Prevalence and antimicrobial resistance profile of Enterobacteriaceae in frugivorous (Eidolon helvum) and insectivorous (Nycteris hispida) bats in Southeast Nigeria

Lynda O. Majesty-Alukagberie; Iniobong C.I. Ugochukwu; Adamma C. Obiapuna; Obichukwu C. Nwobi; Riona I. Okosi; Onyinye J. Okorie-Kanu; Samuel I. Onuorah; Onyemaechi Ugboh; Kenedy F. Chah

doi:10.55779/nsb18212907

Authors

Lynda O. Majesty-Alukagberie University of Nigeria, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Preventive Medicine, Nsukka 402001 (NG) https://orcid.org/0000-0001-7294-3487
Iniobong C.I. Ugochukwu University of Nigeria, Faculty of Veterinary Medicine, Department of Veterinary Pathology, Nsukka 402001 (NG) https://orcid.org/0000-0001-7410-8311
Adamma C. Obiapuna University of Nigeria, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Preventive Medicine, Nsukka 402001 (NG)
Obichukwu C. Nwobi University of Nigeria, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Preventive Medicine, Nsukka 402001 (NG)
Riona I. Okosi National Veterinary Research Institute, Department of Diagnostic and Outstation Services, Vom Plateau State, Vom 930101 (NG)
Onyinye J. Okorie-Kanu University of Nigeria, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Preventive Medicine, Nsukka 402001 (NG) https://orcid.org/0000-0002-8836-9966
Samuel I. Onuorah University of Nigeria, Faculty of Agriculture, Department of Animal Science, Nsukka 402001 (NG)
Onyemaechi Ugboh University of Delta Agbor, Department of Agricultural Economics and Extension, P.O. Box 2090 (NG) https://orcid.org/0009-0005-3970-7438
Kenedy F. Chah University of Nigeria, Faculty of Veterinary Medicine, Department of Veterinary Microbiology and Immunology, Nsukka 402001 (NG)

DOI:

https://doi.org/10.55779/nsb18212907

Keywords:

antimicrobial resistance, bats, Enterobacteriaceae, multidrug resistance, One Health

Abstract

Among the clinically important antimicrobial-resistant bacteria, members of the family Enterobacteriaceae, including Escherichia coli, Klebsiella spp. and Enterobacter spp., are frequently implicated in zoonotic infections and are increasingly detected in non-traditional reservoirs, including wildlife. Bats may contribute to the environmental maintenance and dissemination of Enterobacteriaceae within a One Health context, but data on their occurrence and antimicrobial resistance in Southeast Nigeria remain limited. This study investigated the prevalence and antimicrobial resistance profile of Enterobacteriaceae isolated from frugivorous (Eidolon helvum) and insectivorous (Nycteris hispida) bats in Southeast Nigeria. A total of 540 tissue samples (spleen, liver and intestine) were collected from 180 bats (90 Eidolon helvum and 90 Nycteris hispida). Isolation and identification were performed using standard bacteriological procedures, and selected isolates were confirmed using API 20E. Antimicrobial susceptibility was evaluated by the disk diffusion method. Overall, 229 (42.4%) Enterobacteriaceae isolates were recovered: 117 (51.1%) from Eidolon helvum and 112 (48.9%) from Nycteris hispida. Escherichia coli was the predominant isolate (155/229; 67.7%), followed by Klebsiella pneumoniae/K. oxytoca (31/229; 13.5%), whereas Enterobacter spp. was least frequent (1/229; 0.4%). Resistance was highest to cefuroxime (117/229; 51.1%), followed by ampicillin (83/229; 36.2%) and aztreonam (33/229; 14.4%); resistance to meropenem was low (5/229; 2.2%). Overall, 44 isolates (19.2%) were multidrug-resistant, and the mean multiple antibiotic resistance index was 0.13. Although several taxa were detected at low frequency, the recovery of multidrug-resistant Enterobacteriaceae from bats supports the need for continued One Health-oriented AMR surveillance in wildlife and human-impacted environments.

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References

Adesiyun AA, Stewart-Johnson A, Thompson NN (2009). Isolation of enteric pathogens from bats in Trinidad. Journal of Wildlife Diseases, 45(4): 952–961. https://doi.org/10.7589/0090-3558-45.4.952

Ahmad AA, Alhassan MY, Muhammad NM (2026). Antimicrobial use practices, resistance drivers and policy responses in Nigerian livestock production from a One Health perspective. Discover Public Health, 23: 520. https://doi.org/10.1186/s12982-026-01806-4

Aizpurua O, Alberdi A (2018). Ecology and evolutionary biology of fishing bats. Mammal Review, 48(4): 284–297. https://doi.org/10.1111/mam.12118

Allocati N, Petrucci AG, Di Giovanni P, Masulli M, Di Ilio C, De Laurenzi V (2016). Bat-man disease transmission: zoonotic pathogens from wildlife reservoirs to human populations. Cell Death Discovery, 2: 16048. https://doi.org/10.1038/cddiscovery.2016.48

American Psychological Association (2022). Guidelines for ethical conduct in the care and use of animals. Available at: https://www.apa.org/science/leadership/care/guidelines (accessed 24 May 2026).

