Cystic Echinococcosis (CE) is one of the important zoonotic diseases in humans and animals caused by Echinococcus granulosus sensu lato. It is frequently seen in people and animals in underdeveloped countries, especially in rural areas, and causes serious health problems in humans and significant economic losses in livestock (Richard, 1986). Adult forms of the parasite live in the small intestines of dogs, wolves, jackals and other canids. The hydatid cyst, which is the larval form, resides in various organs of humans and animals, especially the liver and lungs of many domestic and wild animals such as cattle, sheep, goats and pigs (Şimşek et al., 2006). After 20 years of collecting epidemiological, biochemical, and geographic reports on E. granulosus s.l. isolates, as well as comprehensive phylogenetic analysis of nuclear and mitochondrial genes, restriction and conflicts of classification system within E. granulosus s.l. became obvious, as a necessity of a genomic revision. Thus, E. granulosus s.l. is currently classified into E. granulosus sensu stricto (s.s.) (G1 and G3), Echinococcus felidis, Echinococcus equinus, Echinococcus ortleppi and Echinococcus canadensis (G6/G7, G8 and G10) (Vuitton et al., 2020).

A Substantial number of molecular studies in livestock have revealed that E. granulosus s.s (G1 and G3 genotypes) is the prevailing species responsible for sheep, cattle, goat, and camel CE infection in Turkey (Utuk et al., 2008; Simsek et., 2010; Cengiz and Gonenc, 2020; Borhani et al., 2021; Kesik et al., 2022). Echinococcus canadensis (G6/G7) was proportionally detected less in sheep and cattle (Mehmood et al., 2020; Kesik et al., 2021). Additionally, E. granulosus s.s. (G1 and G3) and E. equinus (G4) have been reported in horses, donkeys and mules (Simsek and Cevik, 2014; Simsek et al., 2010; Kesik et al., 2019). Looking at Turkey's neighbours, the dominant species in Iran, Iraq and Greece are E. granulosus s.s. (Roinioti et al., 2016; Hammad et al., 2018; Borhani et al., 2021). E. canadensis (G6/7), E. equinus and E. ortleppi (G5), which was recently reported in camels from Iran (Ebrahimipour et al., 2017; Borhani et al., 2021).

The mechanisms underlying the coexistence of host and parasite in E. granulosus s.l. still remain unclear. The majority of experimental studies over the past 30 years have focused on determining the survival strategies of parasites in their hosts (Mariconti et al., 2019).

Protein-coding genes (exons) constitute approximately 10–14% of the Echinococcus spp genome, while other genes are transcribed as non-coding RNAs (Tsai et al., 2013; Zheng et al., 2013). Non-coding RNAs are classified into two groups according to their molecular weight. First, miRNAs are 18–24 nucleotides in length on average and, second Long non-coding RNAs (LncRNA) are longer than 200 nt (Bartel, 2018; Lekka and Hall, 2018). Previous studies have shown that non-coding RNAs play important roles in physiological and pathological processes in eukaryotes (Barbagallo et al., 2018). It has been reported that miRNAs and LncRNAs are also found in species such as E. granulosus, E. multilocularis and E. canadensis (He et al., 2020). Recent studies have shown that circulating miRNAs of both parasite and host origin are detected in the blood or body fluids of humans and animals with helminth infections (Cai et al., 2016). Therefore, they are seen as potential biomarkers for the early diagnosis of parasitic infection or related diseases (Silakit et al., 2014). It has also been reported that miRNAs identified in Echinococcus species can be important in the host-parasite interaction (Cucher et al., 2015; Macchiaroli et al., 2015). Eighty seven highly conserved miRNAs are thought to have important roles in the development and parasitism of Echinococcus spp (Bai et al., 2014; Cucher et al., 2011). Of the 76 known conserved miRNAs of E. granulosus s.s. miR-2, miR-71, and miR-125 have the highest expression levels (Bai et al., 2014; Cucher et al., 2011).

miR-277, let-7, miR-71, miR-10, miR-2, and miR-9 were specifically expressed in secondary cyst walls and protoscoleces (PSCs) of G1 and G7 genotypes, while miR-125 was detected only in PSCs and pre-microcysts. In addition, three miRNAs (let-7, miR-71, and miR-2) have been reported to be expressed at high levels in PSCs (Cucher et al., 2011). It has been noted that let-7 exhibits significantly increased expression in the PSC and cyst wall, which may be related to the bidirectional growth abilities of E. granulosus (Bai et al., 2014). Also, let-7 and miR-61 expression levels of E. granulosus miRNAs were significantly affected at the microcyst stage after in vitro exposure of benzimidazole. At the same time, it has been reported that the expression of these miRNAs exhibits differential changes in response to albendazole sulfoxide at other developmental stages (Mortezaei et al., 2019).

The observations suggest that miRNAs are important in CE, and can therefore be used as diagnostic or therapeutic targets (He et al., 2020). Studies on the determination of miRNA expression levels in different cyst structures (germinal membrane and/or PSC) by determining haplotype differences in various intermediate hosts (cattle and sheep) are very limited. Mir-71, targeting the Nemo-like kinase gene region, is involved in PSC development and regulates host macrophage functions in CE (Guo et al., 2017; Juvvuna et al., 2012). Therefore, it is important to determine the expression level of mir-71 in PSCs. Mir-7 targets the ECANG7_04919, ECANG7_00818, and ECANG7_03238 gene regions and is known to have a potential role in the developmental morphogenesis of Echinococcus spp (Macchiaroli et al., 2017). On the other hand, mir-96 targets the ECANG7_06901 gene region and its function is not known exactly. It is stated that it has a high expression level especially in the PSC stage (Macchiaroli et al., 2017).

The primary aim of this study was to molecularly characterize and determine the haplotypes of sheep and cattle isolates of E. granulosus. The other aim was to calculate egr-mir-7, egr-mir-71 and egr-mir-96 expression levels in the germinal membrane and PSC's of these isolates and to investigate their relationship with haplotypes.