Search Results (111)

Cronobacter spp. are opportunistic foodborne pathogens that can cause neonatal meningitis, necrotizing enterocolitis, and sepsis. This study conducted a systematic contamination survey and whole-genome epidemiological analysis of 562 low-water-activity food samples in Hunan Province of China. The results showed an overall Cronobacter spp. detection rate of 41.99% (236/562), with spices exhibiting the highest contamination rate (60.06%), and with high-level contamination samples (>110 MPN/g) concentrated in this category. The 236 isolates comprised 6 species, 120 sequence types, and 39 clonal complexes, with C. sakazakii being the most frequently isolated species (64.83%) and high-risk clones ST4, ST1, ST148, and ST64 prevailing. Multiple virulence genes (TraJ, fur, rcsAB, rpoS) and antimicrobial resistance genes (qnrS1, blaTEM-1, blaCTX-M-55, blaLAP-2, aac(3)-IId, aadA2, tet(A), floR, mcr-9.1, sul2) were detected. Core genome multilocus sequence typing (cgMLST) identified two clustering patterns: Cluster C, whose genetic clustering was consistent with transmission associated with potential common upstream raw materials across different brands and provinces, and Cluster G, whose clustering suggested potential persistent colonization in the production environment across multiple batches of the same brand. This study elucidates the contamination characteristics of Cronobacter spp. in low-water-activity foods from Hunan Province and provides a basis for WGS-based active surveillance and supply chain traceability. Full article

Salmonella enterica serovar Choleraesuis (S. Choleraesuis) is a swine-adapted zoonotic pathogen for which multidrug resistance has become an increasing concern. An antimicrobial resistance profile and multidrug resistance pattern in S. Choleraesuis isolates from diseased pig in Taiwan have been reported. This study was designed as a secondary molecular and statistical analysis of 272 isolates recovered from diseased pigs in Taiwan whose minimum inhibitory concentration phenotypes had been reported previously. Using this isolate collection, we evaluated phenotype–genotype concordance and coresistance patterns by combining antimicrobial susceptibility data with targeted polymerase chain reaction screening and quinolone resistance-determining region sequencing. Multidrug resistance was detected in 97.8% of isolates. Among the screened acquired determinants, blaTEM was the most prevalent gene (94.5%), followed by floR (55.9%) and mcr-1 (12.9%); mcr-3 was detected in only one isolate. Significant phenotype–genotype concordance was observed for aphA-1 with kanamycin resistance and mcr-1 with colistin resistance. Sequence analysis of 60 enrofloxacin-resistant isolates revealed that high-level resistance was associated with combined gyrA and parC substitutions, with additional gyrB-region polymorphisms observed in isolates showing the highest minimum inhibitory concentrations. These findings demonstrate frequent coresistance patterns and complex resistance mechanisms in this lineage and support continued genomic surveillance and prudent antimicrobial stewardship in the swine sector. Full article

Objectives: This study aimed to investigate the therapeutic effects and potential mechanisms of Lonicerae japonicae Flos (Jinyinhua, JYH) against respiratory syncytial virus (RSV)-induced pneumonia by integrating lung tissue metabolomics with gut microbiota analysis. Methods: An RSV-infected mouse model was established through intranasal inoculation. Lung pathological changes, viral RNA levels, lung index, and inflammatory cytokine levels were evaluated. Untargeted metabolomics and 16S rRNA gene amplicon sequencing were performed to characterize JYH-mediated alterations in pulmonary metabolites and the gut microbiota. Spearman correlation analysis was conducted to assess associations between differentially abundant bacterial genera and significantly altered metabolites. Results: JYH alleviated RSV-induced pulmonary histopathological injury, reduced viral RNA levels, decreased lung index and interleukin-6 (IL-6) levels, and increased interferon-γ (IFN-γ) levels. Metabolomic profiling identified 46 differential metabolites, among which 26 showed a reversal trend following JYH administration. These metabolites were mainly enriched in pathways associated with the synaptic vesicle cycle, lysosomal function, and Forkhead box O (FoxO) signaling. Gut microbiota analysis showed that JYH increased microbial richness and diversity, whereas KEGG-based functional prediction indicated that the differentially abundant taxa were primarily involved in amino acid, carbohydrate, and nucleotide metabolism. Moreover, correlation analysis revealed significant associations between key bacterial genera, including Gemella, Sutterella, and CC_115, and differential metabolites such as pyridoxamine, uridine monophosphate (UMP), and argininosuccinic acid. Conclusions: JYH may protect against RSV-induced pneumonia by restoring pulmonary metabolic homeostasis and modulating gut microbiota composition. These findings provide new insights into metabolite–microbiota interactions underlying the anti-RSV activity of JYH. Full article

