Postharvest food safety increasingly relies on non-thermal, minimal, or “mild” interventions to preserve product quality while controlling foodborne pathogens. However, microorganisms encountered during postharvest handling are frequently exposed to sequential sub-lethal stresses rather than single lethal events. Accumulating evidence suggests that such stress histories can profoundly reshape bacterial physiology, promoting stress adaptation, phenotypic heterogeneity, and cross-protection against subsequent treatments. This perspective argues that sub-lethal stress history should be considered a central design variable in microbial control rather than an incidental consequence of processing. We discuss how prior exposures influence microbial susceptibility, why intervention efficacy becomes stress history-dependent, and how microbial stress responses complicate the interpretation of conventional validation studies that rely on unstressed cultures. We further examine how hurdle interactions and commodity-specific environments shape stress conditioning and influence downstream treatment performance. From a systems perspective, we argue that the quality-safety tradeoff associated with mild processing should be reconsidered through a stress-aware lens that explicitly accounts for microbial adaptation. Finally, we propose a conceptual framework for integrating stress history into strategy design, challenge testing, process validation, and risk management. Recognizing stress history as a dynamic determinant of microbial behavior may help improve the robustness, predictability, and real-world reliability of postharvest food safety systems across diverse commodities.

We assessed the prevalence, persistence, genetic diversity, and AMR dynamics of Salmonella spp. (SAL) in surface waters (SuWa) of Central Mexico. On-site, 953 samples (10 L each) from 49 watersheds were collected in 24 sampling rounds (2019-2023) using the modified Moore swab technique. SAL was isolated and identified using conventional microbiological procedures and sequenced on Illumina platforms. Overall, the prevalence of SAL was 54%, with higher values (χ2=23.9, P<0.0001) observed in Tlaxcala and the State of Mexico (64%) than in the other regions (42-50%). The top 10 serovars (Agona, Anatum, Newport, London, Adelaide, Derby, Senftenberg, Infantis, Typhimurium, and Muenchen) represented nearly half of the population and were systematically isolated across sampling rounds and years. The most frequent antimicrobial resistance (AMR) phenotypes involved older antibiotics (e.g., tetracycline, streptomycin, and chloramphenicol: 36%, 33%, and 24%, respectively). Approximately 12% of the isolates showed resistance to azithromycin, whereas resistance to cephalosporins, carbapenems, amikacin, and fluoroquinolones was rarely observed (~0-5%). One-third of the isolates exhibited multidrug-resistant (MDR) phenotypes and genotypes. The overall pool of AMR determinants (62 genes and four gene point mutations) encoded 15 different resistance mechanisms at the population level. The prevalence of AMR phenotypes to older antibiotics and the abundance of AMR genes against all antimicrobial classes increased in the post-COVID-19 pandemic period (0.1-0.4 and 0.1-0.6 Log10-fold change, respectively). These results underscore the public health risks associated with agricultural SuWa and the need for further research to identify the sources of SAL contamination.

Cronobacter sakazakii is an opportunistic foodborne pathogen associated with severe infections in infants, linked to powdered infant formula (PIF) and related products. We conducted genomic profiling of C. sakazakii (n=209) from infant and toddler food in the United States, comprising all publicly available genomes for this source, through the integration of antimicrobial resistance (AMR) gene (ARG), plasmid replicon, virulence gene, phylogenetic, and pan-genome analyses. We further applied a machine learning (ML)-driven isolation source classification approach based on pan-genome features to distinguish food and clinical isolates. AMR analysis revealed a conserved resistome dominated by three β-lactam resistance genes (blaCSA, blaCSA-1, and blaCSA-2). Independent co-occurrence and pairwise association analysis of ARGs and plasmid replicons indicated sparse and gene-specific relationships, suggesting that observed AMR patterns were more consistent with conserved resistance determinants than extensive plasmid-mediated dissemination. Phylogenetic analysis identified two major clades, while pan-genome assessment demonstrated an open genome dominated by accessory genes. Using gene presence/absence profiles, a random forest classifier achieved high accuracy in distinguishing food and clinical isolates, highlighting the classification power of pan-genome signatures within the dataset. These findings provide insights into the genomic structure of food-associated C. sakazakii and the utility of integrating comparative genomics with ML for food safety surveillance.

