Development of quantitative real-time PCR assays for detection and quantification of surrogate biological warfare agents in building debris and leachate

Evaluation of the fate and transport of biological warfare (BW) agents in landfills requires the development of specific and sensitive detection assays. The objective of the current study was to develop and validate SYBR green quantitative real-time PCR (Q-PCR) assays for the specific detection and quantification of surrogate BW agents in synthetic building debris (SBD) and leachate. Bacillus atrophaeus (vegetative cells and spores) and Serratia marcescens were used as surrogates for Bacillus anthracis (anthrax) and Yersinia pestis (plague), respectively. The targets for SYBR green Q-PCR assays were the 16S-23S rRNA intergenic transcribed spacer (ITS) region and recA gene for B. atrophaeus and the gyrB, wzm, and recA genes for S. marcescens. All assays showed high specificity when tested against 5 ng of closely related Bacillus and Serratia nontarget DNA from 21 organisms. Several spore lysis methods that include a combination of one or more of freeze-thaw cycles, chemical lysis, hot detergent treatment, bead beat homogenization, and sonication were evaluated. All methods tested showed similar threshold cycle values. The limit of detection of the developed Q-PCR assays was determined using DNA extracted from a pure bacterial culture and DNA extracted from sterile water, leachate, and SBD samples spiked with increasing quantities of surrogates. The limit of detection for B. atrophaeus genomic DNA using the ITS and B. atrophaeus recA Q-PCR assays was 7.5 fg per PCR. The limits of detection of S. marcescens genomic DNA using the gyrB, wzm, and S. marcescens recA Q-PCR assays were 7.5 fg, 75 fg, and 7.5 fg per PCR, respectively. Quantification of B. atrophaeus vegetative cells and spores was linear (R(2) > 0.98) over a 7-log-unit dynamic range down to 10(1) B. atrophaeus cells or spores. Quantification of S. marcescens (R(2) > 0.98) was linear over a 6-log-unit dynamic range down to 10(2) S. marcescens cells. The developed Q-PCR assays are highly specific and sensitive and can be used for monitoring the fate and transport of the BW surrogates B. atrophaeus and S. marcescens in building debris and leachate.     

Cloning and Nucleotide Sequence Analysis of gyrB of Bacillus cereus, B. thuringiensis, B. mycoides, and B. anthracis and Their Application to the Detection of B. cereus in Rice

As 16S rRNA sequence analysis has proven inadequate for the differentiation of Bacillus cereus from closely related species, we employed the gyrase B gene (gyrB) as a molecular diagnostic marker. The gyrB genes of B. cereus JCM 2152^T, Bacillus thuringiensis IAM 12077^T, Bacillus mycoides ATCC 6462^T, and Bacillus anthracis Pasteur #2H were cloned and sequenced. Oligonucleotide PCR primer sets were designed from within gyrB sequences of the respective bacteria for the specific amplification and differentiation of B. cereus, B. thuringiensis, and B. anthracis. The results from the amplification of gyrB sequences correlated well with results obtained with the 16S rDNA-based hybridization study but not with the results of their phenotypic characterization. Some of the reference strains of both B. cereus (three serovars) and B. thuringiensis (two serovars) were not positive in PCR amplification assays with gyrB primers. However, complete sequencing of 1.2-kb gyrB fragments of these reference strains showed that these serovars had, in fact, lower homology than their originally designated species. We developed and tested a procedure for the specific detection of the target organism in boiled rice that entailed 15 h of preenrichment followed by PCR amplification of the B. cereus-specific fragment. This method enabled us to detect an initial inoculum of 0.24 CFU of B. cereus cells per g of boiled rice food homogenate without extracting DNA. However, a simple two-step filtration step is required to remove PCR inhibitory substances.     

