over time.

Microbiomes of China's Space Station During Assembly, Integration, and Test Operations

Sufficient evidence indicates that orbiting space stations contain diverse microbial populations, which may threaten astronaut health and equipment reliability. Understanding the composition of microbial communities in space stations will facilitate further development of targeted biological safety prevention and maintenance practices. Therefore, this study systematically investigated the microbial community of China's Space Station (CSS). Air and surface samples from 46 sites on the CSS and Assembly Integration and Test (AIT) center were collected, from which 40 bacteria strains were isolated and identified. Most isolates were cold- and desiccation-resistant and adapted to oligotrophic conditions. Bacillus was the dominant bacterial genus detected by both cultivation-based and Illumina MiSeq amplicon sequencing methods. Microbial contamination on the CSS was correlated with encapsulation staff activities. Analysis by spread plate and qPCR revealed that the CSS surface contained 2.24 × 10³-5.47 × 10³ CFU/100 cm² culturable bacteria and 9.32 × 10⁵-5.64 × 10⁶ 16S rRNA gene copies/100cm²; BacLight™ analysis revealed that the viable/total bacterial cell ratio was 1.98-13.28%. This is the first study to provide important systematic insights into the microbiome of the CSS during assembly that describes the pre-launch microbial diversity of the space station. Our findings revealed the following. (1) Bacillus strains and staff activities should be considered major concerns for future biological safety. (2) Autotrophic and multi-resistant microbial communities were widespread in the AIT environment. Although harsh cleaning methods reduced the number of microorganisms, stress-resistant strains were not completely removed. (3) Sampling, storage and analytical methods for the space station were thoroughly optimized, and are expected to be applicable to low-biomass environments in general. Microbiology-related future works will follow up to comprehensively understand the changing characteristics of microbial communities in CSS.

Fingerprinting Non-Terran Biosignatures

Most strategies for life detection rely upon finding features known to be associated with terran life, such as particular classes of molecules. But life may be vastly different on other planets and moons, particularly as we expand our efforts to explore ocean worlds like Europa and Enceladus. We propose a new concept for life detection that harnesses the power of DNA sequencing to yield intricate informatics fingerprints, even for life that is not nucleic acid-based. The concept is based on the fact that folded nucleic acid structures (aptamers) have been shown to be capable of binding a wide variety of compounds, whether inorganic, organic, or polymeric, and irrespective of being from a biotic or abiotic source. Each nucleic acid sequence can be thought of as a code, and a combination of codes as a "fingerprint." Over multiple analytes, the "fingerprint" of a non-terran sample can be analyzed by chemometric protocols to provide a classifier of molecular patterns and complexity. Ultimately the chemometric fingerprints of living systems, which may differ significantly from nonliving systems, could provide an empirical, agnostic means of detecting life. Because nucleic acids are exponentially amplified by the polymerase chain reaction, even very small input signals could be translated into a robust readable output. The derived sequences could be identified by a small, portable sequencing device or by capture and optical imaging on a DNA microarray. Without presupposing any particular molecular framework, this agnostic approach to life detection could be used from Mars to the far reaches of the Solar System, all within the framework of an instrument drawing little heat and power. Key Words: Agnostic biosignatures-Astrobiology-Chemometrics-DNA sequencing-Life detection-Proximity ligation assay. Astrobiology 18, 915-922.

Effect of Sterilants on Amplification and Detection of Target DNA from Bacillus cereus Spores

To conceal criminal activity of a bioterrorist or agroterrorist, the site of pathogen generation is often treated with sterilants to kill the organisms and remove evidence. As dead organisms cannot be analyzed by culture, this study examined whether DNA from sterilant-treated Bacillus cereus spores was viable for amplification. The spores were exposed to five common sterilants: bleach, Sterilox®, oxidizer foam (L-Gel), a peroxyacid (Actril®), and formaldehyde vapor. The spores were inoculated on typical surfaces found in offices and laboratories to test for environmental effects. It was found that the surface influenced the efficiency of recovery of the organisms. The DNA isolated from the recovered spores was successfully detected using RT-qPCR for all treatments except for formaldehyde, by amplifying the phosphatidylinositol phospholipase C and sphingomyelinase genes. The results demonstrated that evidence from sites treated with sterilants can still provide information on the uncultured organism, using DNA amplification.

