Search Results (850)

Background/Objectives: This study examines how seasonality, pollution, and sample type (water and sediment) influence the presence and distribution of antibiotic resistance genes (ARGs), with a focus on antibiotic resistance genes (ARGs) located on plasmids (the complete set of plasmid-derived sequences, including ARGs) in a tropical urban river. Methods: Samples were collected from three sites along a pollution gradient in the Virilla River, Costa Rica, during three seasonal campaigns (wet 2021, dry 2022, and wet 2022). ARGs in water and sediment were quantified by qPCR, and metagenomic sequencing was applied to analyze chromosomal and plasmid-associated resistance profiles in sediments. Tobit and linear regression models, along with multivariate ordination, were used to assess spatial and seasonal trends. Results: During the wet season of 2021, the abundance of antibiotic resistance genes (ARGs) such as sul-1, intI-1, and tetA in water samples decreased significantly, likely due to dilution, while intI-1 and tetQ increased in sediments, suggesting particle-bound accumulation. In the wet season 2022, intI-1 remained low in water, qnrS increased, and sediments showed significant increases in tetQ, tetA, and qnrS, along with decreases in sul-1 and sul-2. Metagenomic analysis revealed spatial differences in plasmid-associated ARGs, with the highest abundance at the most polluted site (Site 3). Bacterial taxa also showed spatial differences, with greater plasmidome diversity and a higher representation of potential pathogens in the most contaminated site. Conclusions: Seasonality and pollution gradients jointly shape ARG dynamics in this tropical river. Plasmid-mediated resistance responds rapidly to environmental change and is enriched at polluted sites, while sediments serve as long-term reservoirs. These findings support the use of plasmid-based monitoring for antimicrobial resistance surveillance in aquatic systems. Full article

The perianal skin is a unique “skin–gut” boundary that serves as a critical hotspot for the exchange and evolution of antibiotic resistance genes (ARGs). However, its role in the dissemination of antimicrobial resistance (AMR) has often been underestimated. To characterize the resistance patterns in the perianal skin environment of patients with perianal diseases and to investigate the drivers of AMR in this niche, a total of 51 bacterial isolates were selected from a historical strain bank containing isolates originally collected from patients with perianal diseases. All the isolates originated from the skin site and were subjected to antimicrobial susceptibility testing, whole-genome sequencing, and co-occurrence network analysis. The analysis revealed a highly structured resistance pattern, dominated by two distinct modules: one representing a classic Staphylococcal resistance platform centered around mecA and the bla operon, and a broad-spectrum multidrug resistance module in Gram-negative bacteria centered around tet(A) and predominantly carried by IncFIB and other IncF family plasmids. Further analysis pinpointed IncFIB-type plasmids as potent vehicles driving the efficient dissemination of the latter resistance module. Moreover, numerous unexplained resistance phenotypes were observed in a subset of isolates, indicating the potential presence of emerging and uncharacterized AMR threats. These findings establish the perianal skin as a complex reservoir of multidrug resistance genes and a hub for mobile genetic element exchange, highlighting the necessity of enhanced surveillance and targeted interventions in this clinically important ecological niche. Full article

Contaminated poultry is one of the major sources of food-borne non-typhoidal Salmonella (NTS). The aim of this study was to evaluate the presence of Salmonella along the slaughter process in low- and high-throughput poultry abattoirs in South Africa and to determine their characteristics. Samples were collected from 500 chicken carcass rinsates at various processing stages in three abattoirs. Salmonella detection and identification was conducted in accordance with the ISO 6579 methodology. NTS serotyping was performed with serotype-specific PCRs. The Kirby–Bauer disk diffusion method was used to determine antimicrobial resistance in Salmonella. PCR was used to analyze thirteen antimicrobial genes and four virulence genes. Salmonella spp. was detected in 11.8% (59/500; CI: 9.5–15) of the samples tested. The predominant serovars were Salmonella Enteritidis (n = 21/59; 35.59%) and Salmonella Typhimurium (n = 35; 59.32%). Almost all Salmonella isolates were susceptible to all tested antimicrobials except three. Despite the low resistance to tetracyclines at the phenotypic level, approximately half of the strains carried tetA genes, which may be due to “silent” antimicrobial resistance genes. Diverse virulence genes were detected among the confirmed NTS serotypes. We found a predominance of S. Enteritidis and S. Typhimurium from chicken carcasses with diverse virulence and resistance genes. As we detected differences between the slaughterhouses, an in-depth study should be performed on the risk of Salmonella in low- and high-throughput abattoirs. The integrated monitoring and surveillance of NTS in poultry is warranted in South Africa to aid in the design of mitigation strategies. Full article

