Search Results (320)

Multiple metrics for read-level DNA methylation pattern analysis have provided new insights into DNA methylation modifications. However, the performance of these metrics and their relationship with DNA methylation ratios in identifying biologically meaningful regions have remained unclear. Here, we systematically benchmarked five read-level DNA methylation metrics using whole-genome bisulfite sequencing data from 59 individuals across six healthy tissue types and six tumor types. We found that DNA methylation concurrence (MCR) effectively captured tissue-specific features independent of the DNA methylation ratios. Regions that exhibited decreased MCR (MCDRs) in tumors were significantly enriched in promoter and intergenic regions and strongly overlapped with tumor-gained chromatin accessibility sites. The further analysis of histone modifications, including H3K4me3, H3K27ac, and H3K9ac, confirmed that MCDRs marked active gene regulatory elements. Motif enrichment analysis revealed a strong preference for CTCF binding within MCDRs. Additionally, 3D genome analysis supported a model in which MCDRs, independent of DNA methylation ratios, contribute to active gene regulation by facilitating CTCF binding and long-range chromatin interactions. Full article

Background/Objectives: The rapid emergence of antibiotic-resistant Escherichia coli in food and clinical environments necessitates new, clean-label antimicrobials. This study assessed eight Greek native essential oils—oregano, thyme, dittany, rosemary, peppermint, lavender, cistus and helichrysum—for activity against six genetically and phenotypically diverse E. coli strains (reference, pNorm, mecA, mcr-1, blaOXA and O157:H7). We aimed to identify oils with broad-spectrum efficacy and clarify the chemical constituents responsible. Methods: Disk-diffusion assays measured inhibition zones at dilutions from 50% to 1.56% (v/v). MIC and MBC values were determined by broth microdilution. GC–MS profiling identified dominant components, and Spearman rank-order correlations (ρ) linked composition to activity. Shapiro–Wilk tests (W = 0.706–0.913, p ≤ 0.002) indicated non-normal data, so strain comparisons used Kruskal–Wallis one-way ANOVA with Dunn’s post hoc and Bonferroni correction. Results: Oregano, thyme and dittany oils—rich in carvacrol and thymol—exhibited the strongest activity, with MIC/MBC ≤ 0.0625% (v/v) against all strains and inhibition zones > 25 mm at 50%. No strain-specific differences were detected (H = 0.30–3.85; p = 0.998–0.571; p_adj = 1.000). Spearman correlations confirmed that carvacrol and thymol content strongly predicted efficacy (ρ = 0.527–0.881, p < 0.001). Oils dominated by non-phenolic terpenes (rosemary, peppermint, lavender, cistus, helichrysum) showed minimal or no activity. Conclusions: Phenolic-rich EOs maintain potent, strain-independent antimicrobial effects—including against multidrug-resistant and O157:H7 strains—via a multi-target mode that overcomes classical resistance. Their low-dose efficacy and GRAS status support their use as clean-label food preservatives or adjuncts to antibiotics or bacteriophages to combat antimicrobial resistance. Full article

Acinetobacter baumannii has emerged as a major pathogen responsible for healthcare-associated infections, particularly in intensive care units, contributing to significant morbidity and mortality due to its multidrug resistance and ability to persist in clinical environments. This study aimed to investigate the phenotypic and genomic characteristics of all multidrug-resistant A. baumannii isolates collected between January and June 2022 from two tertiary care hospitals in Thessaloniki, Greece. A total of 40 isolates were included. All isolates exhibited resistance to colistin; however, none harbored the mcr-1 to mcr-9 genes, as confirmed by polymerase chain reaction (PCR). PCR-based screening for virulence-associated genes revealed high prevalence rates of basD (100%), pld (95%), csuE (87.5%), and bap (77.5%). In contrast, ompA and pglC were not detected. Twitching motility ranged from 2 to 50 mm, with 25% of the isolates classified as non-motile and 20% as highly motile. Swarming motility was observed in all strains. Additionally, all isolates demonstrated positive α-hemolysis, suggesting a potential virulence mechanism involving tissue damage and iron acquisition. Pulsed-field gel electrophoresis (PFGE) revealed significant genomic diversity among the isolates, indicating a low likelihood of patient-to-patient or clonal transmission within the hospital setting. These findings highlight the complex relationship between antimicrobial resistance and virulence in clinical A. baumannii isolates and emphasize the urgent need for robust infection control strategies and continued microbiological surveillance. Full article

