Molecular detection of Eimeria species in backyard chickens in the Nakhchivan Autonomous Republic

Sekine Bakhshaliyeva; Rıdvan Kirman; Esin Güven; Turkan Gurbanova; İsmayıl Mammadov

doi:10.33988/auvfd.1833836

Molecular detection of Eimeria species in backyard chickens in the Nakhchivan Autonomous Republic

Abstract

Coccidiosis poses a significant threat to the health and productivity of poultry worldwide. However, there is currently a lack of comprehensive scientific data on the prevalence and species diversity of Eimeria in the Nakhchivan Autonomous Republic. Despite the widespread rearing of backyard chickens in the region, no molecular-level research has yet been conducted to identify the circulating Eimeria species, leaving a critical gap in regional epidemiological knowledge. The aim of this study was to determine the prevalence of Eimeria species in backyard chickens in the Nakhchivan Autonomous Republic and to conduct a molecular analysis for the first time to investigate the presence of seven recognized Eimeria species in the study area. A total of 186 chicken faecal samples were collected from 65 backyard poultry farms in 58 locations from April to September of 2024. The study revealed that 48.9% (91/186) of the faecal samples were positive for Eimeria spp., and the mean OPG value was 1790.1. Eimeria positivity was 60% (63/105) in the group older than six months and 34.6% (28/81) the group younger than six months. The highest prevalence was recorded in the autumn (September) at 64.9%, followed by spring (46.4%) and summer (36.7%) months. The following species were detected in the molecular analysis: E. acervulina (83.5%, 76/91), E. maxima (71.4%, 65/91), E. tenella (61.5%, 56/91), E. necatrix (46.1%, 42/91), E. mitis (46.1%, 42/91), E. praecox (41.8%, 38/91), and E. brunetti (16.5%, 15/91). All positive samples exhibited multiple infections involving three to five Eimeria species. The study results revealed that Eimeria species were widespread in the region, suggesting the possibility of subclinical coccidiosis, which is characterized by low to moderate levels of oocyst shedding, despite the absence of acute infections. Since the disease leads to economic losses, further research is needed to develop sustainable prevention and control methods.

Keywords

References

Amina K, Bachene MS, Mustapha O, et al (2025): Prevalence of coccidiosis in broiler chickens in Medea, Algeria. Comp Immunol Microbiol Infect Dis, 118,102323. DOI: 10.1016/j.cimid.2025.102323.
Andreopoulou M, Chaligiannis I, Sotiraki S, et al (2022): Prevalence and molecular detection of Eimeria species in different types of poultry in Greece and associated risk factors. Parasitol Res, 121, 2051-2063. DOI:10.1007/ s00436-022-07525-4.
Ashenafi H, Tadesse S, Medhin G, et al (2004): Study on coccidiosis of scavenging indigenous chickens in Central Ethiopia. Trop Anim Health Prod, 36, 693-701. DOI:10.1023/b:trop.0000042852.82477.af.
Attree E, Sanchez-Arsuaga G, Jones M, et al (2021): Controlling the causative agents of coccidiosis in domestic chickens; an eye on the past and considerations for the future. CABI Agric Biosci 2, 37. DOI:10.1186/s43170-021-00056-5.
Awais MM, Akhtar M, Iqbal Z, et al (2012): Seasonal prevalence of coccidiosis in industrial broiler chickens in Faisalabad, Punjab, Pakistan. Trop Anim Health Prod 44, 323-328. DOI:10.1007/s11250-011-0024-x.
Bawm S, Win SY, Soe NC, et al (2021): Microscopic and molecular detection of Eimeria maxima and Eimeria praecox naturally infected in free-range village chickens of Myanmar. Acta Parasitol 66, 1074-1078. DOI:10.1007/ s11686-021-00353-z.
Bharti P, Bhat AH, Mir FH, et al (2024): Molecular phylogenetic analysis and seasonal dynamics of Eimeria species infecting broilers of Kashmir, India. Parasitol Res, 123, 322. DOI:10.1007/s00436-024-08343-6.
Blake DP, Knox J, Dehaeck B, et al (2020): Re-calculating the cost of coccidiosis in chickens. Vet Res, 51, 115. DOI:10.1186/s13567-020-00837-2.