This study describes the first complete genomic sequence of an NDM-19 and QnrS11-producing multidrug-resistant (MDR) Escherichia coli isolate collected from a fecal swab from a poultry farm in 2019 in Egypt. The bla_NDM-19 was identified by PCR screening and DNA sequencing. The isolate was then subjected to antimicrobial susceptibility testing, conjugation and transformation experiments, and complete genome sequencing. The chromosome of strain M2-13-1 measures 4,738,278 bp and encodes 4557 predicted genes, with an average G + C content of 50.8%. M2-13-1 is classified under ST167, serotype O101:H5, phylogroup A, and shows an MDR phenotype, having minimum inhibitory concentrations (MICs) of 64 mg/L for both meropenem and doripenem. The genes bla_NDM-19 and qnrS11 are present on 49,816 bp IncX3 and 113,285 bp IncFII: IncFIB plasmids, respectively. M2-13-1 harbors genes that impart resistance to sulfonamides (sul1), trimethoprim (dfrA14), β-lactams (bla_TEM-1B), aminoglycosides (aph(6)-Id, aph(3′)-Ia, aph(3″)-Ib, aac(3)-IV, and aph(4)-Ia), tetracycline (tet(A)), and chloramphenicol (floR). It was susceptible to aztreonam, colistin, fosfomycin, and tigecycline. The genetic context surrounding bla_NDM-19 includes ISAba125-IS5-bla_NDM-19-ble_MBL-trpF-hp1-hp2-IS26. Hierarchical clustering of the core genome MLST (HierCC) indicated M2-13-1 clusters with global ST167 E. coli lineages, showing HC levels of 100 (HC100) core genome allelic differences. Plasmids of the IncX3 group and the insertion sequence (ISAba125) are critical vehicles for the dissemination of bla_NDM and its related variants. To our knowledge, this is the first genomic report of a bla_NDM-19/IncX3-carrying E. coli isolate of animal origin globally. Full article

Water systems serve as multifaceted environmental pools for antibiotic-resistant bacteria (ARB) and resistance genes (ARGs), influencing human, animal, and ecosystem health. This review synthesizes current understanding of how antibiotics, ARB, and ARGs enter surface, ground, and drinking waters via wastewater discharge, agricultural runoff, hospital effluents, and urban stormwater. We highlight key mechanisms of biofilm formation, horizontal gene transfer, and co-selection by chemical stressors that facilitate persistence and spread. Case studies illustrate widespread detection of clinically meaningful ARB (e.g., Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae) and mobile ARGs (e.g., sul1/2, tet, bla variants) in treated effluents, recycled water, and irrigation return flows. The interplay between treatment inefficiencies and environmental processes underscores the need for advanced treatment technologies, integrated monitoring, and policy interventions. Addressing these challenges is critical to curbing the environmental dissemination of resistance and protecting human and ecosystem health. Full article

