Search Results (161)

Salmonella is a major foodborne pathogen, and its increasing antimicrobial resistance poses a significant public health challenge. In this study, we conducted a comprehensive genomic epidemiological investigation of Salmonella isolates recovered from meat products across multiple provinces in China. A total of 141 isolates were collected and subjected to antimicrobial susceptibility testing and whole-genome sequencing. Core genome MLST and hierarchical clustering (HierCC) were performed using EnteroBase, while SNP phylogeny and phylodynamic analyses were conducted to characterize the evolutionary dynamics of Salmonella populations. The predominant serovars were Enteritidis and Infantis, with a high proportion of multidrug-resistant isolates. Potentially transferable plasmids carrying ARGs, such as bla_CTX-M, qnrS1, sul2, and mcr-1.1, were frequently detected, indicating a risk of horizontal transfer during transmission. Genomic epidemiological investigation of our sequenced strains and their associated cgMLST HierCC clusters revealed both persistent Salmonella lineages, such as Enteritidis HC50-87 and Agona HC20-419, and emerging China-specific lineages, including Enteritidis HC20-10145 and Typhimurium HC50-2304. The estimated divergence times of these lineages mostly dated to the late mid-20th century, coinciding with the intensification of poultry farming in China. These findings highlight the power of genomic epidemiology in uncovering antimicrobial resistance patterns and transmission dynamics, underscoring the need for strengthened Salmonella surveillance. Full article

Background/Objectives: Changes in the physiological activity of transforming growth factor-beta (TGF-β) family caused by genetic variability may significantly affect the phenotype of the musculoskeletal system and, consequently, the risk of sports injuries. This study aimed to investigate whether the TGFBI (rs1442), TGFBR3 (rs1805113 and rs1805117), and MSTN (rs11333758) polymorphisms, either individually or in combination, were associated with susceptibility to muscle injury, anterior cruciate ligament (ACL) rupture, and other injuries. Methods: The study group included 202 physically active Caucasians with reported sport injuries and 133 healthy controls. All the samples were genotyped using real-time polymerase chain reaction (real-time PCR). Results: The results revealed that (1) the TGFBR3 rs1805117 TC genotype was nominally associated with increased ACL injury risk; (2) the MSTN rs11333758 heterozygotes was more frequent in the one injury group (vs controls) and in the ACL group, whereas in the multiple vs. one comparison the over-dominant model suggested lower odds for heterozygotes; and (3) the TGFBI rs1442 CG genotype was nominally associated with lower odds of fractures, dislocations or sprains. In addition, simultaneous analysis of chosen SNPs revealed interactions between TGFBR3 rs1805117 and rs1805113, with a nominal association of the rs1805113 G allele with increased injury risk, as did rs11333758 and rs1805113, with a potential effect of rs11333758 on injury status. However, haplotype analysis of the TGFBR3 SNPs revealed no significant associations. After Bonferroni correction, none of the associations remained statistically significant. Conclusions: The results suggested that carrying specific TGFBI, TGFBR3, and MSTN genotypes may be potentially associated with susceptibility to musculoskeletal injuries in a physically active Caucasians. Full article

Background: Carbapenem-resistant Escherichia coli (CREC) producing OXA-48-like carbapenemase was first detected in Hungary in 2022. The aim of the present study was to characterize such strains isolated in 2022–2025 in Baranya County, Hungary. Methods: Antibiotic susceptibility and the whole-genome sequence (WGS) of E. coli isolates, identified as OXA-48-like carbapenemase producers using the CARBA-5 NG test, were established. The transferability of bla_OXA-48-like plasmids was tested by conjugation. Results: Of the 6722 non-repeat E. coli isolates, 6 produced an OXA-48-like carbapenemase. They exhibited variable resistance to ertapenem and were susceptible to imipenem and meropenem. WGS revealed that all OXA-48-like producer E. coli belonged to high-risk clones: two clonally related OXA-181-producer E. coli ST405 were isolated in Hospital A, three OXA-244-producing E. coli ST38 (two identical via cgMLST from Hospital B), and an OXA-48-producing E. coli ST69. The bla_OXA-48 and bla_OXA-244 genes were chromosomally located, while bla_OXA-181 was on a non-conjugative IncFIB-IncFIC plasmid. So far, the bla_OXA-181-bearing plasmid of this incompatibility type has only been described in Ghana, but all bla_OXA-48-like gene-carrying transposons in this study have already been identified in Europe and other continents. The E. coli ST38 isolates, showing close association based on core genome SNP distances to European and Qatari strains, belonged to Cluster A and harbored bla_CTX-M-27. All but the E. coli ST69 isolate had cephalosporinase gene(s). Conclusions: This study describes small-scale intra-hospital transfers of OXA-48-like carbapenemase-producer E. coli. Interestingly, E. coli ST405 of Hungary carried bla_OXA-181 on an IncFIB-IncFIC plasmid, which has only been reported from Africa so far. Full article

