Genome Sequencing and Comparative Genomics of Indian Isolates of Brucella melitensis

Abstract

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.

Phylogenetic Analysis and Comparative Genomics of Brucella abortus and Brucella melitensis Strains in Egypt

“…In this study, B. abortus strains annotation displayed striking similarities in a variety of features to those previously reported in studies (Wang et al 2020 ; Yu et al 2015 ). On the other hand, annotation of B. melitensis strains was agreed upon in a study performed by (Karthik et al 2021 ) and this may be due to the genome stability of Brucella this study’s findings confirm that there are significant resemblances between the two Brucella species according to the homology degree.…”

Whole-genome sequencing for genetic diversity analysis of Iranian Brucella spp. isolated from humans and livestock

“…B. abortus 67/93 was used for rooting the tree. Designation of lineages and genotypes are according to [ 39 , 40 ], respectively. The scale bar indicates the number of nucleotide changes per site.…”

Applications of Bioinformatics on Genomics and Proteomics Levels Highlighted in Brucella Pathogen

“…Comparing to conventional genomics research that emphasis on one genome in study, the comparative genomics gives much supplementary detailed information than that from one analyzed genome (Edwards and Holt, 2013). Additionally, it allows a good interpretation of how species have evolved (Karthik et al, 2021). In this context, pangenome refers to all genes that are found in the analyzed dataset in contrast to core genome is the genes conserved by all analyzed organisms as well as accessory genome is the collection of genes that are exist in 2 or more genomes but not all (Tettelin et al, 2008).…”