Persistence and Decontamination of Bacillus atrophaeus subsp. globigii Spores on Corroded Iron in a Model Drinking Water System

Persistence of Bacillus atrophaeus subsp. globigii spores on corroded iron coupons in drinking water was studied using a biofilm annular reactor. Spores were inoculated at 10⁶ CFU/ml in the dechlorinated reactor bulk water. The dechlorination allowed for observation of the effects of hydraulic shear and biofilm sloughing on persistence. Approximately 50% of the spores initially adhered to the corroded iron surface were not detected after 1 month. Addition of a stable 10 mg/liter free chlorine residual after 1 month led to a 2-log₁₀ reduction of adhered B. atrophaeus subsp. globigii, but levels on the coupons quickly stabilized thereafter. Increasing the free chlorine concentration to 25 or 70 mg/liter had no additional effect on inactivation. B. atrophaeus subsp. globigii spores injected in the presence of a typical distribution system chlorine residual (~0.75 mg/liter) resulted in a steady reduction of adhered B. atrophaeus subsp. globigii over 1 month, but levels on the coupons eventually stabilized. Adding elevated chlorine levels (10, 25, and 70 mg/liter) after 1 month had no effect on the rate of inactivation. Decontamination with elevated free chlorine levels immediately after spore injection resulted in a 3-log₁₀ reduction within 2 weeks, but the rate of inactivation leveled off afterward. This indicates that free chlorine did not reach portions of the corroded iron surface where B. atrophaeus subsp. globigii spores had adhered. B. atrophaeus subsp. globigii spores are capable of persisting for an extended time in the presence of high levels of free chlorine.     

Rapid Immunoassays for Detection of UV-Induced Cyclobutane Pyrimidine Dimers in Whole Bacterial Cells

Immunoassays were developed to measure DNA damage retained by UV-irradiated whole bacterial cells. Active Mycobacterium parafortuitum and Serratia marcescens cells were fixed and incubated with cyclobutane pyrimidine dimer-binding antibodies after being exposed to known UV doses (254 nm). When both fluorescent (Alexa Fluor 488) and radiolabeled (¹²⁵I) secondary antibodies were used as reporters, indirect whole-cell assays were sensitive enough to measure intracellular UV photoproducts in M. parafortuitum and S. marcescens cells as well as photoenzymatic repair responses in S. marcescens cells. For the same UV dose, fluorescent DNA photoproduct detection limits in whole-cell assays (immunofluorescent microscopy) were similar to those in fluorescent assays performed on membrane-bound DNA extracts (immunoslot blot). With either fluorescent or radiolabeled reporters, the intracellular cyclobutane pyrimidine dimer content of UV-irradiated whole bacterial cells could be reliably quantified after undergoing a <0.5-order-of-magnitude decrease in culturability. Immunofluorescent microscopy results showed that photoenzymatic repair competence is not uniformly distributed among exponential-growth UV-irradiated pure cultures.     

Evaluation of the Biological Sampling Kit (BiSKit) for Large-Area Surface Sampling

Current surface sampling methods for microbial contaminants are designed to sample small areas and utilize culture analysis. The total number of microbes recovered is low because a small area is sampled, making detection of a potential pathogen more difficult. Furthermore, sampling of small areas requires a greater number of samples to be collected, which delays the reporting of results, taxes laboratory resources and staffing, and increases analysis costs. A new biological surface sampling method, the Biological Sampling Kit (BiSKit), designed to sample large areas and to be compatible with testing with a variety of technologies, including PCR and immunoassay, was evaluated and compared to other surface sampling strategies. In experimental room trials, wood laminate and metal surfaces were contaminated by aerosolization of Bacillus atrophaeus spores, a simulant for Bacillus anthracis, into the room, followed by settling of the spores onto the test surfaces. The surfaces were sampled with the BiSKit, a cotton-based swab, and a foam-based swab. Samples were analyzed by culturing, quantitative PCR, and immunological assays. The results showed that the large surface area (1 m²) sampled with the BiSKit resulted in concentrations of B. atrophaeus in samples that were up to 10-fold higher than the concentrations obtained with the other methods tested. A comparison of wet and dry sampling with the BiSKit indicated that dry sampling was more efficient (efficiency, 18.4%) than wet sampling (efficiency, 11.3%). The sensitivities of detection of B. atrophaeus on metal surfaces were 42 ± 5.8 CFU/m² for wet sampling and 100.5 ± 10.2 CFU/m² for dry sampling. These results demonstrate that the use of a sampling device capable of sampling larger areas results in higher sensitivity than that obtained with currently available methods and has the advantage of sampling larger areas, thus requiring collection of fewer samples per site.     

