Broad-spectrum antibiotics are frequently used to treat bacteria-induced infections, but the overuse of antibiotics may induce the gut microbiota dysbiosis and disrupt gastrointestinal tract function. Probiotics can be applied to restore disturbed gut microbiota and repair abnormal intestinal metabolism. In the present study, two strains of Enterococcus faecium (named DC-K7 and DC-K9) were isolated and characterized from the fecal samples of infant dogs. The genomic features of E. faecium DC-K7 and DC-K9 were analyzed, the carbohydrate-active enzyme (CAZyme)-encoding genes were predicted, and their abilities to produce short-chain fatty acids (SCFAs) were investigated. The bacteriocin-encoding genes in the genome sequences of E. faecium DC-K7 and DC-K9 were analyzed, and the gene cluster of Enterolysin-A, which encoded a 401-amino-acid peptide, was predicted. Moreover, the modulating effects of E. faecium DC-K7 and DC-K9 on the gut microbiota dysbiosis induced by antibiotics were analyzed. The current results demonstrated that oral administrations of E. faecium DC-K7 and DC-K9 could enhance the relative abundances of beneficial microbes and decrease the relative abundances of harmful microbes. Therefore, the isolated E. faecium DC-K7 and DC-K9 were proven to be able to alter the gut microbiota dysbiosis induced by antibiotic treatment.

Background/Objectives: The global dissemination of tet(X) variants critically threatens tigecycline efficacy as a last-resort antibiotic. The aim of this study was to characterize a tet(X6)-carrying integrative and conjugative element (ICE) in a multidrug-resistant Chryseobacterium lecithinasegens strain, SHZ29, isolated from Shanghai, China. Methods: Minimum inhibitory concentrations (MICs) were determined by broth microdilution for SHZ29. Whole genomic sequencing and bioinformatic analysis were performed to depict the structure of the novel tet(X6)-carrying ICE. Inverse PCR and conjugation experiments were conducted to investigate the transfer ability of the ICE. Results: We depicted a novel tet(X6)-carrying ICE, named ICECleSHZ29, which is 74,906 bp in size and inserted into the 3′ end of tRNA-Met-CAT gene of the C. lecithinasegens strain SHZ29, with 17 bp direct repeats (5′-tcccgtcttcgctacaa-3′). This ICE possesses a 38 kb conserved backbone and four variable regions (VR1-4), with VR3 aggregating multiple resistance genes, including tet(X6), tet(X2), erm(F), ere(D), floR, catB, sul2, ant(6)-I and bla_OXA-1327. NCBI database searching identified 13 additional ICEs sharing a similar backbone to ICECleSHZ29. These ICECleSHZ29-like ICEs could be classified into two types based on their distinct insertion sites: Type I, inserted at the tRNA-Met-CAT gene; and Type II, inserted at the tRNA-Glu-TTC gene. Phylogenetic analysis indicated that differences in integrases may result in differences in the insertion site among these ICEs. A circular intermediate form of ICECleSHZ29 was detected by inverse PCR. However, the conjugation experiments using Escherichia coli EC600 as recipients failed. Conclusions: To our knowledge, this study provides the first report of tet(X6) in C. lecithinasegens and characterizes its carrier, a novel ICE: ICECleSHZ29.

The dissemination of New Delhi metallo-β-lactamase (NDM)-producing Escherichia coli poses a serious threat to public health. Although increasing attention has been paid to the relationship between temperature and antimicrobial resistance (AMR) transmission, research in China’s Xinjiang region remains scarce. In this study, we conducted a cross-sectional survey of 1914 samples from intensive livestock farms across Xinjiang to characterize the detection rate and antimicrobial resistance profiles of bla_NDM-positive E. coli. Using selective culture, PCR, and 16S rRNA sequencing, we identified 140 bla_NDM-positive E. coli (7.3%), predominantly in northern Xinjiang. The highest detection rate of bla_NDM-positive E. coli was found in Tacheng Prefecture (24.0%), followed by Changji Hui Autonomous Prefecture (4.3%) and Bortala Mongol Autonomous Prefecture (0.6%). No bla_NDM-positive E. coli isolates were detected in Bayingolin Mongol Autonomous Prefecture, Kashgar Prefecture, or from pigeon samples. Binomial logistic regression analysis revealed a significant positive association between regional temperature and the detection rate of bla_NDM-positive E. coli. Genotypic analysis identified 35 distinct resistance gene profiles, with predominant resistance genes including bla_TEM (87.9%), ant(3″)-Ia (97.1%), qnrS (92.9%), tet(A) (95.0%), sul1 (70.0%), sul3 (85.0%), and floR (97.1%); mcr-1 and mcr-8 were not detected. Antibiotic susceptibility tests showed that all isolates were resistant to imipenem and exhibited universal resistance to ampicillin, ceftiofur, tetracycline, florfenicol, and enrofloxacin, whereas the majority remained susceptible to amikacin (99.3%), tigecycline (94.3%), and polymyxin (77.1%). These findings indicate that livestock farms, particularly laying-hen systems in northern Xinjiang, may serve as reservoirs of multidrug-resistant bla_NDM-positive E. coli, and that elevated regional temperature is an environmental factor associated with higher detection rates, underscoring a potential climate-associated risk for the spread of AMR.