This study investigated the molecular epidemiology, virulence, antimicrobial resistance, and mobile genetic elements (MGEs) of Salmonella enterica serovar I 4,[5],12:i:- isolates collected in Jeollanam-do, South Korea, between 2021 and 2023. A total of 135 isolates were tested for antimicrobial susceptibility and 14 virulence-associated genes were screened by PCR. Pulsed-field gel electrophoresis (PFGE) assessed clonal relatedness, and whole-genome sequencing (WGS) enabled multilocus sequence typing (MLST), core genome MLST (cgMLST), SNP phylogeny, resistance gene detection, and MGE analysis. Nine virulence profiles (VP1–VP9) were identified. VP1 (74.1%) was strongly associated with multidrug resistance (MDR), while VP2 (14.8%), which carried plasmid-encoded spv genes, remained largely susceptible. Overall, 83.7% of isolates were resistant to at least one antimicrobial, and 65.2% were MDR, with ampicillin and tetracycline consistently forming the backbone of MDR phenotypes. PFGE revealed high genetic diversity, with 72 pulsotypes, yet certain clones (e.g., SMOX01.006, SMOX01.012) were widely distributed and corresponded to VP2 isolates. WGS confirmed two dominant sequence types, ST34 (n = 24) and ST19 (n = 20), with SNP phylogeny showing VP1 isolates mainly clustered with ST34 and VP2 with ST19. Genotype–phenotype concordance showed strong agreement for most antimicrobials, except cefoxitin, ciprofloxacin, amikacin, and trimethoprim/sulfamethoxazole. MGE analysis revealed that tet(B) was consistently associated with ISVsa5, while ISEc59 was linked to multiple resistance genes, though only aac(3)-IV was phenotypically expressed. These findings demonstrate that MDR and virulence gene composition were closely associated with clonal clustering and that MGEs may contribute to resistance gene expression. This study provides a basis for understanding the dissemination of resistant and virulent Salmonella in the region and underscores the need for continuous genomic surveillance. Full article

Growth and carcass traits are key economic traits in beef cattle production, and identifying their associated genetic markers is crucial for improving breeding efficiency. Charolais cattle, as a superior beef breed, exhibit excellent performance in growth rate and meat production. The aim of this study was to utilize the preferred high-coverage whole-genome resequencing (hcWGS) as a replacement for single nucleotide polymorphism (SNP) chips to identify significant SNPs and candidate genes associated with growth (body weight, body height, cross height, body length, and chest measurement across different growth stages) and carcass traits (live backfat thickness and eye muscle area at 18 months) in 240 Charolais cattle, thereby providing guidance for beef cattle breeding. Through hcWGS (approximately 13× coverage) and quality control, 4,088,633 SNPs were identified and subsequently used for genetic analyses. Through FarmCPU-based genome-wide association studies, 196 potentially significant SNPs associated with growth traits and 29 SNPs with carcass traits were identified. Annotation analyses revealed 353 candidate genes (such as RBM33, KCTD17, PTHLH, RAC2, CHD6, TRDN, WBP1L, TLL2, CH25H, and ST13) linked to growth traits and 26 candidate genes linked to carcass traits (such as CHST11, LRRK2, RIOK2, and INTS10). Additionally, three SNPs (g.8674692C>G, g.54418624G>T, and g.71085551G>A) were validated via polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP), enabling efficient marker-assisted selection. Furthermore, eight SNPs in the Acyl-CoA oxidase 1 (ACOX1) gene were found to be associated with growth and backfat thickness traits. These findings provide valuable preliminary insights into the genetic mechanisms underlying growth and carcass traits in Charolais cattle, facilitating genome-assisted breeding. Full article

