Genomic sequence data and single nucleotide polymorphism genotyping of Bacillus anthracis strains isolated from animal anthrax outbreaks in Northern Cape Province, South Africa.
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SUBMITTER: Lekota KE
PROVIDER: S-EPMC6965700 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:Bacillus cereus biovar anthracis (Bcbva) is an emergent bacterium closely related to Bacillus anthracis, the etiological agent of anthrax. The latter has a worldwide distribution and usually causes infectious disease in mammals associated with savanna ecosystems. Bcbva was identified in humid tropical forests of Côte d'Ivoire in 2001. Here, we characterize the potential geographic distributions of Bcbva in West Africa and B. anthracis in sub-Saharan Africa using an ecological niche modeling approach. METHODOLOGY/PRINCIPAL FINDINGS:Georeferenced occurrence data for B. anthracis and Bcbva were obtained from public data repositories and the scientific literature. Combinations of temperature, humidity, vegetation greenness, and soils values served as environmental variables in model calibrations. To predict the potential distribution of suitable environments for each pathogen across the study region, parameter values derived from the median of 10 replicates of the best-performing model for each pathogen were used. We found suitable environments predicted for B. anthracis across areas of confirmed and suspected anthrax activity in sub-Saharan Africa, including an east-west corridor from Ethiopia to Sierra Leone in the Sahel region and multiple areas in eastern, central, and southern Africa. The study area for Bcbva was restricted to West and Central Africa to reflect areas that have likely been accessible to Bcbva by dispersal. Model predicted values indicated potential suitable environments within humid forested environments. Background similarity tests in geographic space indicated statistical support to reject the null hypothesis of similarity when comparing environments associated with B. anthracis to those of Bcbva and when comparing humidity values and soils values individually. We failed to reject the null hypothesis of similarity when comparing environments associated with Bcbva to those of B. anthracis, suggesting that additional investigation is needed to provide a more robust characterization of the Bcbva niche. CONCLUSIONS/SIGNIFICANCE:This study represents the first time that the environmental and geographic distribution of Bcbva has been mapped. We document likely differences in ecological niche-and consequently in geographic distribution-between Bcbva and typical B. anthracis, and areas of possible co-occurrence between the two. We provide information crucial to guiding and improving monitoring efforts focused on these pathogens.
| S-EPMC7082064 | biostudies-literature
Project description:BACKGROUND:Bacillus endophyticus is a soil plant-endophytic bacterium, while B. anthracis is the causative agent of anthrax. The virulence factors of B. anthracis are the plasmid encoded tripartite toxins (pXO1) and poly-?-glutamic acid (PGA) capsule (pXO2). B. endophyticus isolated alongside B. anthracis from animals that died of anthrax in Northern Cape Province (NCP), South Africa, harbored polyglutamate genes. The study compared the characteristics of B. anthracis and B. endophyticus with other Bacillus species with a focus on the presence of the PGA capsule or/and unbound PGA. The morphology and whole genome sequence analysis of B. endophyticus strains and B. anthracis were compared. RESULTS:In conventional microbiology, B. endophyticus showed gram-positive round-shaped rods in single/short chains, which were endospore-forming, non-motile, non-haemolytic with white and dry colonies, and ?-phage resistant. B. anthracis was differentiated from B. endophyticus based on the latter's box-shaped rods in pairs/long chains, white-grey and slimy colonies, encapsulated and ?-phage susceptible. The study identified a PGA polyglutamate synthase operon that consisted of pgsBCA, ?-glutamyltranspeptidase (ggt) and pgsE in B. endophyticus genomes. CONCLUSIONS:PGA regions of B. anthracis contain capBCADE genes located in the pXO2 required for capsulation formation, while B. endophyticus contain the pgsBCAE genes in the chromosome. Whole genome and microbiology analysis identified B. endophyticus, as a non-capsuled endospore-forming bacterium that consists of PGA required for biosynthesis. B. endophyticus strains do not synthesize surface associated PGA, therefore capsule visualization of B. anthracis is a key diagnostic characteristic. The study highlights the significance of using whole genome shotgun sequencing to identify virulence and other important genes that might be present amongst unknown samples from natural outbreaks. None of the B. anthracis related plasmids or virulence genes were found in the B. endophyticus genomes.