We analyzed the prevalence dynamics, genetic diversity, and AMR dynamics of Salmonella spp. (SAL) across surface waters (SuWa) in Central Mexico. On-site, 953 samples (10 L each) from 49 watersheds were collected in 24 sampling rounds (2019–2024) using the modified Moore swab technique. SAL was isolated and identified using conventional microbiological procedures and sequenced on Illumina platforms. Overall, the prevalence of SAL was 54

Cronobacter sakazakii is a rare, life-threatening neonatal pathogen. In this study, we profiled antimicrobial resistance genes (ARGs), plasmid replicons, virulence genes, sequence types (STs), and core-genome phylogeny across all publicly available clinical C. sakazakii genomes from the United States (n = 116). All isolates harbored exclusively chromosomally encoded blaCSA variants. IncFIB and rep cluster 574 co-occurred in 93.1% of isolates as a conserved backbone among 17 replicon types. Among 49 virulence genes, 13 formed a universal core (flagellar motility and type VI secretion); accessory genes such as the yersiniabactin cluster were sporadic. ARG, plasmid replicon, and virulence gene contents were strongly structured by ST, dominated by ST4, ST1, ST8, and ST13. Stratified testing shows most pairwise associations were confounded by clonal lineage, except the IncFIB-rep cluster 574 co-carriage and an IncFII-hcp/tssD association, significant after ST stratification but not multiple testing correction. Core-genome phylogenetics identified 16 clusters, from a large ST4-dominated group to nine singletons, corroborated by ST monophyly; a genomically identical ST1 pair, nine years apart, indicated long-term clonal persistence. Ancestral state reconstruction distinguished stable single acquisitions from features with repeated turnover. Core-genome and gene-content phylogenies demonstrated substantial discordance despite significant overall correlation. These findings provide a genomic framework for clinical C. sakazakii population structure in the United States.

Introduction:Long-term use of chemical pesticides has caused environmental and resistance-related concerns, highlighting the need for environmentally friendly plant immune inducers. This study aimed to prepare curdlan oligosaccharides (CDOS) and evaluate their immune-inducing activity in Arabidopsis thaliana. Methods:CDOS were prepared by enzymatic hydrolysis and purified by dialysis. Their structural characteristics were analyzed by TLC, FTIR, and ESI-MS. Antibacterial activity against Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), disease resistance in A. thaliana, ROS accumulation, defense-related enzyme activities, and immune-related gene expression were further investigated. Results:The purified CDOS preparation mainly consisted of oligosaccharides with a degree of polymerization of 2-3, with a total sugar content of 81.62% and a residual protein content of 3.25%. CDOS showed no direct antibacterial activity against Pst DC3000 but significantly enhanced resistance in A. thaliana, reducing bacterial colonization by approximately 50% at 50 mg/L. CDOS also promoted ROS accumulation, increased POD, SOD, CAT, and PAL activities, and upregulated the SA-associated marker genes PR1, PR2, and PR5, whereas the JA-associated genes VSP and PDF1.2 were not significantly altered. The protective effect was impaired in SA-pathway-deficient mutants but retained in the JA-pathway mutant. Discussion:These findings indicate that CDOS functions primarily as a plant immune elicitor rather than a direct antibacterial agent, and its protective activity is closely associated with SA-dependent defense responses.

