Bovine tuberculosis (bTB) has yet to be eradicated in Brazil. Herds of cattle and buffalo are important sources of revenue to people living in the banks of the Amazon River basin. A better understanding of Mycobacterium bovis (M. bovis) populational structure and transmission dynamics affecting these animals can significantly contribute in efforts to improve their sanitary status. Herein, we sequenced the whole genome of 22 M. bovis isolates (15 from buffalo and 7 from cattle) from 10 municipalities in the region of the Lower Amazon River Basin in Brazil and performed phylogenomic analysis and Single Nucleotide Polymorphism (SNP)-based transmission inference to evaluate population structure and transmission networks. Additionally, we compared these genomes to others obtained in unrelated studies in the Marajó Island (n = 15) and worldwide (n = 128) to understand strain diversity in the Amazon and to infer M. bovis lineages. Our results show a higher genomic diversity of M. bovis genomes obtained in the Lower Amazon River region when compared to the Marajó Island, while no significant difference was observed between M. bovis genomes obtained from cattle and buffalo (p ≥ 0.05). This high genetic diversity is reflected by the weak phylogenetic clustering of M. bovis from the Lower Amazon River region based on geographic proximity and in the detection of only two putative transmission clusters in the region. One of these clusters is the first description of inter-species transmission between cattle and buffalo in the Amazon, bringing implications to the bTB control program. Surprisingly, two M. bovis lineages were detected in our dataset, namely Lb1 and Lb3, constituting the first description of Lb1 in South America. Most of the strains of this study (13/22) and all 15 strains of the Marajó Island carried no clonal complex marker, suggesting that the recent lineage classification better describe the diversity of M. bovis in the Amazon.

巴西的牛结核病（bTB）尚未根除。牛群和水牛群是生活在亚马逊河流域两岸的人们的重要收入来源。更好地了解牛分枝杆菌（牛分枝杆菌）影响这些动物的种群结构和传播动力学可以大大有助于改善其卫生状况。在这里，我们对22个全基因组进行了测序牛分枝杆菌从巴西下亚马逊河盆地地区的10个城市中分离出15株水牛，从牛​​中分离出7株，并进行了系统生物学分析和基于单核苷酸多态性（SNP）的传播推断，以评估种群结构和传播网络。此外，我们将这些基因组与在MarajóIsland（ñ = 15）和全球范围（ñ = 128）以了解亚马逊地区的菌株多样性并进行推断 牛分枝杆菌血统。我们的结果表明，较高的基因组多样性牛肝菌与马拉若岛相比，在下亚马逊河地区获得的两个基因组，而 牛分枝杆菌 从牛和水牛获得的基因组（p≥0.05）。这种高度的遗传多样性反映了该物种的弱系统发育聚类。牛分枝杆菌来自下亚马逊河地区，基于地理邻近性，并且仅检测到该地区中两个假定的传输集群。其中一个集群是亚马逊地区牛与水牛之间种间传播的首次描述，这对bTB控制计划产生了影响。令人惊讶的是，两个牛分枝杆菌在我们的数据集中检测到血统，即Lb1和Lb3，构成了南美对Lb1的第一个描述。这项研究的大多数菌株（13/22）和Marajó岛的所有15株菌株均未带有克隆复杂标记，这表明最近的谱系分类更好地描述了其多样性。牛分枝杆菌 在亚马逊。