Blake DP, Vrba V, Xia D, et al (2021): Genetic and biological characterisation of three cryptic Eimeria operational taxonomic units that infect chickens (Gallus gallus domesticus). Int J Parasitol, 51, 621-634. DOI:10.1016/j.ijpara.2020.12.004.
Blake DP (2025): Eimeria of chickens: the changing face of an old foe. Avian Pathol, 54, 267-278. DOI:10.1080/ 03079457.2024.2441180.
Carrisosa M, Jin S, McCrea BA, et al (2021): Prevalence of select intestinal parasites in Alabama backyard poultry flocks. Animals (Basel), 11, 939. DOI:10.3390/ani11040939.
Carvalho FS, Wenceslau AA, Teixeira M, et al (2011): Diagnosis of Eimeria species using traditional and molecular methods in field studies. Vet Parasitol, 176, 95-100. DOI:10.1016/j.vetpar.2010.11.015.
Chanie M, Negash T, Tilahun SB (2009): Occurrence of concurrent infectious diseases in broiler chickens is a threat to commercial poultry farms in Central Ethiopia. Trop Anim Health Prod, 41, 1309-1317. DOI:10.1007/s11250-009-9316-9.
Coroian M, Fábián-Ravasz TZ, Dobrin PR, et al (2024): Occurrence of Eimeria spp. and intestinal helminths in free-range chickens from northwest and central Romania. Animals (Basel), 14, 563, 2024. DOI:10.3390/ani14040563.
Das M (2021): Diversity of Eimeria species in backyard poultry of subtropical hilly region of Meghalaya, India. J Entomol Zool Stud, 9, 360-365.
Debbou-Iouknane N, Benbarek H, Ayad A (2018): Prevalence and aetiology of coccidiosis in broiler chickens in Bejaia province, Algeria. Onderstepoort J Vet Res, 85, e1-e6. DOI:10.1007/s11686-024-00806-1.
El-Shall NA, Abd El-Hack ME, Albaqami NM, et al (2022): Phytochemical control of poultry coccidiosis: a review. Poult Sci, 101, 101542. DOI:10.1016/ j.psj.2021.101542.
Farrell D (2013): The role of poultry in human nutrition. Available at https://www.fao.org/4/al709e/al709e00.pdf (Accessed September 12, 2025).
Fornace KM, Clark EL, Macdonald SE, et al (2013): Occurrence of Eimeria species parasites on small-scale commercial chicken farms in Africa and indication of economic profitability. PLoS One, 8, e84254. DOI:10.1371/journal.pone.0084254.
Gerhold RW, McDougald LR, Beckstead RB (2015): A novel, simplified technique to amplify Eimeria (Coccidia: Apicomplexa) DNA from oocysts. J Parasitol, 101, 102-103. DOI:10.1645/14-524.1.
Godwin RM, Morgan JA (2015): A molecular survey of Eimeria in chickens across Australia. Vet Parasitol, 214, 16-21. DOI:10.1016/j.vetpar.2015.09.030.
Gökpınar S, Babacan ZB, Dinçel GÇ (2023): Investigation of the prevalence of digestive system parasites in chickens in the Kirikkale region. TJVR, 7, 85-90. DOI:10.47748/tjvr.1280735.
Haug A, Thebo P, Mattsson JG (2007): A simplified protocol for molecular identification of Eimeria species in field samples. Vet Parasitol, 146, 35-45. DOI:10.1016/ j.vetpar.2006.12.015.
Jaramillo-Ortiz JM, Burrell C, Adeyemi O, et al (2023): First detection and characterisation of Eimeria zaria in European chickens. Vet Parasitol, 324, 110068. DOI:10.1016/j.vetpar.2023.110068.
Javaregowda AK, Kavitha Rani B, Revanna SP, et al (2016): Prevalence of gastro-intestinal parasites of backyard chickens (Gallus domesticus) in and around Shimoga. J Parasit Dis, 40, 986-990. DOI:10.1007/s12639-014-0620-6.
Jeni RE, Dittoe DK, Olson EG, et al (2021): An overview of health challenges in alternative poultry production systems. Poult Sci, 100, 101173. DOI:10.1016/j.psj.2021. 101173.
