Tigecycline is a last-resort antibiotic for treating infections caused by carbapenem-resistant Enterobacterales (CRE). The emergence and dissemination of tigecycline-resistant Enterobacterales through the food chain pose a growing public health concern. This study systematically evaluates the global prevalence of tigecycline-resistant Enterobacterales and the tet(X4) carriage rate in foods and food-producing animals, and analyzes the epidemiological characteristics across supply chain stages, bacterial genera, regions, and sample types. We searched PubMed, Scopus, Web of Science, Engineering Index (EI), and China National Knowledge Infrastructure (CNKI) for studies published from January 2015 to December 2025. A random-effects model pooled resistance rates, and subgroup analyses explored heterogeneity. A total of 104 studies (130 reports) were included. The overall resistance rate was 4.36% (95% CI: 2.83%-6.20%); among resistant strains, tet(X4) prevalence (13 reports) was 73.81% (95% CI: 43.79%-94.96%). E.coli accounted for 93.01% of resistant strains. The highest resistance rate was at farms (5.05%), followed by retail markets (2.61%) and fruits and vegetables (3.82%). Asia showed a significantly higher rate (5.30%) than Europe (2.68%). Although overall prevalence is low, tet(X4) is highly prevalent among resistant strains, with E. coli as the predominant host. Farms and Asia are key control points, and resistance in fruits and vegetables warrants vigilance. Strengthening veterinary tetracycline regulation and incorporating tigecycline resistance monitoring into routine food chain surveillance are strongly recommended.

Goat milk is nutritionally valuable and ranks as the second most consumed dairy in China, with Shaanxi Province being the national leader. However, systematic studies on regional quality variations, grading and spoilage mechanisms of it remain limited. In this study, 124 raw milk samples were collected from 14 major dairy goat breeding areas across Shaanxi. Our results revealed that significant spatiotemporal variations, and long-distance transportation affected milk quality by increasing microbial loads and reducing fat content (P < 0.05). The grading model demonstrated high accuracy (91.8%) and reliability (AUC = 98.4%), with fat content being the most critical biomarker. Storage at 10 degrees C accelerated spoilage compared to 4 degrees C, with marked enrichment of Pseudomonas and Enterobacteriaceae. Multi-omics analysis identified seven genus-level microbial biomarkers and five key metabolites, which are linked to goat milk spoilage. This study provides a data-driven tool for raw goat milk quality assessment and grading, reveals core microbiological and metabolic mechanisms, and offers crucial insights for quality control in the dairy industry.

Vibrio-associated foodborne diseases constitute a substantial global health burden, and aquatic products are frequently contaminated with antibiotic-resistant and potentially virulent Vibrio. This meta-analysis aimed to quantify the global prevalence, antibiotic resistance, and virulence genes of Vibrio in aquatic products. From 108 eligible studies, pooled prevalence of Vibrio reached 20.99% (95% CI: 18.04-24.09%), exhibiting a decreasing trend over time. Contamination rates were higher in shellfish (25.43%) than in shrimp (21.69%) and fish (17.63%), and in farm samples (26.31%) compared to retail samples (18.12%). Species and geographic analyses identified V. parahaemolyticus as the predominant species, with Asia and North America as principal hotspots. Among 47 antibiotics tested, resistance to penicillins was most prevalent (67.52%). Resistance to polymyxin B, erythromycin, vancomycin, and tetracycline demonstrated increasing trend over time, accompanied by high frequencies of key resistance genes (blaCTX, blaTEM, ermB, aadA, str, and GyrA associated mutations). Virulence analysis indicated high prevalence of adhesion factors (tcp), secretion systems (type VI secretion system and type III secretion system 1), and hemolysin-related genes (tlh and hlyA). Asian isolates possessed the broadest virulence gene spectrum. Notably, farm-derived isolates exhibited higher prevalence of adhesion- and toxin-related genes, whereas retail-derived isolates harbored more genomic islands and other virulence genes. These findings reveal a high prevalence of Vibrio in aquatic products worldwide, characterized by distinct spatiotemporal distribution patterns, severe antibiotic resistance and diverse virulence attributes. Our results underscore the necessity for integrated surveillance and targeted intervention strategies across the aquaculture-to-retail continuum.