Listeria monocytogenes is a foodborne pathogen of significant public health concern due to its high environmental resilience and ability to cause severe infections in vulnerable populations. The objective of the present study is to characterize foodborne strains of Listeria monocytogenes isolated between 2020 and 2024 in northwestern Italy. Lm was detected through isolation, biochemical confirmation and molecular serogrouping. Next generation sequencing (NGS) analysis was used to characterize the strains in terms of virulence and antibiotic resistance. A total of 39 positive samples were identified from various food matrices, including meat products, fish, cheeses and ready-to-eat foods. The most frequently detected serogroups were IIc and IIa, with a notable presence of the highly virulent IVb group. Next-generation sequencing (NGS) was applied to all isolates, revealing the presence of virulence genes associated with the LIPI-1 island and internalins. In addition to pathogenicity islands, genes related to stress resistance (clpCEP, Gad A, GadB, GadC), biofilm production (agrA, flaA, degU, hfq) and sortase-mediated anchoring of surface protein (strA, strB) have been identified. The presence of antibiotic resistance genes was confirmed, with all isolates harboring the fosX gene. Moreover, four isolates exhibited resistance determinants against antibiotics belonging to two different classes: tetracyclines (tetM) and lincosamides (lsa(A)). Multilocus sequence typing (MLST) showed that clonal complex CC9 was the most prevalent among the isolates. Further, cgMLST and SNP analyses identified a principal cluster of closely related strains, which were isolated from meat products. These findings highlight the need for continuous surveillance of L. monocytogenes. Full article

Background: Metabolic syndrome, a cardiovascular risk cluster, is recognized as a global health priority influenced by gene–diet interactions. The rs2794720 polymorphism has not been previously reported in relation to metabolic syndrome. This study examined the associations between dietary iron, SNP rs2794720, and metabolic syndrome in Chinese metropolitan population, with a focus on sex-specific and genotype-specific effects. Methods: A community-based cross-sectional study enrolled 2639 adults (1254 males, 1385 females) from Shanghai, China. Anthropometric measurements, laboratory analyses, and genotyping for the participants were performed. Dietary assessment utilized the 3-day 24 h dietary recall method. Metabolic syndrome was identified by the presence of at least three out of five metabolic abnormalities according to the NCEP—ATP III criteria. Results: After adjusting for confounders, in males, metabolic syndrome risk was associated with dietary iron (p = 0.002) but not with rs2794720 (p = 0.731). In females, metabolic syndrome risk was associated with rs2794720 (p = 0.014) and dietary iron (p = 0.016), with a significant interaction observed between rs2794720 and dietary iron (p = 0.047). Stratified by rs2794720, among females lacking the C allele, there was a linear trend between dietary iron and metabolic syndrome risk (p = 0.048). Compared to the reference group (lowest-intake GG homozygotes), the Q2–Q4 Ors (95% CI) were 5.31 (1.08, 39.52), 5.50 (1.16, 40.28), and 8.40 (1.80, 41.44)), while the major allele carriers did not show this trend (p = 0.704); compared to the reference group, the Q1–Q4 ORs(95% CI) were 6.13 (1.68, 39.66), 7.53 (2.06, 48.86), 8.10 (2.20, 52.60), and 7.84 (2.07, 51.70)). Conclusions: Our study first identified rs2794720 as a novel SNP associated with metabolic syndrome in Chinese females. The association between dietary iron and metabolic syndrome risk was unique to GG homozygotes (the minority), whereas CC/CG genotypes (the majority) showed no such association. Full article