Kaboudi K, Umar S, Munir MT (2016): Prevalence of coccidiosis in free-range chicken in Sidi Thabet, Tunisia. Scientifica (Cairo), 2016, 7075195. DOI:10.1155/2016/ 7075195.
Khursheed A, Yadav A, Sofi OM, et al (2022): Prevalence and molecular characterization of Eimeria species affecting backyard poultry of Jammu region, North India. Trop Anim Health Prod, 54, 296. DOI:10.1007/s11250-022-03290-9.
Kumar S, Garg R, Moftah A, et al (2014): An optimised protocol for molecular identification of Eimeria from chickens. Vet Parasitol, 199, 24-31. DOI:10.1016/j.vetpar.2013.09.026.
Kundu K, Kumar S, Banerjee PS, et al (2020): Quantification of Eimeria necatrix, E. acervulina and E. maxima genomes in commercial chicken farms by quantitative real time PCR. J Parasit Dis, 44, 374-380. DOI:10.1007/s12639-019-01188-2.
Lawal JR, Jajere SM, Ibrahim UI, et al (2016): Prevalence of coccidiosis among village and exotic breed of chickens in Maiduguri, Nigeria. Vet World, 9, 653-659. DOI:10.14202/vetworld.2016.653-659.
Lew AE, Anderson GR, Minchin CM, et al (2003): Inter- and intra-strain variation and PCR detection of the internal transcribed spacer 1 (ITS-1) sequences of Australian isolates of Eimeria species from chickens. Vet Parasitol, 112, 33-50. DOI:10.1016/s0304-4017(02)00393-x.
Long PL, Joyner LP (1984): Problems in the identification of species of Eimeria. J Protozool, 31, 535-541. DOI:10.1111/j.1550-7408.1984.tb05498.x.
López-Osorio S, Chaparro-Gutiérrez JJ, Gómez-Osorio LM (2020): Overview of poultry Eimeria life cycle and host-parasite interactions. Front Vet Sci, 7, 384. DOI:10.3389/fvets.2020.00384.
Luu L, Bettridge J, Christley RM, et al (2013): Prevalence and molecular characterisation of Eimeria species in Ethiopian village chickens. BMC Vet Res, 9, 208. DOI:10.1186/1746-6148-9-208.
Mammadova S, Abbasov S (2021): Dynamics of associative infection of domestic chickens with eimeriosis and infectious diseases in Azerbaijan. KJSAT, 5, 61-66. DOI:10.5782/2520-6133.2021.5.1.61.
Matsubayashi M, Shibahara T, Matsuo T, et al (2020): Morphological and molecular identification of Eimeria spp. in breeding chicken farms of Japan. J Vet Med Sci, 82, 516-519. DOI:10.1292/jvms.19-0661.
McDougald LR, Fuller L, Mattiello RA (1997): Survey of coccidia on 43 poultry farms in Argentina. Avian Dis, 41, 923-929.
McDougald LR (2003): Coccidiosis. 974-991. In: Saif YM (Ed), Diseases of Poultry. Iowa State University Press, Amsterdam.
McDougald LR, Fitz-Coy SH (2008): Protozoal infection. 1068-1080. In: Saif YM (Ed), Diseases of Poultry. Blackwell Publishing, Ames, IA.
Memmedov İB (1996): Naxçıvan Muxtar Respublikası şəraitində ev toyuqlarının koksidilərlə yoluxmasının yaşdan asılılıq dinamikası. AMEA Naxçıvan Bölməsi Xəbərlər, Təbiət və texniki elmlər seriyası, 2, 179-183. (In Azerbaijani).
Mesa-Pineda C, Navarro-Ruíz JL, López-Osorio S, et al (2021): Chicken coccidiosis: From the parasite life cycle to control of the disease. Front Vet Sci, 8, 787653. DOI:10.3389/fvets.2021.787653.
Ministry of Agriculture, Fisheries and Food (MAFF) (1986): Enumeration of coccidial oocysts. 85-87. In: Manual of Veterinary Parasitological Techniques, Reference Book, H.M. Stationery Office, London.
