Whole Genome Sequence Analysis of Brucella abortus Isolates from Various Regions of South Africa

Phylogenomics of Brucella abortus isolated from African Buffalo in Kruger National Park: New perspectives on wildlife-cattle disease dynamics

In South Africa, Brucella abortus biovar 1 is the primary cause of bovine brucellosis, significantly impacting cattle production and trade. Serological studies have revealed brucellosis in African wildlife, complicating control efforts due to limited epidemiological data. In 1977, B. abortus biovar 1 was isolated from an African buffalo fetus in Kruger National Park (KNP), raising speculation that buffalo may serve as reservoir hosts. This study investigated Brucella spp. in free-ranging buffalo in KNP using serological, molecular, and bacteriological methods. Brucella abortus bv 1 was isolated from lymph nodes and spleens of three sub-adult buffalo in 2022, marking the first documented recurrence in 50 years. Phylogenomic analyses revealed connections between buffalo isolates and cattle strains from South Africa and South America, suggesting spillover and shared origins from Europe. Further genomic and epidemiological surveillance is required to clarify the role of buffalo as reservoir hosts for brucellosis.

Detection and Molecular Diversity of Brucella melitensis in Pastoral Livestock in North-Eastern Ethiopia

Brucellosis is a neglected zoonotic disease affecting livestock and humans that remains endemic in Ethiopia. Despite its prevalence, only a few studies have identified Brucella species circulating in livestock in the country. This study aimed to determine the Brucella species responsible for infections in livestock in the Afar region of Ethiopia and characterize the isolates using whole-genome single nucleotide polymorphism (wgSNP) analysis and in silico multi-locus sequence typing (MLST). Comparisons were made between Ethiopian Brucella and regional and global isolates to determine their phylogenetic relationships. Surveys conducted in May and October-November 2022 in six villages of the Amibara district involved the collection of vaginal swabs (n = 231) and milk samples (n = 17) from 32 sheep and 199 goats kept by 143 pastoral households reporting recent abortions in the animals. Brucella melitensis was detected in three sheep and 32 goats, i.e., 15% (35/231) of animals across 20% (29/143) of households using bacterial culture and PCR-based methods (bcsp31, AMOS, and Bruce-ladder multiplex PCR). Of the 35 positive animals, B. melitensis was isolated from 24 swabs, while the remaining 11 were culture-negative and detected only by PCR. The genomic DNA of the 24 isolates was sequenced using Illumina Novaseq 6000 and assembled using the SPAdes pipeline. Nine- and 21-locus MLST identified 23 isolates as genotype ST12, while one isolate could not be typed. The wgSNP-based phylogenetic analysis revealed that the Ethiopian isolates clustered within the African clade and were closely related to isolates from Somalia. Several virulence factors responsible for adhesion, intracellular survival, and regulatory functions were detected in all isolates. No antimicrobial resistance genes associated with resistance to drugs commonly used for treating brucellosis were detected. Since B. melitensis is prevalent in sheep and goats, vaccination with the B. melitensis Rev-1 vaccine is the recommended strategy in these pastoral systems to protect animal and human health.

Whole-Genome Sequencing of Brucella melitensis Isolates from Kuwait for the Identification of Biovars, Variants, and Relationship within a Biovar

OBJECTIVE

The identification of Brucella genotypes is essential for epidemiological studies. The whole-genome sequencing is emerging as a novel tool for genetic characterization of infectious microbes. The aim of this study was to genotype Brucella melitensis isolates from Kuwait using whole-genome sequencing and variant analysis of the sequence data.

METHODS

DNA was purified from 15 heat-inactivated B. melitensis isolates and used to prepare sequencing libraries employing Nextera XT DNA Sample Preparation Kit (Illumina San Diego, CA, USA) and sequenced on a MiSeq (Illumina). The sequence files were aligned to three biovars of B. melitensis, i.e., biovar 1 str. 16M, biovar 2 str. 63/9, and biovar 3 str. Ether. The alignment and variant calling were performed using "bwa-mem" and SAMtools/VCFtools, respectively.