Antimicrobial resistance (AMR) in Escherichia coli (E. coli) from food-producing animals constitutes a substantial public health concern. This study characterized antimicrobial resistance profiles, phylogenetic diversity, virulence-gene distribution, and plasmid-borne extended-spectrum β-lactamase (ESBL) determinants of E. coli isolates recovered from water buffaloes with subclinical mastitis. Among the 54 ESBL-producing E. coli isolates, all were resistant to ampicillin and cefotaxime. High resistance rates were also observed for cephalothin (75.9%), trimethoprim–sulfamethoxazole (74.0%), ceftiofur (70.4%), florfenicol (68.5%), and cefazolin (63.0%). Lower resistance was recorded for colistin sulfate (40.7%), enrofloxacin (33.3%), and gentamicin (25.9%). Phylogenetic analysis of ESBL producers identified phylogroup B1 (42.6%) as predominant, followed by groups A (29.6%) and D (25.9%). Multilocus sequence typing (MLST) revealed that ST50 (20.4%) was the most common sequence type, and serogroup O150 was dominant (70.4%). Virulence genes, such as iss (81.5%), astA (59.3%), and espP (38.9%), were frequently detected among ESBL isolates. ESBL genes were predominantly bla_CTX-M-1 (27.8%) in all isolates, while the narrow-spectrum β-lactamase genes bla_TEM-1 (55.6%) and bla_OXA-10 (14.8%) were also commonly co-detected. Bioinformatic analysis predicted that all ESBL genes were associated with plasmid-derived contigs, with the predicted plasmid size ranging from approximately 32 to 187 kb and belonging to IncFIB, IncFIA, IncI1, IncFIA + I1, and IncFII replicon types. Conjugation frequencies ranged from 4.8 × 10⁻⁷ to 4.1 × 10⁻², and plasmids were predicted to carry additional resistance genes mediating resistance to chloramphenicol (floR), sulfonamides (sul1, sul3), tetracyclines (tet(A) and tet(B)), and trimethoprim (dfrA1, dfrA12). The co-carriage of ESBL genes with additional antimicrobial resistance and virulence determinants suggests the potential role of water buffaloes as reservoirs of clinically relevant resistance traits that may disseminate through horizontal gene transfer. Full article

Rice grain yield and drought tolerance are critical for global food security. So far, only a few genes have been reported to regulate both traits simultaneously. Here, we characterize OsFLO1, a previously unreported FAD-linked oxidoreductase, as a dual regulator of grain development and drought stress tolerance in rice. Genome-wide association studies (GWAS) revealed natural variation in OsFLO1, with haplotypes showing geographic adaptation to local rainfall. Functional analysis demonstrated that overexpression (OX) lines exhibited larger grains and improved panicle traits, while knockout (CR) lines showed reduced grain size and yield components despite increased tiller number. Regarding drought tolerance, OX lines of OsFLO1 enhanced drought tolerance, as evidenced by increased root length and antioxidant activities, whereas knockout (CR) lines displayed impaired stress responses. We further show that OsWRKY53 directly binds the OsFLO1 promoter, thereby activating its expression and coordinating both grain development and stress responses. Together, these results suggest that OsFLO1 functions as a key regulator coordinating grain development and drought tolerance, making it a promising target for improving rice productivity. Full article