Muñoz-Gómez V, Furrer R, Yin J, et al (2024): Prediction of coccidiosis prevalence in extensive backyard chickens in countries and regions of the Horn of Africa. Vet Parasitol, 327, 110143. DOI:10.1016/j.vetpar.2024.110143.
Musaev M, Gaibova G, Ismailova G, et al (1998): The coccidia of the gallinaceous birds in Azerbaijan. Turk J Vet Anim Sci, 22, 409-414
Nasiri V, Jameie F, Morovati KH (2024): Detection, identification, and characterization of Eimeria spp. from commercial chicken farms in different parts of Iran by morphometrical and molecular techniques. Acta Parasitol, 69, 854-864. DOI:10.1007/s11686-024-00818-x.
Prakashbabu BC, Thenmozhi V, Limon G, et al (2017): Eimeria species occurrence varies between geographic regions and poultry production systems and may influence parasite genetic diversity. Vet Parasitol, 233, 62-72. DOI:10.1016/j.vetpar.2016.12.003.
Samadova SO, Ahmadov EI, Hasanova JV, et al (2017): Blood parasites in galliformes from some districts of Absheron region. J Entomol Zool Stud, 5, 2404-2407.
Schnitzler BE, Thebo PL, Mattsson JG, et al (1998): Development of a diagnostic PCR assay for the detection and discrimination of four pathogenic Eimeria species of the chicken. Avian Pathol, 27, 490-497. DOI:10.1080/03079459808419373.
Schnitzler BE, Thebo PL, Tomley FM, et al (1999): PCR identification of chicken Eimeria: a simplified read-out. Avian Pathol, 28, 89-93. DOI:10.1080/03079459995091.
Sharma S, Iqbal A, Azmi S, et al (2013): Prevalence of poultry coccidiosis in Jammu region of Jammu & Kashmir State. J Parasit Dis, 39, 85-89. DOI:10.1007/s12639-013-0286-5.
Shirley MW, Smith AL, Tomley FM (2005): The biology of avian Eimeria with an emphasis on their control by vaccination. Adv Parasitol, 60, 285-330. DOI:10.1016/ S0065-308X(05)60005-X.
Silva JTd, Alvares FBV, Lima EFd, et al (2022): Prevalence and diversity of Eimeria spp. in free-range chickens in northeastern. Brazil Front Vet Sci, 9, 1031330. DOI:10.3389/fvets.2022.1031330.
Silva JTD, Alvares FBV, Oliveira CSM, et al (2022): Prevalence of endoparasites by microscopic analysis in free-range chickens in a Brazilian semiarid region. Rev Bras Parasitol Vet, 31, e010722. DOI:10.1590/S1984-29612022063.
Singh M, Kaur P, Singla LD, et al (2021): Assessment of risk factors associated with prevalence of gastrointestinal parasites in poultry of central plain zone of Punjab, India. Vet World, 14, 972-977. DOI:10.14202/vetworld.2021. 972-977.
Tamura K, Stecher G, Kumar S (2021): MEGA 11: Molecular evolutionary genetics analysis version 11. Mol Biol Evol, 38, 3022-3027. DOI:10.1093/molbev/msab120.
Temesigen WM, Fentahun WM, Anuar N (2018): Prevalence of coccidiosis in back yard chicken in and around Deberetabere town, south Gondar zone, Amhara regional state, Ethiopia. Cohesive J Microbiol Infect Dis, 1. doi: 10.31031/CJMI.2018.01.000525.
Tomazic ML, Britez JD, Pisón-Martínez ML, et al (2025): Chicken coccidiosis in peri-urban family farming in two south American countries: prevalence and circulating Eimeria spp. Animals (Basel), 15, 982. DOI:10.3390/ani15070982.
Williams R (1998): Epidemiological aspects of the use of live anticoccidial vaccines for chickens. Int J Parasitol, 28, 1089-1098. DOI:10.1016/s0020-7519(98)00066-6.
Win SY, Htun LL, Hmoon MM, et al (2020): Occurrence of gastrointestinal parasites in free ranging village chickens from four townships of Myanmar. Vet Sci Res, 6, 1-6. doi: 10.17582/journal.vsrr/2020/6.1.1.6.