The Janus face of iron on anoxic worlds: iron oxides are both protective and destructive to life on the early Earth and present-day Mars

The surface of the early Earth was probably subjected to a higher flux of ultraviolet (UV) radiation than today. UV radiation is known to severely damage DNA and other key molecules of life. Using a liquid culture and a rock analogue system, we investigated the interplay of protective and deleterious effects of iron oxides under UV radiation on the viability of the model organism, Bacillus subtilis. In the presence of hydrogen peroxide, there exists a fine balance between iron oxide's protective effects against this radiation and its deleterious effects caused by Photo-Fenton reactions. The maximum damage was caused by a concentration of hematite of ∼1 mg/mL. Concentrations above this confer increasing protection by physical blockage of the UV radiation, concentrations below this cause less effective UV radiation blockage, but also a correspondingly less effective Photo-Fenton reaction, providing an overall advantage. These results show that on anoxic worlds, surface habitability under a high UV flux leaves life precariously poised between the beneficial and deleterious effects of iron oxides. These results have relevance to the Archean Earth, but also the habitability of the Martian surface, where high levels of UV radiation in combination with iron oxides and hydrogen peroxide can be found.

Considerations for estimating microbial environmental data concentrations collected from a field setting

In the event of an indoor release of an environmentally persistent microbial pathogen such as Bacillus anthracis, the potential for human exposure will be considered when remedial decisions are made. Microbial site characterization and clearance sampling data collected in the field might be used to estimate exposure. However, there are many challenges associated with estimating environmental concentrations of B. anthracis or other spore-forming organisms after such an event before being able to estimate exposure. These challenges include: (1) collecting environmental field samples that are adequate for the intended purpose, (2) conducting laboratory analyses and selecting the reporting format needed for the laboratory data, and (3) analyzing and interpreting the data using appropriate statistical techniques. This paper summarizes some key challenges faced in collecting, analyzing, and interpreting microbial field data from a contaminated site. Although the paper was written with considerations for B. anthracis contamination, it may also be applicable to other bacterial agents. It explores the implications and limitations of using field data for determining environmental concentrations both before and after decontamination. Several findings were of interest. First, to date, the only validated surface/sampling device combinations are swabs and sponge-sticks on stainless steel surfaces, thus limiting availability of quantitative analytical results which could be used for statistical analysis. Second, agreement needs to be reached with the analytical laboratory on the definition of the countable range and on reporting of data below the limit of quantitation. Finally, the distribution of the microbial field data and statistical methods needed for a particular data set could vary depending on these data that were collected, and guidance is needed on appropriate statistical software for handling microbial data. Further, research is needed to develop better methods to estimate human exposure from pathogens using environmental data collected from a field setting.

Evaluating Composite Sampling Methods of Bacillus Spores at Low Concentrations

Restoring all facility operations after the 2001 Amerithrax attacks took years to complete, highlighting the need to reduce remediation time. Some of the most time intensive tasks were environmental sampling and sample analyses. Composite sampling allows disparate samples to be combined, with only a single analysis needed, making it a promising method to reduce response times. We developed a statistical experimental design to test three different composite sampling methods: 1) single medium single pass composite (SM-SPC): a single cellulose sponge samples multiple coupons with a single pass across each coupon; 2) single medium multi-pass composite: a single cellulose sponge samples multiple coupons with multiple passes across each coupon (SM-MPC); and 3) multi-medium post-sample composite (MM-MPC): a single cellulose sponge samples a single surface, and then multiple sponges are combined during sample extraction. Five spore concentrations of Bacillus atrophaeus Nakamura spores were tested; concentrations ranged from 5 to 100 CFU/coupon (0.00775 to 0.155 CFU/cm2). Study variables included four clean surface materials (stainless steel, vinyl tile, ceramic tile, and painted dry wallboard) and three grime coated/dirty materials (stainless steel, vinyl tile, and ceramic tile). Analysis of variance for the clean study showed two significant factors: composite method (p< 0.0001) and coupon material (p = 0.0006). Recovery efficiency (RE) was higher overall using the MM-MPC method compared to the SM-SPC and SM-MPC methods. RE with the MM-MPC method for concentrations tested (10 to 100 CFU/coupon) was similar for ceramic tile, dry wall, and stainless steel for clean materials. RE was lowest for vinyl tile with both composite methods. Statistical tests for the dirty study showed RE was significantly higher for vinyl and stainless steel materials, but lower for ceramic tile. These results suggest post-sample compositing can be used to reduce sample analysis time when responding to a Bacillus anthracis contamination event of clean or dirty surfaces.

