Occurrence, Molecular Characterization and Antimicrobial Susceptibilityof Sorbitol Non-Fermenting E. coli Isolates, and Assessment of FishHandling Practices along the Supply Chain in Central Oromia, Ethiopia
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Date
2025
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Addis Abeba University
Abstract
Fish-borne diseases are among the global public health concern. Contaminated water bodies and poor handling practices along the fish supply chain can lead to fish contamination. Raw fish consumption is a leading cause of fish-borne infection. Emerging sorbitol non-fermenting Escherichia coli strains including Escherichia coli O157:H7, may transmit to human sthrough contaminated water and fish. However, despite reports of contamination, there islimited information on the occurrence, molecular characteristics, and antimicrobial susceptibility of sorbitol non-fermenting Escherichia coli in Ethiopia. This study, attemptstode termine these aspects in fresh water lakes, fish, and humans in central Oromia, Ethiopia. Data were collected using semi-structured questionnaire interviews and personal observations from a total of 200 purposively selected respondents comprising of 50 fishermen, 10 retailers, 20 food establishments serving fish, and 120 consumers. Moreover, a total of 750 samples including 150 fish meat, 150 fish skin swab, 150 fish feces, 150 fresh water of the lakes, 150human stool samples were collected from five Lakes and three health facilities. Overall, 150fish, 30 fish from each Lake, comprising of six fish species: Oreochromis niloticus, Clariasgariepinus, Tilapia Zilli, Cyprinus carpio, Labeobarbus intermedius, Barbus ethiopicus, whichare commonly used for human consumption were included in the study. Fecal, meat andskinswab samples were taken from each fish. The samples were processed following the standardprotocol recommended by European Food Safety Authority and Kirby–Bauer disc diffusionmethod for detection of the bacteria, and antimicrobial susceptibility tests, respectively. Molecular characterization of presumptive isolates was performed using Whole-Genome Sequencing for sero typing, determination of virulence factors, antimicrobial resistance traits, and genetic linkage of the isolates. The study revealed a wide range of hygienic breaches, including fish processing at unhygienic landing sites, washing filleted fish with contaminated water of the Lakes, use of a single knife for processing all fish with infrequent washing and withnodi sinfection in between. Majority (70%; n=10) of the retailers and all the food establishment strans ported fish in vehicles with no cold chain facilities. Over three-fourths (77%; n =120) of theconsumers preferred consuming raw fish; 80% of them lacked the knowledge of fish borne diseases. Few good hygienic practices appreciated include, the use of refrigerators for storageinall retailers and 70% (n =20) of the food establishments, and the use of vehicles with thermostat for the transportation of fish among 30% of retailers. From a total of 750 microbiological samples analyzed, 3.9% (29/750) was found positive for sorbitol non-fermenting Escherichiacoli; of which 6.7% (n=10), 1.8% (n=8) and 7.3% (n=11) were retrieved from water, fish, anddiarrheic human patients, respectively. Whole-Genome Sequencing confirmed that all the isolates were sorbitol non-fermenting Escherichia coli strains; among which none of them were Escherichia coli O157:H7. Two novel Escherichia coli strains with unknown O-antigen were retrived from fish feces and human stool. All the strains have multiple virulence factors and one or more genes encoding for them. Genetic relatedness was observed among strains from the same sources (water, fish, and humans). Most isolates were resistant to ampicillin (100%), tetracycline (100%), cefotaxime (100%), ceftazidime (100%), meropenem (100%), nalidixicacid(93.1%) and sulfame thoxazole/trimethoprim (79.3%). Majority of the strains were resistant tochlor amphenicol (58.6%) and cipro floxacin (48.3%), while small fraction showed resistance toazi thromycin (3.45%). Isolates have shown an overall multi-drug resistance profile of 87.5%. Majority, (62.1%; n=18) of the strains have acquired multi-drug resistance traits. Genes encoding for mutational resistance and extended spectrum beta-lacta mases were also detected. In conclusion, the study revealed a wide range of hygienic breaches along the fish production and supply chain; lack of infrastructure for post-harvest fish handling and processing, lackof appropriate transportation facilities and presence of knowledge gaps regarding fish borne diseases, and the occurrence of virulent and antimicrobial resistant sorbitol non-fermenting Escherichia coli strains in water, fish, and humans. Although no genetic relatedness was observed among strains from various sources, the genomic clustering among strains from the same sources strongly suggests the potential risk of transmission along the supply chain at the human–fish-environment interface if strict hygienic fish production is not in place. Hence, infrastructural development for hygienic fish production and processing, training for fish producers, consumer retailers and food establishments, and robust genetic study of the new strains with unknown O-antigens is required to improve fish safety and reduce the risk of public health.
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Keywords
Antimicrobial resistance, Contamination, Escherichia coli, Fish-borne diseases, Hygienic practices, Whole-genome sequencing