This study aimed to systematically assess the prevalence, serotype distribution, and antimicrobial resistance of Salmonella in eggs in China. The overall pooled prevalence of Salmonella in Chinese eggs was 7.20%, which is higher than the levels reported in the United States and Europe. Contamination rates were higher on eggshells (8.30%) was than those in egg contents (4.50%), and prevalence was greater in farm samples (9.60%) than that in retail market samples (5.80%), highlighting the importance of hygiene management during production. Spatial analysis revealed significant regional variations, with generally higher prevalence in coastal provinces compared to inland provinces. Serotype analysis identified S. typhimurium and S. enteritidis as the predominant serotypes. Antimicrobial susceptibility testing revealed high resistance rates to several antibiotics, including nalidixic acid. Of particular concern is the notably high prevalence of the mobile colistin resistance gene mcr-1, based on limited data. These findings highlight the serious nature of Salmonella contamination in the Chinese egg supply chain and its potential risk to public health, emphasizing the necessity to strengthen integrated supervision from farm to retail, improve hygiene practices, and strictly regulate antibiotic usage to ensure food safety.

Cronobacter sakazakii is an opportunistic foodborne pathogen linked to severe neonatal infections, and its strong desiccation tolerance enables persistence in low-moisture processing environments. Its survival under sublethal, process-relevant temperatures poses a major challenge to powdered infant formula (PIF) safety. Our previous work associated elevated tolQ expression with heat tolerance in C. sakazakii, but its functional role remained unclear. ΔtolQ mutant of BAA-894 was constructed via a pTmobSacB suicide plasmid and sequence-verified to assess tolQ-mediated stress adaptation. Compared with the wild type, ΔtolQ reduced viable counts by 0.35 log CFU/mL under non-mild heat stress (NMHS; 37 °C) and 0.90 log CFU/mL under mild heat stress (MHS; 52 °C), whereas complementation restored near wild-type growth. During desiccation, the mutant showed reductions of 1.20 and 1.93 log CFU/mL under NMHS and MHS, respectively. Under acid stress (pH 3.5), it maintained viability but lacked wild-type growth increases. Flow cytometry revealed fewer membrane-intact cells, especially under MHS. Transcriptomics identified 1,894 differentially expressed genes enriched in translation, flagellar assembly, envelope integrity, carbon metabolism, and exopolysaccharide biosynthesis. These findings demonstrate that tolQ supports survival and transcriptional homeostasis under sublethal heat, highlighting its potential as a target for improving thermal control in food-processing environments.

Ferrate(VI) is emerging as a promising eco-friendly oxidant for advanced water treatment, yet its interactions with bacterial dormancy states and subsequent water-safety implications remain poorly understood. This study investigated the formation and implications of the viable but non-culturable (VBNC) state in Escherichia coli under ferrate(VI) stress in both saline and surface water matrices. While ferrate(VI) effectively induced a rapid loss of culturability in E. coli, it generated a non-culturable but membrane-intact population associated with physiological adaptation mechanisms, including oxidative stress response, metabolic repression, and membrane remodeling. This adaptive strategy not only supported cellular persistence but also conferred significant cross-resistance to environmental stressors and antibiotics. Crucially, upon resuscitation, the bacteria partially recovered epithelial-cell interaction-associated phenotypes, including adhesion, invasion, and cytotoxicity-related responses in Caco-2 intestinal epithelial cells. These findings demonstrate that ferrate(VI) oxidation may inadvertently select for resilient bacterial populations that evade conventional detection while retaining resuscitation-associated host-cell interaction capacity. This discrepancy between non-detectability and residual physiological activity poses a critical challenge to current culture-dependent water quality standards and engineering dosing strategies. Consequently, this study highlights the necessity of integrating molecular viability assessments into water safety monitoring to manage the hidden risks associated with resuscitable non-culturable bacterial populations in full-scale facilities.

