Tomato (Solanum lycopersicum) is an essential crop worldwide, yet it remains highly vulnerable to severe fungal and bacterial diseases. Traditional chemical-based disease management strategies, aimed at controlling these diseases face increasing scrutiny, due to concerns regarding pathogen resistance, environmental degradation, and potential health risks to humans. This has catalyzed the exploration of sustainable alternatives, with biological control emerging as a viable and promising strategy. Endophytic and epiphytic microorganisms are pivotal as biocontrol agents (BCAs), employing diverse strategies, such as generating antimicrobial substances, enzymes, and volatile organic compounds (VOCs), to suppress pathogen growth and enhance plant health. The efficacy of these antagonistic microorganisms is influenced by the cultivation systems employed, with significant variations observed between soil and hydroponic environments. Factors such as nutrient dynamics and microbial interactions play crucial roles in determining the success of BCAs in these different settings. The advent of metagenomic tools has transformed the landscape of microbial community research, facilitating the identification of functional genes associated with antagonistic activities and the adaptation of these microorganisms to diverse environmental conditions. This review aims to elucidate the potential of endophytic and epiphytic microorganisms in biological control, examining their mechanisms of action, the impact of cultivation systems on their effectiveness, and the application of metagenomics to optimize their use in sustainable disease management strategies for tomato crops.

Diarrheagenic Escherichia coli (DEC) pathotypes are the leading cause of mortality and morbidity in South Asia and sub-Saharan Africa. Daily interaction between people contributes to the spreading of Escherichia coli (E. coli), and fomites are a common source of community-acquired bacterial infections. The spread of bacterial infectious diseases from inanimate objects to the surrounding environment and humans is a serious problem for public health, safety, and development. This study aimed to determine the prevalence and antibiotic resistance of diarrheagenic E. coli found in toilets and kitchen cloths in the Vhembe district, South Africa. One hundred and five samples were cultured to isolate E. coli: thirty-five samples were kitchen cloths and seventy-five samples were toilet swabs. Biochemical tests, API20E, and the VITEK^®-2 automated system were used to identify E. coli. Pathotypes of E. coli were characterised using Multiplex Polymerase Chain Reaction (mPCR). Nine amplified gene fragments were sequenced using partial sequencing. A total of eight antibiotics were used for the antibiotic susceptibility testing of E. coli isolates using the Kirby–Bauer disc diffusion method. Among the collected samples, 47% were positive for E. coli. DEC prevalence was high (81%), with ETEC (51%) harboring lt and st genes being the most dominant pathotype found on both kitchen cloths and toilet surfaces. Diarrheagenic E. coli pathotypes were more prevalent in the kitchen cloths (79.6%) compared with the toilet surfaces. Notably, hybrid pathotypes were detected in 44.2% of the isolates, showcasing the co-existence of multiple pathotypes within a single E. coli strain. The antibiotic resistance testing of E. coli isolates from kitchen cloths and toilets showed high resistance to ampicillin (100%) and amoxicillin (100%). Only E. coli isolates with hybrid pathotypes were found to be resistant to more than three antibiotics. This study emphasizes the significance of fomites as potential sources of bacterial contamination in rural settings. The results highlight the importance of implementing proactive measures to improve hygiene practices and antibiotic stewardship in these communities. These measures are essential for reducing the impact of DEC infections and antibiotic resistance, ultimately safeguarding public health.