Genomic diversity of Bacillus anthracis in endemic settings: novel approaches and data

Anthrax, caused by the spore-forming bacterium Bacillus anthracis, remains endemic in many developing countries where it has significant impacts on the health and livelihoods of livestock-keeping communities. While the global genomic diversity of B. anthracisis is well characterised, few studies have quantified its diversity in endemic settings at more local scales, where this information could be critical for elucidating transmission dynamics and guiding control efforts. We collected samples from 526 anthrax-suspected animal carcasses between 2016 and 2018 in the Ngorongoro Conservation Area in northern Tanzania. Seventy five percent were confirmed positive through qPCR, suggesting that anthrax is responsible for a large proportion of sudden deaths in livestock in this area. A subset of positive samples were cultured for whole genome sequencing (n = 73), including multiple isolates from individual carcasses. All sequenced isolates belonged to the Ancient A lineage of B. anthracis, a common strain in southeastern Africa. No clear spatial clustering was observed, possibly reflecting extensive animal movement related to local nomadic practices. Moreover, high levels of within-host diversity were observed which suggests that cases commonly result from simultaneous infection with multiple strains. Additionally, we trialed a targeted sequence capture approach on 93 samples. This was successful in recovering >80% of the chromosomal genome at > 15X coverage from 60% of samples tested, thus representing a valuable tool for culture-free sequencing of this high-risk bacterium. Our work paves the way for integrating genomic data for B. anthracis into epidemiological studies and monitoring of control programs in endemic areas worldwide.

Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity

Genomic sequencing has revolutionized our understanding of bacterial disease epidemiology, but remains underutilized for zoonotic pathogens in remote endemic settings. Anthrax, caused by the spore-forming bacterium Bacillus anthracis, remains a threat to human and animal health and rural livelihoods in low- and middle-income countries. While the global genomic diversity of B. anthracis has been well-characterized, there is limited information on how its populations are genetically structured at the scale at which transmission occurs, critical for understanding the pathogen's evolution and transmission dynamics. Using a uniquely rich dataset, we quantified genome-wide SNPs among 73 B. anthracis isolates derived from 33 livestock carcasses sampled over 1 year throughout the Ngorongoro Conservation Area, Tanzania, a region hyperendemic for anthrax. Genome-wide SNPs distinguished 22 unique B. anthracis genotypes (i.e. SNP profiles) within the study area. However, phylogeographical structure was lacking, as identical SNP profiles were found throughout the study area, likely the result of the long and variable periods of spore dormancy and long-distance livestock movements. Significantly, divergent genotypes were obtained from spatio-temporally linked cases and even individual carcasses. The high number of SNPs distinguishing isolates from the same host is unlikely to have arisen during infection, as supported by our simulation models. This points to an unexpectedly wide transmission bottleneck for B. anthracis, with an inoculum comprising multiple variants being the norm. Our work highlights that inferring transmission patterns of B. anthracis from genomic data will require analytical approaches that account for extended and variable environmental persistence, as well as co-infection.

A retrospective study (2007-2015) on brucellosis seropositivity in livestock in South Africa