Protein hydrolysates are widely used in health foods, but undisclosed enzymatic sources, particularly porcine pancreas, raising concerns regarding food safety, allergenicity, and dietary restrictions. To address this issue, this study comprehensively characterized the porcine pancreas proteome, identifying 418 proteins and establishing 50 °C autolysis to ensure consistent peptide profiles. Three homologous highly specific α-amylase-derived marker peptides, VTNPSRPW, VVTNPSRPW, and IVVTNPSRPW, were selected and validated, and a targeted LC-MS/MS assay was established with porcine pancreas detection limits of 0.5 %, 1 %, and 5 % (w/w), respectively. Application of this method to commercial products revealed the presence of porcine peptides in samples labeled as "animal-free" which was further proved by on-site investigation. This study provides a robust and practical approach for verifying the species origin of enzymatic preparations in protein hydrolysates, enhancing traceability, food safety, and regulatory compliance. To our knowledge, it represents the first systematic investigation into enzyme source authenticity in such products.

Given the increasing global concern over Salmonella resistance to cephalosporins, such resistance poses serious challenges to food safety and clinical treatment. This study aimed to systematically investigate the global epidemiological characteristics and genetic diversity of bla-harboring Salmonella to further elucidate the association between bla genes and cephalosporin resistance phenotypes. A total of 772,454 Salmonella isolates from the NCBI Pathogen Detection database were analyzed, among which 101,448 isolates harbored bla genes. Most isolates originated from humans, poultry, and pigs, mainly in North America, Europe, and Asia. The dominant serovars were S. 4,[5],12:i:-, S. Typhimurium, S. Infantis, and S. Enteritidis. The most frequent β-lactamase families were blaTEM, blaCMY, and blaCTX-M, with blaTEM-1, blaCMY-2, and blaCTX-M-65 as the predominant subtypes. To further elucidate the correlation between bla genotype and cephalosporin resistance phenotype, we assessed cephalosporin susceptibility of 2,302 Salmonella isolates collected in China. Resistance testing showed ceftriaxone and cefoxitin resistance rates were of 20.68% and 5.82%, respectively, with higher resistance rate observed in chicken isolates than in pork isolates. Twenty-two bla genes were detected, mainly blaTEM-1B, blaOXA-1, and blaCTX-M-65. Correlation and regression analyses indicated that ceftriaxone resistance was primarily driven by CTX-M-type ESBLs, while cefoxitin resistance was linked to blaDHA-1 and blaCMY-2. Machine learning models effectively predicted cephalosporin susceptibility. Genome-wide association study (GWAS) identified multiple functional categories associated with ceftriaxone resistance, including those related to amino acid, carbohydrate, and inorganic ion transport and metabolism, as well as secondary metabolite biosynthesis and catabolism.