Reclaimed fields have a low soil fertility and low productivity compared to conventional arable land, necessitating research on productivity enhancement. The rice–frog co-culture model is an ecologically intensive practice that combines biodiversity objectives with agricultural production needs, offering high ecological and economic value. However, there is a lack of research on this model that has focused on factors other than soil nutrient levels. The present study evaluated the rice–frog co-culture model in a reclaimed paddy field across three experimental plots with varying frog stocking densities: a rice monoculture (CG), low-density co-culture (LRF), and high-density co-culture (HRF). We investigated the effects of the frog density on greenhouse gas emissions throughout the rice growth. The rice–frog co-culture model significantly reduced methane (CH₄) emissions, with fluxes highest in the CG plot, followed by the LRF and then HRF plots. This reduction was achieved by altering the soil pH, the cation exchange capacity, the mcrA gene abundance, and the mcrA/pmoA gene abundance ratio. However, there was a contrasting nitrous oxide (N₂O) emission pattern. The co-culture model actually increased N₂O emissions, with fluxes being highest in the HRF plots, followed by the LRF and then CG plots. The correlation analysis identified the soil nosZ gene abundance, redox potential, urease activity, nirS gene abundance, and ratio of the combined nirK and nirS abundance to the nosZ abundance as key factors associated with N₂O emissions. While the co-cultivation model increased N₂O emissions, it also significantly reduced CH₄ emissions. Overall, the rice–frog co-culture model, especially at a high density, offers a favorable sustainable agricultural production model. Full article

Acinetobacter baumannii is an opportunistic pathogen and a major cause of nosocomial infections worldwide. This study aimed to isolate and characterize phages with lytic activity against multidrug-resistant A. baumannii strains to enable antibacterial alternatives. Eight phages (AKO8a, PS118, B612, MCR, IDQ7, 89P13, CRL20, and CIM23) were isolated and subjected to genomic, phylogenetic, and functional analyses. Antibacterial activity was assessed in vitro against A. baumannii strain AbAK04 by measuring optical density over 17 h at multiplicities of infection (MOIs) of 0.1, 1, and 10, using a repeated-measures design with time as a crossed factor and MOI as a nested factor. Tukey’s post-hoc test identified significant bacterial growth reductions of 57–72% (p < 0.001). Specifically, phages PS118 and 89P13 reduced growth by 71% at MOI 10; CIM23, B612, and CRL20 achieved 68% reduction at MOI 1; and MCR reduced growth by 64% at MOIs 0.1 and 1. Notably, lytic phage MCR encodes a glycosyl hydrolase family 58 (GH58) enzyme, potentially contributing to its antibacterial activity. Genomic analyses confirmed absence of virulence and antibiotic resistance genes, with all phages classified as novel species within the Kagunavirus genus. These findings support the use of these phages as promising candidates for in vivo evaluation. Full article

