BMC Microbiology最新文献

Background: Studying the compositional structure and function of the gut microbiome is essential for evaluating adaptability of wildlife to their environment. Given the high plasticity of the gut microbiome in primates, studying conspecific populations under different habitat quality can provide valuable insights for the conservation and management. To investigate intersite differences in composition and function of the gut microbiome of endangered François' langurs (Trachypithecus francoisi), we employed 16S rRNA and metagenomic sequencing.

Results: The results showed that higher gut microbiota diversity of François' langurs was associated with higher habitat quality, possibly driven by the dietary diversity. In contrast, François' langurs inhabiting lower-quality habitats had a higher relative abundance of Bacillota and more enriched functional genes related to amino acid metabolism and metabolic pathways than those in higher-quality habitats, which support enhanced fiber degradation to meet energy demands. Additionally, the proportion of tetracycline-related ARGs (tetA(58)) was more abundant in lower-quality habitats, likely due to villagers applying livestock and poultry manure.

Conclusion: Our study concludes that intersite differences in gut microbiome are associated with habitat quality in the François' langurs, underscoring its role in habitat adaptation and necessity for physiological indicators to elucidate the mechanisms by which wildlife responds to human disturbance and ecological variability. In addition, we recommend prioritizing the restoration of native vegetation diversity in the langurs' habitats, which leverages their gut microbiota's adaptive potential to provide a suitable fundamental environment for the langurs' long-term survival.

Background: Overuse of carbapenems and other broad-spectrum antibiotics increases both costs and the risk of antimicrobial resistance (AMR). This study assessed whether optimizing antimicrobial susceptibility testing (AST) reports could improve clinical and economic outcomes for hospitalized patients with bloodstream infections (BSIs).

Methods: From June 2022 to May 2023, a series of microbiology laboratory interventions were implemented at the Affiliated Hospital of North Sichuan Medical College, including the use of BacT/Alert Virtuo system (bioMérieux, France) for rapid loading, VITEK MS (bioMérieux, France) for rapid microbiology identification (ID), 24-hour laboratory service, and dual AST cards (N335 + XN04) replacing the single card (GN13). Previous simultaneously reported ID and AST results were successfully replaced by a separate reporting process. Data from BSI patients before (June 2021-May 2022) and after (June 2023-May 2024) interventions were retrospectively analyzed for ID and AST reporting time, antibiotic use, length of stay (LOS), and costs.

Results: A total of 256 BSI patients were analyzed (125 pre-intervention; 131 post-intervention). The post-intervention group had significantly shorter times to ID (median 41.26 vs. 74.35 h) and AST reports (56.02 vs. 74.35 h), with earlier opportunities for targeted antibiotic adjustments. Antibiotic modifications occurred ~ 36 h sooner within the first 72 h. Among all agents, carbapenems underwent the most MIC-based changes (20 additions and 10 discontinuations), reflecting improved carbapenem stewardship driven by expanded AST coverage. Post-intervention patients also showed shorter LOS, reduced antibiotic and testing costs, and a potential improvement in survival, especially in ICU cases.

Conclusions: Optimized microbiology workflows, including dual AST cards and faster AST report, significantly accelerated reporting and facilitated timely, precise antimicrobial therapy, particularly carbapenem stewardship, while reducing clinical and economic burdens.

Background: Carbapenem-resistant Citrobacter freundii is increasingly reported and recognized as an opportunistic host of mobile carbapenemase-encoding elements in healthcare-associated settings. However, lineage-associated plasmid vehicles and their transfer-related features in this species remain incompletely characterized.

Objective: This study aims to characterize the first IncFII(pBK30683)/IncR plasmid carrying bla_KPC-2 in C. freundii ST91, focusing on its transferability, stability, and the role of plasmid lineages in carbapenem resistance dissemination.

Methods: We investigated a urine-derived ST91 C. freundii isolate (MAS5905) through antimicrobial susceptibility testing, whole-genome sequencing, conjugation, 20-day plasmid stability, and growth curve assays. Comparative genomics included plasmid phylogeny of pMAS5905-KPC-like sequences and ST91 phylogenomics.

Results: The 5.64 Mb genome comprised a chromosome and three plasmids. bla_KPC-2 was located on an IncFII(pBK30683)/IncR plasmid pMAS5905-KPC carrying a complete conjugation module, the mer operon, and the anti-CRISPR determinant AcrIE9, with the bla_KPC-2 embedded in an IS26-bracketed ΔTn6296-like module (ISKpn27-bla_KPC-2-ΔISKpn6). The plasmid transferred to E. coli at 1.93 × 10^-5 was retained at 100% over 20 days, and imposed a significant fitness cost. Phenotypically, MAS5905 was resistant to multiple β-lactams (including ertapenem and meropenem) and fluoroquinolones, while remaining susceptible to cefepime, ceftazidime, trimethoprim-sulfamethoxazole, aminoglycosides, tetracyclines, and nitrofurantoin. Plasmid comparisons resolved six IncFII/IncR clades with a conserved backbone and broad host range. ST91 phylogenomics revealed multiple clades and, in the analyzed public dataset, a high carbapenemase gene prevalence (75.76%), dominated by bla_KPC (31.82%) and bla_OXA-48-like (30.30%).