Background/Objectives: Campylobacteriosis in human populations is an ongoing issue in both developed and developing countries. Poultry production is recognized as a reservoir for antimicrobial resistance and main source of human Campylobacter infection. Methods: In this study, sixty-five Campylobacter isolates were cultured from fecal samples collected from 17 flocks of broiler chickens in Alberta, Canada over two years (2015–2016). Susceptibility assays and PCR assays were performed to characterize resistance phenotypes and resistance genes. Conjugation assays were used to examine the mobility of AMR phenotypes. Results: Campylobacter jejuni was the predominant species recovered during both years of sampling. There were no Campylobacter coli isolates found in 2015; however, approximately 33% (8/24) of isolates collected in 2016 were Campylobacter coli. The two most frequent antimicrobial resistance patterns in C. jejuni collected in 2015 were tetracycline (39%) and azithromycin/clindamycin/erythromycin/telithromycin resistance (29%). One isolate collected in 2015 has resistance pattern ciprofloxacin/nalidixic acid/tetracycline. The tetO gene was detected in all tetracycline resistant isolates from 2015. The cmeB gene was detected in all species isolates with resistance to azithromycin/clindamycin/erythromycin/telithromycin, and from two isolates with tetracycline resistance. Alignment of the nucleotide sequences of the cmeB gene from C. jejuni isolates with different resistance patterns revealed several single nucleotide polymorphisms. A variety of multi-drug resistance patterns were observed through conjugation experiments. Conclusions: These data suggest that poultry production may serve as a potential reservoir for and source of transmission of multi-drug resistant Campylobacter jejuni and supports the need for continued surveillance. Full article

Background/objectives: Proteus mirabilis is a frequent causative agent of urinary and wound infections in both community and hospital settings. It develops resistance to expanded-spectrum cephalosporins (ESCs) due to the production of extended-spectrum β-lactamases (ESBLs) or plasmid-mediated AmpC β-lactamases (p-AmpCs). Recently, carbapenem-resistant isolates of P. mirabilis emerged due to the production of carbapenemases, mostly belonging to Ambler classes B and D. Here, we report an outbreak of infections due to carbapenem-resistant P. mirabilis that were observed in a psychiatric hospital in Zagreb, Croatia. The characteristics of ESBL and carbapenemase-producing P. mirabilis isolates, associated with an outbreak, were analyzed. Materials and methods: The antibiotic susceptibility testing was performed by the disk-diffusion and broth dilution methods. The double-disk synergy test (DDST) and inhibitor-based test with clavulanic and phenylboronic acid were applied to screen for ESBLs and p-AmpCs, respectively. Carbapenemases were screened by the modified Hodge test (MHT), while carbapenem hydrolysis was investigated by the carbapenem inactivation method (CIM) and EDTA-carbapenem-inactivation method (eCIM). The nature of the ESBLs, carbapenemases, and fluoroquinolone-resistance determinants was investigated by PCR. Plasmids were characterized by PCR-based replicon typing (PBRT). Selected isolates were subjected to molecular characterization of the resistome by an Inter-Array Genotyping Kit CarbaResisit and whole-genome sequencing (WGS). Results: In total, 20 isolates were collected and analyzed. All isolates exhibited resistance to amoxicillin alone and when combined with clavulanic acid, cefuroxime, cefotaxime, ceftriaxone, cefepime, imipenem, ceftazidime–avibactam, ceftolozane–tazobactam, gentamicin, amikacin, and ciprofloxacin. There was uniform susceptibility to ertapenem, meropenem, and cefiderocol. The DDST and combined disk test with clavulanic acid were positive, indicating the production of an ESBL. The MHT was negative in all except one isolate, while the CIM showed moderate sensitivity, but only with imipenem as the indicator disk. Furthermore, eCIM tested positive in all of the CIM-positive isolates, consistent with a metallo-β-lactamase (MBL). PCR and sequencing of the selected amplicons identified VIM-1 and VIM-4. The Inter-Array Genotyping Kit CarbaResist and WGS identified β-lactam resistance genes bla_VIM, bla_CTX-M-15, and bla_TEM genes; aminoglycoside resistance genes aac(3)-IId, aph(6)-Id, aph(3″)-Ib, aadA1, armA, and aac(6′)-IIc; as well as resistance genes for sulphonamides sul1 and sul2, trimethoprim dfr1, chloramphenicol cat, and tetracycline tet(J). Conclusions: This study revealed an epidemic spread of carbapenemase-producing P. mirabilis in two wards in a psychiatric hospital. Due to the extensively resistant phenotype (XDR), therapeutic options were limited. This is the first report of carbapenemase-producing P. mirabilis in Croatia. Full article