Extraintestinal pathogenic Escherichia coli (ExPEC) poses escalating threats to human and veterinary health amid rising antimicrobial resistance. We isolated a highly virulent ExPEC strain RZ-13 (ST345, O134:H21) from diarrheic calves at a large beef cattle farm in Rizhao City, and conducted whole genome sequencing, conjugation experiments, and antimicrobial susceptibility testing to elucidate its genomic architecture and resistance mechanisms. The RZ-13 genome comprises one chromosome and four plasmids. The chromosome harbors virulence factors for adhesion, invasion, biofilm formation, and iron acquisition. Notably, plasmids pRZ13-1 (265,777 bp, IncHI2-IncHI2A) and pRZ13-3 (74,304 bp, IncFII) carry the majority of resistance genes. Plasmid pRZ13-1 carries 25 resistance genes, including bla_CTX-M-55, floR, qnrS1, sul3, and tet(A), as well as a complete tellurite resistance gene cluster, terABCDEFZY1. Its multidrug resistance (MDR) region features an IS26-mediated tandem amplification and an approximately 29 kb inverted structure. Comparative analysis indicated that the MDR region carried by this plasmid is highly prevalent in both animal-derived and human-derived isolates. Plasmid pRZ13-3 harbors an IS91-mediated mobile region that integrates both antimicrobial resistance and stress adaptation genes, which have been repeatedly identified in plasmids from diverse sources, including animals and humans. Conjugation experiments confirmed both pRZ13-1 and pRZ13-3 plasmids are self-transmissible and confer multidrug-resistant phenotypes to recipient strains, with pRZ13-3 exhibiting an exceptionally high transfer frequency of 8.9 × 10⁻², substantially exceeding that of previously reported IncFII plasmids. These findings demonstrate that pRZ13-1 and pRZ13-3 serve as critical vehicles for resistance dissemination through complex mobile genetic element structures and efficient horizontal transfer, highlighting the urgent need for surveillance of livestock-reservoir ExPEC to mitigate public health risks. Full article

Objective: The main aim of the study was to evaluate the role of wild fishes inhabiting in three anthropogenic-impacted Bays in Chile as reservoirs of antimicrobial resistance genes (ARGs). Methods: A total of 245 antimicrobial-resistant isolates were isolated from fish captured in the Coquimbo (142 isolates), Concepción (44 isolates), and Puerto Montt (59 isolates) Bays, and were identified by 16S rRNA gene sequence analysis, Antimicrobial-resistant isolates were tested for susceptibility to 12 antimicrobials by an agar disk diffusion method, and the carriage of genes encoding for resistance to main antimicrobial classes, such as β-lactams, amphenicols, tetracyclines, and sulfonamides by PCR (Polymerase Chain Reaction). Results: A predominance of the Pseudomonas (37.04%), Vibrio (14.40%), and Shewanella (13.99%) genera. Antimicrobial-resistant isolates were tested for susceptibility to 12 antimicrobials by an agar disk diffusion method, showing highest resistance to streptomycin (82.4%), amoxicillin (67.4%), and furazolidone (63.3%), and lowest resistance to ciprofloxacin (3.7%), meropenem (22.5%), and oxytetracycline (29.8%) and exhibiting a high occurrence of the multi-drug resistance phenotype (76.9%). Furthermore, an important number of isolates recovered from sampled fish species carried plasmids (53.5%), floR gene (36.7%), and tet genes (19.2%), whereas the detection of sul genes and class 1-integron was rare. As an overall result, 10.6% of isolates carried at least one bla gene, encoding an extended-spectrum-β-lactamase, with a high predominance of the bla_CTX-M1 gene (23 isolates), whereas 14 out of 245 isolates (5.7%) were positive for the carriage of carbapenemases encoding genes, which both groups exhibited the β-lactam resistance phenotype. Conclusions: The wide distribution of ARG-carrying bacteria in wild fishes from all sampled Bays provides evidence that wild fish are important reservoirs and drivers of spread of ARGs in the marine environment, prompting the need of a continuous surveillance of these genes in wild fishes inhabiting anthropic impacted coastal marine environments in Chile. Full article