Comparison of UV Inactivation of Spores of Three Encephalitozoon Species with That of Spores of Two DNA Repair-Deficient Bacillus subtilis Biodosimetry Strains

When exposed to 254-nm UV, spores of Encephalitozoon intestinalis, Encephalitozoon cuniculi, and Encephalitozoon hellem exhibited 3.2-log reductions in viability at UV fluences of 60, 140, and 190 J/m², respectively, and demonstrated UV inactivation kinetics similar to those observed for endospores of DNA repair-defective mutant Bacillus subtilis strains used as biodosimetry surrogates. The results indicate that spores of Encephalitozoon spp. are readily inactivated at low UV fluences and that spores of UV-sensitive B. subtilis strains can be useful surrogates in evaluating UV reactor performance.     

Quantitative detection of residual porcine host cell DNA by real-time PCR

All biological products are derived from complex living systems and are often mixed with large numbers of impurities. For reasons of safety, residual host-cell DNA must be eliminated during processing. To assay host-cell DNA content in biopharmaceutical products derived from porcine sources, this study applies the quantitative real-time polymerase chain reaction (Q-PCR) method. The optimized assay in this study is based on the pol region of the porcine endogenous retrovirus (PERV). Assay validation results demonstrate that the proposed assay has appropriate accuracy, preciseness, reproducibility, and sensitivity. Primer and probe specificity are evaluated in real-time Q-PCR reactions using genomic DNA from rabbit, mouse, cat, hamster, monkey, human cell, yeast, and Escherichia coli as templates. The sensitivity of real-time Q-PCR is determined using genomic DNA from the porcine kidney cell line. The reliable detection range is within 0.5–10⁵ pg/reaction. The limit of quantitation is 500 fg. The sensitivity of the assay meets the authority criterion. Moreover, the assay is applied to determine the level of host-cell DNA in recombinant human coagulation factor IX (rhFIX) from transgenic pigs. The real-time Q-PCR assay is thus a promising new tool for quantitative detection and clearance validation of residual porcine DNA when manufacturing recombinant therapeutics.     

Use of a Foam Spatula for Sampling Surfaces after Bioaerosol Deposition

The present study had three goals: (i) to evaluate the relative quantities of aerosolized Bacillus atrophaeus spores deposited on the vertical, horizontal top, and horizontal bottom surfaces in a chamber; (ii) to assess the relative recoveries of the aerosolized spores from glass and stainless steel surfaces with a polyester swab and a macrofoam sponge wipe; and (iii) to estimate the relative recovery efficiencies of aerosolized B. atrophaeus spores and Pantoea agglomerans using a foam spatula at several different bacterial loads by aerosol distribution on glass surfaces. The majority of spores were collected from the bottom horizontal surface regardless of which swab type and extraction protocol were used. Swabbing with a macrofoam sponge wipe was more efficient in recovering spores from surfaces contaminated with high bioaerosol concentrations than swabbing with a polyester swab. B. atrophaeus spores and P. agglomerans culturable cells were detected on glass surfaces using foam spatulas when the theoretical surface bacterial loads were 2.88 × 10⁴ CFU and 8.09 × 10⁶ CFU per 100-cm² area, respectively. The median recovery efficiency from the surfaces using foam spatulas was equal to 9.9% for B. atrophaeus spores when the recovery was calculated relative to the theoretical surface spore load. Using a foam spatula permits reliable sampling of spores on the bioaerosol-exposed surfaces in a wide measuring range. The culturable P. agglomerans cells were recovered with a median efficiency of 0.001%, but staining the swab extracts with fluorescent dyes allowed us to observe that the viable cell numbers were higher by 1.83 log units than culturable organisms. However, additional work is needed to improve the analysis of the foam extracts in order to decrease the limit of detection of Bacillus spores and Gram-negative bacteria on contaminated surfaces.Surface sampling is performed on a frequent basis in all situations where clean environment monitoring is needed, e.g., in health care facilities and in the pharmaceutical industry and food industry. An anthrax bioterrorist event in the fall of 2001 has emphasized the importance of efficient sampling methods for detection of pathogenic microorganisms on surfaces within intentionally contaminated locations (22). Unfortunately, our knowledge on the most effective sampling methodology as well as the level of confidence we may have in the results obtained by wiping, swabbing, and other sample collection strategies is still limited (1). Moreover, in most of the studies performed so far, bacteria and/or spores were collected from test samples or coupons of various materials, inoculated with a suspension of microorganisms that had been placed and spread over the surface, and then dried (14, 15). This may not mimic the true situation of surface contamination by a pathogen that has been intentionally released. Edmonds et al. (12) recently reported lower swabbing efficiencies of different types of swab materials used for sampling glass, polycarbonate, and vinyl surfaces contaminated with dry aerosol-deposited Bacillus atrophaeus spores compared to the surfaces inoculated by spore suspensions. Solid surface contamination from exposure to aerosolized spores fits the real world better than the previous models.Therefore, in our study we decided to generate aerosols of various concentrations of B. atrophaeus spores as well as the vegetative cells of Pantoea agglomerans inside a chamber where the bioaerosol particles were allowed to gravitationally settle on solid surfaces. The aerosolization of P. agglomerans was performed to verify the recovery of Gram-negative bacteria according to the recommendations of Budowle et al. (5). The main goal of our study was to establish the range of detection when bioaerosol-contaminated surfaces were swabbed using a commercially available foam spatula.     

