Identification and antibiotic susceptibility of bacterial microbiota of freshwater fish


  • Alina Klūga Latvia University of Life Sciences and Technologies, Faculty of Veterinary Medicine, Institute of Food and Environmental Hygiene, K. Helmaņa iela 8, Jelgava, LV-3004, Latvia
  • Miroslava Kačániová Slovak University of Agriculture, Faculty of Biotechnology and Food Sciences, Nitra 949 76, Tr. A. Hlinku 2, Slovakia. University of Rzeszow, Faculty of Biology and Agriculture, 35-601 Rzeszow, Zelwerowicza St. 4, Poland,
  • Margarita Terentjeva Latvia University of Life Sciences and Technologies, Faculty of Veterinary Medicine, Institute of Food and Environmental Hygiene, K. Helmaņa iela 8, Jelgava, LV-3004, Latvia



bacteria, freshwater fish, MALDI-TOF MS, antibiotic


The fish meat is an essential part of human diet. However, fish may be contaminated with different microorganisms, including pathogens. Antimicrobial resistance of fish microbiota may facilitate the spread of resistant microorganisms causing serious consequences for human health. The aim of the present study was to detect bacterial contamination in fish gill, gut and skin and to determine antimicrobial susceptibility of the bacterial isolates. Rainbow trout (Oncorhynchus mykiss) and bream (Abramis bram) were obtained from the market in Jelgava city. Chub (Leuciscus cephalus), crucian carp (Carassius carassius) and tench (Tinca tinca) were collected from fishermen. Fish samples were examined for the total bacterial count (TBC), coliforms, EnterobacteriaceaePseudomonas spp. and Aeromonas spp. Testing was done in accordance with International Organization for Standardization (ISO) standards. Identification of all bacteria was accomplished with the Matrix Assisted Laser Desorption Ionization – Time of Flight Mass Spectrometry (MALDI-TOF MS) method. The disc diffusion method was used for the detection of antibiotic susceptibility of isolated bacterial species. TBC ranged from 2.70 to 7.00 log CFU.g-1, coliforms from 0 to 2.67 log CFU.g-1Enterobacteriaceae from 0 to 2.85 log CFU.g-1. The highest contamination with Pseudomonas spp. and Aeromonas spp. was observed in chub gut samples with 1.60 log CFU.g-1 and 2.23 log CFU.g-1, respectively. Altogether, 16 microbial genera and 31 bacterial species were identified. The dominant bacterial species belonged to Pseudomonas spp. (54%) and EnterobacteriaceaePseudomonas spp. were resistant to ticarcillin, susceptibility to ciprofloxacin showed 88% of isolates. All Enterobacteriaceae isolates were susceptible to imipenem. The microbial quality of the fish was acceptable, but the presence of antibiotic resistant bacteria may further cause a negative impact on public health.


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Abd-El-Malek, A. M. 2017. Incidence and virulence characteristics of Aeromonas spp. in fish. Veterinary World, vol. 10, no. 1, p. 34-37. DOI:

Alikunhi, N. M., Batang, Z. B., AlJahdali, H. A., Aziz, M. A. M., Al-Suwailem, A. M. 2017. Culture-dependent bacteria in commercial fishes: Qualitative assessment and molecular identification using 16S rRNA gene sequencing. Saudi Journal of Biological Sciences, vol. 24, no. 6, p. 1105-1116. DOI:

Altun, S., Duman, M., Büyükekiz, A. G., Özyiğit, M. O., Karataş, S., Turgay, E. 2013. Isolation of Citrobacter braakii from rainbow trout (Oncorhynchus mykiss). The Israeli Journal of Aquaculture – Bamidgeh, vol. 65, p. 915-924.

Austin, B. 2006. The bacterial microflora of fish, revised. The Scientific World Journal, vol. 6, p. 931-945. DOI:

Aydin, S., Celebi, S., Akyurt, I. 1997. Clinical, haematological and pathological investigations of Escherichia vulneris in rainbow trout (Oncorhynchus mykiss). Fish Pathology, vol. 32, no. 1, p. 29-34. DOI:

Aydin, S., Erman, Z., Bilgin, O. C. 2011. Investigations of Serratia liquefaciens infection in rainbow trout (Oncorhynchus mykiss Walbaum). Turkish Journal of Veterinary and Animal Sciences, vol. 25, no. 5, p. 643-650.

Cipriano, R. C., Dove, A. 2011. Far from superficial: microbial diversity associated with the skin and mucus of fish. In Bridging America and Russia with Shared Perspectives on Aquatic Animal Health, Third Bilateral Conference between Russia and the United States : proceedings. Maryland, USA : Khaled bin Sultan Living Oceans Foundation, p. 156-167. ISBN: 9780983561101.