During the COVID-19 pandemic, a significant increase in the spread of healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) was observed. Acinetobacter baumannii, particularly carbapenem-resistant strains, poses a serious threat in intensive care units (ICUs). This study aimed to genetically characterize A. baumannii isolates from the ICU of an infectious diseases hospital repurposed for COVID-19 patient treatment. Whole-genome sequencing (WGS) was performed on 56 A. baumannii isolates from patients and environmental surfaces using the Illumina MiSeq platform. Bioinformatic analysis included multi-locus sequence typing (MLST), core-genome MLST (cgMLST), phylogenetic analysis, and in silico detection of antimicrobial resistance genes. Three sequence types (STs) were identified: ST2 (35.7%), ST78 (30.4%), and ST19 (3.5%); while 30.4% of the isolates were non-typeable. Phylogenetic analysis revealed clustering of ST2 with isolates from East Africa, ST78 with European isolates, and ST19 with isolates from Germany and Spain. Resistance genes to eight classes of antimicrobials were detected. All isolates were resistant to aminoglycosides and β-lactams. The blaOXA-23 carbapenemase gene was present in all ST2 isolates. cgMLST analysis (cgST-1746) showed significant heterogeneity among ST2 isolates (24–583 allele differences), indicating microevolution within the hospital. A novel synonymous SNP (T2220G) in the rpoB gene was identified. Environmental sampling highlighted the role of contaminated personal protective equipment (PPE) in transmission, with 47.0% of ST2 and 64.3% of ST78 isolates found on PPE. The study underscores the high resolution of WGS and cgMLST for epidemiological surveillance and confirms the critical role of infection control measures in preventing the spread of multidrug-resistant A. baumannii. Full article

Leptospirosis is a worldwide zoonosis caused by pathogenic Leptospira spp. with small rodents serving as the main reservoir. In Croatia, the serogroup Pomona has been detected most frequently, but its genomic diversity remains insufficiently characterized. This study presents the first whole genome sequencing analysis of 48 Croatian Leptospira spp. isolates collected from small rodents over a 14-year period. Serological typing confirmed that all the isolates belonged to the serogroup Pomona. Genomic analysis assigned them to L. kirschneri based on high genomic similarity using average nucleotide identity (ANI). The isolates were assigned to ST-98 using traditional multilocus sequence typing (MLST), while cgMLST identified seven genotype clusters, many of which showed geographic structuring. Phylogenetic analyses based on single nucleotide polymorphisms (SNPs) supported this structure and revealed a monophyletic clade of Croatian isolates distinct from other global L. kirschneri strains. Serological typing, MLST, and phylogenetic clustering support classification of the isolates as L. kirschneri, serogroup Pomona, most likely serovar Mozdok, although serovar Tsaratsovo cannot be excluded. These results indicate the existence of a geographically restricted and potentially host-adapted lineage of L. kirschneri in Croatia. The integration of ecological, serological, and genomic data in this study emphasizes the value of whole genome sequencing for understanding the population biology of Leptospira spp. serogroup Pomona. Moreover, it supports targeted, country-specific surveillance and control strategies for leptospirosis through the identification of circulating serovars and species in reservoir hosts, in line with a One Health approach. Full article

Background/Objectives: Gestational diabetes (GD) is a common pregnancy complication linked to inflammation. Obesity, a major risk factor, is associated with elevated pro-inflammatory markers (TNF-α, IL-6) and reduced anti-inflammatory IL-10 and adiponectin. This study investigated the role of inflammatory factors (IL-6, TNF-α, IL-10, adiponectin) and their genetic variants (rs1800629, rs1800796, rs1800896, rs266729) in a unique four-group study design of pregnant women. Methods: We collected venous blood from 162 women in the third trimester of pregnancy. We measured IL-6, IL-10, TNF-α, and adiponectin levels and performed real-time PCR genotyping for the selected SNPs. Results: IL-6 levels were significantly higher (p < 0.001) in pregnant women with GD and additional complications. The IL-6 SNP rs1800796 heterozygous CG genotype showed a slightly increased GD risk (OR = 1.41). However, we found no significant associations between GD and TNF-α rs1800629 or IL-10 rs1800896 SNPs. The AdipoQ rs266729 homozygous CC genotype was linked to increased GD risk (p = 0.03 for superdominant model). Importantly, no significant correlations were observed between inflammatory marker levels and gene variants within any study group. Conclusions: Our findings suggest a greater inflammatory burden in GD pregnancies with additional complications. While certain IL-6 and AdipoQ variants might contribute to GD risk, the overall weak association between inflammatory markers and gene variants likely reflects the complex polygenic nature of GD, environmental factors, or the study’s sample size. Full article