Determination of the Efficacy of Two Building Decontamination Strategies by Surface Sampling with Culture and Quantitative PCR Analysis

The efficacy of currently available decontamination strategies for the treatment of indoor furnishings contaminated with bioterrorism agents is poorly understood. Efficacy testing of decontamination products in a controlled environment is needed to ensure that effective methods are used to decontaminate domestic and workplace settings. An experimental room supplied with materials used in office furnishings (i.e., wood laminate, painted metal, and vinyl tile) was used with controlled dry aerosol releases of endospores of Bacillus atrophaeus (“Bacillus subtilis subsp. niger,” also referred to as BG), a Bacillus anthracis surrogate. Studies were performed using two test products, a foam decontaminant and chlorine dioxide gas. Surface samples were collected pre- and posttreatment with three sampling methods and analyzed by culture and quantitative PCR (QPCR). Additional aerosol releases with environmental background present on the surface materials were also conducted to determine if there was any interference with decontamination or sample analysis. Culture results indicated that 10⁵ to 10⁶ CFU per sample were present on surfaces before decontamination. After decontamination with the foam, no culturable B. atrophaeus spores were detected. After decontamination with chlorine dioxide gas, no culturable B. atrophaeus was detected in 24 of 27 samples (89%). However, QPCR analysis showed that B. atrophaeus DNA was still present after decontamination with both methods. Environmental background material had no apparent effect on decontamination, but inhibition of the QPCR assay was observed. These results demonstrate the effectiveness of two decontamination methods and illustrate the utility of surface sampling and QPCR analysis for the evaluation of decontamination strategies.     

Inactivation of Bacillus Endospores in Envelopes by Electron Beam Irradiation

The anthrax incidents in the United States in the fall of 2001 led to the use of electron beam (EB) processing to sanitize the mail for the U.S. Postal Service. This method of sanitization has prompted the need to further investigate the effect of EB irradiation on the destruction of Bacillus endospores. In this study, endospores of an anthrax surrogate, B. atrophaeus, were destroyed to demonstrate the efficacy of EB treatment of such biohazard spores. EB exposures were performed to determine (i) the inactivation of varying B. atrophaeus spore concentrations, (ii) a D₁₀ value (dose required to reduce a population by 1 log₁₀) for the B. atrophaeus spores, (iii) the effects of spore survival at the bottom of a standardized paper envelope stack, and (iv) the maximum temperature received by spores. A maximum temperature of 49.2°C was reached at a lethal dose of ~40 kGy, which is a significantly lower temperature than that needed to kill spores by thermal effects alone. AD₁₀ value of 1.53 kGy was determined for the species. A surface EB dose between 25 and 32 kGy produced the appropriate killing dose of EB between 11 and 16 kGy required to inactivate 8 log₁₀ spores, when spore samples were placed at the bottom of a 5.5-cm stack of envelopes.     