Extended-spectrum β-lactamase (ESBL)-producing Salmonella poses a growing threat to food safety, yet the transmission of blaCTX-M genes in foodborne Salmonella remains incompletely understood. This study investigated the prevalence, antimicrobial resistance profiles, horizontal transferability, and genetic characteristics of blaCTX-Ms in 950 Salmonella isolates recovered from retail chicken and pork in China. A total of 103 (10.8%) blaCTX-M-positive isolates were identified, with a significantly higher prevalence in chicken (20.7%, 96/464) than in pork (1.4%, 7/486). Geographically, blaCTX-M-positive isolates were more prevalent in the 3 northern provinces (19.93%, 59/296) than in the 5 southern provinces (6.73%, 44/654). These isolates represented 11 "sequence type (ST)-serotype" combinations, predominantly ST26 Salmonella enterica serovar Thompson (S. Thompson) (36.9%, 38/103), ST198 S. Kentucky (31.1%, 32/103), and ST17 S.Indiana (13.8%, 18/103). Nine blaCTX-M subtypes were identified, dominated by blaCTX-M-55 (33.0%, 34/103) and blaCTX-M-65 (33.0%, 34/103). Overall, 78.6% (81/103) of blaCTX-M-positive isolates failed to yield detectable transconjugants in Escherichia coli C600, with no transconjugants detected in ST198 S. Kentucky or ST17 S.Indiana. The blaCTX-Ms were mainly carried by IncHI2-HI2A plasmids, which exhibited significantly lower conjugation frequencies than blaCTX-M-positive IncN and IncFII-X1 plasmids. Chromosomal integration of blaCTX-Ms was detected in ST198 S. Kentucky, ST26 S. Thompson, ST17 S.Indiana, and ST13 S. Agona, characterized by signature direct repeats and mediated by ISEcp1, IS15, and IS26. Consistent with these findings, further analysis of 418 blaCTX-M-positive complete Salmonella genomes from the NCBI database showed that 310 plasmids carried blaCTX-Ms, mainly on IncHI2-HI2A plasmids (33.9%, 105/310), whereas 117 isolates carried chromosomal blaCTX-Ms, dominated by blaCTX-M-55 (76.1%, 89/117) and most frequently occurring in ST413 S. Mbandaka, ST198 S. Kentucky, and ST13 S. Agona. Our findings highlight that blaCTX-Ms disseminate in Salmonella through plasmid-mediated transfer and chromosomal integration, providing a mechanistic basis for the long-term persistence of ESBL-producing Salmonella and associated food safety risk.

Food-contact ice serves as an important vector for the transmission of pathogenic microorganisms during the retail stage of frozen chicken. However, microbial cross-contamination between frozen chicken and its associated contact ice remains poorly studied. We hence investigated coliforms contamination and performed whole-genome sequencing to characterize Salmonella isolates from frozen chicken and corresponding contact ice collected from supermarkets. Coliforms were detected in all frozen chicken and in 90.38 % of contact ice samples. Salmonella was isolated from 39.47 % of frozen chicken and 21.15 % of contact ice samples. Phylogenetic analysis of 50 representative Salmonella isolates revealed that strains from contact ice and their corresponding frozen chicken samples commonly belonged to identical clonal lineages and exhibited highly similar profiles of antimicrobial resistance genes, heavy metal resistance genes, and biocide resistance genes. Fourteen serovars and 15 sequence types (STs) were identified from 50 sequenced Salmonella, with ST11 S. Enteritidis, ST909 S. Bareilly, ST198 S. Kentucky, and ST17 S. Indiana being the most common. These findings partially reflect global Salmonella prevalence trends, where S. Kentucky (27.64 %, 11,201/40,518), S. Infantis (23.75 %, 9624/40,518), and S. Enteritidis (17.20 %, 6968/40,518) are the predominant serovars in chicken-derived Salmonella. Notably, ST909 S. Bareilly, which has been predominantly reported in North America (USA, 44.39 %, 1136/2559) and Europe (UK, 38.96 %, 997/2559), and is primarily associated with human sources (87.34 %, 2235/2559), was isolated for the first time from frozen chicken in China. Although it is not yet a major circulating serovar in China, its association with international outbreaks and cross-border transmission potential warrants greater attention.

