NGS‑based characterization of Eimeria spp. prevalence and diversity in broiler farms in northwestern São Paulo State, Brazil.

The aim of this study was to determine the prevalence and diversity of Eimeria spp. in commercial broiler chicken farms (CBCFs) across 20 municipalities in northwestern São Paulo State, Brazil. Eighty-eight fecal samples corresponding to 88 commercial broiler farms were examined by microscopic screening for Eimeria spp. oocysts. All positive samples were subjected to genus-specific nested PCR (18S rRNA gene) followed by next-generation sequencing to identify the Eimeria spp. Microscopy detected Eimeria spp. oocysts in 100% (88/88) of the samples. Next-generation sequencing revealed the following order of prevalence of Eimeria spp. sequences: Eimeria maxima: 83/88 (94.3%; CI: (87.4-97.6); Eimeria acervulina: 75/88 (85.2%; CI: 76.4-91.2); Eimeria necatrix/tenella: 19/88 (21.6%; CI: 14.3-31.3); Eimeria praecox: 19/88 (21.6%; CI: 14.3-31.3); and Eimeria mitis/mivati: 10/88 (11.4%; CI: 6.3-19.7). No sequences corresponding to Eimeria brunetti, Eimeria lata, Eimeria nagambie, and Eimeria zaria were detected. In conclusion, the highest prevalences were observed for E. maxima and E. acervulina, whereas E. tenella/necatrix, E. mitis/mivati, and E. praecox showed lower prevalences. Eimeria brunetti, E. lata, E. nagambie, and E. zaria were not detected in CBCFs from northwestern São Paulo State.