Stropharia rugosoannulata, an ecologically valuable and economically important edible mushroom, faces challenges in strain-level identification and breeding due to limited genomic resources and the lack of high-resolution molecular markers. In this study, we generated high-quality genomic data for 105 S. rugosoannulata strains and identified over 2.7 million SNPs, unveiling substantial genetic diversity within the species. Using core gene-associated multiple nucleotide polymorphism (cgMNP) markers, we developed an efficient and transferable framework for strain discrimination. The analysis revealed pronounced genetic differentiation among cultivars, clustering them into two distinct phylogenetic groups. Nucleotide diversity (π) across 83 core genes varied significantly, highlighting both highly conserved loci under purifying selection and highly variable loci potentially associated with adaptive evolution. Phylogenetic analysis of the most variable gene, Phosphatidate cytidylyltransferase mitochondrial, identified 865 SNPs, enabling precise differentiation of all 85 cultivars. Our findings underscore the utility of cgMNP markers in addressing challenges posed by horizontal gene transfer and phylogenetic noise, demonstrating their robustness in cross-species applications. By providing insights into genetic diversity, evolutionary dynamics, and marker utility, this study establishes a foundation for advancing breeding programs, conservation strategies, and functional genomics in S. rugosoannulata. Furthermore, the adaptability of cgMNP markers offers a universal tool for high-resolution strain identification across diverse fungal taxa, contributing to broader fungal phylogenomics and applied mycology. Full article

The 26S proteasome is a large, ATP-dependent proteolytic complex responsible for degrading ubiquitinated proteins in eukaryotic cells. It plays a crucial role in maintaining cellular protein homeostasis by selectively eliminating misfolded, damaged, or regulatory proteins marked for degradation. In this study, whole-exome sequencing (WES) was performed on an individual presenting with developmental delay and mild intellectual disability, as well as on both of his unaffected parents. This analysis identified a de novo variant, c.959C>G (p.Pro320Arg), in the PSMC5 gene. As predicted, this gene shows a very likely autosomal dominant inheritance pattern. Notably, PSMC5 has not previously been associated with any phenotype in the OMIM database. This variant was recently submitted to the ClinVar database as a variant of uncertain significance (VUS) and remains absent in both gnomAD and dbSNP. Notably, it has been identified in six unrelated individuals presenting with clinical features comparable to those observed in the patient described in this study. Multiple in silico prediction tools classified the variant as pathogenic, and a PhyloP conservation score supports strong evolutionary conservation of the mutated nucleotide. Protein structure predictions using the AlphaFold3 algorithm revealed notable structural differences between the mutant and wild-type PSMC5 proteins. We hypothesize that the p.Pro320Arg substitution alters the structure and function of PSMC5 as a regulatory subunit of the 26S proteasome, potentially impairing the stability and activity of the entire complex. Although functional studies are imperative, this study contributes to a deeper understanding of PSMC5, expands the spectrum of associated neurodevelopmental phenotypes, and highlights its potential as a therapeutic target. Furthermore, this study resulted in the submission of the identified variant to the ClinVar database (SCV006083352), where it was classified as pathogenic. Full article