Detection of aerosolized bacterial spores (Bacillus atrophaeus) using free-flying honey bees (Hymenoptera: Apidae) as collectors

An aerosol cloud of Bacillus atrophaeus (previously B. subtilis variety niger) spores, an anthrax surrogate, was created in a large 0.4 ha (1 ac), bee-containing, open-mesh tent. Bees from a B. atrophaeus uncontaminated hive flying through the cloud adsorbed the spores in statistically significant quantities. After removal of the B. atrophaeus contaminated hive and introduction of another B. atrophaeus uncontaminated hive, the bees again were monitored for the next few days for B. atrophaeus spores. B. atrophaeus spores accumulated on the bees bodies following their exposure to the residual B. atrophaeus contamination in the tent. The spore loads on the bees quickly returned to background levels after the hives were removed from the contaminated tent area. It may therefore be practical to use honey bee colonies to monitor foraging areas for disease-causing spores.     

Detection of aerosolized bacterial spores (<Emphasis Type="Italic">Bacillus atrophaeus</Emphasis>) using free-flying honey bees (Hymenoptera: Apidae) as collectors

An aerosol cloud of Bacillus atrophaeus (previously B. subtilis variety niger) spores, an anthrax surrogate, was created in a large 0.4 ha (1 ac), bee-containing, open-mesh tent. Bees from a B. atrophaeus uncontaminated hive flying through the cloud adsorbed the spores in statistically significant quantities. After removal of the B. atrophaeus contaminated hive and introduction of another B. atrophaeus uncontaminated hive, the bees again were monitored for the next few days for B. atrophaeus spores. B. atrophaeus spores accumulated on the bees bodies following their exposure to the residual B. atrophaeus contamination in the tent. The spore loads on the bees quickly returned to background levels after the hives were removed from the contaminated tent area. It may therefore be practical to use honey bee colonies to monitor foraging areas for disease-causing spores.     

Decontamination Options for Bacillus anthracis-Contaminated Drinking Water Determined from Spore Surrogate Studies

