BMC Microbiology最新文献

Specific pathogen-free (SPF) mice are pivotal preclinical models linking basic microbiology to clinical translation, yet comprehensive high-resolution profiling of their gut microbiome, especially antibiotic resistance genes (ARGs), remains limited. To address this gap, metagenomic sequencing was conducted on cecal contents from C57BL/6 and BALB/c SPF mice from five Shanghai laboratory animal facilities, generating 141 Gbp high-quality sequencing data. From 1,761,909 predicted genes, 1,048,575 non-redundant genes were identified for analysis. Taxonomic annotation identified Bacillota (73.0%), Bacteroidota (16.6%), and Actinomycetota (2.9%) as dominant phyla. At the genus level, microbial communities varied markedly across facilities, with Muribaculaceae prevailing in SHA/SHD and Blautia or Enterococcus enriched in SHB/SHE. Beta diversity analysis showed communities clustered by facility, indicating breeding environment had a stronger impact on gut microbiota diversity than host strain. KEGG, COG, and GO functional annotation revealed broad metabolic and molecular diversity. Antibiotic resistome profiling identified 11 ARG categories, predominantly associated with glycopeptides (18.1%) and tetracycline (11.3%) resistance. The most enriched ARG carriers were Pseudomonadota (acrD, emrB, mdtB etc.), Bacillota (tet(44), tet(M), tet(O) etc.), Bacteroidota (tet(Q), mel, tet(X) etc.), and Actinomycetota (rpoB, ileS). Furthermore, ARGs resistance mechanisms varied between facilities with distinct beta-diversity clustering: SHB and SHE mice mainly employed antibiotic target alteration against glycopeptides, whereas SHA, SHD, and SHC-C57BL/6 primarily utilized antibiotic target protection against tetracyclines. This study presents a high-resolution comparison of gut microbiota and ARGs in SPF mice from multiple facilities, highlighting facility-dependent microbial and resistome variation and providing valuable references for preclinical microbiological standardization and risk assessment.

Yaks are the primary ruminant on the Qinghai-Xizang Plateau, playing a central role in the livelihoods of local farmers and herders. They serve as a vital source of food, clothing, shelter, and transportation in the region. Over the course of long-term natural selection, yaks have evolved distinct regulatory mechanisms related to their physiology, nutritional metabolism and feeding behaviors. Despite these adaptive traits, traditional yak breeding faces challenges such as slow growth, delayed gastrointestinal maturation, and low weaning weights, which lead to reduced breeding efficiency. This study investigated the effects of early supplementary feeding of starter feed on the intestinal health of calves, focusing on the benefits of timely and appropriate supplementation during the early stages of development. Utilizing ITS sequencing and LC-MS non-targeted metabolomics, this study investigated the mechanism by which supplementary feeding of starter feed affects the intestinal health of calves, focusing on changes in the composition of the intestinal microbiota and metabolites present in the calves. The study found that supplementary feeding enhanced the abundance of beneficial fungi, including Plectosphaerella, Mortierella, and Aspergillus, while simultaneously reducing the prevalence of harmful fungi such as Comoclathris, Arthrographis, and Cryptococcus neoformans. Further research utilizing non-targeted metabolomics has revealed that supplementary feeding of starter food influences several metabolic pathways, including fat digestion and absorption, glycerophospholipid metabolism, vitamin digestion and absorption, autophagy (both yeast and animal), and the VEGF signaling pathway. Metabolites such as dexamethasone and benzamidine are commonly associated with inflammatory and protease-inhibition pathways, which can influence gastrointestinal integrity and stress responses in ruminants. This feeding regimen was found to increase the concentrations of metabolites such as dexamethasone, benzamidine, norethindrone acetate, and tamoxifen, while simultaneously reducing the levels of metabolites like dinoterb and monoisobutyl phthalate. In conclusion, early supplementary feeding of starter feed is conducive to the colonization of beneficial fungi in the intestinal tract of calves, reduces the colonization of harmful bacteria, and increases the concentration of metabolites related to anti-inflammation, anti-tumor activity, and signal transduction in the blood of calves. Moreover, a feed formula consisting of 1.4 kg of alfalfa and 1.4 kg of starter feed proves advantageous for maintaining intestinal homeostasis and optimizing blood metabolism in calves, which could improve the overall productivity and health of yak calves.starter feedstarter feed.

Background: Antimicrobial resistance (AMR) has emerged as a critical global health challenge and is currently addressed through a "One Health" approach that investigates its occurrence in humans, animals, and the environment, as well as the transmission pathways linking these reservoirs. In commercial poultry farms, antibiotics are routinely used to treat bacterial infections that are economically significant as well as to promote weight gain. However, data on AMR in Staphylococcus aureus (S. aureus) of poultry origin remain scarce in Nepal. Antimicrobial resistance in S aureus, particularly the emergence of methicillin-resistant (MRSA) and vancomycin-resistant (VRSA) strains in both humans and poultry, poses a significant public health threat worldwide requiring immediate attention. This study aimed to detect the prevalence of multidrug-resistant S. aureus and the distribution of tetA, tetB, ermA, ermB, and ermC genes among S. aureus from litter and soil of poultry farms of Kathmandu Valley.

Methods: Litter and soil samples were processed using serial dilution and spread plate techniques to isolate S. aureus. Antibiotic susceptibility testing was assessed by a modified Kirby-Bauer disc diffusion method. DNA was extracted from the isolates, and polymerase chain reaction (PCR) was performed to detect resistance genes (tetA, tetB, ermA, ermB, and ermC).