Riemerella anatipestifer (R. anatipestifer) is a pathogenic bacterium belonging to the genus Riemerella within the family Flavobacteriaceae, which has multidrug resistance (MDR) and can cause high pathogenicity in waterfowl. The aim of this study was to investigate the antimicrobial resistance and genomic characteristics of R. anatipestifer strains isolated from several regions of China from 2023 to 2024. Two strains were selected for challenge tests, and virulence protection tests were conducted on florfenicol-resistant and florfenicol-sensitive strains. A total of 88 strains of R. anatipestifer were collected from the Shandong, Jiangsu, Guangdong, Hebei and Henan regions. The results showed that the 88 strains included serotypes 1, 2, 5, 6, 7 and 10. Serotype 5 was the most prevalent in the Shandong region. All strains were multidrug-resistant, with the hexaresistance accounting for the highest proportion (42.1%). A total of five resistance genes (tet(X), floR, ermF, qnrS, rmtB) and seven virulence genes were found (ompA, camp, AS87_04050, SIP, Fur, TbdR1, luxE). The challenge test showed that the LD₅₀ of RA12 was 2.75 × 10⁷ CFU/mL, and that of RA26 was 2.57 × 10⁷ CFU/mL. Phylogenetic tree analysis revealed that strain RA26 was closely related to strain 20190403E1-1, and strain RA16 was closely related to strain JW1. In addition, serotypes 2 and 7 identified in this study have been undergoing clonal transmission in China. Virulence protection tests indicated that the results of in vitro drug susceptibility tests were consistent with the therapeutic effects after in vivo treatment, and no R. anatipestifer was found in the visceral tissues of surviving ducklings. This study provides a reference for the rational use of antibiotics. Full article

Salmonella Typhimurium is a major zoonotic pathogen, with pigs and chickens serving as key reservoirs for human infection, yet the genomic determinants of its host adaptation remain incompletely understood. This study integrated comparative genomics, genome-wide association studies (GWASs), and interpretable machine learning on 1654 high-quality genomes of swine- and chicken-origin S. Typhimurium isolates to identify host-associated genetic features. Phylogenetic analysis revealed host-preferred lineages and significantly lower genetic diversity within chicken-adapted subpopulations. Meta-analysis identified distinct host-associated profiles of antimicrobial resistance genes (e.g., higher prevalence of floR and bla_TEM-1 in swine) and virulence factors (e.g., enrichment of allB and the yersiniabactin system in chickens). GWASs pinpointed 1878 host-associated genes and multiple SNPs/indels, functionally enriched in metabolism, regulation, and cell processes. A two-stage Random Forest model, built using the most contributory features, accurately discriminated between swine and chicken origins (AUC = 0.974). These findings systematically revealed the genomic signatures of host adaptation in S. Typhimurium, providing a prioritized set of candidate markers for experimental validation. Full article

Background: Mobile antimicrobial resistance genes (ARGs) on plasmids or other elements enable Salmonella Typhimurium to spread resistance across hosts and environments. The emergence of multi-drug resistance (MDR) Salmonella Typhimurium has raised global concern, yet little is reported about these mobile elements from the Thailand pork supply chain, where this risk of transfer to humans remains largely uncharacterized. Methods: Between March 2023 and February 2024, 25 S. Typhimurium isolates were collected from pig carcasses in slaughterhouses and pork swabs from retail markets in northeastern Thailand. Nine representative isolates, sampled across three seasons, were subjected to Illumina whole-genome sequencing. Assemblies were analyzed for sequence types, phylogenetic relationships, antimicrobial resistance (AMR) determinants, plasmid replicons and mobilization features, functional annotation based on COG (Clusters of Orthologous Groups of proteins) classification, and comparative genomics against a reference strain. Results: Genome assemblies ranged from 4.76 to 5.00 Mb with consistent GC (guanine-cytosine) content (52.0–52.2%). Phylogenetic analysis revealed three sequence types: ST34 (77.8%), ST19, and ST1543. ST34 isolates displayed the broadest AMR gene repertoires, carrying tetracycline (tetA/tetB), sulfonamide (sul1/sul2/sul3), aminoglycoside (aadA, aph(6)-Id, aph(3″)-Ib), phenicol (floR, catA1), and β-lactam (bla_TEM-1B) genes, whereas non-ST34 isolates harbored fewer determinants. ARGs frequently co-localized with IncQ1 and Col-type plasmid replicons, MOB_H/MobA relaxases (enzymes that initiate plasmid transfer), and conjugation modules (type IV secretion and coupling proteins), often alongside virulence loci and metal resistance operons. Functional annotation showed highly conserved metabolic and housekeeping functions, while comparative genomics confirmed >90% core genome conservation, with variability concentrated in genomic islands encoding hypothetical proteins. These genomic patterns were inferred from a limited WGS dataset (nine isolates) and should therefore be considered exploratory and require confirmation in larger collections. Conclusions: Multi-drug resistant ST34 Salmonella Typhimurium predominated in the northeastern Thailand pork supply chain, with diverse resistance genes carried on IncQ1/Col-type plasmids linked to MOB_H relaxases and conjugation modules. The stability of these mobilizable elements underscores their role in sustaining MDR traits and highlights the risk of foodborne AMR transmission, reinforcing the need for continuous genomic surveillance under a One Health framework. Full article

