Whole genome sequencing and identification of Bacillus endophyticus and B. anthracis isolated from anthrax outbreaks in South Africa

Lekota, Kgaugelo Edward; Bezuidt, Oliver; Mafofo, Joseph; Rees, D. J. G.; Muchadeyi, Farai C.; Madoroba, Evelyn; Heerden, Henriëtte van

doi:10.1186/s12866-018-1205-9

Cited by 15 publications

(9 citation statements)

References 46 publications

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“…The identification of species closely related to B. anthracis on diagnostic blood smears can complicate anthrax diagnosis as these species may share similar genetic markers with B. anthracis , leading to false positive results from molecular diagnostics. In addition, other genera, such as Peribacillus and Priestia (Loong et al, 2017, Lekota et al, 2018), can also complicate anthrax diagnosis. These species may not share as many genetic markers with B. anthracis as the B. cereus group, but still have some similarities that could lead to false positive results as seen in this study when performing qPCR diagnostics using only lef , Ba-1, or pagA (BAPA) markers (Figure 6).…”

Section: Discussionmentioning

confidence: 99%

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Comparing microbiological and molecular diagnostic tools for the surveillance of anthrax

Ochai,

Hassim,

Dekker

et al. 2024

Preprint

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The diagnosis of anthrax, a zoonotic disease caused by Bacillus anthracis can be complicated by detection of closely related species. Conventional diagnosis of anthrax involves microscopy, culture identification of bacterial colonies and molecular detection. Genetic markers used are often virulence gene targets such as Bacillus anthracis protective antigen (pagA, as also called BAPA, occurring on plasmid pXO1), lethal factor (lef, on pXO1), as well as chromosomal (Ba1) and plasmid (capsule-encoding capB/C, located on pXO2). Combinations of genetic markers using real-time/quantitative polymerase chain reaction (qPCR) are used to confirm B. anthracis from culture but can also be used directly on diagnostic samples to avoid propagation and its associated biorisks and for faster identification. We investigated how the presence of closely related species could complicate anthrax diagnoses with and without culture to standardise the use of genetic markers using qPCR for accurate anthrax diagnosis. Using blood smears from 2012-2020 from wildlife mortalities (n=1708) in Kruger National Park in South Africa where anthrax is endemic, we contrasted anthrax diagnostic results based on qPCR, microscopy, and culture. From smears, 113/1708 grew bacteria in culture, from which 506 isolates were obtained. Of these isolates, only 24.7% (125 isolates) were positive for B. anthracis based on genetic markers or microscopy. However, among these, merely 4/125 (3.2%) were confirmed B. anthracis isolates (based on morphology, microscopy, and sensitivity testing to penicillin and gamma-phage) from the blood smear, likely due to poor survival of spores on stored smears. This study identified B. cereus sensu lato, which included B. cereus and B. anthracis, Peribacillus spp., and Priestia spp. clusters using gyrB gene in selected bacterial isolates positive for BAPA. Using qPCR on blood smears, 52.1% (890 samples) tested positive for B. anthracis based on one or a combination of genetic markers which included the 25 positive controls. Notably, the standard lef primer set displayed the lowest specificity and accuracy. Interestingly, various marker combinations, such as Ba1+capB, BAPA+capB, Ba-1+BAPA+capB+lef, and BAPA+lef+capB, all demonstrated 100.0% specificity and 98.7% accuracy, while maintaining a sensitivity of 96.6%. The BAPA+lef+Ba-1 combination showed 100% specificity, sensitivity, and accuracy. Using Ba1+BAPA+lef+capB, as well as Ba-1+BAPA+lef with molecular diagnosis accurately detects B. anthracis in the absence of bacterial culture. Systematically combining microscopy and molecular markers holds promise for notably reducing false positives, thereby significantly enhancing the detection and surveillance of diseases like anthrax in southern Africa and beyond and reducing the need for propagation of the bacteria in culture.

