COCCIMORPH is a computational approach for parasite identification in case of Eimeria EGFR inhibitor spp. from the chicken. Digital images of 50 individual unidentified sporulated oocysts of Eimeria spp. were uploaded on to the software. The software then analysed the oocyst on the basis of different features namely, curvature characterisation, size, symmetry and internal structure characterisation for the identification of eimerian species. Identification of Eimeria spp. using COCCIMORPH software revealed the presence of E. acervulina, E. maxima, E. mitis, E. praecox, E. necatrix and E. tenella, in 96.7%, 36.7%, 90.0%, 3.3%, 23.3% and 16.7% of

farms, respectively ( Fig. 1, Supplementary Table 2). E. brunetti was not recorded in any of the farms screened using COCCIMORPH. Nested PCR using ITS-1 primer was standardised with pure DNA of all seven species of Eimeria. Specific PCR amplicons of E. acervulina (321 bp), E. brunetti (311 bp), E. maxima US strain

(145 bp), E. maxima Australian strain (145 bp), E. mitis1 (328 bp), E. mitis5 (193 bp), E. necatrix (383 bp), E. praecox (116 bp) and E. tenella (278 bp) were visualised (data not shown). In field samples, ITS-1 based nested PCR identified E. acervulina, E. brunetti, E. maxima, E. mitis, E. praecox, E. necatrix and E. tenella in 93.3%, 10.0%, 86.7%, 96.7%, 66.7%, 80.0% and 100% farms, respectively ( Fig. 1, Supplementary Table 2). In 16 farms, both the Australian- and US-type strains of E. maxima were identified, while in ten farms only selleck compound the US-type strain of E. maxima was present. Similarly, E. mitis was identified by primers specific for both E. mitis1 and E. mitis5 in all the farms that were positive for E. mitis. Mixed infections of Eimeria spp. were recorded in all farms with a minimum of at least three species (in four broiler farms). All seven Eimeria spp. were identified in three farms. Multiplex PCR using SCAR primers was standardised with pure DNA of all seven species of Eimeria. Amplicons of E. acervulina

(811 bp), E. brunetti (626 bp), E. maxima (272 bp), E. mitis (460 bp), E. necatrix (200 bp), E. praecox (354 bp) and E. tenella (539 bp) were visualised with individual primer pairs as well as in multiplex PCR (data not shown). In field samples, the one-tube multiplex PCR could identify E. maxima, E. mitis, E. necatrix, E. praecox Cell press and E. tenella, in 16.7%, 3.3%, 43.3%, 3.3% and 13.3% farms, respectively. E. acervulina and E. brunetti were not identified in any of the farms screened by one-tube multiplex PCR. A maximum of two Eimeria spp. were identified in six farms, while for 11 farms no Eimeria spp. were recorded by one-tube multiplex PCR. However, two-tube multiplex PCR identified E. acervulina, E. maxima, E. mitis, E. praecox, E. necatrix and E. tenella, in 36.7%, 43.3%, 53.3%, 56.7%, 6.7% and 46.7% farms, respectively ( Fig. 1, Supplementary Table 2). A maximum of five Eimeria species were identified in five farms, while in two farms no Eimeria spp.