In this study, we isolated 214 Vibrio cholerae strains from aquatic (shrimp, crab, grass carp, and crucian carp) and their cultured environment in Shanghai, China. The virulence, serotype, and antimicrobial susceptibility were tested, and polymerase chain reaction (PCR) was used to detect antimicrobial resistance genes. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) was employed for cluster analysis of the isolated strains. The results showed that V. cholerae was found in 47.9% (114/238) of aquatic samples, with the highest detection rate in shrimp (81.1%), and the detection rate was highest in summer (70.0%). Most of the strains were non-O1/O139 groups, and virulence genes rtxC and hap had the highest detection rates of 92.5% and 91.1%. Of the 214 isolates, 69.6% were multidrug-resistant (MDR). The resistance rate of V. cholerae to sulfamethoxazole, ampicillin, and erythromycin was 97.2%, 85.5%, and 70.1%, and that to imipenem, tetracyclines, and aminoglycosides was less than 5%. The MAR index ranged from 0.05 to 0.47. When V. cholerae was screened for antimicrobial resistance genes, β-lactams CARB, chloramphenicol floR, and sulfonamides sul2 were found in 19.6%, 7.9%, and 6.5% of isolates, respectively. The results of ERIC-PCR clustering showed that the isolates had a high degree of genetic diversity. The widespread distribution of virulent and MDR V. cholerae strains poses a potential threat to food safety and public health, calling for improved monitoring and control measures in the aquaculture industry. Full article

The glycemic index (GI) of rice is a complex trait, affected by amylose content (AC), size, and packaging of starch granules (SGs). In this study, the electron microscopy results of starch morphology of nine rice genotypes showed varying AC (6.93–36.9%), and the predicted GI (pGI: 41.07–82.46) in relation to genetic factors revealed that smaller SG surface area (20.06 µm²) and irregular morphology (Hap 3-3 P-11, pGI = 41.07) were associated with a lower pGI, while larger SG surface area (47.68 µm²) and spherical structure were associated with a higher pGI (NON-HAI, pGI = 82.46). The expression of starch biosynthesis and packaging-related genes (OsSSIIb, OsSSIIc, OsSBEIIa, OsISA1, OsISA3, OsGBP, OsFLO6, and OsBT1) revealed downregulation of OsGBP and OsISA3 genes in low pGI lines IRRI-147 (pGI = 56.2) and Hap 3-1-p-18 (pGI = 41.79), respectively, while higher levels of expression of the OsBT1 gene in Makro (pGI = 59.06) and OsSSIIb in Swarna (pGI = 58.06) were observed. All these genotypes had similar AC (~30%), but the difference in expression pattern was correlated with starch granule morphology, suggesting its role in influencing pGI. Further, analysis of allelic variation in eight starch-related genes across 20 rice genotypes showed that allelic variants of only OsGBP were correlated with AC, where allele group 2 showed lower AC (9.62%), while all other allele groups showed consistently high AC (22–24%). These findings underscore the critical role of starch granule morphology and OsGBP allelic variation in determining AC and GI, providing actionable insights for developing low GI rice varieties using tools like CRISPR. Full article