RESULTS

The genome size of all the isolates was around 3.3 mega base pairs and resembled B. melitensis biovar 2. Single-nucleotide polymorphisms (SNPs), insertions, and deletions (indels) were spread all over the genome; but 138 SNPs were common among the 14 isolates, supporting the same ancestral origin. A neighbor-joining tree analysis identified isolate 2 as an outlier. In addition, SNPs (2-478) specific to each isolate were also identified, which divided the B. melitensis biovar 2 into two major groups/genotypes. A further analysis showed that the Kuwaiti isolates of the present study shared phylogeny mainly with strains from the Middle Eastern countries.

CONCLUSIONS

Among the 15 studied isolates from Kuwait, biovar 2 is the most prevalent biovar of B. melitensis. Furthermore, isolate-specific genetic variations were identified, which may be useful in epidemiological investigations.

OBJECTIVE

The identification of Brucella genotypes is essential for epidemiological studies. The whole-genome sequencing is emerging as a novel tool for genetic characterization of infectious microbes. The aim of this study was to genotype Brucella melitensis isolates from Kuwait using whole-genome sequencing and variant analysis of the sequence data.

METHODS

DNA was purified from 15 heat-inactivated B. melitensis isolates and used to prepare sequencing libraries employing Nextera XT DNA Sample Preparation Kit (Illumina San Diego, CA, USA) and sequenced on a MiSeq (Illumina). The sequence files were aligned to three biovars of B. melitensis, i.e., biovar 1 str. 16M, biovar 2 str. 63/9, and biovar 3 str. Ether. The alignment and variant calling were performed using "bwa-mem" and SAMtools/VCFtools, respectively.

RESULTS

The genome size of all the isolates was around 3.3 mega base pairs and resembled B. melitensis biovar 2. Single-nucleotide polymorphisms (SNPs), insertions, and deletions (indels) were spread all over the genome; but 138 SNPs were common among the 14 isolates, supporting the same ancestral origin. A neighbor-joining tree analysis identified isolate 2 as an outlier. In addition, SNPs (2-478) specific to each isolate were also identified, which divided the B. melitensis biovar 2 into two major groups/genotypes. A further analysis showed that the Kuwaiti isolates of the present study shared phylogeny mainly with strains from the Middle Eastern countries.

CONCLUSIONS

Among the 15 studied isolates from Kuwait, biovar 2 is the most prevalent biovar of B. melitensis. Furthermore, isolate-specific genetic variations were identified, which may be useful in epidemiological investigations.

Whole Genome Sequence Analysis of Brucella spp. from Human, Livestock, and Wildlife in South Africa

Brucellosis is an economically important zoonotic disease affecting humans, livestock, and wildlife health globally and especially in Africa. Brucella abortus and B. melitensis have been isolated from human, livestock (cattle and goat), and wildlife (sable) in South Africa (SA) but with little knowledge of the population genomic structure of this pathogen in SA. As whole genome sequencing can assist to differentiate and trace the origin of outbreaks of Brucella spp. strains, the whole genomes of retrospective isolates (n = 19) from previous studies were sequenced. Sequences were analysed using average nucleotide identity (ANI), pangenomics, and whole genome single nucleotide polymorphism (wgSNP) to trace the geographical origin of cases of brucellosis circulating in human, cattle, goats, and sable from different provinces in SA. Pangenomics analysis of B. melitensis (n = 69) and B. abortus (n = 56) was conducted with 19 strains that included B. abortus from cattle (n = 3) and B. melitensis from a human (n = 1), cattle (n = 1), goat (n = 1), Rev1 vaccine strain (n = 1), and sable (n = 12). Pangenomics analysis of B. melitensis genomes, highlighted shared genes, that include 10 hypothetical proteins and genes that encodes for acetyl-coenzyme A synthetase (acs), and acylamidase (aam) amongst the sable genomes. The wgSNP analysis confirmed the B. melitensis isolated from human was more closely related to the goat from the Western Cape Province from the same outbreak than the B. melitensis cattle sample from different cases in the Gauteng Province. The B. melitensis sable strains could be distinguished from the African lineage, constituting their own African sub-clade. The sequenced B. abortus strains clustered in the C2 lineage that is closely related to the isolates from Mozambique and Zimbabwe. This study identified genetically diverse Brucella spp. among various hosts in SA. This study expands the limited known knowledge regarding the presence of B. melitensis in livestock and humans in SA, further building a foundation for future research on the distribution of the Brucella spp. worldwide and its evolutionary background.