| S-EPMC6038202 | biostudies-literature
Project description:The first 1,000 days from conception to 24 months is a critical period for healthy growth and development. In South Africa, stunting (weight-for-length below -2SD from the WHO reference mean) is a major public health issue with significant health consequences. We determined associations between demographic, health, and anthropometric indicators of mothers and their infants. A cross-sectional study was conducted in the Northern Cape. All mothers with 5- to 7-week-old babies visiting PHC facilities were invited to participate. A questionnaire was completed in a structured interview with each mother. Age and length of the baby at 6 weeks were used to determine stunting, while the weight and height of the mother were measured for body mass index (BMI). Eight hundred questionnaires were completed in 92 facilities. The median age of mothers was 26 years (IQR 20-30 years) and 44.9% were married. Only 40.1% had completed school or tertiary education and almost 40% relied on a government grant as the main source of income. Two-thirds (64.9%) had not planned the pregnancy and 17% were on antiretroviral therapy (ART). More than a quarter (26.1%) smoked cigarettes or used snuff during pregnancy, while 9.4% drank alcohol. At 6 weeks, 31% of boys and 14% of girls had a length-for-age below the WHO reference values, while 25.4% of mothers were classified as obese and 24.6% as overweight. More than 70% had a waist circumference above 80 cm. Significantly more mothers with stunted babies weighed less [-6 kg; -1 kg] and were shorter [-4 cm; -1 cm] than mothers with babies who were not stunted. Compared to babies who were not stunted, significantly more babies of mothers who lived in informal housing [-19.7%; -3.2%], relied on a grant [-19.7%; -3.2%], smoked/ snuffed [7.6%; 23.5%], and used alcohol during pregnancy [0.3%; 11.5%] were stunted. The following factors significantly increased the risk of having a stunted baby at 6 weeks: living in informal housing vs. formal housing (RR: 0.68, 95% CI [0.5; 0.9]); smoking or using snuff during pregnancy (RR: 1.74, 95% CI [1.3; 2.3]); using alcohol during pregnancy (RR: 1.5, 95% CI [1.1; 2.2]); both smoking and using alcohol during pregnancy (RR: 1.97, 95% CI [1.4; 2.9]). We confirmed the coexistence of under- and over-nutrition among mothers and their babies, possibly indicating that stunting in childhood may predispose to overweight and obesity in adulthood in a vicious cycle that affects generation after generation. Interventions aimed at poverty alleviation and encouraging healthy lifestyles with an emphasis on healthy eating, smoking cessation and abstaining from alcohol before pregnancy are urgently required.
| S-EPMC7289919 | biostudies-literature
Project description:BackgroundAnthrax, the zoonotic disease caused by the gram-positive bacterium Bacillus anthracis, is nowadays rare in northern parts of Europe including Finland and Scandinavia. Only two minor outbreaks of anthrax in 1988 and in 2004 and one sporadic infection in 2008 have been detected in animals in Finland since the 1970's. Here, we report on two Finnish B. anthracis strains that were isolated from spleen and liver of a diseased calf related to the outbreak in 1988 (strain HKI4363/88) and from a local scrotum and testicle infection of a bull in 2008 (strain BA2968). These infections occurred in two rural Finnish regions, i.e., Ostrobothnia in western Finland and Päijänne Tavastia in southern Finland, respectively.ResultsThe isolates were genetically characterized by PCR-based methods such as multilocus variable number of tandem repeat analysis (MLVA) and whole genome-sequence analysis (WGS). Phylogenetic comparison of the two strains HKI4363/88 and BA2968 by chromosomal single nucleotide polymorphism (SNP) analysis grouped these organisms within their relatives of the minor canonical A-branch canSNP-group A.Br.003/004 (A.Br.V770) or canonical B-branch B.Br.001/002, respectively. Strain HKI4363/88 clustered relatively closely with other members of the A.Br.003/004 lineage from Europe, South Africa, and South America. In contrast, strain BA2968 clearly constituted a new sublineage within B.Br.001/002 with its closest relative being HYO01 from South Korea.ConclusionsOur results suggest that Finland harbors both unique (autochthonous) and more widely distributed, common clades of B. anthracis. We suspect that members of the common clades such as strains HKI4363/88 have been introduced only recently by anthropogenic activities involving importation of contaminated animal products. On the other hand, autochthonous strains such as isolate BA2968 probably have an older history of their introduction into Finland as evidenced by a high number of single nucleotide variant sites in their genomes.