Antibiotics are frequently used in the poultry industry, which has led to the emergence of bacterial strains that are resistant to antimicrobial treatments. The main objectives of this research were to conduct a multimodal risk assessment, to determine the extent of contamination of chicken meat with Escherichia coli, assess the prevalence of strains resistant to extended-spectrum cephalosporins (ESC), and characterise the genes associated with resistance and virulence. A standardised procedure involving enrichment in buffered peptone water and isolation of E. coli on MacConkey agar was carried out on 100 chicken carcasses. Subsequently, the sensitivity of the strains was tested against 21 antibiotic discs. Additionally, ESBL production was detected using a double synergy test. Specific PCRs were employed to identify resistance to critical antibiotics in human medicine (such as cephalosporins, carbapenems, fluoroquinolones, and colistin), as well as the presence of virulence genes. The contamination rate of chicken meat with E. coli was 82%. The prevalence of ESC-resistant isolates was 91.2%. Furthermore, 76.5% of the isolates exhibited ESBL production, with the different beta-lactamase genes (bla_CTXM, bla_TEM, and bla_SHV). The mcr-1 gene, associated with colistin resistance, was detected in four strains (5.9%). Some isolates also carried resistance genes such as sul1, sul2, sul3, tetA, tetB, qnrB, and qnrS. In addition, several virulence genes were detected. In our study, we were able to link the expression of AMR to the iron metabolic regulatory elements using a multimodal machine learning approach; this mechanism could be targeted to mitigate the bacteria virulence and resistance. The high prevalence of ESBL-producing and multi-resistant E. coli strains in poultry presents significant human health risks, with the focus on antibiotic-resistant uropathogenic strains since poultry meat could be an important source of uropathogenic strains, underscoring the danger of hard-to-treat urinary tract infections, stressing the need for controlled antibiotic use and thorough monitoring. Full article

Background: Short food supply chains are commonly perceived as more sustainable and safer alternatives to conventional production systems, often linked to organic, free-range livestock practices. Materials and methods: This study investigates, for the first time, the distribution of antimicrobial resistance genes (ARGs) and characterizes the microbial communities’ composition, using 16S rRNA sequencing and real-time PCR, respectively. Eleven fecal, 76 slaughterhouse surface, 11 cecal, and 11 carcass samples, from 11 poultry farms belonging to the same short food chain, were analyzed in the study. Results: While cleaning and disinfection procedures appeared to reduce the bacterial load on slaughterhouse surfaces, diverse and potentially resistant bacteria, including genera such as Staphylococcus and Streptococcus, persisted both before and after slaughter. ARGs conferring resistance to high-priority critically important antimicrobials (HPCIAs), such as fluoroquinolones and third-generation cephalosporins, were frequently detected on carcasses, with qnrS (76.15%, 95%CI 68.02-84.28%) and bla_CMY2 (57.8%, 95%CI 48.38-67.22%) being the most prevalent. The slaughtering process emerged as a critical step for ARG dissemination via intestinal bacteria, such as genus Lactobacillus. Additionally, the detection of mcr genes and bla_NDM on carcasses but not in the bird gut samples suggests possible anthropogenic contamination. Discussion: These findings highlight that the evisceration process, slaughterhouse environment, and personnel are all contributing factors in ARG spread and underscore the need for enhanced hygiene protocols and reduced gut ARG carriage in domestic birds to mitigate the risk for the consumer. Full article

The emergence of colistin resistance poses a significant threat to its efficacy as a last-line treatment against multidrug-resistant Gram-negative bacterial infections. In this study, 178 multi-drug resistant (MDR) Escherichia coli isolates collected from clinical samples at Queen Sirikit Naval Hospital, Chonburi, Thailand, were evaluated for colistin resistance. Of these, six were identified as mcr gene carriers, mediating colistin resistance. Specifically, mcr-1 was detected in three E. coli isolates, mcr-3 was detected in one E. coli isolate, and mcr-1 and mcr-3 were detected in two E. coli isolates, designated AMR-0220 and AMR-0361. Whole-genome sequencing and bioinformatics analysis revealed that AMR-0220 and AMR-0361 belonged to ST410 and ST617 lineages, respectively. Both isolates carried multiple plasmids, with mcr-1.1 located on an IncX4-type plasmid that is closely related to previously reported mcr-1.1-carrying IncX4 plasmids. In contrast, mcr-3.5 was identified on distinct plasmid backbones: an IncFIB-type plasmid in AMR-0220 and an IncFII-type plasmid in AMR-0361. Overall, our findings demonstrate that the mcr genes found in E. coli isolates in this region are located on different mobile genetic elements, indicating the potential for a widespread dissemination of colistin resistance among Gram-negative bacteria throughout Thailand’s healthcare system. Full article

