Microorganisms, encompassing bacteria, fungi, viruses, protozoa, and algae, are prevalent globally. These microflora communities are generally avirulent. However, pathogenic microbes have contaminated food systems, particularly fresh produce, leading to significant outbreaks of foodborne illnesses. Key pathogens of concern include Salmonella, associated with contamination in tomatoes, seed sprouts, and spices, and Escherichia coli, frequently found in leafy greens like spinach and lettuce.(Carstens et al., 2019) These pathogens can infect produce at any point in the supply chain, from cultivation and harvesting to processing, storage, and distribution. The risk is amplified when produce is consumed raw, such as in salads or as uncooked fruits and vegetables. The increasing prevalence of multidrug-resistant strains among these foodborne pathogens poses a critical public health challenge, complicating treatment and elevating the risk of severe disease outcomes (Helmy et al., 2023). The widespread, persistent presence of antibiotic-resistant bacteria and their associated genes in the environment, largely due to the excessive and inappropriate use of human and veterinary antibiotics, exacerbates this global concern (Sarailoo et al., 2024; Sharma et al., 2024; Zhang et al., 2022).

Gracie's Kitchens has initiated a recall of 150 fruit and vegetable products due to potential contamination with Listeria monocytogenes. This bacterium can cause severe illness, particularly in vulnerable populations such as the elderly, young children, and immunocompromised individuals(Yan et al., 2025). Highlighting the severity of this pathogen, Listeria is responsible for an estimated 1,600 infections and 260 deaths annually in the United States(Self et al., 2019; Sharma et al., 2025). Beyond Listeria, a notable incident involved a multi-state outbreak of E. coli O157:H7 infection linked to recalled yellow onions from Taylor Farms, which were distributed to McDonald's restaurants in several states. This outbreak affected 104 individuals across 14 states, leading to 34 hospitalizations and one fatality. While the specific E. coli strain was not isolated from onion or environmental samples, the recalled onions were identified as the probable source(Mitchell et al., 2024; Racine et al., 2024). Similarly, a multi-state outbreak of Salmonella Africana and Salmonella Braenderup was associated with Bedner Growers, Inc. and Thomas Produce Company in Florida.(Marshall et al., 2020; Mitchell et al., 2024) Although both farms had concluded their growing seasons and no product was actively on the market, Salmonella strains matching those in the outbreak were detected in water samples from both locations. This outbreak resulted in 155 hospitalizations without any reported deaths. Major outbreak events are further detailed in Table 1. These instances underscore the persistent threat posed by foodborne pathogens, particularly those exhibiting antimicrobial resistance, which can lead to widespread public health crises and economic burdens (Iwu & Okoh, 2019) (Rahman et al., 2021).

When considering food safety, pesticide-treated fruits and vegetables present several harmful health effects on the human body(Benbrook et al., 2021). Organic farming avoids synthetic pesticides and relies on more natural methods for fruit and vegetable treatment, reducing chemical residues in pesticide-treated produce (Benbrook et al., 2021; Mie et al., 2016). However, while organic farming reduces chemical residues, it is not immune to contamination by harmful microorganisms such as multidrug-resistant bacteria, even with the use of natural fertilizers(Kiplimo et al., 2025). The presence of MDR bacteria in produce, including organic varieties, poses a significant public health risk as these resistant strains can cause infections that are difficult to treat with conventional antibiotics (Iwu & Okoh, 2019; Rahman et al., 2021). For instance, a 2023 study demonstrated MDR bacteria in fresh fruits in low-cost Ecuadorian markets, highlighting the potential for these pathogens to enter the food chain regardless of farming practices. It is therefore necessary to develop strategies to ensure food security and safety by reducing bacterial contamination in both farm and retail markets and to prevent or reduce the spread of antibiotic-resistant infections within the population. The presence of antibiotic-resistant bacteria and antibiotic resistance genes in fresh produce is increasingly reported as a cause of foodborne disease outbreaks, necessitating comprehensive intervention strategies (Rahman et al., 2021). (Kiplimo et al., 2025; Wu-Wu et al., 2023) Studies indicating a significant risk of outbreaks further amplify this heightened concern a significant risk of outbreaks stemming from antimicrobial resistance and multidrug-resistant pathogens in contaminated fresh produce, underscoring the urgent need to elucidate the mechanisms of farm-level contamination (Glaize et al., 2019).