The seaweed Laminaria japonica possesses a wide range of nutritional and medicinal properties, such as antioxidant and hypoglycemic effects. Previous research has demonstrated that fermenting Laminaria japonica with S. cerevisiae and Lactobacillus enhances its bioactivities. In this study, fermented Laminaria japonica underwent ethanol extraction to recover bioactive compounds. The impact of fermented seaweed extracts (FSE) on renal injury in streptozotocin-induced diabetic nephropathy rats was examined. Through UHPLC-MS/MS analysis, 44 compounds were identified in the fermented seaweed extracts, with carbohydrates and organic acids being the main classes. Fermented seaweed extracts significantly reduced streptozotocin-induced hyperglycemia, improved renal function markers (BUN, SCr, and Umalb), and mitigated kidney morphological changes. Specifically, the FSE-H group exhibited a 49% reduction in fasting glucose levels compared to the model group. Additionally, fermented seaweed extracts treatment downregulated both the transcriptional and protein levels of PI3K, Akt, and mTOR, suggesting involvement of the PI3K/AKT/mTOR-regulated pathway. These findings suggest that fermented seaweed extracts have potential as a therapeutic agent or functional ingredient for the treatment of diabetic nephropathy.

Pre-exposure to sub-lethal stress can increase the resistance of foodborne pathogens to inactivation processes, posing potential risks to food safety. This study examined how sub-lethal stress influences the resistance of Salmonella enterica to ultraviolet-C (UV-C) treatments on raw whole almonds (RWAs) and fresh-cut leafy greens (FCLGs), investigated the role of rpoS in stress-induced cross-protection, and evaluated Enterococcus faecium NRRL B-2354 as a surrogate for S. enterica. Additionally, we assessed the survival of sub-lethally stressed cells on FCLGs under cold or temperature abuse condition post-UV-C treatment. A cocktail of three S. enterica strains, along with S. Typhimurium ATCC 14028 and its ΔrpoS mutant (IB43), were exposed to desiccation stress, heat shock, oxidation stress, or acid stress. Afterward, stressed and unstressed cells were inoculated onto RWAs and FCLGs, and treated with UV-C (500 μW/cm2, 60 min). Treated FCLGs were then stored under cold or temperature abuse condition for 7 days. Results showed that acid-stressed S. enterica exhibited greater UV-C resistance on RWAs, while oxidation-stressed cells had increased survival on FCLGs (p < 0.05). Under temperature abuse, unstressed, oxidation-stressed, or acid-stressed S. enterica were inactivated faster, whereas heat-shocked cells persisted until Day 7. Desiccation-stressed cells rebounded temporarily before inactivation by Day 7. IB43 was more susceptible to UV-C (p < 0.05) than the wild-type strain and lacked cross-protection from prior sub-lethal stress exposure, confirming the crucial role of rpoS in UV-C resistance and stress adaptation. NRRL B-2354 demonstrated comparable or greater survival than S. enterica, supporting its use as a suitable surrogate. These findings highlight the influence of sub-lethal stress on UV-C resistance in S. enterica and emphasize the importance of including stress-adapted pathogens in challenge studies to improve food safety.

Salmonella enterica serotype Typhimurium is a leading cause of foodborne outbreaks linked to chickens in the United States. To investigate the genomic landscape of this population, 1048 chicken-associated S. Typhimurium genomes collected nationwide were analyzed. Overall, 84.5% of isolates carried at least one antimicrobial resistance (AMR) determinant, and 34.3% displayed multidrug resistance (MDR). Sulfonamide and tetracycline resistance were most prevalent (1.03 and 1.01 AMR determinant per isolate, respectively). AMR gene (ARG) co-occurrence analysis identified strong associations among tet(A), sul1, sul2, aac(3)-VIa, and aadA1, with blaCMY-2 emerging within an expanding co-resistance cluster. ARG-plasmid replicon association analysis indicated significant positive links between sul2 and tet(A) with IncC and ColRNAI. Machine learning-driven association rule mining demonstrated that integron carriage perfectly predicted MDR, and their absence in both non-AMR and AMR but non-MDR isolates underscores their pivotal role as the defining marker of MDR. We observed a pan-genome pattern with 3855 core and 9549 accessory genes, reflecting both genomic conservation and diversity. Whole-genome phylogenetic analysis revealed two major clades, with sequence type 19 comprising 99.0% of the isolates. This research provides a comprehensive genomic characterization of chicken-associated S. Typhimurium in the United States, highlighting key AMR mechanisms relevant for food safety and public health.