In Mexico, hospital wastewater (HWW) is a source of chemical and microbiological contamination, and it is released into the municipal sewage system without prior treatment. This water may contain pathogenic bacteria and antimicrobial resistance genes, which represent a risk to Public Health and the environment. So far, there are no studies that analyse this problem comprehensively, relating bacterial population structures, chemical contaminants, and seasonality. The aim of this work was to seasonally characterise the bacterial communities of HWW, including clinically relevant bacteria and resistance genes in Hospital Juárez de México (HJM), and to evaluate the impact of physicochemical factors on their composition. A one-year observational, cross-sectional study was conducted at five HWW discharge points of HJM. Fourteen physicochemical parameters were determined by using standard methodologies, and statistical differences between discharges and seasons were evaluated. Bacterial communities were analysed by targeted amplicon sequencing of the V3-V4 region of the 16S rRNA gene. In addition, the presence of eight antimicrobial resistance genes of local epidemiological importance was assessed. Data were analysed using alpha and beta diversity indices, principal component analysis, and multivariate statistical tests. HWW showed high taxonomic diversity, with Proteobacteria, Firmicutes, and Bacteroidetes standing out. Clinically relevant bacteria were identified in 73.3% of the analyses, with Enterobacter and Escherichia-Shigella predominating. Total and dissolved solids, temperature, nitrate, and pH significantly influenced the bacterial composition of HWW. Seven out of the eight genes evaluated were identified, with bla_KPC, bla_OXA-40, and mcr-1 being the most frequent, showing significant seasonal differences. This study underlines the microbiological and chemical complexity of HWW, highlighting the impact of clinically relevant bacteria and antimicrobial resistance genes on Public Health. The findings emphasise the need to implement hospital waste management programmes and ideally specific treatment plants to minimise the associated risks and protect the environment and human health. Full article

Water table fluctuation alters environment properties and n-alkane transformation, leading to shifts in the groundwater microbial community and functions. A diesel-contaminated aquifer column experiment of seasonal water table fluctuation was designed to explore the mechanisms. Temporal changes in geochemical parameters, n-alkane concentration, bacterial community and functional gene composition were investigated. The results showed that water table fluctuation accelerated the depletion of the diesel n-alkane leakage point. Owing to the variations in the water table, the electron donors (dissolved organic carbon) and electron acceptors (dissolved oxygen, nitrate and sulfate) underwent regular changes, and the bacterial community structure was altered. Dissolved oxygen was the major parameter correlating with the abundance of aerobic functional genes (the sum of the alk_A, alk_R and alk_P) and was beneficial for enhancing the aerobic biodegradation function potential of n-alkanes. However, the static retention of the water table at the highest level inducing water saturation and hypoxia was the critical factor influencing the abundance of anaerobic functional genes (the sum of assA and mcrA) and was favorable for the anaerobic biodegradation function potential of n-alkane. Overall, this study links seasonal water table dynamics to n-alkane biodegradation function potential in aquifers, and suggests that the quality of recharge water, which impacts microbial community assembly and function, should be considered. Full article