Background: Chryseobacterium indologenes, an environmental bacterium, is increasingly recognized as an emerging nosocomial pathogen, particularly in Asia, and is often characterized by multidrug resistance. Objectives: This study aimed to investigate the genomic features of clinical C. indologenes isolates from Maharaj Nakorn Chiang Mai Hospital, Thailand, to understand their mechanisms of multidrug resistance, virulence factors, and mobile genetic elements (MGEs). Methods: Twelve C. indologenes isolates were identified, and their antibiotic susceptibility profiles were determined. Whole genome sequencing (WGS) was performed using a hybrid approach combining Illumina short-reads and Oxford Nanopore long-reads to generate complete bacterial genomes. The hybrid assembled genomes were subsequently analyzed to detect antimicrobial resistance (AMR) genes, virulence factors, and MGEs. Results: C. indologenes isolates were primarily recovered from urine samples of hospitalized elderly male patients with underlying conditions. These isolates generally exhibited extensive drug resistance, which was subsequently explored and correlated with genomic determinants. With one exception, CMCI13 showed a lower resistance profile (Multidrug resistance, MDR). Genomic analysis revealed isolates with genome sizes of 4.83–5.00 Mb and GC content of 37.15–37.35%. Genomic characterization identified conserved resistance genes (bla_IND-2, bla_CIA-4, adeF, vanT, and qacG) and various virulence factors. Phylogenetic and pangenome analysis showed 11 isolates clustering closely with Chinese strain 3125, while one isolate (CMCI13) formed a distinct branch. Importantly, each isolate, except CMCI13, harbored a large genomic island (approximately 94–100 kb) carrying significant resistance genes (bla_OXA-347, tetX, aadS, and ermF). The absence of this genomic island in CMCI13 correlated with its less resistant phenotype. No plasmids, integrons, or CRISPR-Cas systems were detected in any isolate. Conclusions: This study highlights the alarming emergence of multidrug-resistant C. indologenes in a hospital setting in Thailand. The genomic insights into specific resistance mechanisms, virulence factors, and potential horizontal gene transfer (HGT) events, particularly the association of a large genomic island with the XDR phenotype, underscore the critical need for continuous genomic surveillance to monitor transmission patterns and develop effective treatment strategies for this emerging pathogen. Full article

Background/Objectives: Lactiplantibacillus plantarum is widely utilized in the fermentation industry and offers potential health benefits. However, large-scale comparative genomic analyses aimed at exploring its metabolic functions and conducting safety assessments are still lacking. Methods: In this study, we performed a comparative genomic analysis of 324 L. plantarum strains sourced from various origins and geographical locations. Results: The results revealed that L. plantarum possesses a total of 2403 core genes, of which 12.3% have an unknown function. The phylogenetic analysis revealed a mixed distribution from various origins, suggesting complex transmission pathways. The metabolic analysis demonstrated that L. plantarum strains can produce several beneficial metabolites, including lysine, acetate, and riboflavin. Furthermore, L. plantarum is highly capable of degrading various carbohydrates and proteins, increasing its adaptability. Further, we profiled the antimicrobial peptides (AMPs) in the genomes of L. plantarum. We identified a widely distributed AMP and its variants, presenting in a total of 280 genomes. In our biosafety assessment of L. plantarum, we identified several antibiotic resistance genes, such as Tet(M), ANT(6)-Ia, and mdeA, which may have potential for horizontal gene transfer within the Lactobacillaceae family. Conclusions: This study provides genomic insights into the genetic diversity, metabolic functions, antimicrobial properties, and biosafety of L. plantarum, underscoring its potential applications in biotechnology and environmental adaptation. Full article