Listeria monocytogenes is a foodborne pathogen that poses threat to food safety and public health. Generally, the rates of resistance to clinically important antibiotics in L. monocytogenes are low. This study aimed to investigate the prevalence and genetic characteristics of L. monocytogenes with acquired multidrug resistance (MDR) in food samples from China between 2012 and 2022. Of 8344 isolates collected, 34 (0.41 %) were identified as acquired MDR. The majority of acquired MDR isolates (n = 31, 92.3 %) belonged to hypovirulent clonal complex (CC) 9 (Lineage II, IIc), including 3 sequence types (ST) (ST9, n = 29; ST2458, n = 1; ST9-1LV, n = 1), which has remained dominant over the past decade. In 2022, three additional acquired MDR clones emerged: CC87/ST87 (Lineage I, IIb), CC8/ST8 (Lineage II, IIa), and CC155/ST705 (Lineage II, IIa), with CC87/ST87 and CC8/ST8 being notably associated with human listeriosis in Asia. The rep25_2_M640p00130 plasmid was the most common mobile genetic element among these acquired MDR isolates, consistently harboring seven types of antibiotic resistance genes, including aminoglycosides (ant(6)-Ia; aph(3')-III), trimethoprim (dfrG), macrolides, lincosamides and streptogramin B (MLSb) (erm(B)), lincosamides (lnu(B)), pleuromutilins, lincosamides and streptogramin A (PLSA) (lsa(E)), tetracyclines (tet(S)), and phenicols (catA), and flanked on one side by IS1216E. However, the diversity of acquired MDR-carrying plasmids increased from 2017 to 2022, with an increased prevalence among replicons including rep26_2_repA, rep26_4_repA, and rep26_1_pli0070/rep32_1_pli0023. Importantly, compared to the dominant hypovirulent CC9, which contained premature stop codons in the internalin gene inlA associated with adhesion and invasion, the newly emerged acquired MDR L. monocytogenes CC8/ST8 and CC155/ST705 maintained intact inlA gene and exhibited stronger adhesion and invasion phenotype in Caco-2 cells. These findings emphasize the need for continuous surveillance of acquired MDR L. monocytogenes, particularly the virulent CC8/ST8 and CC155/ST705, to mitigate risks to food safety and human health.

Global bacterial antibiotic resistance threatens health, food safety, and sustainability. The food supply chain is a critical "One Health" pathway, linking agriculture, environment, and processing. However, systematic reviews addressing the impact of coexisting stressors on antibiotic resistance emergence and transmission across this continuum are lacking. This review innovatively synthesizes environmental inputs (antibiotic residues, fertilizers, heavy metals, pesticides, microplastics, climate change, and grazing) and processing/transport stressors (temperature, nonthermal technologies, pH, osmosis, disinfectants, food additives, probiotics, and trade), focusing on their individual and synergistic effects. These stressors enhance resistance and horizontal gene transfer by activating bacterial stress responses (sigma factors, SOS), altering membranes, and triggering mutations/efflux pumps. Coexisting stressors can further intensify, accelerate, and amplify resistance emergence and transmission. We propose multilevel mitigation strategies across the food chain, including curbing selective pressures at the source, optimizing food processing techniques to avoid stress-induced resistance, guiding consumer behavior, and strengthening international regulatory governance.

OBJECTIVE:To explore the genomic epidemiological characteristics of Salmonella in fruits, vegetables, and irrigation water in China. METHODS:A total of 410 samples of fruits, vegetables and irrigation water were collected from Hubei and Shaanxi Provinces from June to December 2022. Salmonella strains were detected and identified referenced in the United States Food and drug administration&apos;s bacteriological analytical manual. The antimicrobial susceptibility to 17 antibiotics in 9 classes was assessed by broth microdilution, and the serotype and antibiotic resistance genes(ARG) were predicted by whole genome sequencing technology. RESULTS:In total, 29 strains of Salmonella were collected. There were 3 strains isolated from fruits and vegetables, 25 from irrigation water, and 1 from soil fertilizers. The detection rate in irrigation water(22.32%) was higher than that in fruits, vegetables(1.46%), and soil fertilizers(1.08%). The individual detection rate(13.01%) was higher than the large-scale monitoring point detection rate(4.03%). Based on the analysis of the whole genome sequencing, a total of 19 serotypes were identified, with S. Thompson being the most frequently detected serotype(24.14%).31.0% of isolates showed resistance to the tested drugs and showed the highest resistance to cotrimoxazole, tetracycline, ampicillin.24.1% were multi-drug resistant strains and were resistant to 14 kinds of antimicrobial compounds belonging to 8 categories. Moreover, based on the whole-genome sequence analysis of antibiotic resistance genes, it was found that the carriage rate of aminoglycoside ARGs was 100%, and the carriage rates of other ARGs were folate pathway antagonists, fosfomycins, tetracyclines, phenicols, sulfonamids, quinolones, beta-lactam, macrolids and rifamycins were 31.03%, 27.59%, 27.59%, 27.59%, 24.14%, 20.69%, 6.90%, and 6.90%, respectively. Over 30% of the strains carried more than 6 antibiotic resistance genes. CONCLUSION:Salmonellas were detected in fruits, vegetables, irrigation water and soil fertilizer in Hubei and Shaanxi Provinces. The strains isolated from irrigation water exhibiting a diverse range of serotypes and carrying numerous antibiotic resistance genes. More intensive efforts should be made on the monitoring of Salmonella and its antibiotic resistance in irrigation water.