Cwiková, O. 2016. Microbiological evaluation of fish. Potravinarstvo, vol. 10, no. 1, p. 407-412. DOI:

Da Silva, M., Matte, G., Germano, P., Matte, M. 2010. Occurrence of pathogenic microorganisms in fish sold in Sao Paulo, Brazil. Journal of Food Safety, vol. 30, no. 1, p. 94-110. DOI:

Dekker, J., Frank, K. 2015. Salmonella, Shigella, and Yersinia. Clinics in Laboratory Medicine, vol. 35, no. 2, p. 225-246. DOI:

Doménech-Sánchez, A., Laso, E., Perez, M. J., Berrocal, C. I. 2011. Emetic disease caused by Bacillus cereus after consumption of tuna fish in a beach club. Foodborne Pathogens and Disease, vol. 8, no. 7, p. 835-837. DOI:

EFSA, ECDC. 2017. The European Union summary report on trends and sources of zoonoses, zoonotic agents and food‐borne outbreaks in 2016. EFSA Journal, vol. 15, no. 12, p. 1-228. DOI:

Eizenberga, I., Terentjeva, M., Valciņa, O., Novoslavskij, A., Ošmjana, J., Strazdiņa, V., Bērziņš, A. 2015. Evaluation of microbiological quality of freshwater fish in Usma lake. Acta Biologica Universitatis Daugavpiliensis, vol. 15, no. 1, p. 65-73.

EUCAST (The European Committee on Antimicrobial Susceptibility Testing). 2018. Breakpoint tables for interpretation of MICs and zone diameters. Version 8.1. Available at:

Fernandes, R. 2009. Microbiology handbook – fish and seafood. UK : Leatherhead Food International, 256 p. ISBN: 978-1-905224-76-0.

Flores-Tena, F. J., Guerrero-Barrera, A. L., Avelar-González, F. J., Ramírez-López, E. M., Martínez-Saldaña, M. C. 2007. Pathogenic and opportunistic Gram-negative bacteria in soil, leachate and air in San Nicolás landfill at Aguascalientes, Mexico. Revista Latinoamericana de Microbiología, vol. 49, no. 1-2, p. 25-30.

Ge, Y., Zhu, J., Ye, X., Yang, Y. 2016. Spoilage potential characterization of Shewanella and Pseudomonas isolated from spoiled large yellow croaker (Pseudosciaena crocea). Letters in Applied Microbiology, vol. 64, no. 1, p. 86-93. DOI:

Guyomard-Rabenirina, S., Dartron, C., Falord, M., Sadikalay, S., Ducat, C., Richard, V., Breurec, S., Gros, O., Talarmin, A. 2017. Resistance to antimicrobial drugs in different surface waters and wastewaters of Guadeloupe. Plos One, vol. 12, no. 3, p. 155-173. DOI:

Hassan, EL., Farag, S. M. 2006. Incidence of haemolysin producing motile Aeromonas in some shellfish and their public health significance in Port-said city. Journal of Applied Sciences Research, vol. 2, no. 11, p. 972-979.

Heuer, O. E., Kruse, H., Grave, K., Collignon, P., Karunasagar, I., Angulo, F. J. 2009. Human health consequences of use of antimicrobial agents in aquaculture. Clinical Infectious Diseases, vol. 49, no. 8, p. 1248-1253. DOI:

ISO 13720: 2010. Meat and meat products – Enumeration of presumptive Pseudomonas spp.

ISO 21528: 2017. Microbiology of the food chain – Horizontal method for the detection and enumeration of Enterobacteriaceae – Part 2: Colony-count technique.

ISO 4832: 2006. Microbiology of food and animal feeding stuffs – Horizontal method for the enumeration of coliforms – Colony-count technique.

Kačániová, M., Terentjeva, M., Vukovic, N., Puchalski, C., Roychoudhury, S., Kunová, S.; Klūga, A., Tokár, M., Kluz, M., Ivanišová, E. 2017. The antioxidant and antimicrobial activity of essential oils against Pseudomonas spp. isolated from fish. Saudi Pharmaceutical Journal, vol. 25, no. 8, p. 1108-1116. DOI:

Keren, Y., Keshet, D., Eidelman, M., Geffen, Y., Raz-Pasteur, A., Hussein, K. 2014. Is Leclercia adecarboxylata a new and unfamiliar marine pathogen? vol. 52, no. 5, p. 1775-1776. DOI:

Kholil, Md. I., Hossain, Md. M. M., Neowajh, Md. S., Islam, Md. S., Kabir, M. 2015. Comparative efficiency of some commercial antibiotics against Pseudomonas infection in fish. International Journal of Fisheries and Aquatic Studies, vol. 2, no. 3, p. 114-117. DOI:

Kim, D. H., Brunt, J., Austin, B. 2007. Microbial diversity of intestinal contents and mucus in rainbow trout (Oncorhynchus mykiss). Journal of Applied Microbiology, vol. 102, no. 6, p. 1654-64. DOI:

Larsen, A. M. 2014. Studies on the microbiota of fishes and the factors influencing their composition : dissertation theses. Auburn, Alabama, USA : Auburn University. 242 p.

