Traore, A. N.Potgieter, N.Lukheli, Elelwani2025-09-162025-09-162025-09-05Lukheli, E. 2025. Identification and characterization of enterobacter species causing decay of onions and their antimicrobial susceptibility. . .https://univendspace.univen.ac.za/handle/11602/2953M.Sc. (Microbiology)Department of Biochemistry and MicrobiologyBackground: Plants are susceptible to a range of health problems, and onions are no exception. While onions are relatively resilient, they are not immune to diseases and pathogens. Onions that are packed before being fully dried are prone to rapid decay. Research has shown that water can facilitate the transmission of pathogens and contribute to microbial contamination of fresh produce, including Salmonella and E. coli. Salmonella can enter the soil through agricultural practices such as pesticide application, the use of fertilizers derived from animal manure, and irrigation with contaminated water. Since irrigation water can come from various sources—such as municipal supplies, treated wastewater, rivers, or groundwater—farmers are advised to safeguard their water sources to reduce the risk of contamination. Objective: To identify and characterize Enterobacter species causing decay of bulb onions and their antimicrobial susceptibility. Methods: This study was carried out in the Vhembe district in the Limpopo province. The focus was on farms in various municipalities, including both commercial and subsistence farms, as well as the rivers surrounding these farms. Water, soil, and onion samples were collected. The presence of total coliform and E. coli was determined using the Colilert Quanti tray method. Collected samples were further analyzed for Enterobacteriaceae using membrane filtration and culture-based methods. Biochemical tests (Vitek-2-system) were used to identify and confirm the isolates. E. coli pathotypes were characterized using multiplex PCR. The characterization of strains from Enterobacter species was done using Sanger Sequencing. Results: Measured temperatures ranged from 19.8°C to 25°C, with Farm 2 showing slightly elevated values. Electrical conductivity (EC) values were within acceptable limits (<540 μS/cm) across all farms, though Farm 3 exhibited higher total dissolved solids (TDS) levels, reaching up to 450 mg/L. The pH values across farms ranged from 5.0 to 6.4, lower than the recommended 6.5–8.5 for agricultural water. Elevated TDS and acidic pH in Farm 3 was observed. High levels of total coliforms (up to 2419.6 MPN/100 mL) and the presence of E. coli were detected in water and onion samples, particularly from Farms 2 and 3. PCR analysis identified multiple E. coli pathotypes, including EPEC, ETEC, EAEC, and EIEC, with greater diversity in Farms 2 and 3. Membrane filtration and culture methods confirmed the presence of gram-negative bacteria (GNB) in most samples. Pathogens such as Enterobacter cloacae, Klebsiella oxytoca, and Pseudomonas aeruginosa were isolated and confirmed with the Vitek 2 system. Enterobacter cloacae was consistently detected in onion samples, Antimicrobial Resistance: Antibiotic susceptibility testing revealed multidrug resistance among Enterobacter cloacae, Klebsiella oxytoca, and Pseudomonas aeruginosa. Resistance to ampicillin, colistin was noted. Most of the strains identified as Enterobacter cloacae by phenotypic methods were identified as Enterobacter Ludwigii. These findings highlight the potential risks of waterborne pathogen transmission and the need for stringent water treatment and management practices to safeguard agricultural and public health.1 online resource (xi, 55 leaves): color illustrationsenUniversity of VendaEnterobactriaceaeUCTDIrrigation waterOnion decaySoilVitek-2579.34EnterobacteriaceaeEnterobacterGram-negative bacteriaDissertationLukheli E. Identification and characterization of enterobacter species causing decay of onions and their antimicrobial susceptibility. []. , 2025 [cited yyyy month dd]. Available from:Lukheli, E. (2025). <i>Identification and characterization of enterobacter species causing decay of onions and their antimicrobial susceptibility</i>. (). . Retrieved fromLukheli, Elelwani. <i>"Identification and characterization of enterobacter species causing decay of onions and their antimicrobial susceptibility."</i> ., , 2025.TY - Dissertation AU - Lukheli, Elelwani AB - Background: Plants are susceptible to a range of health problems, and onions are no exception. While onions are relatively resilient, they are not immune to diseases and pathogens. Onions that are packed before being fully dried are prone to rapid decay. Research has shown that water can facilitate the transmission of pathogens and contribute to microbial contamination of fresh produce, including Salmonella and E. coli. Salmonella can enter the soil through agricultural practices such as pesticide application, the use of fertilizers derived from animal manure, and irrigation with contaminated water. Since irrigation water can come from various sources—such as municipal supplies, treated wastewater, rivers, or groundwater—farmers are advised to safeguard their water sources to reduce the risk of contamination. Objective: To identify and characterize Enterobacter species causing decay of bulb onions and their antimicrobial susceptibility. Methods: This study was carried out in the Vhembe district in the Limpopo province. The focus was on farms in various municipalities, including both commercial and subsistence farms, as well as the rivers surrounding these farms. Water, soil, and onion samples were collected. The presence of total coliform and E. coli was determined using the Colilert Quanti tray method. Collected samples were further analyzed for Enterobacteriaceae using membrane filtration and culture-based methods. Biochemical tests (Vitek-2-system) were used to identify and confirm the isolates. E. coli pathotypes were characterized using multiplex PCR. The characterization of strains from Enterobacter species was done using Sanger Sequencing. Results: Measured temperatures ranged from 19.8°C to 25°C, with Farm 2 showing slightly elevated values. Electrical conductivity (EC) values were within acceptable limits (<540 μS/cm) across all farms, though Farm 3 exhibited higher total dissolved solids (TDS) levels, reaching up to 450 mg/L. The pH values across farms ranged from 5.0 to 6.4, lower than the recommended 6.5–8.5 for agricultural water. Elevated TDS and acidic pH in Farm 3 was observed. High levels of total coliforms (up to 2419.6 MPN/100 mL) and the presence of E. coli were detected in water and onion samples, particularly from Farms 2 and 3. PCR analysis identified multiple E. coli pathotypes, including EPEC, ETEC, EAEC, and EIEC, with greater diversity in Farms 2 and 3. Membrane filtration and culture methods confirmed the presence of gram-negative bacteria (GNB) in most samples. Pathogens such as Enterobacter cloacae, Klebsiella oxytoca, and Pseudomonas aeruginosa were isolated and confirmed with the Vitek 2 system. Enterobacter cloacae was consistently detected in onion samples, Antimicrobial Resistance: Antibiotic susceptibility testing revealed multidrug resistance among Enterobacter cloacae, Klebsiella oxytoca, and Pseudomonas aeruginosa. Resistance to ampicillin, colistin was noted. Most of the strains identified as Enterobacter cloacae by phenotypic methods were identified as Enterobacter Ludwigii. These findings highlight the potential risks of waterborne pathogen transmission and the need for stringent water treatment and management practices to safeguard agricultural and public health. DA - 2025-09-05 DB - ResearchSpace DP - Univen KW - Enterobactriaceae KW - Irrigation water KW - Onion decay KW - Soil KW - Vitek-2 LK - https://univendspace.univen.ac.za PY - 2025 T1 - Identification and characterization of enterobacter species causing decay of onions and their antimicrobial susceptibility TI - Identification and characterization of enterobacter species causing decay of onions and their antimicrobial susceptibility UR - ER -