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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

Comparative genomic characterization and antimicrobial resistance of bacteremia-causing Enterococcus faecium and Enterococcus faecalis in a Chinese hospital.

Enterococci are common commensals of the human gut and important opportunistic pathogens, with Enterococcus faecium and Enterococcus faecalis being the most clinically prevalent species. A significant epidemiological shift has emerged with an increasing clinical burden of E. faecium. To compare genomic evolution of E. faecium and E. faecalis, we performed whole-genome sequencing on 93 E. faecium and 32 E. faecalis isolates causing bloodstream infections at a single hospital (2022-2024). Analysis of patient demographics revealed that E. faecium infections originated from fewer sources than E. faecalis, with a higher proportion deriving from intra-abdominal infections. Multilocus sequence typing identified ST78 and ST789 as the predominant sequence types for E. faecium, whereas ST16 and ST179 were most common for E. faecalis. E. faecium carried more antimicrobial resistance genes and putative virulence marker (PVM)-type virulence genes than E. faecalis, with vancomycin resistance predominantly mediated by vanHAX (33/93, 35.5%) and a single E. faecalis isolate also carrying vanHAX (1/32, 3.1%); the structurally incomplete vanHMX gene cluster was detected in 11 E. faecium isolates. Pan-genome analysis indicated a larger core genome in E. faecalis compared to E. faecium, consistent with greater plasmid replicon diversity in the latter. Intra-host comparisons showed that two E. faecalis pairs from the same patient were clonally related, with one isolate acquiring a vanHAX plasmid conferring vancomycin resistance. In contrast, E. faecium isolates exhibited marked genomic diversity even among clonally related pairs. These findings suggest that E. faecium possesses greater genomic plasticity and adaptive potential to the clinical environment.IMPORTANCEThis study provides a detailed comparison of clinical and genomic features between Enterococcus faecium and Enterococcus faecalis from the same hospital setting. We show that E. faecium isolates, mainly ST78/ST789, carry more antimicrobial resistance genes and a higher number of putative virulence marker (PVM) genes than E. faecalis, reflecting their hospital-adapted nature. E. faecium also exhibits a smaller core genome and greater diversity of plasmid replicon types, indicating higher genomic plasticity and capacity for horizontal gene transfer. By contrast, E. faecalis retains a larger core genome and a set of classical virulence factors, and its within-host isolates are clonally related. These distinct genomic profiles help to understand how the two species adapt to clinical environments and may inform more targeted infection control strategies and resistance surveillance.

Enterococcus faecium↗