Bobate S, Mahalle S, Dafale NA, Bajaj A (2023). Emergence of environmental antibiotic resistance: mechanism, monitoring and management. Environmental Advances, 13: 100409. https://doi.org/10.1016/j.envadv.2023.100409

Castanheira M, Huband MD, Mendes RE, Flamm RK (2017). Meropenem-vaborbactam tested against contemporary Gram-negative isolates collected worldwide during 2014, including carbapenem-resistant, KPC-producing, multidrug-resistant and extensively drug-resistant Enterobacteriaceae. Antimicrobial Agents and Chemotherapy, 61(5): e00567-17. https://doi.org/10.1128/AAC.00567-17

Che H, Hu B, Cui X, Yang J, Zeng J, Dong L, Wang R, Cai Y (2025). Carbapenem treatment options for metallo-beta-lactamase: drug screening and dose optimization of meropenem-based combinations against NDM- or IMP-producing Klebsiella pneumoniae. Frontiers in Microbiology, 16: 1490372. https://doi.org/10.3389/fmicb.2025.1490372

CLSI (Clinical and Laboratory Standards Institute) (2025). Performance standards for antimicrobial disk and dilution susceptibility tests for bacteria isolated from animals. CLSI Standard VET01S, 7th ed. Clinical and Laboratory Standards Institute, Malvern, PA, USA.

CLSI (Clinical and Laboratory Standards Institute) (2025). Performance standards for antimicrobial susceptibility testing. CLSI Standard M100, 35th ed. Clinical and Laboratory Standards Institute, Malvern, PA, USA.

Cocoș DI, Dumitrescu E, Muselin F, Brezovan D, Degi J, Boldura OM, Cristina RT (2025). Prevalence and antimicrobial resistance of Enterobacteriaceae in wild birds across Europe: a systematic review. Antibiotics, 14(9): 905. https://doi.org/10.3390/antibiotics14090905

Daniel DS, Ng YK, Chua EL, Arumugam Y, Wong WL, Kumaran JV (2013). Isolation and identification of gastrointestinal microbiota from the short-nosed fruit bat Cynopterus brachyotis brachyotis. Microbiological Research, 168(8): 485–496. https://doi.org/10.1016/j.micres.2013.02.001

EFSA (European Food Safety Authority), ECDC (European Centre for Disease Prevention and Control) (2024). The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2021/2022. EFSA Journal, 22(2): e8583. https://doi.org/10.2903/j.efsa.2024.8583

Ejikeme JNU (2021). Ogbunike cave in Nigeria: a tourism potential asset in Anambra State. Ikenga International Journal of Institute of African Studies, 22(1): 1–19.

Ellison LE, O’Shea TJ, Wimsatt J, Pearce RD, Neubaum DJ, Neubaum MA, Bowen RA (2006). Sampling blood from big brown bats (Eptesicus fuscus) in the field with and without anesthesia: impacts on survival. Journal of Wildlife Diseases, 42(4): 849–852. https://doi.org/10.7589/0090-3558-42.4.849

Esther J, Onyebuchi OB, Eugenia OE, Ann OC, Adamma NM, Chiaka IG, Omowumi F, Odunke NS, Nkeiruka F, Blessing UI (2025). Antimicrobial resistance in Nigeria’s healthcare system: a comprehensive narrative review and policy implications. Discover Public Health, 22: 460. https://doi.org/10.1186/s12982-025-00859-1

Eya EB, Enyanwu OB, Chukwu OA (2026). A retrospective assessment of antimicrobial resistance patterns in WHO-access, watch, and reserve-classified antibiotics across two large hospitals in a resource-limited setting. Scientific Reports, 16: 6519. https://doi.org/10.1038/s41598-026-37665-x

Ferreira MRS, Cleary DFR, Coelho FC, Gomes NC, Huang YM, Polónia AM, de Voogd NJ (2020). Geographical location and habitat predict variation in prokaryotic community composition in Suberites diversicolor. Annals of Microbiology, 70: 14. https://doi.org/10.1186/s13213-020-01559-0

Garrity GM (Ed.) (2005). Bergey’s Manual of Systematic Bacteriology. Vol. 2B: The Gammaproteobacteria (Enterobacteriaceae Section). Springer, New York, NY, USA.