The increasing prevalence of antimicrobial resistance has raised significant concern globally. Colistin is currently considered a last resort for treating Gram-negative bacterial infections. However, the emergence of colistin resistance has led to a difficult situation against bacterial infections. Therefore, the monitoring of colistin resistance is of great importance for the control of bacterial infections. The mobile colistin resistance (mcr) gene has been identified as a colistin resistance gene, and ten mcr genes (mcr-1 to mcr-10) have been identified to date. Hence, the detection of mcr genes can help predict bacterial colistin resistance at the molecular level. However, there have not been reported multiplex PCR methods for simultaneously detecting mcr-1 to mcr-10 until now. In this study, we established a one-step multiplex PCR method for simultaneous detection of mcr-1 to mcr-10 for the first time. Furthermore, we retrospectively investigated the prevalence of the ten mcr genes in Escherichia coli (E. coli) and Salmonella isolates in China. The results showed that the mcr detection rate of Salmonella isolated during 2004-2019 was 4.73 % (16/338), and only mcr-9 was harbored. As well, the mcr detection rate of E. coli isolated during 2012-2015 was 20.42 % (49/240) and only mcr-1 was identified. Moreover, we also investigated the relationship between mcr harboring and colistin phenotype-resistance. The broth micro-dilution assay results showed that all mcr-1-positive E. coli isolates were colistin-resistant. However, all mcr-9-positive Salmonella isolates did not represent colistin-resistance. Our findings are beneficial for the monitoring and control of colistin resistance.

ABSTRACT Salmonella enterica is a significant foodborne pathogen frequently associated with produce contamination through irrigation with untreated surface water. This study investigated the effects of sampling replication and selective media on S. enterica serovar recovery and diversity in surface waters across Paraíba State, Brazil. Water samples ( n = 200) were collected from 10 reservoirs using modified Moore swabs (MMSs), with three replicates per sampling site, yielding 600 samples. The prevalence of S. enterica was 53.5% in individual samples, increasing to 68.5% when combining results from triplicate samples. Statistical analyses demonstrated that triplicate sampling significantly enhanced both recovery rates and serovar diversity compared with single samples ( P < 0.05). Alpha diversity metrics revealed a 39% increase in serovar richness when using triplicate versus single samples. The parallel use of multiple enrichment broths and selective agars proved essential for maximum serovar detection, as certain serovars were recovered exclusively under specific culture conditions. While triplicate sampling provided optimal detection sensitivity, duplicate sampling emerged as a cost-effective alternative, maintaining sufficient statistical power. These findings demonstrate the effectiveness of MMS combined with replicate sampling for comprehensive S. enterica surveillance in surface waters, with implications for water quality monitoring programs and public health risk assessment. IMPORTANCE Salmonella contamination in irrigation water poses a major threat to food safety, as contaminated produce can cause widespread foodborne illness outbreaks affecting thousands of people. Current water monitoring methods often miss these hazardous bacteria, creating blind spots in our food safety systems. This research addresses a critical gap by demonstrating that taking multiple water samples from the same location, rather than just single samples, improves our ability to detect Salmonella contamination. The study shows that collecting three samples instead of one increases the detection rate from 54% to 69% and reveals nearly 40% more serovars. This enhanced detection capability is crucial for protecting public health, as it provides more accurate information about the occurrence of Salmonella in natural surface waters. Lastly, our findings provide practical guidance for improving surveillance programs worldwide, offering a cost-effective approach that significantly strengthens our defense against Salmonella contamination in the food supply chain.

We report the draft genome sequences of 94 multidrug-resistant Salmonella isolates (S. Infantis, Enteritidis, and Typhimurium) from organic and conventional retail chickens in Maryland, USA (average genome size = 4.97 Mb; guanine-cytosine content = 52.12%). These isolates harbored diverse antimicrobial resistance and virulence genes, Salmonella pathogenicity islands, and plasmids, highlighting potential public health risks.