Foodborne illnesses represent a significant public health challenge, with an estimated 48 million individuals experiencing such diseases annually(Mather et al., 2024). These illnesses are also widely documented as transmissible(Vourc’h et al., 2022). Compounding this issue, several of these bacteria exhibit resistance to common medications(Farrukh et al., 2025). Future pandemics may not solely be caused by viruses like Covid, but rather by dangerous pathogens such as methicillin-resistant Staphylococcus aureus(Carrel et al., 2024). Treating antibiotic-resistant bacteria is significantly more difficult and would likely lead to elevated mortality rates, expensive medical treatments, and increased hospitalization(Baltazar & Campos, 2025). Therefore, understanding which bacteria are commonly resistant to antibiotics and their origins is crucial.

Antibiotics are vital medications that inhibit the growth of microorganisms, effectively preventing bacterial infections. The mechanisms of commonly used antibiotics are detailed in Table 2. However, bacterial pathogens, such as Escherichia coli, can develop resistance to antibiotics and transfer this resistance to other bacteria, thereby diminishing the effectiveness of standard treatments for common bacterial infections^[2]. Of particular concern are certain strains of E. coli that have become multidrug-resistant (MDR), exhibiting resistance to multiple classes of antibiotics. The global rise of MDR microorganisms poses a significant threat to public health, rendering many infections untreatable with conventional therapies(Ahmed et al., 2024). These pathogens, including MDR E. coli, have developed resistance to critical antibiotics, such as cephalosporins and carbapenems, often through the production of extended-spectrum beta-lactamases (ESBL).

The development of antibiotic resistance arises from multiple mechanisms, including natural selection, genetic mutations, and the acquisition of resistance-conferring genes. Bacteria can acquire resistance through horizontal gene transfer, which involves the direct exchange of genetic material between cells (Elshobary et al., 2025; Schindel, 2013; Urban-Chmiel et al., 2022). Due to their prokaryotic nature, bacteria have a remarkable ability to share resistance genes, enabling rapid dissemination across populations. These horizontally acquired genes often confer resistance to specific antimicrobial agents. A key example is efflux pumps, which actively expel antibiotics from the bacterial cell, preventing the buildup of therapeutic concentrations (Lomovskaya & Watkins, 2001; Nishino et al., 2021). This mechanism typically targets particular antibiotics, allowing resistant strains to survive and multiply during treatment. Highly resistant pathogens, such as methicillin-resistant Staphylococcus aureus and multidrug-resistant Mycobacterium tuberculosis, exemplify the severe challenges of antibiotic resistance (Halawa et al., 2024). MRSA is a leading cause of healthcare-associated infections, while MDR-TB represents a major global health threat due to resistance to multiple first-line antituberculosis drugs (Karnan et al., 2024). Bacteria producing extended-spectrum beta-lactamases further complicate treatment, enzymes that degrade key antibiotics like cephalosporins and penicillins, rendering them ineffective (Alen et al., 2023; Shaikh et al., 2014). As a result, ESBL-producing infections are difficult to treat and often lead to poor outcomes. Table 3 outlines additional key mechanisms of antibiotic resistance.

Resistant bacteria spread via various routes, including person-to-person contact, airborne transmission, and environmental contamination. In food safety contexts, these bacteria can contaminate products throughout production and handling, posing substantial public health risks (Bava et al., 2024; Samtiya et al., 2022).

The rising prevalence of antibiotic resistance highlights the need to understand its mechanisms, curb its spread, and develop effective interventions. Essential strategies to combat this crisis and preserve antibiotic efficacy include enhanced surveillance, rigorous hygiene, and innovative approaches (Elshobary et al., 2025; Mmbando et al., 2025; Singha et al., 2024). These include antibiotic stewardship programs (Elshobary et al., 2025), phage therapy (Singha et al., 2024), probiotics to reshape microbial communities, predatory bacteria, combination antibiotic therapies to boost effectiveness and hinder resistance, and real-time monitoring of multidrug resistance. This multifaceted approach is critical to address the complex challenge of antibiotic resistance, which stems from various bacterial mechanisms including enzymatic modification, reduced binding affinity, changes in cell permeability, and the overexpression of efflux pumps (Elshobary et al., 2025).(Darby et al., 2022; Elshobary et al., 2025)

This study comprehensively evaluated the prevalence of multidrug-resistant bacteria in local community environments and agricultural products, confirming substantial contamination risks. The study collected bacterial samples from diverse sources, including public schools, organic produce, and conventionally grown produce, followed by rigorous testing and analysis that definitively characterized their antimicrobial and MDR profiles. The study successfully identified agricultural products with high levels of resistant bacteria, demonstrated the superior efficacy of probiotics over specific antibiotics against these strains, and validated practical strategies using readily available tools to effectively curb resistance dissemination. Moreover, artificial intelligence-based methodologies robustly monitor resistance patterns, enhance clinical interventions, and optimize preventive measures(Lastra et al., 2024; Saeed et al., 2023). These findings directly inform and enable targeted interventions to manage MDR bacteria in community and agricultural settings.