Gopee NV, Adesiyun A, Caesar KA (2000). A longitudinal study of Escherichia coli strains isolated from captive mammals, birds and reptiles in Trinidad. Journal of Zoo and Wildlife Medicine, 31(3): 351–360. https://doi.org/10.1638/1042-7260(2000)031[0351:ALSOEC]2.0.CO;2

Guitart-Matas J, Espunyes J, Illera L, Gonzalez-Escalona N, Ribas MP, Marco I, Migura-Garcia L (2024). High-risk lineages of extended-spectrum cephalosporinase-producing Escherichia coli from Eurasian griffon vultures (Gyps fulvus) foraging in landfills in north-eastern Spain. Science of The Total Environment, 909: 168625. https://doi.org/10.1016/j.scitotenv.2023.168625

Handrova L, Kmet V (2019). Antibiotic resistance and virulence factors of Escherichia coli from eagles and goshawks. Journal of Environmental Science and Health, Part B, 54(8): 605–614. https://doi.org/10.1080/03601234.2019.1600289

Happold DCD (1987). The Mammals of Nigeria. Clarendon Press, Oxford, UK.

Janda JM, Abbott SL (2021). The changing face of the family Enterobacteriaceae (order Enterobacterales): new members, taxonomic issues, geographic expansion, and new diseases and disease syndromes. Clinical Microbiology Reviews, 34(2): e00118-20. https://doi.org/10.1128/CMR.00118-20

Jesser KJ, Trueba G, Konstantinidis KT, Levy K (2023). Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador. Gut Microbes, 15(2): 2281010. https://doi.org/10.1080/19490976.2023.2281010

Mbehang Nguema PP, Onanga R, Ndong Atome GR, Obague Mbeang JC, Mabika Mabika A, Yaro M, Bretagnolle F (2020). Characterization of ESBL-producing Enterobacteria from fruit bats in an unprotected area of Makokou, Gabon. Microorganisms, 8(1): 138. https://doi.org/10.3390/microorganisms8010138

McDougall F, Boardman W, Gillings M, Power M (2019). Bats as reservoirs of antibiotic resistance determinants: a survey of class 1 integrons in grey-headed flying foxes (Pteropus poliocephalus). Infection, Genetics and Evolution, 70: 107–113. https://doi.org/10.1016/j.meegid.2019.02.006

Merinda M, Ramoni-Perazzi FG, Muñoz MR (2016). Inventory of bats culturable Proteobacteria from Cueva las Escaleras (Táchira, Venezuela): evidence of potential human health risk. Journal of Cave and Karst Studies, 78(3): 174–182. https://doi.org/10.4311/2015MB0123

Milbank C, Vira B (2022). Wildmeat consumption and zoonotic spillover: contextualising disease emergence and policy responses. The Lancet Planetary Health, 6(5): e439–e448. https://doi.org/10.1016/S2542-5196(22)00064-X

Mühldorfer K (2013). Bats and bacterial pathogens: a review. Zoonoses and Public Health, 60(1): 93–103. https://doi.org/10.1111/j.1863-2378.2012.01536.x

Nowak K, Fahr J, Weber N, Lübke-Becker A, Semmler T, Weiss S, Mombouli JV, Wieler LH, Guenther S, Leendertz FH, Ewers C (2017). Highly diverse and antimicrobial susceptible Escherichia coli display a naïve bacterial population in fruit bats from the Republic of Congo. PLOS ONE, 12(7): e0178146. https://doi.org/10.1371/journal.pone.0178146

Obodoechi LO, Carvalho I, Chenouf NS, Martínez-Álvarez S, Sadi M, Nwanta JA, et al. (2021). Antimicrobial resistance in Escherichia coli isolates from frugivorous (Eidolon helvum) and insectivorous (Nycteris hispida) bats in Southeast Nigeria, with detection of CTX-M-15 producing isolates. Comparative Immunology, Microbiology and Infectious Diseases, 75: 101613. https://doi.org/10.1016/j.cimid.2021.101613

Olorunleke SO, Kirchner M, Duggett N, AbuOun M, Okorie-Kanu OJ, Stevens K, et al. (2022). Molecular characterization of extended-spectrum cephalosporin-resistant Escherichia coli isolated from livestock and in-contact humans in Southeast Nigeria. Frontiers in Microbiology, 13: 937968. https://doi.org/10.3389/fmicb.2022.937968

Pătrînjan RT, Morar A, Ban-Cucerzan A, Popa SA, Imre M, Morar D, Imre K (2024). Systematic review of the occurrence and antimicrobial resistance profile of foodborne pathogens from Enterobacteriaceae in wild ungulates within European countries. Pathogens, 13(12): 1046. https://doi.org/10.3390/pathogens13121046

Reichard JD, Fuller NW, Kunz TH (2011). Condition of wings is an important criterion of bat health: a response to Francl et al. Journal of Wildlife Diseases, 47(4): 1050–1051. https://doi.org/10.7589/0090-3558-47.4.1050

RIM (Resources Inventory and Management Ltd) (1993). Nigeria National Livestock Survey. Federal Department of Livestock and Pest Control Services, Abuja, Nigeria.

