Slaughtering should only take place in slaughterhouses supervised by veterinarians and with strict
adherence to hygiene protocols to guarantee the production of high-quality meat. This study
aimed to compare the hygiene of several slaughterhouses using total aerobic plate count (TAPC)
and isolation of specific hygiene-indicating bacteria, such as Staphylococcus spp., Escherichia
coli (E. coli), and Salmonella spp. 480 samples comprise swabs collected from various sources,
such as knives (slaughter and skinning knifes), slaughterhouse buildings (wall, floor, and tap
water samples), swabs from carcasses, and workers’ shoes and hands. Based on our findings, the
hygiene indicator microorganisms are negatively correlated with the biosecurity level. The TAPC
was predominantly high in samples collected from slaughterhouse B, which had the lowest
biosecurity score. The highest frequency of Staphylococcus spp., E. coli, and Salmonella spp.
was (94.17%), (54.17%), and (5%), in slaughterhouses B, A, and C, respectively. PCR targeting
the NUC gene was used for molecular confirmation of randomly selected Staphylococcus spp. as
S. aureus. Only 60% of S. aureus isolates were positive for the biofilm-forming gene (BAP gene)
in PCR. According to serological identification of E. coli isolates, the most popular E. coli
serotypes in the cattle slaughterhouses were O44: K74, O142: K86, O119: K69, O164: K-, and
O26: K60, while S. enterica sub-SP Salamae was the most frequent salmonella serotype. In
conclusion, good personal hygiene and biosecurity measures serve as the primary safeguard
against zoonotic infections in employees and bacterial colonization of livestock.