Acanthamoeba is a free-living opportunistic protozoan Amoeba which widely distributed in soil, water sources, dust and contact lens solutions. Acanthamoeba keratitis (AK) which causes a sight-threating infection of the cornea is going to rise in Iran and worldwide. The aim of this study was: to compare three different methods; PCR, microscopic examination and culture for detection of Acanthamoeba in clinical samples, and genotyping of Acanthamoeba by sequencing of 18SrRNA gene.

18 specimens of corneal scrapes were obtained from suspected AK patients that referred to the Ophthalmology Hospital of Khatam-al-Anbia of Mashhad, Iran, between August 2017 and November 2018.The samples were divided in three parts and subjected to direct microscopic examination, cultivation onto the non-nutrient agar plate and PCR Technique

The results showed that 13(72%) of these patients infected with AK. Majority of patients were female (61%). Appearance of a stromal ring shaped infiltrate was the most common sign. On using culture as the gold standard, sensitivity and specificity of PCR and direct microscopic examination were 100 % (95% CI, 59.0 - 100.0%), 45.45% (95% CI, 16.7 -76.6%), 57.14% (95% CI, 18.4 - 90.1%) and 90.9% (95% CI, 58.7 - 99.8%), respectively. Also positive predictive value, negative predictive value of PCR and direct microscopic examination were calculated 53.8%, 80%, 100% and 76.9%. Sequencing analysis demonstrated that all strains belonged to T4 genotype.

PCR based on 18S ribosomal DNA (rDNA) is a reliable and sensitive method in the diagnosis of AK in clinically suspected cases. It can set up in diagnostic laboratories as an easy diagnostic tool.