All reagents were purchased from Amazon unless otherwise specified.

Across 34 isolate-level susceptibility profiles spanning nine antibiotics (chloramphenicol, neomycin, penicillin, kanamycin, novobiocin, streptomycin, erythromycin, tetracycline, and ampicillin), resistance patterns were strongly dependent on sample source (organic produce, traditional/conventional produce, and “community site”). Employing the scoring scheme depicted in the table (R = 1, I = 0.5, S = 0) to derive a composite "total resistance" score per isolate, isolates from organic produce demonstrated low overall resistance (mean = 1.34, median = 0.5, n = 19), while those from traditional produce exhibited predominantly multidrug resistance (mean = 6.94, median = 7.5, n = 9). Community site isolates displayed near-universal resistance across the antibiotic panel (mean = 8.42, median = 9, n = 6), with most profiles showing "R" in nearly every category. Applying an operational MDR threshold of resistance to ≥3 antibiotic classes yielded prevalences of 15.8% in organic isolates, 88.9% in traditional isolates, and 100% in community isolates. Notably, the organic dataset encompassed both fully susceptible isolates and sporadic instances of elevated resistance, highlighting intra-group heterogeneity (Table 4 and Figure 1).

When aggregating data across all samples, kanamycin and erythromycin exhibited the highest weighted resistance burdens (weighted resistance fraction ≈0.515 each), followed by penicillin (≈0.50) and streptomycin (≈0.456). Tetracycline displayed the lowest overall resistance (weighted fraction ≈0.353) among the antibiotics evaluated (Figure 1). Stratification by sample source indicated that this global resistance profile was primarily propelled by isolates from traditional produce and community sites, whereas organic isolates were largely susceptible across the panel, with only infrequent resistant or intermediate outcomes.

A minor discrepancy was noted in one "community site" entry: comprising two intermediates and seven resistant isolates, it should sum to 8.0 per the scoring scheme (R=1, I=0.5, S=0), yet the table lists 7.0. This likely reflects a transcription, rounding, or scoring anomaly that warrants correction during manuscript revision to uphold reproducibility. Further rigorous data validation and re-evaluation of the scoring rubric will be undertaken to ensure the utmost accuracy and consistency in the reported resistance profiles. A semi-quantitative antagonism screen was performed using four probiotic consortia against bacterial isolates recovered from eight produce categories. Inhibition outcomes were categorically scored as strong inhibition (I), intermediate inhibition, or no inhibition.

The Lactobacillus + Bifidobacterium consortium showed the broadest activity, producing I in 7/8 conditions and only failing to inhibit isolates from conventional strawberry (with intermediate inhibition against organic strawberry, suggesting partial but incomplete suppression in that matrix). By contrast, the Lactobacillus consortium displayed more selective activity: it inhibited isolates from organic apple, organic strawberry, and organic capsicum, but failed against those from conventional apple, conventional strawberry, conventional lettuce, organic lettuce, and conventional capsicum indicating a narrower spectrum or reduced competitiveness under several isolate backgrounds. (Figure 2)

The Bacillus consortium exhibited the weakest overall performance, showing NI across 6/8 produce categories and only intermediate inhibition against isolates from organic strawberry and organic capsicum, which highlights its limited antagonistic potential in this screen. Meanwhile, the Bifidobacterium consortium demonstrated strong inhibition against both apple categories and conventional lettuce, intermediate inhibition against both strawberry categories and organic lettuce, but no inhibition against both capsicum categories revealing a produce-type-dependent profile distinct from the Lactobacillus-dominant formulations.

Overall, these data suggest that probiotic consortia efficacy in inhibiting bacterial growth depends heavily on both the specific strains employed and the environmental context of the bacterial isolate, underscoring the challenges in developing universal probiotic interventions.

The present study investigated antibiotic and multidrug resistance phenotypes in bacterial isolates from organic, traditionally grown produce, and community-sourced environmental samples. These data reveal marked enrichment of MDR in isolates from traditional produce and community sites compared to organic produce. Near-pan-resistant community profiles suggest environments harboring broad intrinsic resistance, repeated antimicrobial selection, or cross-contamination amplifying resistant strains. In contrast, organic isolates predominantly showed full susceptibility or minimal resistance, though occasional high-resistance cases indicate that organic status alone does not preclude exposure risks from point-source events.