Sati NM, Card RM, Barco L, Muhammad M, Luka PD, Chisnall T, Fagbamila IO, Cento G, Nnadi NE, Kankya C, et al. (2024). Antimicrobial resistance and phylogenetic relatedness of Salmonella serovars in indigenous poultry and their drinking water sources in North Central Nigeria. Microorganisms, 12(8): 1529. https://doi.org/10.3390/microorganisms12081529

Sens-Junior H, Trindade WA, Oliveira AF, Zaniolo MM, Serenin GF, Araujo-Ceranto JB, Goncalves DD, Germano MR (2018). Bacterial resistance in bats from Phyllostomidae family and its relationship with One Health. Pesquisa Veterinária Brasileira, 38(6): 1207–1216. https://doi.org/10.1590/1678-5150-PVB-5185

Sweeney MT, Lubbers BV, Schwarz S, Watts JL (2018). Applying definitions for multidrug resistance, extensive drug resistance and pandrug resistance to clinically significant livestock and companion animal bacterial pathogens. Journal of Antimicrobial Chemotherapy, 73(6): 1460–1463. https://doi.org/10.1093/jac/dky043

Swift BMC, Bennett M, Waller K, Dodd C, Murray A, Gomes RL, Humphreys B, Hobman JL, Jones MA, Whitlock SE, et al. (2019). Anthropogenic environmental drivers of antimicrobial resistance in wildlife. Science of The Total Environment, 649: 12–20. https://doi.org/10.1016/j.scitotenv.2018.08.108

Thrusfield M (1995). Veterinary Epidemiology. 3rd ed. Blackwell Science, Oxford, UK, pp. 233–234.

Tripathi N, Zubair M, Sapra A (2025). Gram staining. In: StatPearls [Internet]. StatPearls Publishing, Treasure Island, FL, USA. PMID: 32965827.

Tschäpe H, Prager R, Streckel W (1995). Verotoxigenic Citrobacter freundii associated with severe gastroenteritis and cases of haemolytic uraemic syndrome in a nursery school. Epidemiology and Infection, 114(3): 441–450. https://doi.org/10.1017/S0950268800052148

Türkyılmaz O, Darcan C (2026). Molecular basis of ampicillin resistance: combinatorial mechanisms and future strategies. World Journal of Microbiology and Biotechnology, 42: 79. https://doi.org/10.1007/s11274-026-04826-z

Vengust M, Knapic T, Weese JS (2018). The faecal bacterial microbiota of bats in Slovenia. PLOS ONE, 13(5): e0196728. https://doi.org/10.1371/journal.pone.0196728

Vidanović D, Vasković N, Dmitrić M, Tešović B, Debeljak M, Stojanović M, Budinski I (2025). Identification and characterization of viral and bacterial pathogens in free-living bats of Kopaonik National Park, Serbia. Veterinary Sciences, 12(5): 401. https://doi.org/10.3390/vetsci12050401

Walana W, Vicar EK, Kuugbee ED, Sakida F, Yabasin IB, Faakuu E, Amfoabegyi S, Ziem JB (2023). Antimicrobial resistance of clinical bacterial isolates according to the WHO AWaRe and the ECDC-MDR classifications: the pattern in Ghana’s Bono East Region. Frontiers in Antibiotics, 2: 1291046. https://doi.org/10.3389/frabi.2023.1291046

Wang S, Li W, Wang Z, Yang W, Li E, Xia X, Yan F, Chiu S (2024). Emerging and reemerging infectious diseases: global trends and new strategies for their prevention and control. Signal Transduction and Targeted Therapy, 9: 223. https://doi.org/10.1038/s41392-024-01917-x

WHO Regional Office for Europe, European Centre for Disease Prevention and Control (2022). Antimicrobial Resistance Surveillance in Europe 2022 - 2020 Data. Publications Office of the European Union, Luxembourg. https://doi.org/10.2900/112339

Zanichelli V, Sharland M, Cappello B, Moja L, Getahun H, Pessoa-Silva C, Sati H, van Weezenbeek C, Balkhy H, Simão M, et al. (2023). The WHO AWaRe antibiotic book and prevention of antimicrobial resistance. Bulletin of the World Health Organization, 101(4): 290–296. https://doi.org/10.2471/BLT.22.290323