Considering the increasing reports of Salmonella enterica strains resistant to quinolones, antimicrobials frequently employed as therapeutic agents globally, our goal was to investigate the occurrence of plasmid-mediated quinolone resistance (PMQR) determinants in S. enterica recovered from natural surface waters in Paraíba state, Brazil. Water samples (n = 230) were collected monthly in triplicate using modified Moore swabs from 29 sampling sites belonging to 10 large dams. After conventional microbial isolation, representative isolates (n = 938) were submitted to whole genome sequencing, assembly and annotation. Antimicrobial resistance genes (ARGs) were identified, and core genome multilocus sequence typing (cgMLST) was used to infer phylogenetic relationships. Among recovered S. enterica, 130 (13.9%) isolates harboured PMQR determinants; 124 (95.4%) harboured qnrB19, while 6 (4.6%) harboured qnrS1. Multiple other ARGs associated with resistance to aminoglycosides, β-lactams, sulphonamides, tetracyclines and fosfomycin were identified. The diversity of ARGs and plasmids suggests a highly complex resistance landscape. Phylogenetic analysis revealed clustering by serovar and sequence type but not by resistance profile or geographic origin. The absence of association between phylogeny and ARGs highlights the potential role of horizontal gene transfer in disseminating resistance genes in water. Our findings reinforce the importance of antimicrobial resistance surveillance in surface waters.

Salmonella enterica remains a major foodborne pathogen globally but little attention has been paid to infrequent serovars in environmental settings. We report the occurrence of 30 rare S. enterica serovars isolated from environmental water sources between 2021 and 2022 in semiarid northeastern Brazil. We conducted two risk-based field campaigns at shoreline access points in 10 reservoirs associated with the three largest river basins in the state. Salmonella enterica was recovered from 175 out of 230 water samples, yielding 2903 isolates. Of these, 938 were selected for whole-genome sequencing (WGS). Genome assembly and downstream analyses identified 65 unique serovars, including 68 isolates belonging to 30 rare serovars. Salmonella Carrau (n = 14), S. Oran (n = 9), S. Gaminara (n = 5), and S. Urbana (n = 4) were the most frequent rare serovars. WGS analysis revealed the presence of antimicrobial resistance genes (ARGs) in all isolates. The highest abundances were associated with ARGs conferrying resistance to aminoglycosides [aac(6')-Iaa (100%)], quinolones (parC:p.T57S [98.1%] and qnrB19 [3.77%]), and fosfomycin (fosA7 [3.77%]). Some isolates carried plasmids (IncX3, IncFII [S], IncFII [Cf], Col [pHAD28], and IncFII [SARC14]) that could facilitate the spread of antimicrobial resistance. Phylogenetic analysis indicated the presence of distinct clades for each serovar. Interestingly, 20 serovars are endemic lineages circulating in Brazil, except S. Kiambu, which belongs to an international lineage. These findings underscore the importance of environmental monitoring and understanding the distribution of Salmonella in water sources to safeguard public health and prevent the spread of antimicrobial resistance.

Laminaria japonica is a kind of brown algal with good nutritional and medicinal value. Our previous studies demonstrated that the phytochemical components and bioactivities of Laminaria japonica were markedly enhanced by fermentation. However, the specific activity and underlying mechanism of fermented Laminaria japonica (FLJ) against NAFLD remain poorly understood. For this study, Laminaria japonica was fermented using S. cerevisiae and Lactiplantibacillus . In vitro assays were employed to evaluate the efficacy of FLJ in regulating cholesterol reduction and fat binding. In addition, the hepatoprotective effects and underlying mechanisms of FLJ in the treatment of NAFLD were evaluated using oleic acid (OA)–induced HepG2 cells and NAFLD mice. Our data revealed that FLJ significantly promoted fat‐binding and cholesterol‐reducing activity in vitro . Moreover, FLJ alleviated hepatic lipid accumulation, oxidative stress, and the inflammatory response in high‐fat diet (HFD)–induced NAFLD mice and in OA–induced HepG2 cells. The underlying protective mechanisms of FLJ against NAFLD may be attributed to the activation of the SIRT1 signaling pathway. These observations suggested that FLJ could be developed as a functional food supplement for the prevention or improvement of NAFLD.