Background/Objectives: The global dissemination of tet(X) variants critically threatens tigecycline efficacy as a last-resort antibiotic. The aim of this study was to characterize a tet(X6)-carrying integrative and conjugative element (ICE) in a multidrug-resistant Chryseobacterium lecithinasegens strain, SHZ29, isolated from Shanghai, China. Methods: Minimum inhibitory concentrations (MICs) were determined by broth microdilution for SHZ29. Whole genomic sequencing and bioinformatic analysis were performed to depict the structure of the novel tet(X6)-carrying ICE. Inverse PCR and conjugation experiments were conducted to investigate the transfer ability of the ICE. Results: We depicted a novel tet(X6)-carrying ICE, named ICECleSHZ29, which is 74,906 bp in size and inserted into the 3′ end of tRNA-Met-CAT gene of the C. lecithinasegens strain SHZ29, with 17 bp direct repeats (5′-tcccgtcttcgctacaa-3′). This ICE possesses a 38 kb conserved backbone and four variable regions (VR1-4), with VR3 aggregating multiple resistance genes, including tet(X6), tet(X2), erm(F), ere(D), floR, catB, sul2, ant(6)-I and bla_OXA-1327. NCBI database searching identified 13 additional ICEs sharing a similar backbone to ICECleSHZ29. These ICECleSHZ29-like ICEs could be classified into two types based on their distinct insertion sites: Type I, inserted at the tRNA-Met-CAT gene; and Type II, inserted at the tRNA-Glu-TTC gene. Phylogenetic analysis indicated that differences in integrases may result in differences in the insertion site among these ICEs. A circular intermediate form of ICECleSHZ29 was detected by inverse PCR. However, the conjugation experiments using Escherichia coli EC600 as recipients failed. Conclusions: To our knowledge, this study provides the first report of tet(X6) in C. lecithinasegens and characterizes its carrier, a novel ICE: ICECleSHZ29. Full article

An outbreak characterized by clinical signs of diarrhea and paralysis, occasionally progressing to fatal outcomes, occurred at an ostrich breeding facility. Conventional antibiotic treatments proved ineffective. To investigate the etiology of the disease, brain and liver specimens were collected for diagnostic analysis. An Escherichia coli (E. coli) isolate, designated strain HZDC01, was obtained from cerebral tissues, and whole-genome sequencing was performed for genomic characterization. Genomic analysis revealed that the chromosomal DNA harbors numerous resistance genes, conferring multidrug resistance through complex mechanisms. Furthermore, a p0111-type plasmid carrying the bla_CTX-M-55 gene and an IncX1-type plasmid harboring rmtB, sul1, APH(6)-Id, tet(A), AAC(3)-IIc, aadA2, bla_TEM-1B, and floR genes were identified. These plasmids carry numerous mobile genetic elements that can disseminate via horizontal gene transfer, thereby amplifying the risk of resistance-gene spread within bacterial populations. Additionally, the ibeB and ibeC genes, which encode proteins involved in the invasion of brain microvascular endothelial cells, were identified. These genes may facilitate E. coli penetration of the blood–brain barrier, potentially leading to meningitis and posing a life-threatening risk to the host. This is the first report of the isolation and characterization of extended-spectrum beta-lactamase E. coli from the brain of an ostrich with paralysis. The findings provide valuable genomic insights into the antimicrobial resistance profiles and pathogenic mechanisms of ostrich-derived E. coli isolates. Full article

This study aimed to evaluate the protective effects of Inula japonica leaf extract against PM₁₀-induced oxidative stress in normal human keratinocytes. Keratinocytes were pretreated with various concentrations of Inula japonica leaf extract and subsequently exposed to PM10. Cell viability, ROS production, gene and protein expression (qRT-PCR and Western blot), and UHPLC-MS profiling were assessed. Network pharmacology analysis was conducted using database-predicted compounds of Inulae Flos. The extract significantly reduced PM₁₀-induced ROS generation and restored the expression of epidermal barrier-related genes such as loricrin. It also inhibited phosphorylation of MAPKs (ERK, p38) and modulated apoptotic and inflammatory markers including Bax, p53, MMP-9, and COX-2. UHPLC-MS analysis identified eight compounds not previously reported in our earlier study, which may contribute to the extract’s protective effects. Inula japonica leaf extract exerts protective effects against PM₁₀-induced skin damage by reducing oxidative stress and inflammation in keratinocytes. These findings support its potential as a therapeutic candidate for pollution-related skin disorders. Full article