| S-EPMC6122712 | biostudies-literature
Project description:Through full genome analyses of four atypical Bacillus cereus isolates, designated B. cereus biovar anthracis, we describe a distinct clade within the B. cereus group that presents with anthrax-like disease, carrying virulence plasmids similar to those of classic Bacillus anthracis. We have isolated members of this clade from different mammals (wild chimpanzees, gorillas, an elephant and goats) in West and Central Africa (Côte d'Ivoire, Cameroon, Central African Republic and Democratic Republic of Congo). The isolates shared several phenotypic features of both B. anthracis and B. cereus, but differed amongst each other in motility and their resistance or sensitivity to penicillin. They all possessed the same mutation in the regulator gene plcR, different from the one found in B. anthracis, and in addition, carry genes which enable them to produce a second capsule composed of hyaluronic acid. Our findings show the existence of a discrete clade of the B. cereus group capable of causing anthrax-like disease, found in areas of high biodiversity, which are possibly also the origin of the worldwide distributed B. anthracis. Establishing the impact of these pathogenic bacteria on threatened wildlife species will require systematic investigation. Furthermore, the consumption of wildlife found dead by the local population and presence in a domestic animal reveal potential sources of exposure to humans.
| S-EPMC5015827 | biostudies-literature
Project description:BackgroundAnthrax, a zoonotic disease caused by the spore-forming bacterium Bacillus anthracis, remains a major global public health concern, especially in countries with limited resources. Sierra Leone, a West African country historically plagued by anthrax, has almost been out of report on this disease in recent decades. In this study, we described a large-scale anthrax outbreak affecting both animals and humans and attempted to characterize the pathogen using molecular techniques.MethodsThe causative agent of the animal outbreak in Port Loko District, Sierra Leone, between March and May 2022 was identified using the nanopore sequencing technique. A nationwide active surveillance was implemented from May 2022 to June 2023 to monitor the occurrence of anthrax-specific symptoms in humans. Suspected cases were subsequently verified using quantitative polymerase chain reaction. Full-genome sequencing was accomplished by combining long-read and short-read sequencing methods. Subsequent phylogenetic analysis was performed based on the full-chromosome single nucleotide polymorphisms.ResultsThe outbreak in Port Loko District, Sierra Leone, led to the death of 233 animals between March 26th and May 16th, 2022. We ruled out the initial suspicion of Anaplasma species and successfully identified B. anthracis as the causative agent of the outbreak. As a result of the government's prompt response, out of the 49 suspected human cases identified during the one-year active surveillance, only 6 human cases tested positive, all within the first month after the official declaration of the outbreak. The phylogenetic analysis indicated that the BaSL2022 isolate responsible for the outbreak was positioned in the A.Br.153 clade within the TransEuroAsian group of B. anthracis.ConclusionsWe successfully identified a large-scale anthrax outbreak in Sierra Leone. The causative isolate of B. anthracis, BaSL2022, phylogenetically bridged other lineages in A.Br.153 clade and neighboring genetic groups, A.Br.144 and A.Br.148, eventually confirming the spillover of anthrax from West Africa. Given the wide dissemination of B. anthracis spores, it is highly advisable to effectively monitor the potential reoccurrence of anthrax outbreaks and to launch campaigns to improve public awareness regarding anthrax in Sierra Leone.