ABSTRACT Surface waters function as ecological niches where Salmonella enterica can persist and disseminate to fresh produce production systems. We examined the genomic characteristics of S. enterica serotypes Agona (n = 86), Braenderup (n = 47), Muenchen (n = 53), and Panama (n = 69) isolates from surface waters in Chile, Mexico, and Brazil between 2019 and 2022. Mexican isolates consistently displayed a higher occurrence of genotypic antimicrobial resistance (AMR) than Chilean and Brazilian isolates. All S. Agona isolates exhibited the presence of fosA7.2, while qnrB19 emerged as the predominant AMR gene (ARG) among S. Braenderup isolates. S. Muenchen isolates from Chile displayed an absence of any ARGs, while those from Mexico and Brazil predominantly carried qnrB19. Among S. Panama isolates from Chile, aadA1, floR, sat2, and tet(B) were the most prevalent ARGs, whereas those from Mexico and Brazil harbored tet(A), and floR and tet(A) as the leading ARGs, respectively. ARG sharing among isolates and ARG co-occurrence within individual isolates were prevalent across countries and serotypes. All isolates containing integrons exhibited genotypic multidrug resistance. The principal coordinates analysis reveals distinct clustering patterns based on country, serotype, number of ARGs per isolate, and plasmid and integron presence/absence. The whole-genome phylogenetic analysis demonstrates clear clusters, each associated with their respective countries. However, a notable exception was observed with one S. Agona isolate from Brazil closely related to two isolates from Chile, differing by only 18 and 19 single-nucleotide polymorphisms, respectively.IMPORTANCEThis comprehensive study explored the intricate genomic landscapes of S. Agona, Braenderup, Muenchen, and Panama isolates from surface waters across Chile, Mexico, and Brazil. By filling important knowledge gaps related to the genomic characteristics of these serotypes, the research offers a nuanced understanding of these serotypes as potential reservoirs for multidrug resistance. Our findings emphasize the urgency of targeted interventions to mitigate the emergence and dissemination of multidrug-resistant Salmonella enterica. This work underscores the need for informed policies and collaborative efforts to address the risks posed by S. enterica in Latin American surface waters.

Sub-lethal stress can induce cross-protection in pathogens, complicating food processing. We evaluated the combined effects of chlorine dioxide (CD) and ultraviolet-C (UV-C) on sub-lethally stressed Salmonella enterica on raw whole almonds (RWAs) and fresh-cut leafy greens (FCLGs), post-treatment survival on FCLGs, and Enterococcus faecium NRRL B-2354 as a S. enterica surrogate. S. enterica cocktails (RWAs: S. Enteritidis, Newport, Typhimurium; FCLGs: S. Enteritidis Montevideo, Typhimurium) were subjected to desiccation, oxidation, heat shock, or acid stress. Stressed and unstressed S. enterica and NRRL B-2354 were inoculated onto RWAs and FCLGs, and treated with CD (0-0.6 mg/L, 0-30 min) or CD + UV-C [CD (0-0.4 mg/L, 0-15 min) followed by UV-C (254 nm, 0-450 mJ/cm2, 0-15 min)]. Treated FCLGs were stored under cold storage (4 °C) or temperature abuse (35 °C for 2 h, then 4 °C) for seven days. CD + UV-C produced < 5.6- and ≥ 5.6-log reductions on RWAs and FCLGs, respectively, while CD achieved < 2.0- and < 2.5-log reductions, respectively. Desiccation- or oxidation-stressed cells were more resistant (P < 0.05) than unstressed or other stressed cells. Treatment (CD vs. CD + UV-C) and microorganism (S. enterica vs. NRRL B-2354) were dominant factors influencing inactivation. Association rule mining identified CD + UV-C on S. enterica yielding high reductions. Stressed cells declined more rapidly under cold storage, while desiccation-stressed cells persisted under temperature abuse. NRRL B-2354 showed lower reductions than S. enterica (P < 0.05), supporting its use as a surrogate with safety margin. These results support CD + UV-C as an effective hurdle strategy and highlight the importance of stress adaptation in validating interventions.