Molecular epidemiology of Brucella abortus isolated from the environment in Ningxia Hui autonomous region, China

Brucellosis is among the key zoonotic infectious diseases in China, and The Ningxia Hui Autonomous Region represents a major endemic area, and it is one of the main causes of poverty in the region due to illness. In Ningxia, there is substantial research on Brucella melitensis, studies on the molecular epidemiology of Brucella abortus are notably scarce. Consequently, this study aims to undertake pathogenic isolation and molecular epidemiological research on Brucella abortus isolated from the environment in Ningxia, providing insights and evidence to advance the prevention and control measures for brucellosis in the region. Building on traditional pathogenic detection methods, this research employs whole-genome sequencing(WGS) techniques and bioinformatics software to conduct a phylogenetic comparison of Ningxia strains and strains of Brucella abortus from various geographical origins. The results indicate that four Brucella abortus strains are classified as biovar 3 and MLST type ST2. It is shown that the local strains were closer phylogenetic relationships with strains from Asian and European countries. The presence of Brucella abortus in certain environmental sectors of Ningxia indicates a risk of transmission from the environment to animals and subsequently to humans. In conclusion, the Brucella abortus exists in some farming environments in Ningxia, and exists for a long time. Therefore, it is necessary to strengthen the monitoring of the disinfection effect of the farming environment to provide a basis for the forward movement of the gate of brucellosis prevention and control.

Molecular typing methods to characterize Brucella spp. from animals: A review

Brucellosis is an infectious disease of animals that can infect humans. The disease causes significant economic losses and threatens human health. A timely and accurate disease diagnosis plays a vital role in the identification of brucellosis. In addition to traditional diagnostic methods, molecular methods allow diagnosis and typing of the causative agent of brucellosis. This review will discuss various methods, such as Bruce-ladder, Suiladder, high-resolution melt analysis, restriction fragment length polymorphism, multilocus sequence typing, multilocus variable-number tandem repeat analysis, and whole-genome sequencing single-nucleotide polymorphism, for the molecular typing of Brucella and discuss their advantages and disadvantages.

Comparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains

Brucella abortus and Brucella melitensis are the primary etiological agents of brucellosis in large and small ruminants, respectively. There are limited comparative genomic studies involving Brucella strains that explore the relatedness among both species. In this study, we involved strains (n=44) representing standard, vaccine and Indian field origin for pangenome, single nucleotide polymorphism (SNP) and phylogenetic analysis. Both species shared a common gene pool representing 2884 genes out of a total 3244 genes. SNP-based phylogenetic analysis indicated higher SNP diversity among B. melitensis (3824) strains in comparison to B. abortus (540) strains, and a clear demarcation was identified between standard/vaccine and field strains. The analysis for virulence genes revealed that virB3, virB7, ricA, virB5, ipx5, wbkC, wbkB, and acpXL genes were highly conserved in most of the Brucella strains. Interestingly, virB10 gene was found to have high variability among the B. abortus strains. The cgMLST analysis revealed distinct sequence types for the standard/vaccine and field strains. B. abortus strains from north-eastern India fall within similar sequence type differing from other strains. In conclusion, the analysis revealed a highly shared core genome among two Brucella species. SNP analysis revealed B. melitensis strains exhibit high diversity as compared to B. abortus strains. Strains with absence or high polymorphism of virulence genes can be exploited for the development of novel vaccine candidates effective against both B. abortus and B. melitensis.