Extraction of Aerosol-Deposited Yersinia pestis from Indoor Surfaces To Determine Bacterial Environmental Decay

Public health and decontamination decisions following an event that causes indoor contamination with a biological agent require knowledge of the environmental persistence of the agent. The goals of this study were to develop methods for experimentally depositing bacteria onto indoor surfaces via aerosol, evaluate methods for sampling and enumerating the agent on surfaces, and use these methods to determine bacterial surface decay. A specialized aerosol deposition chamber was constructed, and methods were established for reproducible and uniform aerosol deposition of bacteria onto four coupon types. The deposition chamber facilitated the control of relative humidity (RH; 10 to 70%) following particle deposition to mimic the conditions of indoor environments, as RH is not controlled by standard heating, ventilation, and air conditioning (HVAC) systems. Extraction and culture-based enumeration methods to quantify the viable bacteria on coupons were shown to be highly sensitive and reproducible. To demonstrate the usefulness of the system for decay studies,Yersinia pestis persistence as a function of surface type at 21 °C and 40% RH was determined to be >40%/min for all surfaces. Based upon these results, at typical indoor temperature and RH, a 6-log reduction in titer would expected to be achieved within 1 h as the result of environmental decay on surfaces without active decontamination. The developed approach will facilitate future persistence and decontamination studies with a broad range of biological agents and surfaces, providing agent decay data to inform both assessments of risk to personnel entering a contaminated site and decontamination decisions following biological contamination of an indoor environment.

IMPORTANCE

Public health and decontamination decisions following contamination of an indoor environment with a biological agent require knowledge of the environmental persistence of the agent. Previous studies on Y. pestis persistence have utilized large liquid droplet deposition to provide persistence data. As a result, methods were developed to deposit aerosols containing bacteria onto indoor surfaces, reproducibly enumerate bacteria harvested from coupons, and determine surface decay utilizing Y. pestis The results of this study provide foundational methods required to evaluate surface decay of bacteria and potentially other biological agents, such as viruses, in aerosol particles as a function of surface type and environment. Integrating the data from both aerosol and liquid deposition surface decay studies will provide medical and public health personnel with a more complete understanding of agent persistence on surfaces in contaminated areas for assessment of health risks and to inform decontamination decisions.

False-negative rate, limit of detection and recovery efficiency performance of a validated macrofoam-swab sampling method for low surface concentrations of Bacillus anthracis Sterne and Bacillus atrophaeus spores

AIMS

We sought to evaluate the effects of Bacillus species, low surface concentrations, and surface material on recovery efficiency (RE), false-negative rate (FNR) and limit of detection for recovering Bacillus spores using a validated macrofoam-swab sampling procedure.

METHODS AND RESULTS

The performance of a macrofoam-swab sampling method was evaluated using Bacillus anthracis Sterne (BAS) and Bacillus atrophaeus Nakamura (BG) spores applied at nine low target surface concentrations (2 to 500 CFU per plate or coupon) to positive-control plates and test coupons (25·8064 cm(2) ) of four surface materials (glass, stainless steel, vinyl tile and plastic). The Bacillus species and surface material had statistically significant effects on RE, but surface concentration did not. Mean REs were the lowest for vinyl tile (50·8% with BAS and 40·2% with BG) and the highest for glass (92·8% with BAS and 71·4% with BG). FNR values (which ranged from 0 to 0·833 for BAS and from 0 to 0·806 for BG) increased as surface concentration decreased in the range tested. Surface material also had a statistically significant effect on FNR, with FNR the lowest for glass and highest for vinyl tile. Finally, FNR tended to be higher for BG than for BAS at lower surface concentrations, especially for glass.

CONCLUSIONS

Concentration and surface material had significant effects on FNR, with Bacillus species having a small effect. Species and surface material had significant effects on RE, with surface concentration having a nonsignificant effect.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results provide valuable information on the performance of the macrofoam-swab method for low surface concentrations of Bacillus spores, which can be adapted to assess the likelihood that there is no contamination when all macrofoam-swab samples fail to detect B. anthracis.

