Table_4_Whole genome sequencing of Ethiopian Brucella abortus isolates expands the known diversity of an early branching sub-Saharan African lineage.xlsx

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.

布鲁氏菌病（Brucellosis）仍是全球范围内最具危害的人畜共患病之一，其不仅会造成大量人类发病病例，还会通过影响畜禽生产力引发重大经济损失。尽管如此，包括撒哈拉以南非洲地区在内的众多中低收入国家，在该领域仍存在显著的研究证据空白。本研究首次报道了来自埃塞俄比亚的布鲁氏菌属（Brucella sp.）菌株的分子特征分析结果：研究人员通过细菌培养与分子生物学方法，从埃塞俄比亚中部某牛群的暴发疫情中分离得到15株布鲁氏菌属菌株，并将其鉴定为牛布鲁氏菌（Brucella abortus）。对埃塞俄比亚牛布鲁氏菌分离株进行测序后，研究团队利用全基因组单核苷酸多态性（whole genome single nucleotide polymorphisms, wgSNP）技术，将其与411株不同地理来源的牛布鲁氏菌菌株开展系统发育比较。结果显示，埃塞俄比亚分离株隶属于一个此前仅由两株菌株数据代表的早期分支谱系（谱系A），这两株菌株均来自撒哈拉以南非洲地区（分别为肯尼亚与莫桑比克来源）。本研究同时鉴定出第二个牛布鲁氏菌谱系（谱系B），该谱系同样仅包含撒哈拉以南非洲来源的菌株。绝大多数菌株则隶属于另外两个地理分布范围更广的谱系。基于多位点序列分型（multi-locus sequence typing, MLST）与多位点可变数目串联重复序列分析（multi-locus variable-number tandem repeat analysis, MLVA）的进一步分析，扩充了可与埃塞俄比亚分离株进行比对的牛布鲁氏菌菌株数量，其结果与全基因组单核苷酸多态性分析的结论一致。埃塞俄比亚分离株的多位点序列分型图谱，拓展了牛布鲁氏菌早期分支谱系（即全基因组单核苷酸多态性谱系A）的序列型（sequence type, ST）多样性。另一组序列型更为多样的簇（对应全基因组单核苷酸多态性谱系B）则仅由撒哈拉以南非洲来源的菌株构成。对牛布鲁氏菌多位点可变数目串联重复序列分型图谱（n=1891）的分析同样证实，埃塞俄比亚分离株形成了一个独特的簇，仅与两株现有菌株亲缘关系相近，且与绝大多数其他撒哈拉以南非洲来源菌株存在显著差异。本研究结果拓展了我们对牛布鲁氏菌代表性不足谱系的已知多样性，并提示该病原体可能起源于东非。除了阐明埃塞俄比亚境内现存布鲁氏菌属物种的相关信息外，本研究还为进一步探究这一重要人畜共患病病原体的全球种群结构与进化历史奠定了基础。