Phylogenomics of Brucella abortus isolated from African buffalo in Kruger National Park : new perspectives on wildlife-cattle disease dynamics
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Elsevier
Abstract
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.
Description
DATA AVAILABILITY : Whole genome sequences were deposited in GenBank under BioProject accession number: PRJNA1139423.
SUPPLEMENTARY MATERIAL : TABLE S1. Table of MLVA16 profiles of 2205 B. abortus strains used to produce the MST tree in Fig. 2. TABLE S2. Table of 661 B. abortus cgMLST profiles used to produce the MST tree in Fig. 3. TABLE S3. List of 490 B. abortus genomes included in the kSNP analysis. FIGURE S1. Figure depicting macro- and microscopical (Gram staining) aspect of the three confirmed Brucella abortus cultures isolated from buffaloes SAN63, SAN68 and SAN94. FIGURE S2. Minimum spanning tree representing cgMLST results between 529 reference genomes and isolates from South Africa (KNP buffalo and SA cattle). Numbers on branches length indicate allelic distance. The node radius is scaled on the count of strains sharing the sequence type. Branches having allelic distances minor than 18 were collapsed to facilitate visualization of the plot. Colour legend provides stratification per continent of isolation. Subtree on the left represents Kruger National Park (KNP) buffalo isolates (sequence types ST47, ST48 and ST49) and closest match corresponding to Argentinian (cgST318 and cgST302-303) and Portuguese (cgST365) isolates. Subtree on the right represents South African cattle isolates (ST1-10) and closest strains from Zimbabwe (cgST288), Mozambique (cgST315) and India (cgST352, cgST563-564, cgST594). FIGURE S3. Phylogeny of 328 strains assigned to Brucella abortus clade D “New World”. Maximum parsimony tree deduced from 3770 core genome SNPs called from WGS data. Nodes are colored according to geographic origin as indicated. The African strains are colored in red and shown by arrows. Isolates from UK and Republic of Ireland are colored in dark blue, and isolates from Northern Ireland or Ireland are circled. Lineages L1 to L5 defined by Kamath et al. 2016 in the description of B. abortus in Yellowstone National Park are shown together with estimated dating points (blue stars). The 95% highest probability density (HPD) for the year 1770 dating estimate is 1650-1860. The HPD estimate for year 1870 dating is 1810-1910. The green stars indicate dating points estimated by (Suarez-Esquivel et al., 2020) regarding the introduction of B. abortus in Costa Rica (Central America). The red star indicates the position of the root or most recent common ancestor (MRCA) of Clade D “New world”. The two red dots located on internal nodes show the position of the last node towards the KNP and Cattle South African isolates which was still rooted in Europe. The export occurred at some point downstream these dots. The distance between the nearest blue star dating point and the red dots is 40 SNPs and 9 SNPS along the “Cattle” and “KNP” lineages respectively. The average 1 SNP/4 years estimated by L’Hôte et al 2024 based on fossil data would suggest that the exports from Europe occurred during the nineteenth or early twentieth century.
SUPPLEMENTARY MATERIAL : TABLE S1. Table of MLVA16 profiles of 2205 B. abortus strains used to produce the MST tree in Fig. 2. TABLE S2. Table of 661 B. abortus cgMLST profiles used to produce the MST tree in Fig. 3. TABLE S3. List of 490 B. abortus genomes included in the kSNP analysis. FIGURE S1. Figure depicting macro- and microscopical (Gram staining) aspect of the three confirmed Brucella abortus cultures isolated from buffaloes SAN63, SAN68 and SAN94. FIGURE S2. Minimum spanning tree representing cgMLST results between 529 reference genomes and isolates from South Africa (KNP buffalo and SA cattle). Numbers on branches length indicate allelic distance. The node radius is scaled on the count of strains sharing the sequence type. Branches having allelic distances minor than 18 were collapsed to facilitate visualization of the plot. Colour legend provides stratification per continent of isolation. Subtree on the left represents Kruger National Park (KNP) buffalo isolates (sequence types ST47, ST48 and ST49) and closest match corresponding to Argentinian (cgST318 and cgST302-303) and Portuguese (cgST365) isolates. Subtree on the right represents South African cattle isolates (ST1-10) and closest strains from Zimbabwe (cgST288), Mozambique (cgST315) and India (cgST352, cgST563-564, cgST594). FIGURE S3. Phylogeny of 328 strains assigned to Brucella abortus clade D “New World”. Maximum parsimony tree deduced from 3770 core genome SNPs called from WGS data. Nodes are colored according to geographic origin as indicated. The African strains are colored in red and shown by arrows. Isolates from UK and Republic of Ireland are colored in dark blue, and isolates from Northern Ireland or Ireland are circled. Lineages L1 to L5 defined by Kamath et al. 2016 in the description of B. abortus in Yellowstone National Park are shown together with estimated dating points (blue stars). The 95% highest probability density (HPD) for the year 1770 dating estimate is 1650-1860. The HPD estimate for year 1870 dating is 1810-1910. The green stars indicate dating points estimated by (Suarez-Esquivel et al., 2020) regarding the introduction of B. abortus in Costa Rica (Central America). The red star indicates the position of the root or most recent common ancestor (MRCA) of Clade D “New world”. The two red dots located on internal nodes show the position of the last node towards the KNP and Cattle South African isolates which was still rooted in Europe. The export occurred at some point downstream these dots. The distance between the nearest blue star dating point and the red dots is 40 SNPs and 9 SNPS along the “Cattle” and “KNP” lineages respectively. The average 1 SNP/4 years estimated by L’Hôte et al 2024 based on fossil data would suggest that the exports from Europe occurred during the nineteenth or early twentieth century.
Keywords
Brucellosis, Wildlife disease, Genomics, African buffalo (Syncerus caffer), Zoonosis, Kruger National Park (KNP), Kruger National Park (South Africa)
Sustainable Development Goals
SDG-03: Good health and well-being
SDG-15: Life on land
SDG-15: Life on land
Citation
Cossu, C.A., Garofolo, G., Janowicz, A. et al. 2025, 'Phylogenomics of Brucella abortus isolated from African buffalo in Kruger National Park : new perspectives on wildlife-cattle disease dynamics', Veterinary Microbiology, vol. 304, art. 110493, pp. 1-8, doi : 10.1016/j.vetmic.2025.110493.