Identification of oxidoreductases from the petroleum Bacillus safensis strain

A gram-positive bacterium, denominated CFA-06, was isolated from Brazilian petroleum in the Campos Basin and is responsible for the degradation of aromatic compounds and petroleum aromatic fractions. The CFA-06 strain was identified as Bacillus safensis using the 16S rRNA and gyrase B sequence. Enzymatic assays revealed the presence of two oxidoreductases: a catalase and a new oxidoreductase. The oxidoreductases were enzymatically digested and analyzed via ESI-LTQ-Orbitrap mass spectrometry. The mass data revealed a novel oxidoreductase (named BsPMO) containing 224 amino acids and 89% homology with a hypothetic protein from B. safensis (CFA-06) and a catalase (named BsCat) with 491 amino acids and 60% similarity with the catalase from Bacillus pumilus (SAFR-032). The new protein BsPMO contains iron atom(s) and shows catalytic activity toward a monooxygenase fluorogenic probe in the presence of cofactors (NADH, NADPH and NAD). This study enhances our knowledge of the biodegradation process of petroleum by B. safensis.

Development of an ELISA for evaluation of swab recovery efficiencies of bovine serum albumin

After a potential biological incident the sampling strategy and sample analysis are crucial for the outcome of the investigation and identification. In this study, we have developed a simple sandwich ELISA based on commercial components to quantify BSA (used as a surrogate for ricin) with a detection range of 1.32–80 ng/mL. We used the ELISA to evaluate different protein swabbing procedures (swabbing techniques and after-swabbing treatments) for two swab types: a cotton gauze swab and a flocked nylon swab. The optimal swabbing procedure for each swab type was used to obtain recovery efficiencies from different surface materials. The surface recoveries using the optimal swabbing procedure ranged from 0–60% and were significantly higher from nonporous surfaces compared to porous surfaces. In conclusion, this study presents a swabbing procedure evaluation and a simple BSA ELISA based on commercial components, which are easy to perform in a laboratory with basic facilities. The data indicate that different swabbing procedures were optimal for each of the tested swab types, and the particular swab preference depends on the surface material to be swabbed.

Vulnerability of Bacillus spores and of related genera to physical impaction injury with particular reference to spread-plating

AIMS

To examine whether bacterial spores are vulnerable to impaction injury during standard spread-plating or to other modes of physical impaction.

METHODS AND RESULTS

Employing heat-challenged spores of Bacillus pumilus, Bacillus subtilis, Bacillus thuringiensis, Lysinibacillus, Paenibacillus and Brevibacillus spp. from day-4 to day-10 nutrient agar (NA) plates in 50% ethanol, plating the spore suspension to the extent of just drying the agar surface on fresh NA (50-60 s; SP-B) was tested in comparison with the spreader-independent approach of spotting-and-tilt-spreading (SATS), or a brief plating (<10 s; SP-A). Spore CFU was significantly reduced with SP-B in different organisms (23-40%) over SATS independent of the spore size. Comparing 4-, 7- and 10-day-old B. pumilus spores, the former two displayed significant CFU reduction in SP-B indicating a spore age-related effect. Continuous plating for 2-5 min showed a reduction in spore CFU in all organisms depending on plating duration. CFU reduction effect with SP-B was less manifest on refrigerated plates where no friction was experienced but acute on prewarmed and surface-dried plates. Spreader movement over agar surface subsequent to the exhaustion of free moisture proved highly detrimental to spores. A simulated plating study by plating the spores over a plastic film till drying showed a significant reduction in spore CFU. DAPI staining and glass bead-vortexing studies confirmed spore disruption through physical impaction.

CONCLUSIONS

Bacterial spores are vulnerable to injury during spread-plating or with other forms of physical impaction with variable effects on different genotypes independent of the spore size but altered by spore age.

SIGNIFICANCE AND IMPACT OF THE STUDY

Implications during spore CFU estimations employing spread-plating and during spore surveillance, and the recommendation of SATS as an easier and safer alternative for spore CFU enumeration.