Multidrug-resistant Salmonella is becoming a public health hazard. This study aimed to investigate the genomic diversity of the selected Salmonella serovars isolated from organic and non-organic chickens using whole-genome sequencing (WGS). A total of 94 Salmonella isolates [Infantis (n = 71), Enteritidis (n = 13), Typhimurium (n = 10)] recovered from organic and non-organic retail chickens were subjected to WGS using Illumina MiSeq. All Salmonella isolates contained at least one antibiotic resistance (AR) gene (ARG). All S. Typhimurium and S. Enteritidis isolates, and 98.6 % of S. Infantis isolates possessed aac(6')-Iaa which predicted resistant to aminoglycosides. Most isolates harbored ARGs for sulfonamides, β-lactamase inhibitors, tetracyclines, and fluoroquinolone/quinolone resistance regardless of chicken types. Fisher's exact test indicated a significantly higher prevalence of ARGs in Salmonella isolated from organic chickens. The virulence genes that stimulate Salmonella pathogenicity island 1 (SPI1) encoding, type three secretion system 1 (TTSS-1) translocated effectors, SPI2 encoding, TTSS-2 translocated effectors, fimbrial adherence determinants, serum resistance, stress adaptation and Mg2+ uptake were observed in every serovar regardless of chicken types. Seven plasmids were detected in Salmonella isolates from non-organic chicken, including IncFIB(pN55391), IncFIB(S), Col(BS512), IncFII(S), IncX1, IncC, and ColpVC, whereas Salmonella isolates from organic chicken carried only three plasmids [IncFIB(pN55391), Col(BS512), and IncC]. Phylogenetic analysis confirmed that a significant portion of the isolates had single nucleotide polymorphism (SNP) distances greater than the threshold (SNP ≤ 20), indicating genetic distance among them. These results suggest that the Salmonella isolates from organic and non-organic chickens possessed various AR and virulence genes and thus have the potential to cause salmonellosis.

Surface water ecosystems are intimately intertwined with anthropogenic activities and have significant public health implications as primary sources of irrigation water in agricultural production. Our extensive metagenomic analysis examined 404 surface water samples from four different geological regions in Chile and Brazil, spanning irrigation canals (n = 135), rivers (n = 121), creeks (n = 74), reservoirs (n = 66), and ponds (n = 8). Overall, 50.25 % of the surface water samples contained at least one of the pathogenic or contaminant bacterial genera (Salmonella: 29.21 %; Listeria: 6.19 %; Escherichia: 35.64 %). Furthermore, a total of 1,582 antimicrobial resistance (AMR) gene clusters encoding resistance to 25 antimicrobial classes were identified, with samples from Brazil exhibiting an elevated AMR burden. Samples from stagnant water sources were characterized by dominant Cyanobacteriota populations, resulting in significantly reduced biodiversity and more uniform community compositions. A significant association between taxonomic composition and the resistome was supported by a Procrustes analysis (p < 0.001). Notably, regional signatures were observed regarding the taxonomic and resistome profiles, as samples from the same region clustered together on both ordinates. Additionally, network analysis illuminated the intricate links between taxonomy and AMR at the contig level. Our deep sequencing efforts not only mapped the microbial landscape but also expanded the genomic catalog with newly characterized metagenome-assembled genomes (MAGs), boosting the classification of reads by 12.85 %. In conclusion, this study underscores the value of metagenomic approaches in surveillance of surface waters, enhancing our understanding of microbial and AMR dynamics with far-reaching public health and ecological ramifications.

Paired-end short reads of Illumina HiSeq, MiSeq, and NovaSeq of simulated bacterial communities from fresh spinach and surface water were generated in silico at various sequencing depths. Multidrug-resistant Salmonella enterica serotype Indiana was included in the spinach community, while the water community contained multidrug-resistant Pseudomonas aeruginosa.