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In the present study, out of 1156 neonatal goat kids, 238 showing clinical diarrhea were used for detection of toxinotypes of Clostridium perfringens, Enteropathogenic E. coli (EPEC), Group A rotavirus (GARV) and Bovine coronavirus (BCV). Isolation and toxinotyping of isolates were done by multiplex Polymerase chain reaction (PCR) using primers for cpa, cpb, cpb2, etx and iap genes. For EPEC, isolation and identification were done using bfpA gene and SYBR green based real time PCR (qPCR). GARV and BCV were detected, by one-step RT-PCR (osRT-PCR). The incidence of C. perfringens was 15.13% with 75% isolates toxinotype A, 25% type D and 61.11% of isolates carrying the β2-toxin gene. The incidence of EPEC was 68.07% based on qPCR, whereas 21.85% were positive for GARV and 15.97% for BCV by osRT-PCR. There was mixed infection of C. perfringens and EPEC in 11.76% and 3.78% for C. perfringens and GARV and 2.1% of C. perfringens and BCV. EPEC and GARV was 19.74% and EPEC plus BCV positivity was 11.34%. GARV and BCV was 5.88%, and 4.20% had mixed infection of EPEC, GARV and BCV. Of the total diarrheic kids sampled, 0.84% had mixed infection of C. perfringens, GARV, BCV and EPEC. On the basis of the above findings, it may be concluded that isolation, multiplex PCR and real time PCR facilitated the characterization of circulating C. perfringens toxinotypes and EPEC in goats reared under semi-arid conditions. The importance of enteritis caused by GARV and BCV and their role in mixed infection in goats requires extensive screening and pathogenicity studies to associate the symptoms with disease., U populaciji od 1156 neonatalnih jarića 238 je pokazivalo kliničke znakove proljeva. Od njih su uzeti uzorci izmeta za dokazivanje toksinskih tipova bakterije Clostridium perfringens, enteropatogenih sojeva bakterije E. coli (engl. enteropathogenic E. coli, EPEC), rotavirusa skupine A (engl. group A rotavirus, GARV) i goveđeg koronavirusa (engl. bovine coronavirus, BCV). Izdvajanje i toksinska tipizacija izolata provedeni su višestrukom lančanom reakcijom polimerazom (PCR) upotrebom početnica za gene cpa, cpb, cpb2, etx i iap. Izdvajanje i identifikacija EPEC-a provedeni su pretragom na gen bfpA i PCR-om u stvarnom vremenu, uz upotrebu SYBR zelenila (qPCR). Za dokaz rotavirusa skupine A i goveđeg koronavirusa upotrijebljena je RT-PCR (osRT-PCR). Incidencija bakterije C. perfringens iznosila je 15,13 %. Od toga je 75 % izolata pripadalo toksinskom tipu A, 25 % tipu D, dok je 61,11 % izolata imalo gen za toksin β2. Incidencija EPEC-a iznosila je 68,07 %, a 21,85 % pretraženih uzoraka bilo je pozitivno na GARV te 15,97 % na BCV. Mješovita infekcija bakterijom C. perfringens i EPEC-om utvrđena je u 11,76 % uzoraka, C. perfringens i GARV u 3,78 % te C. perfringens i BCV u 2,1 % pretraženih uzoraka. Mješovita infekcija EPEC-om i GARV-om utvrđena je u 19,74 %, a EPEC-om i BCV-om u 11,34 %. Mješovita infekcija rotavirusom i koronavirusom bila je ustanovljena u 5,88 %, a mješovita infekcija EPEC-om, GARV-om i BCV-om u 4,20 % uzoraka. Od ukupnog broja pretražene jaradi s proljevom u njih 0,84 % dokazana je mješovita infekcija bakterijom C. perfringens, rotavirusom skupine A, goveđim koronavirusom i EPEC-om. Na osnovi prikazanih rezultata može se zaključiti da izdvajanje, višestruki PCR te PCR u stvarnom vremenu omogućuju karakterizaciju i praćenje kolanja toksinskih tipova bakterija C. perfringens i EPEC-a u koza uzgajanih u sušnim uvjetima. Važnost enteritisa uzrokovanog rotavirusom skupine A i goveđim koronavirusom te njihova uloga kod mješovitih infekcija u koza zahtijevaj