Quantification of encapsulated bioburden in spacecraft polymer materials by cultivation-dependent and molecular methods

Bioburden encapsulated in spacecraft polymers (such as adhesives and coatings) poses a potential risk to jeopardize scientific exploration of other celestial bodies. This is particularly critical for spacecraft components intended for hard landing. So far, it remained unclear if polymers are indeed a source of microbial contamination. In addition, data with respect to survival of microbes during the embedding/polymerization process are sparse. In this study we developed testing strategies to quantitatively examine encapsulated bioburden in five different polymers used frequently and in large quantities on spaceflight hardware. As quantitative extraction of the bioburden from polymerized (solid) materials did not prove feasible, contaminants were extracted from uncured precursors. Cultivation-based analyses revealed <0.1–2.5 colony forming units (cfu) per cm³ polymer, whereas quantitative PCR-based detection of contaminants indicated considerably higher values, despite low DNA extraction efficiency. Results obtained from this approach reflect the most conservative proxy for encapsulated bioburden, as they give the maximum bioburden of the polymers irrespective of any additional physical and chemical stress occurring during polymerization. To address the latter issue, we deployed an embedding model to elucidate and monitor the physiological status of embedded Bacillus safensis spores in a cured polymer. Staining approaches using AlexaFluor succinimidyl ester 488 (AF488), propidium monoazide (PMA), CTC (5-cyano-2,3-diotolyl tetrazolium chloride) demonstrated that embedded spores retained integrity, germination and cultivation ability even after polymerization of the adhesive Scotch-Weld 2216 B/A. Using the methods presented here, we were able to estimate the worst case contribution of encapsulated bioburden in different polymers to the bioburden of spacecraft. We demonstrated that spores were not affected by polymerization processes. Besides Planetary Protection considerations, our results could prove useful for the manufacturing of food packaging, pharmacy industry and implant technology.

Lessons learned from the microbial analysis of the Herschel spacecraft during assembly, integration, and test operations

Understanding microbial diversity in spacecraft assembly clean rooms is of major interest with respect to planetary protection considerations. A coordinated screening of different clean rooms in Europe and South America by three German institutes [Deutsches Zentrum für Luft- und Raumfahrt (DLR), Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), and the Institute of Microbiology and Archaea Center, University of Regensburg] took place during the assembly, test, and launch operations of the Herschel spacecraft in 2006-2009. Through this campaign, we retrieved critical information regarding the microbiome within these clean rooms and on the Herschel spacecraft, which served as a model for upcoming ESA mission preparations. This "lessons learned" document summarizes and discusses the data we obtained during this sampling campaign. Additionally, we have taken the opportunity to create a database that includes all 16S rRNA gene sequences ever retrieved from molecular and cultivable diversity studies of spacecraft assembly clean rooms to compare the microbiomes of US, European, and South American facilities.

Enhancement of anion binding in lanthanide optical sensors

In the design of molecular sensors, researchers exploit binding interactions that are usually defined in terms of topology and charge complementarity. The formation of complementary arrays of highly cooperative, noncovalent bonding networks facilitates protein-ligand binding, leading to motifs such as the "lock-and-key". Synthetic molecular sensors often employ metal complexes as key design elements as a way to construct a binding site with the desired shape and charge to achieve target selectivity. In transition metal complexes, coordination number, structure and ligand dynamics are governed primarily by a combination of inner-sphere covalent and outer-sphere noncovalent interactions. These interactions provide a rich variable space that researchers can use to tune structure, stability, and dynamics. In contrast, lanthanide(III)-ligand complex formation and ligand-exchange dynamics are dominated by reversible electrostatic and steric interactions, because the unfilled f shell is shielded by the larger, filled d shell. Luminescent lanthanides such as terbium, europium, dysprosium, and samarium display many photophysical properties that make them excellent candidates for molecular sensor applications. Complexes of lanthanide ions act as receptors that exhibit a detectable change in metal-based luminescence upon binding of an anion. In our work on sensors for detection of dipicolinate, the unique biomarker of bacterial spores, we discovered that the incorporation of an ancillary ligand (AL) can enhance binding constants of target anions to lanthanide ions by as much as two orders of magnitude. In this Account, we show that selected ALs in lanthanide/anion systems greatly improve sensor performance for medical, planetary science, and biodefense applications. We suggest that the observed anion binding enhancement could result from an AL-induced increase in positive charge at the lanthanide ion binding site. This effect depends on lanthanide polarizability, which can be established from the ionization energy of Ln(3+) → Ln(4+). These results account for the order Tb(3+) > Dy(3+) > Eu(3+) ≈ Sm(3+). As with many lanthanide properties, ranging from hydration enthalpy to vaporization energy, this AL-induced enhancement shows a large discrepancy between Tb(3+) and Eu(3+) despite their similarity in size, a phenomenon known as the "gadolinium break". This discrepancy, based on the unusual stabilities of the Eu(2+) and Tb(4+) oxidation states, results from the half-shell effect, as both of these ions have half-filled 4f-shells. The high polarizability of Tb(3+) explains the extraordinarily large increase in the binding affinity of anions for terbium compared to other lanthanides. We recommend that researchers consider this AL-induced enhancement when designing lanthanide-macrocycle optical sensors. Ancillary ligands also can reduce the impact of interfering species such as phosphate commonly found in environmental and physiological samples.