Brucellosis Seropositivity Using Three Serological Tests and Associated Risk Factors in Abattoir Workers in Gauteng Province, South Africa

Abattoir workers are liable to zoonotic infections from animals and animal products, primarily to diseases with asymptomatic and chronic clinical manifestations in animals, such as brucellosis. No published reports exist on the seroprevalence of brucellosis in abattoir workers in South Africa. Therefore, this cross-sectional study was conducted to estimate the occurrence and risk factors for Brucella exposure in abattoir workers in Gauteng Province. A total of 103 abattoir workers and managers from 6 abattoirs, where brucellosis-positive slaughtered cattle and sheep were previously detected, were interviewed and tested with serological assays using the Rose Bengal test (RBT), BrucellaCapt, and IgG-ELISA. A pre-tested questionnaire was administered to consenting respondents to obtain information on risk factors for brucellosis. Of the 103 respondents tested, the distribution of female and male workers was 16 (15.5%) and 87 (84.5%), respectively. The seroprevalence for exposure to brucellosis was 21/103 (20.4%, 95%CI: 13.1-29.5) using a combination of RBT, BrucellaCapt, or IgG-ELISA. For test-specific results, seroprevalences by RBT, BrucellaCapt, and IgG-ELISA were 13/103 (12.6%, 95%CI: 6.9-20.6), 9/103 (8.74%, 95%CI: 4.1-15.9), and 18/103 (17.5%, 95%CI: 10.7-26.2), respectively. Low-throughput abattoirs were identified as associated risks, as 29.3% of workers were seropositive compared with 12.7% of workers in high-throughput abattoirs, which highlights that direct contact at abattoirs poses higher risk to workers than indirect and direct contact outside abattoirs. This study confirms the occurrence of Brucella spp. antibodies among abattoir workers in South Africa, possibly due to occupational exposure to Brucella spp., and highlights the occupational hazard to workers. Furthermore, findings underscore that abattoir facilities can serve as points for active and passive surveillance for indicators of diseases of public health importance. We recommend periodic implementation of brucellosis testing of abattoir workers country-wide to establish baseline data for informing appropriate preventive practices and reducing the potential burden of infection rates among these high-risk workers.

Original and introduced lineages co-driving the persistence of Brucella abortus circulating in West Africa

Introduction

Brucellosis, a serious public health issue affecting animals and humans, is neglected in West Africa (WA).

Methods

In the present study, bio-typing, multi-locus sequence typing (MLST), multiple-locus variable-number tandem repeat analysis (MLVA), and whole genome sequencing single-nucleotide polymorphism (WGS-SNP) analysis were used to characterize the Brucella abortus (B. abortus) strains from WA.

Results

All of the 309 strains analyzed in this study were extracted and downloaded from the international MLVA bank and were from 10 hosts (cattle, humans, ovine, buffalo, dromedaries, horse, sheep, zebu, dog, and cat) distributed in 17 countries in WA. Based on the bio-typing, three biovars, dominated by B. abortus bv.3, were observed and reported across seven decades (1958–2019). With MLST, 129 B. abortus strains from the present study were sorted into 14 STs, with ST34 as the predicted founder. These 14 STs clustered into the global MLST data into three clone complexes (C I–C III) with the majority of strains clustering in C I, while C II forms an independent branch, and C III harbors three STs shared by different continents. These data revealed that most cases were caused by strains from native lineages. According to the MLVA-11 comparison, 309 strains were divided into 22 MLVA-11 genotypes, 15 of which were unique to WA and the remaining seven had a global distribution. MLVA-16 analysis showed that there were no epidemiological links among these strains. Based on the MLVA data, B. abortus strains from WA have high genetic diversity, and predominated genotypes were descended from a native lineage. While the MLVA-16 globally highlights that the dominant native and few introduced lineages (from Brazil, the USA, South Korea, Argentina, India, Italy, Portugal, the UK, Costa Rica, and China) co-driving the B. abortus ongoing prevalence in WA. The high-resolution SNP analysis implied the existence of introduced B. abortus lineages, which may be reasonably explained by the movement and trade of dominant hosts (cattle) and/or their products.

