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Sequence-based Polymerase Chain Reaction (PCR) has been introduced as an effective and reliable method for bacterial strain typing, which could provide a reliable typing approach for clinical laboratories. This study aimed to describe the reproducibility and performance of the Outer Membrane Protein 31 (Omp31)-based PCR, as a molecular genotyping tool for Brucella melitensis (B. melitensis) typing. The 31 KD outer-membrane protein of Brucella, which encodes the Omp31 gene, can be applied as an antigen to diagnose brucellosis. For this purpose, 146 samples were taken from human blood samples, bovine and camel lymph nodes, as well as sheep and goat aborted fetuses, including fetal kidney, abomasum, liver, lung, spleen, and heart for bacteriological investigation. The molecular detection of the Omp31 and IS711 genes was performed using the isolated B. melitensis (n=14). The sequencing of the Omp31 gene of B. melitensis in the Iranian field isolates was also performed for the whole gene sequencing. The homology of all sequences was then checked with the reported National Center for Biotechnology Information sequences using a basic local alignment search tool for the nucleotide diversity evaluation. The findings revealed that B. melitensis isolates were recovered from 14 examined cases and confirmed by the IS711-based PCR with a PCR product of 731 bp. Moreover, 14 Iranian B. melitensis sequences clustered together as a monophyletic grouping with bootstrap support of 63, and they were closely related to the B. melitensis reference isolates. This Omp31-based phylogenetic placement strongly indicates the monophyletic origin of the Iranian B. melitensis in different animals and human hosts. [ABSTRACT FROM AUTHOR]