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Section: Discussionmentioning

confidence: 99%

“…Specifically, Lekota et al (2018) demonstrated that the capsular region or polyglutamate regions ( capABC ) are the ones that complicate anthrax diagnosis. Lekota et al (2018) reported that capC is not specific to B. anthracis . Thus, combining capsule markers such as the capB in this study with other markers increased the specificity.…”

Section: Discussionmentioning

confidence: 99%

Comparing microbiological and molecular diagnostic tools for the surveillance of anthrax

Ochai,

Hassim,

Dekker

et al. 2024

Preprint

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“…Interestingly, we found a species of Bacillus ( B. endophyticus ) that significantly promotes growth of Coccidioides . This species of Bacillus has been co-cultured with other pathogens and has been implicated in providing virulence factors via plasmid exchange [ 49 ].…”

Section: Discussionmentioning

confidence: 99%

Combating the Dust Devil: Utilizing Naturally Occurring Soil Microbes in Arizona to Inhibit the Growth of Coccidioides spp., the Causative Agent of Valley Fever

Kollath

Morales

Itogawa

et al. 2023

JoF

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The fungal disease Valley fever causes a significant medical and financial burden for affected people in the endemic region, and this burden is on the rise. Despite the medical importance of this disease, little is known about ecological factors that influence the geographic point sources of high abundance of the pathogens Coccidioides posadasii and C. immitis, such as competition with co-occurring soil microbes. These “hot spots”, for instance, those in southern Arizona, are areas in which humans are at greater risk of being infected with the fungus due to consistent exposure. The aim of this study was to isolate native microbes from soils collected from Tucson, Arizona (endemic area for C. posadasii) and characterize their relationship (antagonistic, synergistic, or neutral) to the fungal pathogen with in vitro challenge assays. Secreted metabolites from the microbes were extracted and described using analytical techniques including high-performance liquid chromatography (HPLC) and mass spectrometry. Bacteria belonging to the genus Bacillus and fungi in the Fennellomyces and Ovatospora genera were shown to significantly decrease the growth of Coccidioides spp. In vitro. In contrast, other bacteria in the Brevibacillus genus, as well as one species of Bacillus bacteria, were shown to promote growth of Coccidioides when directly challenged. The metabolites secreted from the antagonistic bacteria were described using HPLC and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The microbes identified in this study as antagonists to Coccidioides and/or the metabolites they secrete have the potential to be used as natural biocontrol agents to limit the amount of fungal burden at geographic point sources, and therefore limit the potential for human infection.

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“…Additionally, colonial characteristics and the Gram staining reaction of DPM17 were in general agreement with those reported for Bacillus sp. [42].…”

Section: Discussionmentioning

confidence: 99%

Plant Growth-Promoting Bacterium from Non-Agricultural Soil Improves Okra Plant Growth

2022

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Beneficial soil microorganisms influence nutrient recycling, soil fertility, plant growth, and productivity and reduce chemical fertilizer application. This study aimed to isolate bacteria from non-agricultural soils in the Al-Ahsa region and characterize the bacteria with the best biostimulating characteristics at the physiological, biochemical, and molecular level. DPM17, a bacterial isolate, promotes plant growth through phosphate solubilization, nitrogen fixation, and ammonia production. DPM17 also produces the phytohormones, indole acetic acid (IAA; 4.516 μg mL−1) and gibberellin (1.33 µg mL−1), and ammonia (0.06 µg mL−1). Additionally, DPM17 grows in the presence of up to 10% NaCl, indicating its halophilic nature. DPM17 was identified as Bacillus baekryungensis based on comparative sequence analysis of the 16S rRNA gene, and neighbor-joining phylogenetic analyses indicated that DPM17 was 96.51% identified to Bacillus sp. DPM17 inoculation substantially improved Abelmoschus esculentus (okra) root length, lateral root count, and dry weight from 7.03 to 9.41 (p = 0.03), 3.2 to 7.2, and 6 to 13 mg (p = 0.032), respectively. The results suggest that DPM17 enhances plant growth and can be exploited to develop efficient formulations for sustainable agriculture and food security in Saudi Arabia.

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Whole genome sequencing and identification of Bacillus endophyticus and B. anthracis isolated from anthrax outbreaks in South Africa

Cited by 15 publications

References 46 publications

Comparing microbiological and molecular diagnostic tools for the surveillance of anthrax

Comparing microbiological and molecular diagnostic tools for the surveillance of anthrax

Combating the Dust Devil: Utilizing Naturally Occurring Soil Microbes in Arizona to Inhibit the Growth of Coccidioides spp., the Causative Agent of Valley Fever

Plant Growth-Promoting Bacterium from Non-Agricultural Soil Improves Okra Plant Growth

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