ObjectiveTo understand the influence of cultivation conditions on the formation of Salmonella biofilm and provide basis for ensure food safety.MethodsCongo red staining and crystal violet staining method were used to screen biofilm （BF） formation strains from 400 foodborne Salmonella. Scanning electron microscope was applied to observe BF formation. Whole-genome sequencing analysis was used to identify BF formation related genes. Tube culture and microplate quantitative detection methods were used to determine BF formation of Salmonella under different culture conditions. The effect of different culture time， medium type， glucose content， peptone content and Vitamin B1 （VB1） content to Salmonella BF formation were studied.ResultsEight （2.00%） BF-forming Salmonella isolates were obtained. Compared to LB medium， BHI was more suitable for BF formation for Salmonella. When cultured for 96 h， the BF formation of Salmonella on BHI was much more than that on LB. Fifteen BF-related genes including trx2， fadI， bsmA， bssS， tabA， bcsE， csgD， csgA， B， C， seqA， dam， fliZ， flhD and motB were detected in BJ44D， ZZSR2-2008， NYSR94-08 and yl19Ta. The best BF formation nutrient conditions for Salmonella were that 0.6% or 0.8% glucose， 4.0% peptone， and 50 mg/L VB1 were respectively supplemented in BHI broth （P<0.05）.ConclusionIt is indicated that different culture conditions significantly correlated with BF formation of Salmonella and have strain-specificity， and can provide theoretical basis for BF formation control of Salmonella in the food production chain.

With the continuous advancements in high-throughput genome sequencing technologies and the development of innovative bioinformatics tools, bacterial genome-wide association studies (BGWAS) have emerged as a transformative approach for investigating the genetic variations underlying diverse bacterial phenotypes at the population genome level. This review provides a comprehensive overview of the application of BGWAS in elucidating genetic determinants of bacterial drug resistance, pathogenicity, host specificity, biofilm formation, and probiotic fermentation characteristics. We systematically summarize the BGWAS workflow, including study design, data analysis pipelines, and the bioinformatics software employed at various stages. Furthermore, we highlight specialized tools tailored for BGWAS and discuss their unique features and applications. We also discuss confounding factors that can influence the accuracy and reliability of BGWAS results, including population structure, linkage disequilibrium, and multiple testing. By incorporating recent advancements, this review serves as a comprehensive reference for researchers utilizing BGWAS to uncover the genetic basis of bacterial phenotypes.