New Delhi metallo-β-lactamase (NDM) is an enzyme that can degrade a wide range of β-lactam antibiotics. The widespread dissemination of the bla_NDM gene, which encodes NDM, in animal-derived settings poses a threat to public health security. Live poultry markets represent critical nodes in public health surveillance. However, there is currently limited reporting on the spread of the bla_NDM gene within these markets under the One Health approach. This study investigated the prevalence of the bla_NDM gene in live poultry markets and, by integrating newly sequenced genomes with publicly available database entries, performed an in-depth analysis of its association networks with other genetic elements across species. A total of 233 bla_NDM-positive strains, comprising 218 Escherichia coli strains, 4 Enterobacter cloacae strains, 7 Klebsiella pneumoniae, 2 Klebsiella aerogenes, 1 Providencia rettgeri, and 1 Proteus mirabilis were isolated from two live poultry markets in Jiangsu, China. Among the bla_NDM-positive strains, multiple variants were identified, primarily bla_NDM-5, followed by bla_NDM-1, bla_NDM-13, bla_NDM-27, and bla_NDM-39. The coexistence of bla_NDM-5 and mcr-1 was detected in five E. coli strains. Additionally, we found one E. coli strain in which bla_NDM-5 coexisted with estT and tet(X4), and another E. coli strain where bla_NDM-5 coexisted with estT. Spearman correlation analysis of publicly available genomes revealed that the genetic element preferences of bla_NDM variants vary significantly across species (|R| > 0.3, p < 0.05). The element preferences of E. coli strains carrying bla_NDM-5 are similar to those of Klebsiella pneumoniae harboring bla_NDM-1. In Klebsiella aerogenes, Enterobacter cloacae, and Proteus mirabilis, strains carrying bla_NDM-1, have opposite genetic element preferences when compared with strains harboring bla_NDM-5 or bla_NDM-7. Notably, we report the first evidence of the bla_NDM-1 gene transfer mediated by ISKpn13, ISSpu2, and MITEKpn1. The findings highlight that live poultry markets are important transmission hotspots of AMR and thus require continuous surveillance. Full article

The global dissemination of plasmid-mediated mcr genes, which confer resistance to the last-resort antibiotic colistin, represents a critical public health challenge driven by the interplay of clinical, agricultural, and environmental factors. This review examines the genetic and ecological dynamics of mcr-bearing plasmids, focusing on their role in disseminating colistin resistance across diverse bacterial hosts and ecosystems. Key plasmid families demonstrate distinct evolutionary strategies, including IncI2, IncHI2, and IncX4. IncI2 plasmids favor stability in livestock and clinical settings. IncHI2 plasmids, on the other hand, leverage transposons to co-select for multidrug resistance, while IncX4 plasmids achieve global dissemination through streamlined, conjugation-efficient architectures. The pervasive spread of mcr genes is exacerbated by their integration into chromosomes via mobile genetic elements and co-selection with resistance to other antibiotic classes, amplifying multidrug-resistant phenotypes. Environmental reservoirs, food chains, and anthropogenic practices further facilitate cross-niche transmission, underscoring the interconnectedness of resistance under the One Health framework. Addressing this crisis requires coordinated strategies, including reducing colistin misuse in agriculture, enhancing surveillance of high-risk plasmid types, and fostering international collaboration to preserve antimicrobial efficacy and mitigate the threat of untreatable infections. Full article

Background: Antimicrobial resistance (AMR) is a global threat in the public healthcare sector. The emergence of carbapenem-resistant Enterobacterales (CRE) has become a serious public health threat in South Africa. The spread of CRE has led to the use of colistin for treating severe infections. Colistin is a cationic, lipopeptide antibacterial agent that is effective against most Gram-negative bacteria through its disruption of the bacterial cell membrane. This study aims to determine the colistin resistance (MIC) and mobile colistin resistance (mcr-1) gene in clinical isolates from healthcare facilities in Mthatha and its surrounding areas. Methods: Fifty-three CRE isolates were collected from health facilities between January 2019 and June 2021 and stored in skim milk 10% and 5% inositol broth. The carbapenemase confirmatory test involved a RESIST-4 O.K.N.V assay (Coris BioConcept, Gembloux, Belgium), which was conducted following manufacturer protocol. Broth microdilution was performed according to the ISO standard method (20776-1) using A ComAspTM colistin 0.25–16 μg/mL MIC Broth. Conventional polymerase reaction (PCR) was performed for the detection of mcr-1. Results: N = 53 (100%) isolates were used. A total of 53% were defined as Klebsiella pneumoniae, Escherichia coli constituted 8%, Enterobacter cloacae 8%, Serratia marcescens 8%, Serratia fonticola 2%, Enterobacter aerogenes 2%, Klebsiella oxytoca 2%, Citrobacter koseri 2%, and Citrobacter freundii 2%. The specimens were from the following wards: Pediatric and Neonatal 38%, Medical 30%, Gynecology, Labour, and Maternity 11%, OPD and A&E 11%, ENT 4%, and Others—Male TB ward, Trauma, and adult ICU 6%. In total, 13% of the isolates were resistant and 86% were sensitive to colistin. The common CRE genes detected were OXA-48 at 47%, NDM at 13%, VIM at 1%, and a combination of OXA-48 and NDM at 5%. Of the isolates, 66% were positive for the production of carbapenamase. In this study, we found that all N = 53 (100%) isolates did not have the mobile colistin resistance gene (mcr-1). Conclusions: Antimicrobial resistance is associated with the emergence of carbapenemases genes. Increasing resistance to colistin in clinical settings can lead to difficulties in treating CRE infections, which may lead to clinical failure. In our study, 13% of isolates were phenotypically resistant to colistin. Full article