Detection of Streptococcus pneumoniae from Different Types of Nasopharyngeal Swabs in Children

BACKGROUND

A better understanding of the epidemiology of nasopharyngeal carriage of Streptococcus pneumoniae is important to assess the impact of vaccination and the pathogenesis of pneumococcal disease. We compared the recovery of S. pneumoniae from nylon flocked, Dacron and rayon swabs.

METHODS

The recovery of S. pneumoniae from mocked specimens using flocked, Dacron and rayon swabs were compared by culture. The yield from paired nasopharyngeal (NP) samples obtained from healthy children sampled with flocked and Dacron swabs was also determined using culture and lytA-targeted real-time polymerase chain reaction (qPCR).

RESULTS

Using mock specimen, the percentage recovery of S. pneumoniae ATCC 49619 (serotype 19F) strain from the flocked swabs was 100%, while it was 41% from Dacron swabs and 7% from rayon swabs. Similar results were observed for S. pneumoniae serotypes 1 and 5. S. pneumoniae was cultured from 18 of 42 (43%) paired NP samples from the healthy children (median age 8 [interquartile range (IQR) 5-16] months). The median number of colony-forming units (CFU) recovered from flocked swabs was two-fold higher (8.8×10(4) CFU/mL [IQR, 2.0×10(2) - 4.0×10(5) CFU/mL]) than Dacron swabs (3.7×10(4) CFU/mL [IQR, 4.0×10(2)-3.2×10(5) CFU/mL], p = 0.17). Using lytA-targeted qPCR from paired NP samples, the median copy number of S. pneumoniae detected from flocked swabs was significantly higher than from Dacron swabs (3.0×10(5) genome copies/mL [IQR, 1.3×10(2)-1.8×10(6)] vs. 9.3×10(4) genome copies/mL [IQR, 7.0×10(1)-1.1×10(6)]; p = 0.005).

CONCLUSION

Flocked swabs released more S. pneumoniae compared to both Dacron and rayon swabs from mock specimens. Similarly, higher bacterial loads were detected by qPCR from flocked swabs compared with Dacron swabs from healthy children.

Archaea on human skin

The recent era of exploring the human microbiome has provided valuable information on microbial inhabitants, beneficials and pathogens. Screening efforts based on DNA sequencing identified thousands of bacterial lineages associated with human skin but provided only incomplete and crude information on Archaea. Here, we report for the first time the quantification and visualization of Archaea from human skin. Based on 16 S rRNA gene copies Archaea comprised up to 4.2% of the prokaryotic skin microbiome. Most of the gene signatures analyzed belonged to the Thaumarchaeota, a group of Archaea we also found in hospitals and clean room facilities. The metabolic potential for ammonia oxidation of the skin-associated Archaea was supported by the successful detection of thaumarchaeal amoA genes in human skin samples. However, the activity and possible interaction with human epithelial cells of these associated Archaea remains an open question. Nevertheless, in this study we provide evidence that Archaea are part of the human skin microbiome and discuss their potential for ammonia turnover on human skin.