The global dissemination of ciprofloxacin-resistant Escherichia coli (CIPRE. coli) poses a critical public health threat, with poultry products as predominant transmission vehicles to humans. To investigate the genomic characteristics and resistance profiles of CIPRE. coli in a global context, we collected 274 retail chicken samples from seven regions in Shaanxi, China, between October 2022 and April 2023. From these, 64 representative strains underwent antimicrobial susceptibility testing, whole-genome sequencing, and comparative analysis with 1043 global CIPRE. coli (G-CIPRE. coli) genomes retrieved from the NCBI database. Results showed the detection rate of CIPRE. coli in Shaanxi chicken (SC-CIPRE. coli) was 96.0%, significantly higher than in G-CIPRE. coli (16.1%, P < 0.01). Moreover, SC-CIPRE. coli isolates harbored more antimicrobial resistance genes (ARGs) per isolate (16.55 vs. 6.51, P < 0.01). Both groups showed high quinolone resistance determined region (QRDR) mutation frequencies (95.3% vs. 87.1%), with conserved major substitutions (GyrA-Ser83Leu, ParC-Ser80Ile, GyrA-Asp87Asn). IncFIB was the common predominant plasmid group (79.7% vs 75.2%), and 77.8% of ARGs were plasmid-associated, underscoring the pivotal role of plasmids in resistance dissemination. Multilocus Sequence Typing (MLST) analysis showed that ST162 (30.0%) was dominant in SC-CIPRE. coli, while ST131 (35.1%) and ST1193 (13.4%) prevailed globally. Notably, ST10 strains were widely distributed and exhibited enhanced ARGs carriage capacity. Phylogenetic analysis provided evidence for cross-host and cross-regional transmission potential of CIPRE. coli, suggesting that highly resistant strains from retail chicken in Shaanxi may pose a broader risk to public health.

Salmonella is a major foodborne pathogen, frequently linked to poultry and posing serious food safety and public health risks. To investigate its epidemiology in retail chicken in Shaanxi Province, China, we conducted a comprehensive study integrating whole-genome sequencing (WGS), Clusters of Orthologous Groups (COG) analysis, and machine learning (ML). Genomic data of 331 S. Kentucky and 614 S. enteritidis isolates from the NCBI database were also analyzed to assess genetic relatedness between local strains and those from other sources across China. From 280 chicken samples collected in seven cities, 92 (32.86 %) were Salmonella-positive, yielding 132 isolates representing 29 serotypes. S. Kentucky predominated in wet markets, whereas S. enteritidis dominated supermarkets. All isolates were resistant to at least one antibiotic, with 87.88 % showing multidrug resistance (MDR) and 38.64 % exhibiting extensive drug-resistance (XDR). WGS of 78 representative isolates identified 61 antimicrobial resistance genes (ARGs) and seven quinolone resistance-determining region (QRDR) mutations, with ParC (Thr57Ser) being most frequent. It is worth noting that the high prevalence (100.00 %) of Yersinia high-pathogenicity island (HPI) genes detected in S. infantis in this study has hardly been reported previously. Phylogenetic analysis revealed S. Kentucky and S. enteritidis, which are the predominant serotypes detected in the investigation, showing close genetic relationship (SNP < 10) with those from chicken, pork, aquatic products, and humans in other provinces and host sources. Pan-genomic analysis showed that the number of accessory genes in S. Kentucky was higher than that in S. enteritidis, and supermarket- and human-origin Salmonella isolates possessed a higher proportion of accessory genes. This indicates that the genomes of these isolates are more open and have greater potential for acquiring exogenous elements. Functional enrichment analysis on the core and auxiliary genomes of S. Kentucky and S. enteritidis based on COG clustering indicated that significant differences could be found in the functions of the accessory genomes between the two serotypes. ML-based screening identified intS3, which is implicated in genomic stability and DNA damage repair, as a key feature gene in wet market isolates. Key feature genes identified in S. Kentucky and S. enteritidis from chicken were torI and rfaF, respectively, both associated with environmental adaptability. In human-derived isolates, ccmA and oadB1 were identified as feature genes, contributing to bacterial proliferation and host adaptation. This study provides comprehensive genomic and epidemiological insights into Salmonella in Shaanxi retail chicken, emphasizing the widespread MDR/XDR burden and cross-regional dissemination, and underscoring the need for strengthened genomic surveillance to protect food safety and public health.

