Genomic characterization of clinical Brucella melitensis isolates from southern Tunisia reveals their clonal relatedness within the national and global population
© The Author(s), 2026. Licensed under CC BY-NC 4.0.
Abstract
Brucellosis remains a significant public health concern in Tunisia, particularly due to the consumption of unpasteurized dairy products. The diagnosis of human brucellosis mainly relies on serology and culture, often without identifying the Brucella (B.) species or biovar. Limited biosafety infrastructure and scarce genomic data hinder understanding of the genetic diversity of Tunisian strains and their regional and global relationships. This study reports the genomic characteristics of three B. melitensis strains isolated from blood samples of human brucellosis cases associated with the consumption of dairy products in Gabès, southern Tunisia. Hybrid short- and long-read sequencing was performed to investigate the relatedness to national and international isolates, their antimicrobial resistance determinants, and virulence factors. All isolates were identified as B. melitensis biovar 3 and were assigned to ST89 according to the MLST-21 scheme. Using the MLST-9 scheme, two strains sharing 8 of 9 loci were assigned to 3 closely related STs (ST11, ST12, and ST91). Core-genome SNP (cgSNP) analysis showed that the three studied strains were closely related (0–37 SNPs) and clustered with all available Tunisian B. melitensis genomes, with pairwise core-genome SNP distances ranging from 0 to 141 SNPs. In a broader geographical context, the isolates clustered within Lineage I, the West Mediterranean clade, and were highly related to strains from Algeria, Austria, and Italy. In silico antimicrobial resistance analysis revealed no classical resistance determinants. However, mprF, bepCDEFG genes, and mutations in parC genes were identified in all isolates. In silico virulence-associated gene analysis identified 74 genes, predominantly involved in lipopolysaccharide biosynthesis and the type IV secretion system. Our findings provide valuable genomic insights into three human B. melitensis isolates and highlight the value of genomic surveillance for characterizing Brucella species in Tunisia.