Evaluation of surface sampling for Bacillus spores using commercially available cleaning robots

Five commercially available domestic cleaning robots were evaluated on their effectiveness for sampling aerosol-deposited Bacillus atrophaeus spores on different indoor material surfaces. The five robots tested include three vacuum types (R1, R2, and R3), one wet wipe (R4), and one wet vacuum (R5). Tests were conducted on two different surface types (carpet and laminate) with 10(6) colony forming units of B. atrophaeus spores deposited per coupon (35.5 cm × 35.5 cm). Spores were deposited on the center surface (30.5 × 30.5 cm) of the coupon's total surface area (71.5 × 71.5 cm), and the surfaces were sampled with an individual robot in an isolation chamber. Chamber air was sampled using a biofilter sampler to determine the potential for resuspension of spores during sampling. Robot test results were compared to currently used surface sampling methods (vacuum sock for carpet and sponge wipe for laminate). The test results showed that the average sampling efficacies for R1, R2, and R3 on carpet were 26, 162, and 92% of vacuum sock sampling efficacy, respectively. On laminate, R1, R2, R3, R4, and R5 average sampling efficacies were 8, 11, 2, 62, and 32% of sponge wipe sampling efficacy, respectively. We conclude that some robotic cleaners were as efficacious as the currently used surface sampling methods for B. atrophaeus spores on these surfaces.

A rapid and repeatable method to deposit bioaerosols on material surfaces

A simple method for repeatably inoculating surfaces with a precise quantity of aerosolized spores was developed. Laboratory studies were conducted to evaluate the variability of the method within and between experiments, the spatial distribution of spore deposition, the applicability of the method to complex surface types, and the relationship between material surface roughness and spore recoveries. Surface concentrations, as estimated by recoveries from wetted-wipe sampling, were between 5×10(3) and 1.5×10(4)CFUcm(-2) across the entire area (930cm(2)) inoculated. Between-test variability (Cv) in spore recoveries was 40%, 81%, 66%, and 20% for stainless steel, concrete, wood, and drywall, respectively. Within-test variability was lower, and did not exceed 33%, 47%, 52%, and 20% for these materials. The data demonstrate that this method is repeatable, is effective at depositing spores across a target surface area, and can be used to dose complex materials such as concrete, wood, and drywall. In addition, the data demonstrate that surface sampling recoveries vary by material type, and this variability can partially be explained by the material surface roughness index. This deposition method was developed for use in biological agent detection, sampling, and decontamination studies, however, is potentially beneficial to any scientific discipline that investigates surfaces containing aerosol-borne particles.

Improved recovery of Bacillus spores from nonporous surfaces with cotton swabs over foam, nylon, or polyester, and the role of hydrophilicity of cotton in governing the recovery efficiency

Evaluating different swabbing materials for spore recovery efficiency (RE) from steel surfaces, we recorded the maximum RE (71%) of 10(7) Bacillus subtilis spores with Tulips cotton buds, followed by Johnson's cotton buds and standard Hi-Media cotton, polyester, nylon, and foam (23%) swabs. Among cotton swabs, instant water-absorbing capacity or the hydrophilicity index appeared to be the major indicator of RE, as determined by testing three more brands. Tulips swabs worked efficiently across diverse nonporous surfaces and on different Bacillus spp., registering 65 to 77% RE.

Abundance and diversity of microbial inhabitants in European spacecraft-associated clean rooms

The determination of the microbial load of a spacecraft en route to interesting extraterrestrial environments is mandatory and currently based on the culturable, heat-shock-surviving portion of microbial contaminants. Our study compared these classical bioburden measurements as required by NASA's and ESA's guidelines for the microbial examination of flight hardware, with molecular analysis methods (16S rRNA gene cloning and quantitative PCR) to further develop our understanding of the diversity and abundance of the microbial communities of spacecraft-associated clean rooms. Three samplings of the Herschel Space Observatory and its surrounding clean rooms were performed in two different European facilities. Molecular analyses detected a broad diversity of microbes typically found in the human microbiome with three bacterial genera (Staphylococcus, Propionibacterium, and Brevundimonas) common to all three locations. Bioburden measurements revealed a low, but heterogeneous, abundance of spore-forming and other heat-resistant microorganisms. Total cell numbers estimated by quantitative real-time PCR were typically 3 orders of magnitude greater than those determined by viable counts, which indicates a tendency for traditional methods to underestimate the extent of clean room bioburden. Furthermore, the molecular methods allowed the detection of a much broader diversity than traditional culture-based methods.