Discussion

Our results indicated that B. abortus strains in WA consist of native and introduced strains that necessitate control such as vaccination, testing, slaughtering, and movement control by the relevant country authorities to reduce brucellosis in livestock.

Whole genome sequencing of Ethiopian Brucella abortus isolates expands the known diversity of an early branching sub-Saharan African lineage

Brucellosis remains one of the most significant zoonotic diseases globally, responsible for both considerable human morbidity and economic losses due to its impacts on livestock productivity. Despite this, there remain significant evidence gaps in many low- and middle-income countries, including those of sub-Saharan Africa. Here we report the first molecular characterisation of Brucella sp. from Ethiopia. Fifteen Brucella sp. isolates from an outbreak in cattle from a herd in central Ethiopia were identified as Brucella abortus, using bacterial culture and molecular methods. Sequencing of the Ethiopian B. abortus isolates allowed their phylogenetic comparison with 411 B. abortus strains of diverse geographical origins, using whole genome single nucleotide polymorphisms (wgSNP). The Ethiopian isolates belonged to an early-branching lineage (Lineage A) previously only represented by data from two strains, both of sub-Saharan African origin (Kenya and Mozambique). A second B. abortus lineage (Lineage B), also comprised solely of strains originating from sub-Saharan Africa, was identified. The majority of strains belonged to one of two lineages of strains originating from a much broader geographical range. Further analyses based on multi-locus sequence typing (MLST) and multi-locus variable-number tandem repeat analysis (MLVA) expanded the number of B. abortus strains available for comparison with the Ethiopian isolates and were consistent with the findings from wgSNP analysis. MLST profiles of the Ethiopian isolates expanded the sequence type (ST) diversity of the early branching lineage of B. abortus, equivalent to wgSNP Lineage A. A more diverse cluster of STs, equivalent to wgSNP Lineage B, was comprised solely of strains originating from sub-Saharan Africa. Similarly, analysis of B. abortus MLVA profiles (n = 1891) confirmed that the Ethiopian isolates formed a unique cluster, similar to only two existing strains, and distinct from the majority of other strains of sub-Saharan African origin. These findings expand the known diversity of an under-represented lineage of B. abortus and suggest a potential evolutionary origin for the species in East Africa. In addition to providing information concerning Brucella species extant within Ethiopia this work serves as the basis for further studies on the global population structure and evolutionary history of a major zoonotic pathogen.

An integrated platform for Brucella with knowledge graph technology: From genomic analysis to epidemiological projection

Motivation:Brucella, the causative agent of brucellosis, is a global zoonotic pathogen that threatens both veterinary and human health. The main sources of brucellosis are farm animals. Importantly, the bacteria can be used for biological warfare purposes, requiring source tracking and routine surveillance in an integrated manner. Additionally, brucellosis is classified among group B infectious diseases in China and has been reported in 31 Chinese provinces to varying degrees in urban areas. From a national biosecurity perspective, research on brucellosis surveillance has garnered considerable attention and requires an integrated platform to provide researchers with easy access to genomic analysis and provide policymakers with an improved understanding of both reported patients and detected cases for the purpose of precision public health interventions.

Results: For the first time in China, we have developed a comprehensive information platform for Brucella based on dynamic visualization of the incidence (reported patients) and prevalence (detected cases) of brucellosis in mainland China. Especially, our study establishes a knowledge graph for the literature sources of Brucella data so that it can be expanded, queried, and analyzed. When similar “epidemiological comprehensive platforms” are established in the distant future, we can use knowledge graph to share its information. Additionally, we propose a software package for genomic sequence analysis. This platform provides a specialized, dynamic, and visual point-and-click interface for studying brucellosis in mainland China and improving the exploration of Brucella in the fields of bioinformatics and disease prevention for both human and veterinary medicine.