Table_2_Genome Sequencing and Comparative Genomics of Indian Isolates of Brucella melitensis.XLSX

Brucella melitensis causes small ruminant brucellosis and a zoonotic pathogen prevalent worldwide. Whole genome phylogeny of all available B. melitensis genomes (n = 355) revealed that all Indian isolates (n = 16) clustered in the East Mediterranean lineage except the ADMAS-GI strain. Pangenome analysis indicated the presence of limited accessory genomes with few clades showing specific gene presence/absence pattern. A total of 43 virulence genes were predicted in all the Indian strains of B. melitensis except 2007BM-1 (ricA and wbkA are absent). Multilocus sequence typing (MLST) analysis indicated all except one Indian strain (ADMAS-GI) falling into sequence type (ST 8). In comparison with MLST, core genome phylogeny indicated two major clusters (>70% bootstrap support values) among Indian strains. Clusters with <70% bootstrap support values represent strains with diverse evolutionary origins present among animal and human hosts. Genetic relatedness among animal (sheep and goats) and human strains with 100% bootstrap values shows its zoonotic transfer potentiality. SNP-based analysis indicated similar clustering to that of core genome phylogeny. Among the Indian strains, the highest number of unique SNPs (112 SNPs) were shared by a node that involved three strains from Tamil Nadu. The node SNPs involved several peptidase genes like U32, M16 inactive domain protein, clp protease family protein, and M23 family protein and mostly represented non-synonymous (NS) substitutions. Vaccination has been followed in several parts of the world to prevent small ruminant brucellosis but not in India. Comparison of Indian strains with vaccine strains showed that M5 is genetically closer to most of the Indian strains than Rev.1 strain. The presence of most of the virulence genes among all Indian strains and conserved core genome compositions suggest the use of any circulating strain/genotypes for the development of a vaccine candidate for small ruminant brucellosis in India.

羊布鲁氏菌（Brucella melitensis）可引发小型反刍动物布鲁氏菌病，是一种在全球范围内流行的人畜共患病原菌。本研究对所有已公开的羊布鲁氏菌基因组（n=355）开展全基因组系统发育分析（whole genome phylogeny），结果显示除ADMAS-GI菌株外，全部16株印度分离株均聚类于东地中海谱系中。泛基因组（pangenome）分析表明，该菌的附属基因组（accessory genome）规模有限，仅少数进化枝呈现特异性的基因存在/缺失模式。除2007BM-1菌株（缺失ricA与wbkA基因）外，所有印度羊布鲁氏菌菌株均预测携带43个毒力基因。多位点序列分型（Multilocus Sequence Typing, MLST）分析显示，除ADMAS-GI菌株外，其余印度分离株均归于序列型ST8。与MLST分析结果相比，核心基因组系统发育分析（core genome phylogeny）在印度分离株中鉴定出两个主要聚类（自展支持率（bootstrap support values）>70%）；自展支持率<70%的聚类则代表进化起源各异、分别寄居于动物与人体的菌株。动物（绵羊与山羊）分离株与人体分离株之间呈现100%自展支持率的遗传相关性，证实了其跨物种人畜共患传播的潜力。基于单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的分析结果与核心基因组系统发育分析的聚类模式一致。在印度分离株中，来自泰米尔纳德邦的3株菌株构成的进化分支携带数量最多的独特SNP位点（共112个）。该分支的SNP位点涉及U32、M16失活结构域蛋白、Clp蛋白酶家族蛋白及M23家族蛋白等多个肽酶基因，且多数为非同义替换（non-synonymous, NS）。全球多个地区已通过疫苗接种防控小型反刍动物布鲁氏菌病，但印度尚未推行此类措施。将印度分离株与疫苗株比对后发现，相较于Rev.1疫苗株，M5疫苗株与多数印度分离株的遗传亲缘关系更为接近。所有印度分离株均携带多数毒力基因，且核心基因组组成保守，这提示可选取印度国内流行的任意菌株/基因型，用于开发适配本国的小型反刍动物布鲁氏菌病候选疫苗。