Pasteurella multocida (Pm) is a zoonotic pathogen that poses a significant threat to animal health and causes substantial economic losses, further aggravated by rising tetracycline resistance. To restore the efficacy of tetracyclines to Pm, we evaluated the synergistic antibacterial activity of doxycycline combined with metformin, an FDA-approved antidiabetic agent. Among several non-antibiotic adjuvant candidates, metformin exhibited the most potent in vitro synergy with doxycycline, especially against capsular serogroup A strain (PmA). The combination demonstrated minimal cytotoxicity and hemolysis in both mammalian and avian cells and effectively inhibited resistance development under doxycycline pressure. At 50 mg/kg each, the combination of metformin and doxycycline significantly reduced mortality in mice and ducks acutely infected with PmA (from 100% to 60%), decreased pulmonary bacterial burdens, and alleviated tissue inflammation and damage. Mechanistic validation confirmed that metformin enhances membrane permeability in Pm without compromising membrane integrity, dissipates membrane potential, increases intracellular doxycycline accumulation, and downregulates the transcription of the tetracycline efflux gene tet(B). Morphological analyses further revealed pronounced membrane deformation and possible leakage of intracellular contents. These findings highlight metformin as a potent, low-toxicity tetracycline adjuvant with cross-species efficacy, offering a promising therapeutic approach for managing tetracycline-resistant Pm infections. Full article

Water environments and sediments are important reservoirs for antibiotic resistance genes (ARGs). Under the pressure of antibiotics, ARGs can transform between microorganisms. Lanthanum-modified bentonite (LMB) is a phosphorus passivation material with good prospects in water environment restoration. After a treatment with LMB, the phosphorus forms in water and sediments will change, which may have an impact on microorganisms and the transmission of ARGs. To investigate the effects of LMB and antibiotics on ARGs and bacterial communities in sediment and aquatic environments, LMB and tetracycline (Tet) were added individually and in combination to mixed samples of sediment and water. The results showed that the addition of either LMB or Tet increased the abundance of intI1 and tetA genes in both the sediment and water, with the Tet addition increasing ARGs to more than 1.5 times the abundance in the control group. However, when LMB and Tet were present simultaneously, the abundance of ARGs showed no significant difference compared to the control group. Tet and LMB also affected the bacterial community structure and function in the samples and had different effects on the sediment and water. A correlation analysis revealed that the potential host bacteria of the intI1 and tetA genes were unclassified_Geobacteraceae, Geothrix, Flavobacterium, Anaeromyxobacter, and Geothermobacter. These findings indicate that Tet or LMB may increase the dissemination of ARGs by affecting microbial communities, while LMB may reduce the impact of Tet through adsorption, providing a reference for the safety of the LMB application in the environment and its other effects (alleviating antibiotic pollution) in addition to phosphorus removal. Full article

Epigenetic regulation, particularly DNA methylation, plays a crucial role in embryonic development by controlling gene expression patterns. The disruption of this regulation by environmental factors can have long-lasting consequences. Opioid drugs, such as morphine, are known to cross the placental barrier and affect the developing central nervous system, yet their precise epigenetic effects during early development remain unclear. This study aimed to elucidate the impact of chronic morphine exposure on the DNA methylation landscape and gene expression in mouse embryonic stem cells (mESCs). mESCs were chronically exposed to morphine (10 μM for 24 h). Genome-wide bisulfite sequencing was performed to identify DNA methylation changes, while RNA sequencing (RNA-Seq) assessed corresponding gene expression alterations. Global levels of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) were quantified using mass spectrometry. Morphine exposure induced global DNA hypomethylation and identified 16,808 differentially methylated genes (DMGs) related to development, cell signalling, metabolism, and transcriptional regulation. Integrative transcriptomic analysis with RNA-Seq data revealed 651 overlapping genes, including alterations in key epigenetic regulators involved on DNA methylation machinery. Specifically, Tet1 was upregulated with promoter hypomethylation, while Dnmt1 was downregulated, without changes in promoter methylation after morphine exposiure. Mass spectrometry results confirmed a global decrease in 5mC levels alongside increased 5hmC, indicating the involvement of both passive and active demethylation pathways. These findings demonstrate for the first time that morphine disrupts the epigenetic homeostasis of mESCs by promoting global and gene-specific DNA demethylation, which might be key to the phenotypic changes that occur in adulthood. This work provides novel mechanistic insights into how opioid exposure during early development may lead to persistent epigenetic alterations, with potential long-term implications for neurodevelopment and disease susceptibility. Full article