Results: A total of 32 S. aureus were obtained, comprising 20 isolates from litter and 12 isolates from the soil of poultry farms. A total of 59.3% (19/32) of S. aureus isolates were multidrug-resistant (MDR); from which 65% (13/20) were from litter and 50% (6/12) from soil. A Chi-square test revealed no statistically significant association between MDR isolates and the source (litter vs. soil) (p > 0.05). The antibiotic susceptibility results showed high degree of resistance towards erythromycin (68.8%) followed by tetracycline (59.4%). In PCR analysis, the majority of isolates (96.8%) showed the tetA gene, while none of the isolates showed the tetB gene. Only 15 and 11 isolates out of 32 showed the ermB (46.8%) and ermC (34.3%) genes, respectively, while all isolates tested negative for ermA. Additionally, 5 S. aureus isolates carried both ermB and ermC genes. Chi-square analysis showed no significant association between AMR gene occurrence and the source of S. aureus isolates.

Conclusion: The high incidence of multidrug-resistant S. aureus and detection of antibiotic resistance genes in poultry litter and soil highlight a significant risk of transmission to farm workers, butchers, and consumers, as well as possible environmental contamination through manure application. These findings underscore the urgent need for strict antimicrobial stewardship, improved biosecurity, and policy measures to prevent the spread of resistant S. aureus from poultry farms to the wider community.

Background: Candidozyma auris is a multidrug resistant fungal pathogen classified by the World Health Organization (WHO) as a critical priority species. Broth microdilution (BMD) is the recommended reference method for antifungal susceptibility testing (AFST), with interpretation based on tentative breakpoints proposed by the Centers for Disease Control and Prevention (CDC) and, more recently, EUCAST clinical breakpoints published in 2025. However, automated systems such as VITEK 2 currently lack validated susceptibility interpretations for C. auris. This study aimed to evaluate the performance of the VITEK 2 system for AFST of C. auris isolates by comparison with the BMD method and to assess the impact of applying CDC and EUCAST breakpoints on susceptibility interpretation.

Methods: Antibiotic susceptibility testing (AFST) was performed simultaneously on 88 C. auris isolates using the VITEK 2 system and the BMD method. Susceptibility results were interpreted according to both CDC and EUCAST clinical breakpoints. The clade distribution of the isolates was determined by multiplex PCR.

Results: All isolates were identified as clade I. Categorical agreement (CA) between VITEK 2 and BMD was 31.8% for amphotericin B, 76.1% for fluconazole, and 92.0% for both caspofungin and micafungin. Based on CDC breakpoints, no very major errors (VME) were observed for amphotericin B, caspofungin, or micafungin using VITEK 2, whereas a VME rate of 15.0% was detected for fluconazole. Major error (ME) rates for VITEK 2 were 93.7% for amphotericin B, 68.7% for fluconazole, and 7.9% for caspofungin and micafungin, all exceeding the acceptable performance threshold (ME ≤ 3%). Concordance between CDC- and EUCAST-based interpretations was high for micafungin (VITEK 2: 93.1%; BMD: 96.5%) but markedly lower for amphotericin B (VITEK 2: 59.0%; BMD: 27.2%).

Conclusion: In conclusion, VITEK 2 showed a high level of agreement with the BMD method in the echinocandin susceptibility test of C. auris, while very high ME and VME ratios were observed for amphotericin B and fluconazole. These findings indicate that VITEK 2 amphotericin B and fluconazole AFST results should be interpreted carefully and validated using reference methods. Furthermore, the differences between CDC and EUCAST breakpoint interpretations, particularly for amphotericin B, highlight the significant impact of breakpoint selection on antifungal susceptibility categorization in C. auris.

Background: The emergence and dissemination of carbapenem-resistant Klebsiella pneumoniae (CRKP) within healthcare settings is recognized as an "urgent threat" to public health. CRKP infections in pediatric patients exhibit distinct genetic and phenotypic features compared to those observed in adult patients.

Methods: This study performed whole-genome sequencing on 92 CRKP isolates collected from pediatric patients at Children's Hospital, Zhejiang University School of Medicine over a 6-year period (2019-2024), and systematically characterized the profiles of antimicrobial resistance genes, virulence factors, capsular types, and antimicrobial resistance (AMR) prevalence.

Results: Ninety-two CRKP isolates were collected, NDM-type was the predominant carbapenemase (64/92). Capsule typing analysis demonstrated that KL2 was the most prevalent type, comprising 43.48% (40/92) of all isolates. All KL2 isolates harbored the bla_NDM-1 gene and exhibited resistance to ceftazidime/avibactam (CZA). Comparative analysis of the plasmid genomic sequences of ST25-KL2 CRKP with those of all available K. pneumoniae isolates in the National Center for Biotechnology Information (NCBI) database revealed that the DY1928 strain, isolated from Hangzhou, Zhejiang Province, exhibited high sequence homology to the plasmid genomes identified in this study. In addition to harboring a conservative structural sequence (bla_NDM-1-ble-trpF-dsbD) located downstream of the bla_NDM-1 gene, the strain also carries the resistance genes bla_CTX-M-104, bla_TEM-1-B, and rmtB.

Conclusions: We performed genomic analysis and epidemiological studies on the CRKP among pediatric patients in China over six years and report the emergence of a specific clone. Our research results indicate that clonal dissemination of ST25-KL2, which requires enhanced monitoring of this situation in the future.