Conclusion: To our knowledge, this is the first characterization of an IncFII(pBK30683)/IncR plasmid carrying bla_KPC-2 in a clinical C. freundii ST91 isolate. The findings highlight plasmid lineages as drivers of carbapenem resistance dissemination and underscore the need for plasmid-focused genomic surveillance, particularly for monitoring transferable resistance vehicles across clinically relevant hosts.

Background: The nasal cavity serves as a primary contact site and is a common location for colonization by symbiotic, opportunistic, and potentially pathogenic bacteria. Diabetic patients are more susceptible to colonization by opportunistic microorganisms due to impaired immune function, altered normal flora, and increased exposure to healthcare. This study aimed to investigate the nasal colonization of Gram-positive (Staphylococcus aureus) and Gram-negative (Enterobacteriaceae) bacteria in diabetic and non-diabetic individuals, assessing phenotypic traits including antibiotic resistance and biofilm production, as well as investigating the presence of resistant genes.

Materials and methods: In this cross-sectional study, nasal swabs were collected from 150 diabetic and 150 non-diabetic individuals. Isolates were identified and evaluated phenotypically (Antibiotic resistance using the disk diffusion method and biofilm formation by the microtiter plate method) and genotypically (resistance genes including mecA, bla_CTX, bla_SHV, and bla_TEM) by PCR.

Results: The rate of S. aureus colonization was higher in diabetics (18.7%) than in non-diabetics (12.7%) and MRSA colonization was significantly higher in diabetics (8% vs. 1.3%). High antibiotic resistance was not observed except for tetracycline (nearly 50%) in S. aureus isolates from both groups. There was no statistically significant difference in the occurrence of MDR S. aureus between the diabetic (32.1%) and non-diabetic (31.6%) groups. Enterobacteriaceae colonization was 3.3% in diabetics and 7.3% in non-diabetics. Although none were phenotypically ESBL-positive, bla_CTX, bla_TEM, and bla_SHV genes were present in about 40% of the isolates.

Conclusion: Nasal MRSA colonization was more common among diabetic patients than non-diabetics. The findings of this study highlight the need for ongoing monitoring of nasal colonization of MRSA in different populations and settings, which may lead to the development of effective preventive and therapeutic strategies to control infections caused by nasal colonization.

Background: Kanamycin, an aminoglycoside, is an effective broad-spectrum antimicrobial agent against bacterial infections. However, the clinical efficacy of aminoglycosides has been overshadowed by the emergence of resistance mechanisms involving enzyme-mediated covalent modifications. Aminoglycoside nucleotidyltransferases (ANTs) inactivate aminoglycosides via AMP group transfer. Elucidating their molecular mechanisms and identifying effective inhibitors are critical for combating antimicrobial resistance.

Methods: Exiguobacterium sp. PL221A was isolated from hospital sewage under selection with 16 mg/L aminoglycosides. Following genomic sequencing using the Oxford Nanopore and BGISEQ-500 platforms, the eanT-1 gene encoding an ANT was identified, cloned, and expressed in Escherichia coli DH5α. Minimum inhibitory concentrations (MICs) against kanamycin were determined. Protein-ligand interactions between Eant-1 and kanamycin, virtual mutations of EanT-1, and inhibitor screening were assessed using the MaXFlow platform. To evaluate the catalytic mechanism, eant-1 mutants were expressed in vitro and their kinetic parameters were characterized. The impact of bicuculline on MICs and time-kill curves was also evaluated.

Results: Strain PL221A exhibited notable resistance to neomycin, kanamycin, and gentamicin (all MICs > 128 mg/L). Heterologous expression indicated that EanT-1 confers kanamycin resistance. Mutation of residues D43A and D98A abrogated enzymatic activity, whereas alanine substitutions at R51 and T100 had no apparent effect. Bicuculline, an isoquinoline alkaloid compound, was identified as an effective EanT-1 inhibitor, showing stronger binding affinity (-8.72 kcal/mol) for EanT-1 than kanamycin (-7.51 kcal/mol) and an ability to occupy aspartate residues critical for electrophilic polarization. Its hydroxyl-free alkaloid scaffold may prevent adenylation, enabling competitive binding with kanamycin at the catalytic site and inactivating EanT-1. Additionally, the combination of kanamycin and bicuculline effectively inhibited the growth of eanT-1-expressing bacteria.

Conclusions: The ANT encoded by eanT-1 in Exiguobacterium sp. PL221A mediates resistance to kanamycin, which can be counteracted by the alkaloid bicuculline through inhibition of its catalytic activity.