Five parameters were evaluated with surrogates of Bacillus anthracis spores to determine effective decontamination alternatives for use in a contaminated drinking water supply. The parameters were as follows: (i) type of Bacillus spore surrogate (B. thuringiensis or B. atrophaeus), (ii) spore concentration in suspension (10² and 10⁶ spores/ml), (iii) chemical characteristics of the decontaminant (sodium dichloro-S-triazinetrione dihydrate [Dichlor], hydrogen peroxide, potassium peroxymonosulfate [Oxone], sodium hypochlorite, and VirkonS), (iv) decontaminant concentration (0.01% to 5%), and (v) exposure time to decontaminant (10 min to 1 h). Results from 138 suspension tests with appropriate controls are reported. Hydrogen peroxide at a concentration of 5% and Dichlor or sodium hypochlorite at a concentration of 2% were highly effective at spore inactivation regardless of spore type tested, spore exposure time, or spore concentration evaluated. This is the first reported study of Dichlor as an effective decontaminant for B. anthracis spore surrogates. Dichlor''s desirable characteristics of high oxidation potential, high level of free chlorine, and a more neutral pH than that of other oxidizers evaluated appear to make it an excellent alternative. All three oxidizers were effective against B. atrophaeus spores in meeting the EPA biocide standard of greater than a 6-log kill after a 10-min exposure time and at lower concentrations than typically reported for biocide use. Solutions of 5% VirkonS and Oxone were less effective as decontaminants than other options evaluated in this study and did not meet the EPA''s efficacy standard for a biocide, although they were found to be as effective for concentrations of 10² spores/ml. Differences in methods and procedures reported by other investigators make quantitative comparisons among studies difficult.Developing a decontamination approach that can be safely and effectively applied to civilian water resources and facilities following a terrorist or catastrophic release of Bacillus anthracis spores poses many challenges. For example, if a municipal drinking water system were contaminated directly or indirectly during or after such an incident, it would be essential to assess the potential health risks posed by water consumption or other water uses (e.g., recreational and bathing) and then to apply one or more proven technologies, if deemed necessary, to decontaminate the water supply quickly and cost-effectively. Treatment of drinking water implies the use of a decontamination approach that would not pose adverse health risks to humans or result in unacceptable damage to the environment. A major obstacle in killing spores of Bacillus spp. on or in virtually any matrix is their high level of resistance to treatments such as harsh chemicals, heat, desiccation, and UV light (14, 20). Because of the substantial and widely reported resistance of Bacillus spores to inactivation, a decontaminant proven to be efficacious in killing such spores for site-specific applications is likely to be effective against all other biological warfare agents as well.Whereas nearly all biological warfare agents are intended for aerosol application, many have strong potential as waterborne threats and could inflict heavy casualties when ingested (2). B. anthracis in particular has been identified as a “probable” (12) or an actual (24) water threat. Even though the principal risk associated with the consumption of water containing B. anthracis spores would likely arise from an ingestion hazard, water used for bathing, showering, or recreational purposes might also pose cutaneous as well as aerosol exposure hazards. There is controversy regarding the long-term viability of B. anthracis in water, and experimental evidence is limited. However, according to a review of nonkinetic studies on survival of virulent strains in the environment (21), B. anthracis spores can survive from 2 to 18 years in pond water and 20 months in seawater or distilled water. B. anthracis spores have been reported by others to be stable in water for 2 years (24).Various decontamination approaches have been evaluated for efficacy against biological warfare agents, including Bacillus spores, on hard, nonporous surfaces. Recommendations by the U.S. Environmental Protection Agency (EPA) include the use of sodium hypochlorite (1:9 dilution of bleach to 5,250 to 6,000 ppm, corrected to pH 7, with a 60-min contact time at 20°C [6, 17]), and liquid chlorine dioxide with a 30-min wet contact time at 20°C (7). Liquid hydrogen peroxide/peroxyacetic acid (known as peroxy compounds and marketed as ready-to-use solutions), generally with a 15- to 20-min wet contact time and concentration as specified by the manufacturer, has also been recommended (13). Other products, such as hydrogen peroxide solution (3 to 25%) and potassium peroxymonosulfate, have been evaluated for efficacy against Bacillus spores as well (27). Although disinfectants at various concentrations have been tested previously against the spores of B. anthracis and their surrogates, wide variations in test protocols make meaningful comparisons among studies virtually impossible (9, 11, 17).In contrast to surface cleanup of spores, fewer assessments of efficacy utilizing suspension tests with the aforementioned chemicals or other methods have been reported for the decontamination of Bacillus species spores in water, and much of the published work has assessed only relatively high concentrations of spores in water. For example, one previous investigation commenced evaluations with 0.2-ml suspensions of approximately 10⁹ spores/ml of various Bacillus spp. to which 20 ml of aqueous ozone or 20 ml of hydrogen peroxide solution was added to assess sporicidal action (10), and others have reported mechanisms of deactivating B. subtilis spores prepared in concentrations of up to approximately 10⁸ spores/ml (26) and approximately 10⁹ spores/ml (17). Inactivation by chlorination of various Bacillus spp. with initial concentrations of approximately 1 × 10⁴ CFU/ml has also been tested (16). However, relatively low spore concentrations would be expected to result from dilutions following contamination of a large public water system. Therefore, it is reasonable to evaluate the effectiveness of decontaminants or other methods against even lower spore concentrations in water than have been previously assessed. In addition to assessing the parameter of Bacillus spore concentration in water, it is essential to identify the most effective commercially available chemical that will kill all the spores or minimize population growth, while considering the effects of the chemical on the environment and in humans.Several objectives served to focus our investigation. First, five potential candidate decontaminants were selected because of their relative safety and ultimate degradation in the environment without substantive adverse consequences. The five chemicals were also chosen as a way of comparing the effectiveness of available free chlorine content, pH, and oxidation potential on spore inactivation. From an evaluation of those chemical parameters, we sought to determine the most effective option for inactivating Bacillus spore surrogates suspended in water. As a second objective, we attempted to identify the lowest concentration of the selected chemicals necessary to achieve the EPA''s biocide standard of a >6-log kill. As a third objective, we wanted to assess the effect of reduced spore concentration on chemical biocide efficacy. As an important step in ascertaining an efficient, safe, and cost-effective water treatment method that could potentially provide safe water to the general population in the event of B. anthracis contamination—and limit the potential risk of contracting gastrointestinal or cutaneous anthrax as well—the following parameters were evaluated: chemical decontaminant type, chemical decontaminant concentration (0.01% to 5%), contact time of spores with chemical decontaminant (10 min to 1 h), spore type (Bacillus atrophaeus or Bacillus thuringiensis), and low versus relatively high spore concentrations (approximately 10² and 10⁶ spores/ml, respectively).Use of B. atrophaeus and B. thuringiensis spores as surrogates for B. anthracis is widely reported in the literature. For example, Szabo et al. (23) used B. atrophaeus subsp. globigii spores as a surrogate for B. anthracis to investigate the persistence and decontamination of those surrogates on corroded iron in a model drinking water system, and Rice et al. (16) used spores of B. thuringiensis as an “appropriate surrogate for spores of B. anthracis” for determining the sporicidal activity of chlorination as commonly used in drinking water treatment. Furthermore, the EPA (5) concluded that “B. globigii can serve as a conservative surrogate for B. anthracis during studies of inactivation by chlorination.”     