In South Africa, brucellosis testing and record-keeping are done by several laboratories, thus it is difficult to access any organized data to assess the status of the disease. This study evaluated the seropositivity for brucellosis using Rose Bengal test and complement fixation test in suspect cattle, sheep, goats and pigs sera submitted to Bacterial Serology Laboratory, Agricultural Research Council-Onderstepoort Veterinary Research (ARC-OVR) from nine provinces in the country during the period 2007-2015. This retrospective data analysis was conducted to estimate the occurrence of brucellosis in the country from the submitted samples, identify variables that affected seropositivity for brucellosis, investigate existing gaps in data recording and make recommendations on important variables to facilitate better data capture and inferences on brucellosis. Nine years of data were collated and analysed to detect association (seropositivity over time regarding animal species and location). Of the 764,276 animals tested, the distribution of samples was 90.50% (691,539/764,276), 5.19% (39,672/764,276), 3.92% (29,967/764,276) and 0.41% (3,098/764,276) for cattle, sheep, goats and pigs, respectively. The seropositivity for brucellosis by animal species was 6.31% (43,666/691,539, 95% CI: 6.26-6.37), 2.09% (828/39,672, 95% CI: 1.95-2.23), 0.63% (189/29,967, 95% CI: 0.55-0.73) and 0.13% (4/3,098, 95% CI: 0.05-0.33) in cattle, sheep, goats and pigs respectively. The data available did not capture information on the age, sex, breed and other host risk factors that would have been related to seropositivity for brucellosis. The data provide an understanding of the disease occurrence and confirm that brucellosis is enzootic in South Africa. Improved and standardized data collection can be used to pro-actively drive, monitor, change or formulate policies to mitigate the challenges brought about by brucellosis in the livestock sector in South Africa.

Investigating selective media for optimal isolation of Brucella spp. in South Africa

Bovine brucellosis in South Africa is caused mainly by Brucella abortus biovar (bv.) 1 and less frequently by B. abortus bv. 2. Bacterial isolation is regarded as the gold standard for diagnosis of Brucella species; however, it is not very sensitive. The aim of this study was to determine the selective medium with optimum antibiotic composition that will allow the growth of Brucella species (spp.) while inhibiting moulds, yeast and most, if not all, Gram-negative contaminants in South Africa. In the controlled experiment, modified Agrifood Research and Technology Center of Aragon (CITA) medium (mCITA) seemed to be the optimum selective medium for isolation of Brucella spp. as compared with Farrell's medium (FM) and modified Thayer Martin (mTM), while FM inhibited the growth of most fungal and bacterial contaminants. Mean comparison between the three media used to culture B. abortus resulted in lower mean difference ranging from 0 to 2.33. In case of Brucella ovis, high mean difference was obtained when comparing FM with mCITA (10.33) and mTM (12). However, the mean differences of 0.67 and 1.67 were obtained when comparing mCITA and mTM media used to, respectively, culture pasteurised and raw milk spiked with B. ovis. Further optimisation at the Agricultural Research Council - Onderstepoort Veterinary Research Institute resulted in a comparable performance between FM and mCITA; however, mCITA allowed optimal growth of the fastidious B. ovis, which is generally inhibited on FM. Generally, mCITA seemed to be the optimum selective medium for isolation of Brucella spp., while FM inhibits the growth of most fungal and bacterial contaminants. Thus, veterinary laboratories can use mCITA and/or FM but should take into consideration the detection of factious Brucella isolated in the country or region.

Blowflies as vectors of Bacillus anthracis in the Kruger National Park

Anthrax, caused by Bacillus anthracis, is endemic in the Kruger National Park (KNP). The epidemiology of B. anthracis is dependent on various factors including vectors.The aims of this study were to examine non-biting blowflies for the presence of B. anthracis externally and internally after feeding on an anthrax-infected carcass and to determine the role of flies in disseminating B. anthracis onto the surrounding vegetation.During an anthrax outbreak in 2014 in the endemic Pafuri region, blowflies associated with two 2–3-day-old anthrax-positive carcasses (kudu and impala) as well as surrounding vegetation were collected and investigated for the presence of B. anthracis spores.The non-biting blowflies (n = 57) caught included Chrysomya albiceps, Ch. marginalis and Lucilia spp. Bacillus anthracis spores were isolated from 65.5% and 25.0% of blowflies collected from the kudu and impala carcasses, respectively.Chrysomya albiceps and Ch. marginalis have the potential to disseminate B. anthracis to vegetation from infected carcasses and may play a role in the epidemiology of anthrax in the KNP. No B. anthracis spores were initially isolated from leaves of the surrounding vegetation using selective media. However, 170 and 500 spores were subsequently isolated from Abutilon angulatum and Acacia sp. leaves, respectively, when using sheep blood agar.Conservation implications: The results obtained in this study have no direct conservation implications and only assist in the understanding of the spread of the disease.

