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Background   Acanthamoeba  spp. are the causative agents of a severe keratitis occurring mainly in contact lens wearers. The genus comprises more than 24 species that are currently divided into 20 different genotypes (T1-T20) according to sequence variations in the  18S  rRNA gene. The objective of this study was to identify the genotypes and sub-genotypes of  Acanthamoeba  isolates collected at the Parasitology Laboratory of the Public Health Institute of Chile, the only laboratory in the country where  Acanthamoeba  screening is performed. This is the first report of genotypic identification of clinical isolates of  Acanthamoeba  in Chile and one of the few in South America.    Results  In this study, 114  Acanthamoeba  isolates from 76  Acanthamoeba  keratitis patients, obtained between 2005–2016, were genotyped. T4 was the predominant genotype; T2 and T11 genotypes, which are scarcely reported worldwide, were also identified in Chilean patients (one and two patients, respectively). This is the first report of T2 and T11 genotypes isolated from  Acanthamoeba  keratitis patients in South America. It is also the first report of the T2 genotype circulating in this continent. Analysis of the diagnostic fragment 3 region of the  18S  rRNA gene showed 24 T4 variants, with a predominance of the sub-genotype T4/A, followed by T4/B, T4/G, T4/C and T4/D. Bayesian analysis revealed three groups among the T4 variants: two well supported groups that included 12 and 7 sub-genotypes, respectively, and a weakly supported group that included 5 sub-genotypes. Most of the predominant T4 sub-genotypes belonged to the same group, which included 71.3% of the patients, while some minority variants lied mainly in the other two clusters.    Conclusions  T2, T4 and T11 genotypes were predominantly isolated from the  Acanthamoeba  keratitis patients in Chile. Chilean predominant T4 sub-genotypes, which have also been reported worldwide, formed a separate cluster of the minority T4 variants. This study provides useful information about the predominant genotypes and subgenotypes that would be useful in selecting suitable strains to develop immunological and/or molecular diagnostic assays in Chile.    Electronic supplementary material  The online version of this article (10.1186/s13071-019-3302-5) contains supplementary material, which is available to authorized users.

Genotypic diversity of Acanthamoeba strains isolated from Chilean patients with Acanthamoeba keratitis