Use of Quantitative Real-Time PCR for Direct Detection of Serratia marcescens in Marine and Other Aquatic Environments

Serratia marcescens is the etiological agent of acroporid serratiosis, a distinct form of white pox disease in the threatened coral Acropora palmata. The pathogen is commonly found in untreated human waste in the Florida Keys, which may contaminate both nearshore and offshore waters. Currently there is no direct method for detection of this bacterium in the aquatic or reef environment, and culture-based techniques may underestimate its abundance in marine waters. A quantitative real-time PCR assay was developed to detect S. marcescens directly from environmental samples, including marine water, coral mucus, sponge tissue, and wastewater. The assay targeted the luxS gene and was able to distinguish S. marcescens from other Serratia species with a reliable quantitative limit of detection of 10 cell equivalents (CE) per reaction. The method could routinely discern the presence of S. marcescens for as few as 3 CE per reaction, but it could not be reliably quantified at this level. The assay detected environmental S. marcescens in complex sewage influent samples at up to 761 CE ml⁻¹ and in septic system-impacted residential canals in the Florida Keys at up to 4.1 CE ml⁻¹. This detection assay provided rapid quantitative abilities and good sensitivity and specificity, which should offer an important tool for monitoring this ubiquitous pathogen that can potentially impact both human health and coral health.     

Burkholderia pseudomultivorans sp. nov., a novel Burkholderia cepacia complex species from human respiratory samples and the rhizosphere

Eleven Burkholderia cepacia-like isolates of human clinical and environmental origin were examined by a polyphasic approach including recA and 16S rRNA sequence analysis, multilocus sequence analysis (MLSA), DNA base content determination, fatty acid methyl ester analysis, and biochemical characterization. The results of this study demonstrate that these isolates represent a novel species within the B. cepacia complex (Bcc) for which we propose the name Burkholderia pseudomultivorans. The type strain is strain LMG 26883^T (=CCUG 62895^T). B. pseudomultivorans can be differentiated from other Bcc species by recA gene sequence analysis, MLSA, and several biochemical tests including growth at 42 °C, acidification of sucrose and adonitol, lysine decarboxylase and β-galactosidase activity, and esculin hydrolysis.     

