AimsThis study investigated the possible role of Fayoumi chickens and pigeons in the transmission of multidrug resistant (MDR) Salmonella with zoonotic potential. Methods and ResultsMorbid Fayoumi chickens (70) and pigeons (30) were examined to detect the prevalence and antibiotic resistance of Salmonella and to detect and sequence sodC-1 gene as a zoonotic and phylogenetic marker. Salmonella isolates were detected in 143 and 20% of the examined Fayoumi chickens and pigeons, respectively. Salomonella subspecies salamae (438%) and S. subspecies enterica serovar Bukuru (313%) were the most prevalent isolates. All tested Salmonella isolates were MDR to at least five classes of antibiotics. S. salamae and S. Bukuru isolates that carried bla(TEM), qnrS, aadA2 and floR genes expressed phenotypic resistance to cefotaxime, ciprofloxacin, streptomycin and chloramphenicol, respectively. The aacC gene was detected in one of each S. salamae and S. Bukuru isolate, although only the S. Bukuru isolate showed phenotypic resistance to gentamicin. The sequence analysis of the sodC-1 gene from Salmonella isolates showed clear inter- and intra-subspecies phylogenetic segregation. ConclusionsFayoumi chickens and pigeons could act as reservoirs of MDR Salmonella. Significance and Impact of the StudyThis study highlights the possible emergence of Salmonella subspecies salamae with zoonotic potential.