First Report of Enterobacter ludwigii and Other Potentially Pathogenic Enteric Bacteria in Onions, Soil, and Irrigation Water from the Vhembe Region, South Africa.

The presence of antimicrobial-resistant bacteria in fresh produce constitutes a significant public health concern, particularly in rural areas where untreated water is commonly used for irrigation. Certain Enterobacter species have been reported as causal agents of onion bulb rot, with Enterobacter cloacae experimentally demonstrated to cause bulb rot in onions. However, there is poor documentation of its effects in the Vhembe District, South Africa. This study investigated the detection and identification of enteric bacteria in onions, soil, and irrigation water, as well as the characterisation of the identified isolates. Thirty-six samples were analysed, comprising 13 onion samples, 4 irrigation water samples, and 9 soil specimens collected from three farms using selective and differential agar. Identification and enumeration in water and onion samples were performed with the Colilert Quanti-Tray. Physicochemical analysis of irrigation water indicated that Farm 3 had the highest electrical conductivity (EC) and total dissolved solids (TDS), as well as the lowest pH, while Farm 2 exhibited the greatest diversity of pathogenic Escherichia coli pathotypes, including enteroinvasive E. coli (EIEC), which was absent in Farm 3. Culture-based methods yielded 72 presumptive bacterial isolates, which were characterized using the VITEK 2 system. Identified species included Pseudomonas aeruginosa, Klebsiella pneumoniae, Klebsiella oxytoca, Citrobacter amalonaticus, Raoultella ornithinolytica, and members of the Enterobacter cloacae complex. Phylogenetic analysis revealed that most Enterobacter isolates closely matched reference strains of Enterobacter ludwigii. Antimicrobial susceptibility testing against 19 antibiotics demonstrated varied resistance patterns among the isolates. The Enterobacter cloacae complex exhibited the highest resistance (10/19 antibiotics), followed by Klebsiella pneumoniae (9/19) and Citrobacter amalonaticus (7/19). All isolates were resistant to colistin but remained susceptible to ciprofloxacin, with most also sensitive to gentamicin and amikacin. Future research should include additional farms and investigate antibiotic resistance at the genetic level to elucidate its origins.