A retrospective study of anthrax on the Ghaap Plateau, Northern Cape province of South Africa, with special reference to the 2007-2008 outbreaks

Anthrax is a zoonotic disease caused by the gram-positive, endospore-forming and soil-borne bacterium Bacillus anthracis. When in spore form, the organism can survive in dormancy in the environment for decades. It is a controlled disease of livestock and wild ungulates in South Africa. In South Africa, the two enzootic regions are the Kruger National Park and the Ghaap Plateau in the Northern Cape province. Farms on the Plateau span thousands of hectares comprising of wildlife - livestock mixed use farming. In 2007-2008, anthrax outbreaks in the province led to government officials intervening to aid farmers with control measures aimed at preventing further losses. Because of the ability of the organism to persist in the environment for prolonged periods, an environmental risk or isolation survey was carried out in 2012 to determine the efficacy of control measures employed during the 2007-2008, anthrax outbreaks. No B. anthracis could be isolated from the old carcass sites, even when bone fragments from the carcasses were still clearly evident. This is an indication that the control measures and protocols were apparently successful in stemming the continuity of spore deposits at previously positive carcass sites.

Use of <i>Brucella abortus</i> species specific polymerase chain reaction assay for the diagnosis of bovine brucellosis

Serology is primarily used in the diagnosis of bovine brucellosis. Bacterial culture and isolation is the gold standard in diagnosing brucellosis but, like serology, it does not offer complete (100%) diagnostic sensitivity and specificity. Polymerase chain reaction (PCR) has been suggested to offer better specificity and sensitivity. In this study, we evaluated the performance of Brucella abortus species specific (BaSS) PCR directly from different samples in the diagnosis of bovine brucellosis in naturally infected cattle in KwaZulu-Natal province of South Africa with known infectious status from culture. The BaSS PCR had a low diagnostic sensitivity (DSe) of 70%, but was able to identify vaccine strains using abomasal fluid from aborted foetuses and detect Brucella DNA from decomposing samples. The best sample for the BaSS PCR was abomasal fluid.

An evaluation of serological tests in the diagnosis of bovine brucellosis in naturally infected cattle in KwaZulu-Natal province in South Africa

The diagnostic sensitivity (DSe) of the Rose Bengal test (RBT), the complement fixation test (CFT), the serum agglutination test (SAT), the competitive enzyme-linked immunosorbent assay (cELISA) and the indirect ELISA (iELISA) were determined in naturally infected cattle in KwaZulu-Natal province of South Africa with known infectious status from culture (gold standard). Natural brucellosis infection status of animals was determined by culturing and identification of Brucella abortus biovar 1 from abomasal fluid, milk, hygroma fluid, lymph nodes or uterine discharges samples. The diagnostic specificity (DSp) of the tests mentioned above was determined using samples from known negative herds. There was no statistically significant difference between the tests in their ability to diagnose brucellosis. The RBT and iELISA had the highest DSe of 95.8%, whereas RBT and CFT had the highest DSp of 100%. In South African laboratories, the RBT and CFT serological tests are used, because of the cost efficacy of CFT when compared to the less labour intensive but more expensive iELISA.

Polyphasic characterization of Bacillus species from anthrax outbreaks in animals from South Africa and Lesotho

INTRODUCTION

Bacillus anthracis is the causative agent of anthrax, a disease endemic in regions of Northern Cape Province and Kruger National Park of South Africa. Accurate identification of virulent B. anthracis is essential but challenging due to its close relationship with other members of B. cereus group. This study characterized B. anthracis and Bacillus species that were recovered from animals and the environment where animals died of anthrax symptoms in southern Africa using a polyphasic approach.

METHODOLOGY

For this purpose, 3 B. anthracis and 10 Bacillus isolates were subjected to microbiology tests, BiologOmniLog identification system (Biolog), 16S ribosomal RNA (rRNA) sequence analysis, polymerase chain reaction (PCR) detection of protective antigen (pag) and capsule (cap) regions, and real-time PCR using hybridization probes targeting chromosomal, pag, and capC genes.

