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PubMed2026

Mobilization of blaVIM genes via the Tn6292 transposon among carbapenem-resistant Enterobacter cloacae complex isolates from colonized patients in a Spanish hospital.

UNLABELLED: The aim of this study was to perform molecular characterization of the carbapenem-resistant Enterobacter cloacae complex (ECC) isolates from colonized patients in a hospital using whole-genome sequencing (WGS) technology. As part of routine surveillance for multidrug-resistant bacterial colonization, 21 ECC isolates were recovered from patients at San Carlos Hospital in Madrid (Spain) between December 2020 and November 2024. WGS was used to determine their genetic relatedness. Furthermore, species identification, sequence type (ST), resistome, plasmid content, and flanking mobile genetic elements (MGEs) of the carbapenemase genes were derived from the WGS data. The most prevalent carbapenemase gene identified was blaVIM-1 (n = 18, 85.7%), with other notable genes including blaKPC-2 (n = 1, 4.8%), blaKPC-3 (n = 1, 4.8%), and blaOXA-48 (n = 1, 4.8%). Several blaACT and blaESBL variants were also found among the carbapenem-resistant ECC isolates. All of them carried at least one blaACT gene, with blaACT-7 (11/21) and blaTEM-type (14/21) genes being the most common AmpC and ESBL-encoding genes, respectively. Additionally, two isolates exhibited the presence of the mcr-9 gene. Overall, E. hormaechei subsp. steigerwaltii (ST93), followed by E. hormaechei subsp. hoffmanii (ST78 and ST50), were the predominant species and STs circulating among the carbapenem-resistant ECC strains. The blaVIM-1 gene was part of class 1 integrons located within a Tn3-family transposon, Tn6292. blaKPC and blaOXA-48 were linked to Tn4401 and Tn1999 transposons, respectively. In conclusion, the presence of the blaVIM within a transposon Tn6292 enhances its mobility across bacterial genomes, underscoring the value of high-throughput sequencing in monitoring the spread of carbapenem-resistant ECC isolates. IMPORTANCE: This study highlights why monitoring the spread of antibiotic-resistant bacteria in hospitals is critical. By analyzing the complete DNA of carbapenem-resistant bacteria, antibiotics were considered a last line of treatment. We found that the resistance genes are not isolated. Instead, they are embedded within mobile elements called transposons. This means that they can "jump" between different bacteria, accelerating the spread of resistance. These findings emphasize the importance of high-resolution genomic technologies to track and control the spread of these dangerous bacteria in clinical settings, helping preserve the effectiveness of life-saving treatments.

Humans↗

PubMed2026

The Conjugative Megaplasmid pMD9A Mediates Transferring Antibiotic Resistance Genes.

Pseudomonas asiaticais an emerging opportunistic pathogen with a broad host range. Current evidence suggests that some isolates exhibit multidrug resistance, which may complicate treatment. In this study, a multidrug-resistant P. asiatica strain MD9 was isolated from aquaculture water. We aimed to characterize its complete genome sequence and investigate the role of its conjugative megaplasmid pMD9A in the horizontal transfer of antibiotic resistance genes. The genome of MD9 consists of one circular chromosome (5,956,782 bp, with a G + C content of 62.5%) and one circular megaplasmid, pMD9A (455,169 bp, with a G + C content of 56.5%). Genome annotation identified 65 antibiotic resistance genes and 148 putative virulence factor-encoding genes in the MD9 genome. The megaplasmid pMD9A carries 29 antibiotic resistance genes conferring resistance to β-lactams, chloramphenicol/florfenicol, aminoglycosides, and macrolides. A class 1 integron (intI1) and multiple autonomous conjugative transfer elements were identified in pMD9A. Conjugation experiments demonstrated that the β-lactam resistance gene blaOXA-246 could be horizontally transferred from the donor MD9 strain to the recipient Escherichia coli 25DN strain. The megaplasmid pMD9A not only carries a broad array of antibiotic resistance genes, but also facilitates their horizontal spread among environmental bacteria, thereby potentially contributing to the dissemination of multidrug-resistant bacteria.

Pseudomonas asiatica↗

PubMed2025

Genomic and phenotypic insights into ST164 blaNDM-1-positive Acinetobacter baumannii from intestinal colonization in China.

BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAB) poses a critical global threat, especially in ICUs. Yet, reports on ST164 CRAB harboring blaNDM-1 remain scarce. This study investigates two clinical CRAB isolates, L4773hy and L4796hy, derived from intestinal colonization in Hangzhou, China, focusing on their phenotypic and genomic characteristics as well as the broader transmission of ST164 A. baumannii. METHODS: Bacterial identification was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) mass spectrometry. Antimicrobial susceptibility was assessed via agar and broth microdilution. Whole-genome sequencing employed Illumina NovaSeq 6000 and Oxford Nanopore platforms. Resistance genes, insertion elements, transposons, and integrons were detected using ResFinder, PlasmidFinder, VFDB, ISFinder, pdifFinder, and IntegronFinder. Strains were typed by MLST, and a phylogenetic tree was constructed with kSNP3.0. Genetic environment diagrams were generated using Easyfig 2.2.5. RESULTS: Two blaNDM-1-carrying A. baumannii isolates exhibiting extensive resistance to carbapenems, cephalosporins, and fluoroquinolones. Whole-genome sequencing and genetic environment analysis revealed the presence of a conserved structural sequence (ISAba14-ISAba14-aphA-ISAba125-blaNDM-1-bleMBL) on their chromosomes. Phylogenetic and clonal dissemination analysis showed that ST164 CRAB is primarily distributed in China and exhibits clonal spread. Pathogenicity studies indicated that blaNDM-1-positive ST164 strains have enhanced survival under immune pressure but do not display increased virulence in infection models. CONCLUSION: This study provides the genomic and phenotypic characterization of intestinally colonized ST164 blaNDM-1 positive CRAB in Hangzhou, China. The elucidation of the genetic environment of blaNDM-1 further confirms the clonal dissemination of ST164 isolates, highlighting the importance of enhanced surveillance and infection control measures to mitigate the spread of these multidrug-resistant pathogens.

Acinetobacter baumannii↗

PubMed2025

Drug resistant Klebsiella pneumoniae from patients and hospital effluent: a correlation?

BACKGROUND: The application of wastewater-based epidemiology has gained traction as a cost effective tool in antimicrobial resistance (AMR) surveillance with studies showing a correlation between the presence of resistant bacteria from hospital sewage and patients. This study compared Klebsiella pneumoniae from patients and hospital effluent in terms of antibiotic resistance patterns, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and phylogenomic relationships. RESULTS: Pooled effluent samples were collected from the final effluent point of a regional hospital and K. pneumoniae isolates were identified on selective media. Clinical isolates were also collected from the same hospital. Antimicrobial susceptibility testing (AST) was performed using the VITEK® 2 system. DNA was extracted prior to whole genome sequencing (WGS). The resistome, mobilome, and phylogenetic lineages of sequenced isolates were assessed using bioinformatics analysis. A total of 10 randomly selected presumptive and 10 clinical K. pneumoniae constituted the sample and were subjected to AST. Total resistance was observed in the clinical samples to cefuroxime, cefotaxime, piperacillin/tazobactam, gentamicin, tobramycin and trimethoprim/sulfamethoxazole. The effluent isolates exhibited total susceptibility to most antibiotics but showed resistance to amoxicillin/clavulanic acid and piperacillin/tazobactam (100%), and tigecycline (10%). The effluent isolates did not exhibit a diverse resistome, while the clinical isolates harboured genes conferring resistance to aminoglycoside (aph(6)-Id, aph(3'')-Ib, aac(6')-Ib-cr, aadA16), ß-lactam (blaSVH group, blaOXA group, blaTEM group), and fluoroquinolone (oqxA, oqxB) antibiotics. Only class 1 integrons were identified. Phylogenetic analysis revealed that effluent isolates from this study were not closely related to the clinical isolates. CONCLUSION: This study showed no correlation between the resistance profiles of the clinical and effluent isolates. The relationship between AMR in hospital effluent and clinical resistance may depend on the antimicrobial agents and bacterial species studied.

Klebsiella pneumoniae↗

PubMed2026

Genomic surveillance reveals escalating antimicrobial resistance and plasmid diversity in clinical Salmonella 1,4,[5],12:i:- ST34 isolates from Guizhou Province, China.