tet(X4)-positive IncHI1 plasmids are widely prevalent in various bacteria. To understand their transmission characteristics, we analyzed two extensively drug-resistant (XDR) Escherichia coli strains isolated from pet dog feces in Henan Province, China. Strain T28R harbored tet(X4)-positive IncHI1, IncF18:A-:B-, and mcr-1-positive IncI2 plasmids, while T16R carried tet(X4)-positive IncHI1, F16:A-:B-, and mcr-1-positive IncX4 plasmids. Four representative fusion plasmids, pT28R-F1, pT28R-F2, pT28R-F3, and pT16R-F1, in transconjugants were analyzed using WGS and PCR mapping. The results showed that IS26 from the IncF18:A-:B--plasmid attacked the conjugative transfer-associated genes trhc and rsp on the IncHI1 plasmid, generating pT28R-F1 and pT28R-F2. pT28R-F3 was generated through ISCro1- and ISCR2-mediated homologous recombination, deleting the Tra1 region of the IncHI1 plasmid. T16R-F1 emerged from ISCR2- and IS1B-mediated homologous recombination, losing transfer regions of parental plasmids. Notably, fusion plasmids lost the temperature sensitivity of the IncHI1 plasmid, with conjugation frequencies between 1.57 × 10⁻⁴ and 3.84 × 10⁻⁵ at 28 °C and 37 °C. The findings suggest that tet(X4)-positive IncHI1 plasmids could be mobilized with the assistance of conjugative helper plasmids and that fusion events enhance the adaptability of these plasmids, thus facilitating the spread of antibiotic resistance, posing a growing public health threat. Full article

Pathogenic Escherichia coli can cause a variety of intestinal and extra-intestinal infections in humans and animals. The availability and subsequent misuse of antimicrobials, especially in poultry production systems, has contributed immensely to the emergence and spread of multidrug-resistant E. coli. This study investigated the genotypic characterization of colistin-resistant E. coli and selected antimicrobial-resistance encoding genes along with their phenotypic resistant pattern and the multiple antimicrobial resistant (MAR) index from village chickens in Kelantan. Sixty E. coli isolates obtained from a previous study’s stock culture were enriched and analyzed using routine microbiological methods: Kirby–Bauer disc diffusion method, minimum inhibitory concentration (MIC), and PCR amplification of E. coli species-specific and multidrug-resistance mcr-positive E. coli. All the isolates were confirmed as E. coli and 16.6% (10/60) were positive for mcr. Five isolates were positive for mcr-1, three for mcr-4, and two for mcr-9. The mcr-positive isolates showed varying degrees of resistance to different antimicrobials. The isolates were resistant to gentamicin (100%), chloramphenicol (100%), and tetracycline (89.4%) and susceptible to ceftaxidime (2.26%) and imipenem (18%). Furthermore, 100%, 94.7%, and 89.4% of isolates from village chickens belonged to phylogroup C, B2, and E, while 21.0% and 42.1% of the isolates belonged to phylogroup A and B1, respectively. Sequence types (STs) of selected E. coli isolates were further analyzed using multi-locus sequence typing, and 10 different STs were identified. This study showed the emerging threats of multidrug-resistant mcr-positive E. coli gene in village chickens that are believed to be raised with minimal or no antibiotics. Full article