Shiga-toxin-producing E. coli (STEC) is a leading causing of bacterial foodborne and zoonotic illnesses in the USA. Whole-genome sequencing (WGS) is a powerful tool used in public health and microbiology for the detection, surveillance, and outbreak investigation of STEC. In this study, we applied three WGS-based subtyping methods, high quality single-nucleotide polymorphism (hqSNP) analysis, whole genome multi-locus sequence typing using chromosome-associated loci [wgMLST (chrom)], and core genome multi-locus sequence typing (cgMLST), to isolate sequences from 11 STEC outbreaks. For each outbreak, we evaluated the concordance between subtyping methods using pairwise genomic differences (number of SNPs or alleles), linear regression models, and tanglegrams. Pairwise genomic differences were highly concordant between methods for all but one outbreak, which was associated with international travel. The slopes of the regressions for hqSNP vs. allele differences were 0.432 (cgMLST) and 0.966 wgMLST (chrom); the slope was 1.914 for cgMLST vs. wgMLST (chrom) differences. Tanglegrams comprised of outbreak and sporadic sequences showed moderate clustering concordance between methods, where Baker’s Gamma Indices (BGIs) ranged between 0.35 and 0.99 and Cophenetic Correlation Coefficients (CCCs) were ≥0.88 across all outbreaks. The K-means analysis using the Silhouette method showed the clear separation of outbreak groups with average silhouette widths ≥0.87 across all methods. This study validates the use of cgMLST for the national surveillance of STEC illness clusters using the PulseNet 2.0 system and demonstrates that hqSNP or wgMLST can be used for further resolution. Full article

Multiple myeloma is a neoplastic disease characterised by the proliferation of clonal, atypical plasma cells. In cancer cells, the balance between two paths of cell death, necroptosis and apoptosis, is disrupted. The aim of this study was to analyse the occurrence of polymorphisms in genes encoding key proteins for the necroptosis process, i.e., RIPK-1, RIPK-3 and MAPKAPK2. We investigated the potential relations between the occurrence of genetic variability and the clinical course of the disease. We analysed six single-nucleotide polymorphisms in a population of patients with multiple myeloma (n = 205) and healthy volunteers (n = 100): RIPK1 rs2272990, RIPK1 rs9391981, RIPK3 rs724165, RIPK3rs3212243, MAPKAPK2, rs45514798 and MAPKAPK2 rs4073250. We found that genotypes rs9391981 CG, rs724165 CG, rs3212243 GG, and rs4073250 AA were independent predictors of overall survival, while genotype MAPKAPK2 rs4073250 AA was an independent predictor of progression-free survival. MAPKAPK2 rs45514798 AA was associated with polyneuropathy after thalidomide therapy. In conclusion, some of the SNPs tested have potential prognostic value and could be used as marker of survival in patients with multiple myeloma. Full article

Mastitis is an important disease limiting milk production in dairy cows. Somatic cell score is commonly used as one of the main ways to gauge the level of mastitis in dairy cows, with higher somatic cell scores usually indicating possible mastitis. However, the main molecular markers affecting somatic cell scores remain unknown. The aim of this study was to investigate the association between single nucleotide polymorphisms in the SLC11A1 gene and somatic cell score in Chinese Holstein cows. In this study, 210 Chinese Holstein cows were genotyped and potential SNPs were detected by DNA sequencing, PCR-SSCP and PCR-RFLP analysis. Our results revealed two SNPs were identified in the CDS region of SLC11A1: c.723C>T and c.1144C>G. For the c.723C>T polymorphic site, two genotypes (AA, AB) were found and the genotype frequencies were 0.790 and 0.210, respectively. The results of the association analysis showed that the mean somatic cell score of the AA genotypes were significantly lower than those of the AB genotypes, suggesting that the A allele is a potential marker for improving mastitis resistance in Chinese Holstein cows. For the c.1144C>G polymorphic site, three genotypes (CC, CD, and DD) were found and the genotype frequencies were 0.629, 0.352 and 0.019, respectively. The association analysis revealed that the mean somatic cell score of CC genotypes was lower than that of CD and DD genotypes, however, no significant differences were observed among the various genotype groups when subjected to pair-wise comparisons. The bioinformatic analysis showed that these mutations affected the secondary and tertiary structure of SLC11A1 mRNA, suggesting that they may affect gene expression or protein translation and function. Finally, we predicted the SLC11A1 protein interaction network and found that SPI1, NOD2, TLR2 and S100A12 interacted with SLC11A1 and were reported as candidate genes associated with mastitis resistance. The results indicated that the SNP (c.723C>T) could be potential molecular marker for improving mastitis resistance traits in Chinese Holstein cows. We recommend further validation of this SNP in larger populations and its potential integration into breeding programs to enhance mastitis resistance in dairy cows. Full article