Mastan, S. A. 2013. Pseudomonas septicemia in Labeo rohita (ham.) and Cyprinus carpio (linn.) in andhra pradesh–natural occurrence and artificial challenge. International Journal of Pharmacy and Pharmaceutical Sciences, vol. 5, no. 2, p. 564-568.

Oliveira, R. V., Oliveira, M. C., Pelli, A. 2017. Disease infection by Enterobacteriaceae family in fishes: a review. Microbiology & Experimentation, vol. 4, no. 5, p. DOI:

Petersen, A., Andersen, J. S., Kaewmak, T., Somsiri, T., Dalsgaard, A. 2002. Impact of integrated fish farming on antimicrobial resistance in a pond environment. American Society for Microbiology, vol. 68, no. 12, p. 6036-6042. DOI:

Picot, L., Abdelmoula, S. M., Merieau, A., Leroux, P., Cazin, L., Orange, N., Feuilloley, M. G. 2001. Pseudomonas fluorescens as a potential pathogen: adherence to nerve cells. Microbes and Infection, vol. 3, no. 12, p. 985-995. DOI:

Prasad, M. P. 2014. Molecular characterization of enterotoxigenic Bacillus cereus species isolated from tropical marine fishes using RAPD markers. International Journal of Pure & Applied Bioscience, vol. 2, no. 4, p. 189-195.

Rasool, U., Ahmad, A., Badroo, G. A., Mudasir, M., Fayaz, S., Mustafa, R. 2017. Isolation and Identification of Bacillus cereus from fish and their handlers from Jammu, India. International Journal of Current Microbiology and Applied Sciences, vol. 6, no. 8, p. 441-447. DOI:

Singer, A. C., Shaw, H., Rhodes, V., Hart, A. 2016. Review of antimicrobial resistance in the environment and its relevance to environmental regulators. Frontiers in Microbiology, vol. 7, p. 1-22. DOI:

Starliper, C. E. 2001. Isolation of Serratia liquefaciens as a pathogen of Arctic char, Salvelinus alpinus. Journal of Fish Diseases, vol. 24, p. 53-56. DOI:

Stock, I., Wiedemann, B. 1999. Natural antibiotic susceptibility of Escherichia coli, Shigella, E. vulneris, and E. hermannii strains. Diagnostic Microbiology and Infectious Disease, vol. 33, no. 3, p. 187-199. DOI:

Stratev, D., Vashin, I., Daskalov, H. 2015. Microbiological status of fish products on retail markets in the Republic of Bulgaria. International Food Research Journal, vol. 22, no. 1, p. 64-69.

Terentjeva, M., Eizenberga, I., Novoslavskij, A., Strazdiņa, V., Valciņa, O., Ošmjana, J., Bērziņš, A. 2015. Bacterial microflora of freshwater fish originated from Usmas Lake in Latvia. The Journal of Microbiology, Biotechnology and Food Sciences, vol. 4, no. 1, p. 74-77. DOI:

Tortorello, M. L. 2003. Indicator organisms for safety and quality—uses and methods for detection: minireview. Journal of AOAC International, vol. 86, no. 6, p. 1208-1217. DOI:

Tosun, Ş.Y., Üçok Alakavuk, D., Mol S. 2016. Isolation of Salmonella spp. and other members of Enterobacteriaceae from horse mackerel (Trachurus trachurus), sold in public markets of Istanbul, Turkey. Journal of Food and Health Science, vol. 2, no. 2, p. 82-89. DOI:

Wamala, S. P., Mugimba, K. K., Mutuloki, S., Evensen, Ø., Mdegela, R., Byarugaba, D. K., Sørum, H. 2018. Occurrence and antibiotic susceptibility of fish bacteria isolated from Oreochromis niloticus (Nile tilapia) and Clarias gariepinus (African catfish) in Uganda. Fisheries and Aquatic Science, vol. 21, no. 1, p. 1-10. DOI:

Yagoub, S.O. 2009. Isolation of Enterobacteriaceae and Pseudomonas spp. from raw fish sold in fish market in Khartoum state. Journal of Bacteriology Research, vol. 1, no. 7, p. 85-88.



How to Cite

Klūga, A. ., Kačániová, M. ., & Terentjeva, M. . (2019). Identification and antibiotic susceptibility of bacterial microbiota of freshwater fish. Potravinarstvo Slovak Journal of Food Sciences, 13(1), 408–414.

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