Optimization of a sample processing protocol for recovery of Bacillus anthracis spores from soil

Persistence in time: the hunt for Bacillus anthracis at a historic tannery site in Austria reveals genetic diversity thought extinct

Identifying and analyzing historic anthrax loci may provide a treasure trove to fill in the gaps of persistence in time and genetic diversity of Bacillus anthracis. In countries where anthrax has become a disease of the past, detailed knowledge of the exact location and stability of spores in soil reservoirs is limited. Reviewing archival records may provide valuable clues to unearthing such forgotten sites. Knowledge of anthrax diversity in Austria is scarce, as the only available isolates-originating from the last outbreak in Austria in 1988-cluster in the B.Br.004 (CNEVA) canonical single-nucleotide polymorphism (canSNP) group. Thus, we analyzed archival records on anthrax incidents in Austria to locate historic B. anthracis soil reservoirs. In parallel, we tested the performance of different soil processing protocols for the isolation of B. anthracis spores to establish a suitable workflow for screening historical anthrax loci. Using an optimized workflow, we were able to isolate viable B. anthracis spores 80 years after the last occurrence of anthrax at an abandoned tannery identified through our archival work. Genome analysis of the isolated strains allowed to improve the phylogeographic resolution within the hitherto poorly covered A.Br.064 (V770) canSNP group by linking historical records to genetic information. Furthermore, our results re-emphasize that B. anthracis can survive for decades at historic sites and may pose a health threat when such sites are eventually reactivated by climatic factors or human intervention.

IMPORTANCE

Bacillus anthracis is a continuing threat from a One Health perspective since it leads to severe infections in animals and humans. Ongoing climate change or human activities can reactivate historical B. anthracis loci, previously considered inactive or forgotten. Therefore, knowledge of historic anthrax incidents at abandoned animal processing facilities, such as tanneries or farmyards, along with robust detection protocols, is of prime interest when monitoring this important zoonosis. As shown here, archival records of possible origins of anthrax-contaminated goods received at tanneries are valuable sources and support these efforts. Investigation for viable spores at such historical sites could not only provide new insights into the past genetic diversity and population structure of B. anthracis but also provide important information for taking appropriate measures to prevent future outbreaks originating from these sites.

Evaluation of sample processing methods to improve the detection of Bacillus anthracis in difficult sample matrices

Large area sampling approaches have been developed and implemented by the US Environmental Protection Agency (EPA) to increase sample sizes, and potentially representativeness, in outdoor urban environments (e.g., concrete, asphalt, grass/landscaping). These sampling approaches could be implemented in response to an outdoor biological contamination incident or bioterrorism attack to determine the extent of contamination and for clearance following remediation. However, sample collection over large areas often contains an extensive amount of co-collected debris and native background microorganisms that interfere with the detection of biological threat agents. Sample processing methods that utilize basic laboratory equipment amenable to field deployment were selected and applied to turbid aqueous samples (TAS) to reduce particulates and native environmental organisms prior to culture and rapid viability-polymerase chain reaction (RV-PCR) analytical methods. Bacillus anthracis Sterne (BaS) spores were spiked into TAS collected by soil grab, wet vacuum collection from an outdoor concrete surface, or storm water runoff from an urban parking lot. The implementation of a sample processing method improved the sensitivity of culture and RV-PCR analytical methods for BaS spore detection in soil and wet vacuum TAS samples compared to baseline (minimal to no field processing methods applied). For soil, when the processing method was applied, samples with 15 colony forming units (CFU)/ml (60 CFU/g) and 1.5 CFU/mL (6 CFU/g) BaS spore load were detected using culture and RV-PCR, respectively. Most notably, the processing methods greatly improved the sensitivity of the RV-PCR analytical method for the wet vacuum TAS from no detection at the 1500 CFU/mL BaS spore load level to as low as 1.5 CFU/mL BaS spore load.

No hints for abundance of Bacillus anthracis and Burkholderia pseudomallei in 100 environmental samples from Cameroon

BACKGROUND

Little is known on the abundance of the pathogens Bacillus anthracis and Burkholderia pseudomallei in environmental samples in Cameroon. Therefore, 100 respective samples were assessed in a proof-of-principle assessment.

METHODS

DNA residuals from nucleic acid extractions of 100 environmental samples, which were collected between 2011 and 2013 in the Mapé Basin of Cameroon, were screened for B. anthracis and B. pseudomallei by real-time PCR. The samples comprised soil samples with water contact (n = 88), soil samples without water contact (n = 6), plant material with water contact (n = 3), water (n = 2), and soil from a hospital dressing room (n = 1).

RESULTS

B. anthracis and B. pseudomallei were detected in none of the samples assessed.

CONCLUSION

The results indicate that at least a quantitatively overwhelming, ubiquitous occurrence of B. anthracis and B. pseudomallei in the environment in Cameroon is highly unlikely. However, the number and choice of the assessed samples limit the interpretability of the results.

Enzyme-Linked Phage Receptor Binding Protein Assays (ELPRA) Enable Identification of Bacillus anthracis Colonies

Bacteriophage receptor binding proteins (RBPs) are employed by viruses to recognize specific surface structures on bacterial host cells. Recombinant RBPs have been utilized for detection of several pathogens, typically as fusions with reporter enzymes or fluorescent proteins. Identification of Bacillus anthracis, the etiological agent of anthrax, can be difficult because of the bacterium's close relationship with other species of the Bacillus cereussensu lato group. Here, we facilitated the identification of B. anthracis using two implementations of enzyme-linked phage receptor binding protein assays (ELPRA). We developed a single-tube centrifugation assay simplifying the rapid analysis of suspect colonies. A second assay enables identification of suspect colonies from mixed overgrown solid (agar) media derived from the complex matrix soil. Thus, these tests identified vegetative cells of B. anthracis with little processing time and may support or confirm pathogen detection by molecular methods such as polymerase chain reaction.

Colony-Forming Unit Spreadplate Assay versus Liquid Culture Enrichment-Polymerase Chain Reaction Assay for the Detection of Bacillus Endospores in Soils

A liquid culture enrichment-polymerase chain reaction (E-PCR) assay was investigated as a potential tool to overcome inhibition by chemical component, debris, and background biological impurities in soil that were affecting detection assay performance for soil samples containing Bacillus atrophaeus subsp. globigii (a surrogate for B. anthracis). To evaluate this assay, 9 g of matched sets of three different soil types (loamy sand [sand], sandy loam [loam] and clay) was spiked with 0, ~4.5, 45, 225, 675 and 1350 endospores. One matched set was evaluated using a previously published endospore concentration and colony-forming unit spreadplate (CFU-S) assay and the other matched set was evaluated using an E-PCR assay to investigate differences in limits of detection between the two assays. Data illustrated that detection using the CFU-S assay at the 45-endospore spike level started to become sporadic whereas the E-PCR assay produced repeatable detection at the ~4.5-endospore spike concentration. The E-PCR produced an ~2-log increase in sensitivity and required slightly less time to complete than the CFU-S assay. This study also investigated differences in recovery among pure and blended sand and clay soils and found potential activation of B. anthracis in predominately clay-based soils.