Details

Primary Language

English

Subjects

Veterinary Parasitology

Journal Section

Research Article

Authors

Sekine Bakhshaliyeva This is me
0009-0005-8103-9568
Azerbaijan

Rıdvan Kirman ^*
0000-0001-5437-089X
Türkiye

Esin Güven
0000-0001-7067-8819
Türkiye

Turkan Gurbanova This is me
0000-0002-5923-5600
Azerbaijan

İsmayıl Mammadov This is me
0009-0005-4796-1882
Azerbaijan

Early Pub Date

May 25, 2026

Publication Date

-

Submission Date

December 1, 2025

Acceptance Date

May 5, 2026

Published in Issue

Year 2026 Number: Advanced Online Publication

DOI

https://doi.org/10.33988/auvfd.1833836

IZ

https://izlik.org/JA66WW27MJ

Cite

RIS / Bibtex

APA

Bakhshaliyeva, S., Kirman, R., Güven, E., Gurbanova, T., & Mammadov, İ. (2026). Molecular detection of Eimeria species in backyard chickens in the Nakhchivan Autonomous Republic. Ankara Üniversitesi Veteriner Fakültesi Dergisi, Advanced Online Publication. https://doi.org/10.33988/auvfd.1833836

AMA

1.Bakhshaliyeva S, Kirman R, Güven E, Gurbanova T, Mammadov İ. Molecular detection of Eimeria species in backyard chickens in the Nakhchivan Autonomous Republic. Ankara Univ Vet Fak Derg. 2026;(Advanced Online Publication). doi:10.33988/auvfd.1833836

Chicago

Bakhshaliyeva, Sekine, Rıdvan Kirman, Esin Güven, Turkan Gurbanova, and İsmayıl Mammadov. 2026. “Molecular Detection of Eimeria Species in Backyard Chickens in the Nakhchivan Autonomous Republic”. Ankara Üniversitesi Veteriner Fakültesi Dergisi, no. Advanced Online Publication. https://doi.org/10.33988/auvfd.1833836.

EndNote

Bakhshaliyeva S, Kirman R, Güven E, Gurbanova T, Mammadov İ (May 1, 2026) Molecular detection of Eimeria species in backyard chickens in the Nakhchivan Autonomous Republic. Ankara Üniversitesi Veteriner Fakültesi Dergisi Advanced Online Publication

IEEE

[1]S. Bakhshaliyeva, R. Kirman, E. Güven, T. Gurbanova, and İ. Mammadov, “Molecular detection of Eimeria species in backyard chickens in the Nakhchivan Autonomous Republic”, Ankara Univ Vet Fak Derg, no. Advanced Online Publication, May 2026, doi: 10.33988/auvfd.1833836.

ISNAD

Bakhshaliyeva, Sekine - Kirman, Rıdvan - Güven, Esin - Gurbanova, Turkan - Mammadov, İsmayıl. “Molecular Detection of Eimeria Species in Backyard Chickens in the Nakhchivan Autonomous Republic”. Ankara Üniversitesi Veteriner Fakültesi Dergisi. Advanced Online Publication (May 1, 2026). https://doi.org/10.33988/auvfd.1833836.

JAMA

1.Bakhshaliyeva S, Kirman R, Güven E, Gurbanova T, Mammadov İ. Molecular detection of Eimeria species in backyard chickens in the Nakhchivan Autonomous Republic. Ankara Univ Vet Fak Derg. 2026. doi:10.33988/auvfd.1833836.

MLA

Bakhshaliyeva, Sekine, et al. “Molecular Detection of Eimeria Species in Backyard Chickens in the Nakhchivan Autonomous Republic”. Ankara Üniversitesi Veteriner Fakültesi Dergisi, no. Advanced Online Publication, May 2026, doi:10.33988/auvfd.1833836.

Vancouver

1.Sekine Bakhshaliyeva, Rıdvan Kirman, Esin Güven, Turkan Gurbanova, İsmayıl Mammadov. Molecular detection of Eimeria species in backyard chickens in the Nakhchivan Autonomous Republic. Ankara Univ Vet Fak Derg. 2026 May 1;(Advanced Online Publication). doi:10.33988/auvfd.1833836