Evaluation of new gyrB-based real-time PCR system for the detection of B. fragilis as an indicator of human-specific fecal contamination

A rapid and specific gyrB-based real-time PCR system has been developed for detecting Bacteroides fragilis as a human-specific marker of fecal contamination. Its specificity and sensitivity was evaluated by comparison with other 16S rRNA gene-based primers using closely related Bacteroides and Prevotella. Many studies have used 16S rRNA gene-based method targeting Bacteroides because this genus is relatively abundant in human feces and is useful for microbial source tracking. However, 16S rRNA gene-based primers are evolutionarily too conserved among taxa to discriminate between human-specific species of Bacteroides and other closely related genera, such as Prevotella. Recently, one of the housekeeping genes, gyrB, has been used as an alternative target in multilocus sequence analysis (MLSA) to provide greater phylogenetic resolution. In this study, a new B. fragilis-specific primer set (Bf904F/Bf958R) was designed by alignments of 322 gyrB genes and was compared with the performance of the 16S rRNA gene-based primers in the presence of B. fragilis, Bacteroides ovatus and Prevotella melaninogenica. Amplicons were sequenced and a phylogenetic tree was constructed to confirm the specificity of the primers to B. fragilis. The gyrB-based primers successfully discriminated B. fragilis from B. ovatus and P. melaninogenica. Real-time PCR results showed that the gyrB primer set had a comparable sensitivity in the detection of B. fragilis when compared with the 16S rRNA primer set. The host-specificity of our gyrB-based primer set was validated with human, pig, cow, and dog fecal samples. The gyrB primer system had superior human-specificity. The gyrB-based system can rapidly detect human-specific fecal source and can be used for improved source tracking of human contamination.     

Development of a Combined Selection and Enrichment PCR Procedure for Clostridium botulinum Types B, E, and F and Its Use To Determine Prevalence in Fecal Samples from Slaughtered Pigs

A specific and sensitive combined selection and enrichment PCR procedure was developed for the detection of Clostridium botulinum types B, E, and F in fecal samples from slaughtered pigs. Two enrichment PCR assays, using the DNA polymerase rTth, were constructed. One assay was specific for the type B neurotoxin gene, and the other assay was specific for the type E and F neurotoxin genes. Based on examination of 29 strains of C. botulinum, 16 strains of other Clostridium spp., and 48 non-Clostridium strains, it was concluded that the two PCR assays detect C. botulinum types B, E, and F specifically. Sample preparation prior to the PCR was based on heat treatment of feces homogenate at 70°C for 10 min, enrichment in tryptone-peptone-glucose-yeast extract broth at 30°C for 18 h, and DNA extraction. The detection limits after sample preparation were established as being 10 spores per g of fecal sample for nonproteolytic type B, and 3.0 × 10³ spores per g of fecal sample for type E and nonproteolytic type F with a detection probability of 95%. Seventy-eight pig fecal samples collected from slaughter houses were analyzed according to the combined selection and enrichment PCR procedure, and 62% were found to be PCR positive with respect to the type B neurotoxin gene. No samples were positive regarding the type E and F neurotoxin genes, indicating a prevalence of less than 1.3%. Thirty-four (71%) of the positive fecal samples had a spore load of less than 4 spores per g. Statistical analysis showed that both rearing conditions (outdoors and indoors) and seasonal variation (summer and winter) had significant effects on the prevalence of C. botulinum type B, whereas the effects of geographical location (southern and central Sweden) were less significant.     

Killing bacterial spores by organic hydroperoxides

Killing of wild-type spores of Bacillus subtilis by t-butyl hydroperoxide, cumene hydroperoxide and peracetic acid was not through DNA damage, as shown by the absence of mutations in the survivors and the identical sensitivity of spores of strains with or without a recA mutation. In contrast, B. subtilis spores (termed α⁻β⁻) lacking the DNA protective α/β-type small, acid-soluble spore proteins (SASP) were more sensitive to t-butyl hydroperoxide and cumene hydroperoxide, and their killing was in large part through DNA damage, as shown by the high frequency of mutations in the survivors and the greater sensitivity of α⁻β⁻ recA spores. Analysis of t-butyl hydroperoxide-treated spores showed that generation of DNA damage in α⁻β⁻ spores was more rapid than in wild-type spores; α/β-type SASP also protected against DNA strand breakage in vitro caused by t-butyl hydroperoxide. α/β-Type SASP appeared to play no role in protection of spores from killing by peracetic acid; wild-type and α⁻β⁻ spores exhibited identical peracetic acid sensitivity and their killing by this agent appeared to be not through DNA damage. Received 17 December 1996/ Accepted in revised form 13 March 1997