INTRODUCTION: Salmonella 1,4,[5],12:i:- ST34 has emerged as a significant public health issue due to its association with various antimicrobial resistance genes (ARGs) and transferable plasmids. However, its genomic characteristics and potential influence on public health in Guizhou have not been comprehensively assessed. METHODS: From 2019 to 2023, a 5-year surveillance was conducted in nine cities (prefectures) of Guizhou Province. We integrated phenotypic and genomic analyses of 281 clinical Salmonella 1,4,[5],12:i:- ST34 isolates to investigate the prevalence of ARGs and plasmids and to analyze the molecular epidemiology and evolution. RESULTS: The isolates exhibited resistance to first-line antibiotics, with 22.4% for ciprofloxacin, 11.4% for azithromycin, 18.5% for ceftazidime, and 39.1% for cefotaxime. ARGs showed substantial agreement with phenotypes for tetracycline, macrolides, third-generation cephalosporins (3GCs), carbapenems, and colistin (80.8-100.0% consistency; Kappa: 0.50-1.00). Plasmid analysis identified IncQ1 (84.3%) and IncHI2/IncHI2A (26.3%) as the main replicons, with the variety of plasmid replicons increasing from 7 to 21 over the 5 years. ARGs associated with resistance to critically important antibiotics (CIAs) were frequently predicted to be located on plasmid-associated contigs, with significant associations observed between IncHI2/IncHI2A plasmids and ARGs conferring resistance to fluoroquinolones, macrolides, and cephalosporins (P < 0.05). Molecular typing divided 281 isolates into 37 cgSTs, with cgST52428 being the most common. Molecular epidemiological analysis revealed that Guizhou isolates primarily clustered together, sharing close genetic ties with those from Sichuan and Guangdong, and exhibited the highest genetic similarity to pork-derived isolates. Phylogenetic analysis revealed clustering of CIA-resistant ARGs and plasmids in Clades 4 and 5, with a significant association between IncHI2/IncHI2A plasmids and CIA-resistant ARGs (χ2 = 112.12, P < 0.001). Additionally, class 1 integron was associated with higher ARG burdens, while virulence-associated genes were conserved and predominantly chromosome-associated. Gene-content analysis revealed that isolates in Clades 4 and 5 harbored the largest mean gene complements, and cgST52428 isolates also harbored the largest among dominant cgSTs. DISCUSSION: This study presents a comprehensive genomic profile of Salmonella 1,4,[5],12:i:- ST34 in Guizhou, providing essential data for exploring the resistance characteristics and investigating the molecular epidemiology of Salmonella 1,4,[5],12:i:-.

ST34↗

PubMed2026

Carbapenem-resistant Gram-negative pathogens: molecular epidemiology, diagnostic advances, and emerging therapeutic strategies.

Carbapenem-resistant Gram-negative pathogens (CR-GNPs) have become an important global health problem, contributing significantly to healthcare-associated infections, extended hospital stays, high mortality rates, and higher healthcare costs. The dissemination of carbapenem resistance is mainly attributed to the spread of carbapenemase-encoding genes, such as the Klebsiella pneumoniae carbapenemase (KPC), the New Delhi metallo-β-lactamase (NDM), the Verona integron-encoded metallo-β-lactamase (VIM), the imipenemase (IMP), and the oxacillinase-48 (OXA-48)-like enzymes associated with clinically important Gram-negative pathogens, including Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa. As well as carbapenemase production, resistance can also develop via alteration of porins, upregulation of efflux pumps, and the buildup of several resistance factors, generating highly adaptable and hard-to-treat microbes. Phenotypic resistance patterns may not predict the underlying mechanism and accurate laboratory detection remains challenging. The identification and monitoring of carbapenem-resistant organisms have undergone improvement in recent years thanks to molecular diagnostics, rapid phenotypic tests, whole-genome sequencing and metagenomics. At the same time, new drugs have been developed, such as ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, cefiderocol and combinations of aztreonam, offering increased treatment options, but with emerging resistance an issue. This mini review covers the molecular epidemiology of CR-GNPs, the latest developments and challenges in diagnosing these infections, new therapeutic options, and future perspectives on genomic surveillance, antimicrobial stewardship, and precision medicine strategies to address the increasing threat of carbapenem resistance.

Gram-negative pathogens↗

PubMed2025

Reduction in ARGs and Mobile Genetic Elements Using 2-Bromoethane Sulfonate in an MFC-Powered Fenton System.

The integration of an MFC-powered Fenton (MFC-Fenton) system into the traditional anaerobic composting process can promote excess dewatered sludge (ES) decomposition. However, the antibiotic resistance gene (ARG) profiles in ES treated by MFC-Fenton systems remain poorly understood; in addition, the effect of adding 2-bromoethane sulfonate (BES, a methane inhibitor) during ES treatment using an MFC-Fenton system on ARG levels is largely unexplored. The present work focused on investigating the effects of BES and bioelectrochemical processes on ARG and MGE abundances and unraveling the ARG attenuation mechanism. According to our findings, adding BES promoted ARG reduction in ES in an MFC-Fenton system. The average ARG levels in the MFC-Fenton samples containing high BES contents (0.4 or 0.5 g BES/g VSS) markedly declined relative to those in samples containing lower BES levels. Moreover, macrolide transporter ATP-binding protein, macrolide-efflux protein, and macB levels markedly decreased as BES levels increased. BES supplementation and bioelectrochemical assistance were crucial for altering the ARG composition in the MFC-Fenton system. Changes in the microbial community composition had the greatest effect on the variation in ARG composition. Furthermore, the Actinobacteria and Firmicutes levels accounted for 52.8% of the overall ARG variation. Among MGEs, plasmids, insertion sequences, and integrons showed lower levels within the sludge metagenomes. Typically, sulI, sulII, tetG, and bla TEM levels were positively correlated with metal resistance genes (MRGs), and their levels markedly declined following the MFC-Fenton process. Thus, the collective evidence indicates that BES synergizes with bioelectrogenesis to reduce ARG abundance.

Sewage↗