The uses and abuses of rapid bioluminescence-based ATP assays

Bioluminescence-based ATP testing of solid surfaces has become well established in the food processing industry as part of general hazard analysis and critical control points (HACCP) measures. The rise in healthcare associated infections (HAIs) at the turn of the century focussed attention on the environment as a potential reservoir of the agents responsible for such infections. In response to the need for objective methods of assessing the efficiency of cleaning in healthcare establishments and for rapid methods for detecting the presence of the pathogens responsible for HAIs, it was proposed that ATP testing of environmental surfaces be introduced. We examine the basis behind the assumptions inherent in these proposals. Intracellular ATP levels are shown to vary between microbial taxa and according to environmental conditions. Good correlations between microbial numbers and ATP levels have been obtained under certain specific conditions, but never within healthcare settings. Notwithstanding, ATP testing may still have a role in providing reassurance that cleaning regimes are being carried out satisfactorily. However, ATP results should not be interpreted as surrogate indicators for the presence of microbial pathogens.

False-negative rate and recovery efficiency performance of a validated sponge wipe sampling method

Recovery of spores from environmental surfaces varies due to sampling and analysis methods, spore size and characteristics, surface materials, and environmental conditions. Tests were performed to evaluate a new, validated sponge wipe method using Bacillus atrophaeus spores. Testing evaluated the effects of spore concentration and surface material on recovery efficiency (RE), false-negative rate (FNR), limit of detection (LOD), and their uncertainties. Ceramic tile and stainless steel had the highest mean RE values (48.9 and 48.1%, respectively). Faux leather, vinyl tile, and painted wood had mean RE values of 30.3, 25.6, and 25.5, respectively, while plastic had the lowest mean RE (9.8%). Results show roughly linear dependences of RE and FNR on surface roughness, with smoother surfaces resulting in higher mean REs and lower FNRs. REs were not influenced by the low spore concentrations tested (3.10 × 10(-3) to 1.86 CFU/cm(2)). Stainless steel had the lowest mean FNR (0.123), and plastic had the highest mean FNR (0.479). The LOD(90) (≥1 CFU detected 90% of the time) varied with surface material, from 0.015 CFU/cm(2) on stainless steel up to 0.039 on plastic. It may be possible to improve sampling results by considering surface roughness in selecting sampling locations and interpreting spore recovery data. Further, FNR values (calculated as a function of concentration and surface material) can be used presampling to calculate the numbers of samples for statistical sampling plans with desired performance and postsampling to calculate the confidence in characterization and clearance decisions.

Influence of home characteristics on airborne and dustborne endotoxin and β-D-glucan

The aim of this study was to assess the associations between airborne and dustborne microbial contaminants (endotoxin and β-D-glucan) and estimate the effects of home characteristics on exposure levels of these microbial contaminants. Endotoxin and β-D-glucan concentrations in airborne inhalable particles, airborne PM1 (<1 μm) and vacuumed dust from 184 residential homes were determined using specific Limulus amebocyte assays. Home characteristics were recorded by visual inspection and questionnaires. Linear regression and correlation analyses were performed. Inhalable endotoxin correlated with dust endotoxin (r = 0.34, p < 0.001) and PM1 endotoxin (r = 0.33, p < 0.001). Inhalable β-D-glucan correlated with dust β-D-glucan (r = 0.18, p < 0.01), but not with PM1 β-D-glucan. Significant correlation was also found between PM1 and dust concentrations for endotoxin (r = 0.26, p < 0.001), but not for β-D-glucan. Multivariate regression analyses showed only one significant association between airborne contaminants and environmental characteristics: inhalable β-D-glucan was positively associated with relative humidity with an effect size (change in the dependent variable corresponding to a unit increase in the independent variable) of 2.32 and p < 0.05. In contrast, several associations were found between dust concentrations and environmental characteristics. Dust endotoxin was positively associated with temperature (2.87, p < 0.01) and number of inhabitants (2.76, p < 0.01), whereas dust β-D-glucan was inversely associated with the presence of dogs (-2.24, p < 0.05) and carpet (-3.05, p < 0.01) in the home. In conclusion, dustborne contaminants were more strongly affected by home characteristics than airborne contaminants. Furthermore, even though statistically significant, the correlations between airborne and dustborne contaminants were weak. This indicates that airborne concentrations cannot be reliably predicted based on dustborne concentrations.