RESULTS

The Bacillus isolates were non-hemolytic, non-motile, and susceptible to penicillin, which is typical of B. anthracis, but resistant to gamma phage, unlike typical B. anthracis. The Biolog system and 16S rRNA gene sequence analysis identified most of the Bacillus isolates as B. endophyticus (7 of 10). Conventional PCR revealed that most of the Bacillus isolates contained capBCA gene regions. This highlights the limitation of the specificity of conventional PCR and the fact that the real-time PCR is more specific and reliable for anthrax diagnosis.

CONCLUSIONS

Real-time PCR, 16S rRNA sequencing, and confirmatory microbiology tests including phage resistance distinguished Bacillus isolates from B. anthracis in this study. Identification of B. anthracis should be done using a polyphasic approach.

Detection of Brucella abortus in Chiredzi district in Zimbabwe

Brucellosis is an endemic disease in Zimbabwe caused by the genus Brucella. Brucella seroprevalence was recently reported to be high in the wildlife-livestock interface in the Chiredzi district and the neighbouring Gonarezhou National Park (GNP) in Zimbabwe, and higher amongst communal cattle with an abortion history and access to grazing in GNP than amongst communal cattle with no abortion history or access to grazing in GNP. The aim of this study was to investigate Brucella species in brucellosis seropositive cattle in the Chiredzi district with access to GNP using isolation and identification. Isolation of Brucella species from whole blood (n = 18) and milk samples (n = 10) from seropositive animals with an abortion history was based on the rose Bengal test (RBT) and enzyme-linked immunoassays (enzyme- linked immunosorbent assay [ELISA]; indirect ELISA and complement ELISA), using microbiology and polymerase chain reaction (PCR) methods. Brucella abortus was cultured and identified from blood and milk collected from seropositive cows in both communal areas. The Brucella-specific 16-23S intergenic spacer (ITS) PCR and multiplex AMOS-PCR assays verified the identification of the cultures. Our results confirmed that B. abortus is present in cattle on communal farms in the Chiredzi district in Zimbabwe and might cause cattle abortions. The need for implementing control measures and raising public awareness on zoonotic transmission of brucellosis are recommended.

The Kümm isolate of Ehrlichia ruminantium: in vitro isolation, propagation and characterization

An effective culture system for Ehrlichia (Cowdria) ruminantium comb. nov. was first established in 1985 and many stocks were subsequently isolated and propagated in vitro. A notable exception, however, was the Kümm isolate that resisted all attempts at in vitro culture until the successful experiment described here. In one experiment white blood cells were harvested from heparinized blood derived from a sheep infected with the Kümm isolate. The cells were added to DH 82 cells and incubated at 37 degrees C. The high metabolic activity of the DH 82 cells necessitated that cell growth be retarded by the addition of cycloheximide. Colonies were first detected 19 days after culture initiation and, once the cultures were established, they could be passaged every 3 days. Bovine and sheep endothelial cells were readily infected with culture supernatant obtained from the infected DH 82 cells. In a further experiment another sheep was infected, using a higher dose of the same batch of Kümm stabilate, and we attempted to infect several different cell lines: these were DH 82 cells, bovine aorta (BA 886) cells, sheep brain endothelial (SBE 189) cells and sheep fibroblastoid cells (E2). Ten days after culture initiation only the E2 cells had become positive for E. ruminantium. Culture supernatant from the first cultured isolate (Kümm-1) was less virulent for mice than that of the second cultured isolate (Kümm-2) which killed all mice. Upon molecular characterization with E. ruminantium 16S probes we found that Kümm-1 hybridized with a Senegal 16S genotype probe, whereas Kümm-2 hybridized only with an Omatjenne 16S genotype probe. The original stabilate used to infect the sheep hybridized with both probes. These results clearly indicate that two different stocks had been isolated in culture.