| S-EPMC10788998 | biostudies-literature
Project description:BackgroundThe use of animals and animal-derived materials in traditional medicine constitutes an important part of the belief systems of indigenous African cultures. It is believed to be rapidly expanding in South Africa, where traditional healers are estimated to outnumber western doctors by 2000:1 in some areas, with an overall clientele consisting of 60-80% of South African citizens. Despite concerns about the impact of the trade in traditional medicine on biodiversity, there has been only limited research on this topic in South Africa.MethodsTraditional Xhosa and Sotho healers operating from impoverished, rural communities in the Boland Region of the Western Cape Province were consulted to provide a comprehensive inventory of the number and frequency of animals used and sold. Species richness estimators, diversity indices, and a relative cultural importance (RCI) index were used to highlight species of concern and assess market dynamics.ResultsA total of 26 broad use categories for 12 types of animal parts or products from 71 species or morphospecies were recorded. The most commonly sold items were skin pieces, oil or fat, and bones. Results showed that leopard, chacma baboon, Cape porcupine, monitor lizard species, puff adder, African rock python, and black-backed jackal were the species most used in the traditional medicinal trade.ConclusionsThis study extends existing knowledge on the trade of animals in South African healing practices and provides the first attempt in the Western Cape to quantify wildlife use for cultural traditions. The results have relevance for setting conservation priorities and may assist in effective policy development inclusive of ecological sustainability priorities, as well as cultural demands.
| S-EPMC6617652 | biostudies-literature
Project description:Environmental reservoirs are essential in the maintenance and transmission of anthrax but are poorly characterized. The anthrax agent, Bacillus anthracis was long considered an obligate pathogen that is dormant and passively transmitted in the environment. However, a growing number of laboratory studies indicate that, like some of its close relatives, B. anthracis has some activity outside of its vertebrate hosts. Here we show in the field that B. anthracis has significant interactions with a grass that could promote anthrax spore transmission to grazing hosts. Using a local, virulent strain of B. anthracis, we performed a field experiment in an enclosure within a grassland savanna. We found that B. anthracis increased the rate of establishment of a native grass (Enneapogon desvauxii) by 50% and that grass seeds exposed to blood reached heights that were 45% taller than controls. Further we detected significant effects of E. desvauxii, B. anthracis, and their interaction on soil bacterial taxa richness and community composition. We did not find any evidence for multiplication or increased longevity of B. anthracis in bulk soil associated with grass compared to controls. Instead interactions between B. anthracis and plants may result in increased host grazing and subsequently increased transmission to hosts.
| S-EPMC4046938 | biostudies-literature
Project description:We used quantitative real-time RT-PCR to not only investigate the mRNA levels of anthrax toxin receptor 1 (ANTXR1) and 2 (ANTXR2) in the murine J774A.1 macrophage cells and different tissues of mice, but also evaluate the effect of anthrax edema toxin and Bacillus anthracis Sterne spores on the expression of mRNA of these receptors. The mRNA transcripts of both receptors were detected in J774A.1 cells and mouse tissues such as the lung, heart, kidney, spleen, stomach, jejunum, brain, skeleton muscle, and skin. The ANTXR2 mRNA level was significantly higher than that of ANTXR1 in J774A.1 cells and all tissues examined. The mRNA expression of both receptors in the lung was the highest among the tissues evaluated. Interestingly, the mRNA expression of both receptors in J774A.1 cells was upregulated by edema toxin. In addition, ANTXR mRNA expression in the lung was downregulated after subcutaneous inoculation of B. anthracis Sterne spores as well as after intranasal administration of anthrax toxin-based vaccine BioThrax. These results suggest that anthrax edema toxin and B. anthracis Sterne spore are involved in the ANTXR mRNA regulation in host cells.
| S-EPMC1973154 | biostudies-literature
Project description:The ability to control fire was a crucial turning point in human evolution, but the question when hominins first developed this ability still remains. Here we show that micromorphological and Fourier transform infrared microspectroscopy (mFTIR) analyses of intact sediments at the site of Wonderwerk Cave, Northern Cape province, South Africa, provide unambiguous evidence--in the form of burned bone and ashed plant remains--that burning took place in the cave during the early Acheulean occupation, approximately 1.0 Ma. To the best of our knowledge, this is the earliest secure evidence for burning in an archaeological context.
| S-EPMC3356665 | biostudies-literature