Cronobacter spp. exhibit remarkable resilience to extreme environmental stresses, including thermal, acidic, desiccation, and osmotic conditions, posing significant challenges to food safety. Their thermotolerance relies on heat shock proteins (HSPs), thermotolerance genomic islands, enhanced DNA repair mechanisms, and metabolic adjustments, ensuring survival under high-temperature conditions. Acid tolerance is achieved through internal pH regulation, acid efflux pumps, and acid tolerance proteins, allowing survival in acidic food matrices and the gastrointestinal tract. Desiccation tolerance is mediated by the accumulation of protective osmolytes like trehalose, stabilizing proteins and membranes to withstand dryness, especially in dry food products. Similarly, osmotic stress resilience is supported by compatible solutes such as trehalose and glycine betaine, along with metabolic adaptations to balance osmotic pressures. These mechanisms highlight the adaptability of Cronobacter spp. to diverse environments. Moreover, exposure to sublethal stresses, including heat, osmotic, dry, and pH stresses, may induce homologous or cross-resistance, complicating control strategies. Understanding these survival mechanisms is essential to mitigate the risks of Cronobacter spp., especially in powdered infant formula (PIF), and ensure food safety.

As emerging environmental pollutants, antibiotic resistance genes (ARGs) are prevalent in livestock farms and their surrounding environments. Although existing studies have focused on ARGs in specific environmental media, comprehensive research on ARGs within farming environments and their adjacent areas remains scarce. This review explores the sources, pollution status, and transmission pathways of ARGs from farms to the surrounding environment. Drawing on the "One Health" concept, it also discusses the potential risks of ARGs transmission from animals to human pathogens and the resulting impact on human health. Our findings suggest that the emergence of ARGs in livestock farming environments primarily results from intrinsic resistance and genetic mutations, while their spread is largely driven by horizontal gene transfer. The distribution of ARGs varies according to the type of resistance genes, seasonal changes, and the medium in which they are present. ARGs are disseminated into the surrounding environment via pathways such as manure application, wastewater discharge, and aerosol diffusion. They may be absorbed by humans, accumulating in the intestinal microbiota and subsequently affecting human health. The spread of ARGs is influenced by the interplay of microbial communities, antibiotics, heavy metals, emerging pollutants, and environmental factors. Additionally, we have outlined three control strategies: reducing the emergence of ARGs at the source, controlling their spread, and minimizing human exposure. This article provides a theoretical framework and scientific guidance for understanding the cross-media migration of microbial resistance in livestock farming environments.

Azithromycin is commonly recommended for the treatment of invasive salmonellosis, although the emergence of azithromycin resistance has become a new public health issue, it was seldomly investigated in China. This study analyzed 1230 non-typhoidal Salmonella (NTS) isolates from diverse sources in China (2006-2018), identifying 101 azithromycin-resistant NTS isolated from chicken, pork and human with minimum inhibitory concentration (MIC) values of 32-64 μg/mL of azithromycin across seven serotypes, primarily ST17 S. Indiana (n = 68) and ST52 S. Blockley (n = 26). All azithromycin-resistant NTS isolates exhibited multidrug resistance pattern with 48 isolates exhibited resistance to nine antibiotic categories. Genomic analysis identified six kinds of distinct macrolide resistance genes in azithromycin-resistant NTS isolates: mph(A) (n = 94), mph(E)-msr(E) (n = 4), erm(42) (n = 2), erm(G) (n = 1) and erm(T) (n = 1). mph(A) (93.07 %) was most prevalent and found within the genetic environment mph(A)-mrx-mphR(A)-IS6100. No mutation associated with azithromycin resistance was discovered in the 23S rRNA gene, and 50S ribosomal protein L22 and L4 encoding sequences. A total of 22 distinct plasmid replicons were identified, with IncX1 being the most prevalent (58.42 %, 59/101). Notably, mph(A) gene in all ST52 S. Blockley strains (n = 26) were exclusively located on the chromosome. In contrast, mph(A) in other six serotypes, and erm(42), erm(T), mph(E)-msr(E) were predicted to be on plasmids. Specifically, the erm(T) gene was associated with IncQ1 plasmids. These findings underscore the necessity of continuous surveillance of azithromycin resistance in NTS across the food chain to better understand and mitigate its potential public health impact.