Mechanistically, elevated β-lactam and aminoglycoside resistance in high-resistance groups aligns with common environmental bacterial mechanisms like enzyme inactivation, efflux, and permeability changes, while strong erythromycin resistance reflects widespread macrolide determinants across Gram-positive and -negative taxa. Lower tetracycline resistance may stem from underrepresentation of resistant taxa or phenotypic assay limits for borderline cases in mixed communities. These phenotypic data capture only culturable fractions under specific conditions—not the full microbiome—potentially underestimating the resistance reservoir, as unculturable components harbor diverse mechanisms (Rodríguez et al., 2006).

These findings justify probiotic screening strain selection: traditional and community isolates form a stringent panel, while organic isolates serve as low-resistance comparators to discern broad- from resistance-specific inhibition. This manuscript specifies unique isolates advanced from each category and any enrichment of resistant profiles. Absent standardized breakpoints for environmental bacteria, interpretations relied on clinical thresholds for E. coli and S. aureus as proxies (Mafiz et al., 2021; VOİDAROU et al., 2009).

Finally, several limitations should be acknowledged: (1) the dataset appears to represent a modest number of isolates per produce type and category (with some categories having n=1 entry), limiting statistical power; (2) intermediate calls were incorporated as 0.5 by convention, but interpretation thresholds may vary by organism and guideline, and (3) “community place” is operationally broad—defining the sampling context (surface type, handling, and environmental conditions) will strengthen causal interpretation. Addressing these points will make the resistance dataset a strong foundation for the subsequent probiotic efficacy results and the overall argument that targeted biocontrol strategies may be necessary to reduce the MDR load associated with certain produce-handling environments.

Furthermore, future research could benefit from integrating metagenomic approaches to provide a more holistic understanding of the resistome, including non-culturable bacteria and mobile genetic elements, which are crucial for the dissemination of antibiotic resistance genes within urban agricultural systems (Harrelson et al., 2025). Such molecular characterization would allow the identification of specific genetic mechanisms underlying resistance and elucidate potential horizontal gene transfer events (Abraham et al., 2025).

Probiotics are live microorganisms that have beneficial effects on the body and improve or restore the gut microbiota. Probiotic bacteria have the ability to influence particular immune functions and immunological homeostasis by interacting with and stimulating commensal microflora and intestinal immune cells(Mazziotta et al., 2023). Probiotics have the potential to improve gut microflora by encouraging the growth of beneficial bacteria and suppressing the growth of harmful pathogens, such as MDR bacteria(Wieërs et al., 2021). Wieërs et al., 2021 suggested that patients treated with probiotics upon admission to the hospital had fewer MDR pathogens like Pseudomonas aeruginosa in the digestive tract. Broad-spectrum vs selective inhibition

The most prominent finding is the superior breadth of Consortium 1 (Lactobacillus + Bifidobacterium multi-species), which inhibited isolates from nearly all produce categories. Broad-spectrum activity in multi-strain lactobacilli/ bifidobacteria blends is biologically plausible because such consortia can deploy multiple inhibitory mechanisms simultaneously, including organic acidification, competitive nutrient depletion, bacteriocin-like antimicrobials, and quorum-interference effects mechanisms that often vary by strain and collectively increase coverage against heterogeneous target isolates. In contrast, the narrower profile of Consortium 2 (two Lactobacillus spp.) suggests either (i) reduced mechanistic diversity, (ii) insufficient inhibitory metabolite production under the assay conditions, or (iii) mismatch between probiotic strains and the dominant isolate taxa recovered from certain produce types (notably lettuce and conventional samples).

Overall, phenotypic susceptibility profiling showed a strong source-dependent resistance burden, with isolates from traditional produce and community sampling sites exhibiting markedly higher multidrug resistance than isolates recovered from organic produce. These findings justify prioritizing high-resistance isolates as stringent challenge strains for downstream probiotic-consortium screening and support the need for targeted interventions to reduce the MDR-associated microbial load in produce handling environments. Furthermore, the multi-species Lactobacillus + Bifidobacterium consortium showed the broadest inhibitory activity across produce-derived isolates, whereas the Bacillus consortium exhibited minimal inhibition and the smaller Lactobacillus/Bifidobacterium blends showed produce-dependent selectivity. These results support prioritizing the multi-species consortium for confirmatory, quantitative testing in produce-surface models to validate robustness and real-world applicability.