Microplastic particles (MPs) are an emerging global pollutant of increasing concern due to their widespread occurrence, persistence, and multifaceted impact on aquatic ecosystems. This study provides a comprehensive review of peer-reviewed literature from 2011 to 2025, analysing the presence, distribution, and microbiological associations of MPs in surface waters across five continents. The findings confirm that MPs are present in both marine and freshwater systems, with concentrations varying by region, hydrology, and proximity to anthropogenic sources. Polyethylene and polypropylene were identified as the most common polymers, often enriched in river mouths, estuaries, and aquaculture zones. A key focus of this review is the plastisphere—microbial biofilms colonizing MPs—which includes both environmental and pathogenic bacteria such as Vibrio, Pseudomonas, and Acinetobacter. Notably, MPs serve as vectors for the spread of antibiotic resistance genes (ARGs), including sul1, tetA and ermF, and β-lactamase genes like blaCTX-M. This highlights their role in enhancing horizontal gene transfer and microbial dissemination. The results emphasize the need for standardized monitoring protocols and further interdisciplinary research. In light of the One Health approach, understanding the microbial dimension of MP pollution is essential for managing risks to environmental and public health. Full article

Staphylococcus saprophyticus (S. saprophyticus) is an opportunistic coagulase-negative staphylococcus (CoNS) known to cause urinary tract infections in humans and is increasingly recognized in veterinary medicine. The aim of this study was to provide an epidemiological characterization of S. saprophyticus strains and to identify potential virulence factors that may contribute to interspecies transmission. This research is particularly important, as companion animals represent an understudied reservoir of this microorganism, and their role in the spread of resistant pathogens remains insufficiently understood. A total of 61 S. saprophyticus strains isolated from humans, dogs, and cats were analyzed. Identification was performed using MALDI-TOF MS and confirmed by PCR targeting the hrcA gene. Antimicrobial susceptibility was assessed using the disk diffusion and broth microdilution methods, while resistance genes were detected by PCR. The blaZ and mecA genes were present in all strains; additionally, the majority harbored the resistance genes ermA, ermB, tetM, and tetK. Multidrug resistance (MDR) was identified in 21/61 strains (34.4%). Biofilm-forming capacity was temperature-dependent, with the strongest biofilm production observed at 37 °C (70.5%). At 38 °C and 39 °C, the proportion of strong biofilm producers decreased to 50.8% and 52.5%, respectively. All tested strains demonstrated pathogenic potential in the Galleria mellonella larvae infection model, with the highest mortality recorded for selected feline and canine strains. These findings indicate that S. saprophyticus strains from both humans and companion animals possess notable virulence and multidrug resistance. The detection of genotypically and phenotypically resistant strains in animals highlights their potential role as reservoir for zoonotic transmission. Full article

Escherichia coli (E. coli) is an opportunistic pathogen widely distributed in nature, and multi-drug resistance (MDR) E. coli has been widely recognized as a critical reservoir of resistance genes, posing severe health threats to humans and animals. A total of 288 E. coli strains were isolated and purified from fresh fecal samples of forest musk deer collected from farms in Sichuan, Shaanxi, and Yunnan Provinces of China between 2013 and 2023. This study aimed to conduct antibiotic susceptibility testing and resistance gene detection on the isolated forest musk deer-derived E. coli, analyze the correlations between them, investigate the presence of CRISPR systems within the strains, and perform bioinformatics analysis on the CRISPR systems carried by the strains. Results showed that 138 out of 288 E. coli strains were MDR, with the highest resistance to tetracycline (48.3%), cefalexin (45.1%), and doxycycline (41.7%). Prevalent genes were tetA (41.0%), sul2 (30.2%), blaTEM (27.1%), with 29 gene–phenotype pairs correlated. CRISPR system-negative strains had higher resistance rates to 16 antibiotics and lower detection rates only for aac (6′)-Ib-cr, qnrA, and qnrB compared to CRISPR system-positive strains. Regional analysis showed that the problem of drug resistance in Sichuan and Shaanxi was more serious, and that the detection rate of antibiotic resistance genes was relatively high. This study guides E. coli infection control in forest musk deer and enriches resistance research data. Full article