Polish journal of microbiology最新文献

Carbapenems, as the preferred treatment for multidrug-resistant Pseudomonas aeruginosa, are increasingly facing issues of insufficient therapeutic efficacy. This study aims to investigate the antimicrobial resistance mechanisms of clinical P. aeruginosa isolates to carbapenems. The whole genome sequencing revealed various β-lactamase genes, including the intrinsic genes bla _PAO and bla _OXA-50-like, as well as the acquired bla _GES-5 (n = 6), and bla _OXA-101 (n = 10) in 40 carbapenem-resistant P. aeruginosa (CRPA) isolates. These isolates were categorized into 18 different sequence types, with ST235 (n = 6) and ST270 (n = 10) being the most prevalent. Single nucleotide polymorphism (SNP) analysis revealed that the collected isolates can be divided into two evolutionary branches, with some exhibiting high homogeneity. Isolates belonging to ST207, ST235, ST270, and ST277 may have contributed to small-scale outbreaks of infection in the hospital. A total of 5 different class 1 integrons, including a new gene cassette array bla _GES-5 -gcuE15-aph(3')-XV-ISPa21e, were detected in this study. All 40 CRPAs were found to have mutations in the outer membrane porin OprD. The efflux pump gene mexY showed the highest overexpression frequency at 55.00% (22/40). The CRPAs that overexpress mexY showed a higher resistance rate to various antimicrobial agents than those with normal levels of mexY expression (p < 0.05). Of 40 CRPAs, four isolates carried four antimicrobial resistance mechanisms simultaneously (bla _GES-5, OprD mutation, high expression of efflux pump, and biofilm formation). To the best of our knowledge, a new gene cassette array of class 1 integron, bla _GES-5-gcuE15-aph(3')-XV-lSPa21e, was reported for the first time in this study.

Bacteriophage-based biocontrol is a cost-effective, sustainable strategy with low ecological impact, which can control the growth of bacteria such as Escherichia coli that impacts public health problems. This work aimed to perform a meta-analysis to evaluate the implementation of bacteriophages as a biocontrol strategy to prevent the contamination of meat products with E. coli. The search was performed by two field experts to avoid reviewer bias. The initial search identified 2,695 bibliographic sources, of which 2,480 were discarded because they did not meet the inclusion criteria, which were the origin of phage, application method, phage taxonomy, E. coli pathotype and meat products, getting 157 articles because they were duplicates, and 47 because they lacked the necessary numerical data. Finally, 11 articles were selected for quantitative analysis. Likewise, phage characteristics (p < 0.05) and E. coli pathotype (p < 0.05), showed that the bacteriophage-bacteria ratio is an item that should be taken into account for the design of bacteriophage application strategies. This meta-analysis evaluates the use of phages in the reduction of E. coli in meat products, considering multiple methodological criteria. Studies were included that specify the origin of the phages (natural or modified), their method of application (direct in meat, in solution, in aerosol, etc.), their taxonomic classification, as well as the pathotype of the target E. coli (EHEC, ETEC, etc.). In addition, the different types of meat products were analyzed, including beef, pork, and chicken. These criteria help clarify the factors affecting phage therapy efficacy in the meat industry.

This study aimed to explore the combined detection of secreted frizzled-related protein-2 (SFRP2), Syndecan-2 (SDC2), and Fusobacterium nucleatum (Fn) in fecal samples for early colorectal cancer (CRC) screening. Public datasets were analyzed to evaluate the expression of SFRP2, SDC2, and Fn. The study included 30 pairs of tissue and 196 fecal samples. Gene expression of SFRP2, SDC2, F. nucleatum antigen adhesinA (fadA), and N-utilization substance G (nusG) was measured by qPCR. Correlations with Ki67, P53 expression, and immune infiltration were examined. The diagnostic performance of the combined markers was assessed using ROC curve analysis. SFRP2 and SDC2 were underexpressed (p < 0.001), while Fn was notably enriched in CRC (p < 0.0001). Expression of SFRP2 and SDC2 correlated with immune cell infiltration, whereas Fn abundance showed a negative correlation with immune infiltration. ROC analysis indicated that the combined detection of these markers outperformed single-gene tests, CEA, and FOBT in early CRC detection. This combined detection approach offers a promising, non-invasive, and cost-effective method for early CRC screening.

Due to their hazardous effects on human health and air quality, benzene and xylene constitute the primary pollutants. Coupling the physicochemical strategies with bacterial bioremediation is an emerging mode of decontamination. Considering the limited understanding of benzene and xylene degradation pathways in the genus Bacillus, failure of earlier documented bacteria to degrade these compounds due to poor optimization and complicated real-world contamination scenarios, we initiated the current project. It is an attempt to explore the gene repertoire and pathways associated with the bioremediation of benzene and xylene in new and efficient bacteria. Eleven bacteria were isolated from tannery industry soil in a previous study. Bacterial DNA was extracted by the organic method. To prepare a sample for whole genome sequencing (WGS) analysis, a mixture of genomic DNA was made by adding DNA from each isolate in equimolar concentration (100 ng). The sample was subjected to WGS. Results obtained as FASTq files were submitted to Sequence Read Archives (SRA), NCBI, to get the accession number assigned. Taxonomic profiling revealed that the sample was composed of phyla Proteobacteria (76%), Firmicutes (16%) and unclassified phyla (8%). Functional annotation unraveled the presence of benzoate, m-, p- and o-xylene isomers, benzene, aminobenzoate, 2-, 3- and 4-fluorobenzoate, toluene, chloroalkane and chloroalkene, naphthalene, polycyclic aromatic hydrocarbons (PAHs), dioxin, caprolactum, atrazine, styrene, and chlorobenzene and chlorocyclohexane degradation enzymes and pathways. It is the first ever study documenting the benzene degradation pathway similar to Gram-negative bacteria, in the genus Bacillus, inhabiting the tannery soil and coexistence of metabolic pathways for multiple organic pollutants.

Streptococcus pyogenes is a significant pathogen in postpartum women and neonates. This study aimed to determine its prevalence, antibiotic susceptibility, clinical features, and associated risk factors in tertiary care hospitals in Khyber Pakhtunkhwa, Pakistan. A total of 384 clinical samples were collected from postpartum women (n = 192) and neonates (n = 192) in maternity wards. S. pyogenes isolates were identified using standard microbiological methods, and antibiotic susceptibility was assessed via the Kirby-Bauer disk diffusion assay. The emm typing was performed through PCR and sequencing. Clinical features and risk factors were analyzed statistically. The overall prevalence of S. pyogenes was 14.3% (55/384), with 16.7% in postpartum women and 11.9% in neonates. Isolates exhibited high sensitivity to β-lactams (penicillin ≥ 95%, ampicillin ≥ 91%) but moderate resistance to cephalosporins (cefepime ~12%) and macrolides (erythromycin 23.5-29.0%). Fluoroquinolones and tetracyclines showed the highest resistance rates (ciprofloxacin 38.7-43.5%, tetracycline 32.1-37.5%). Molecular typing revealed diverse emm types, with emm44, emm77, and emm12 being predominant. Fever and sepsis were common, with postpartum women experiencing more wound infections (33.3%) and neonates exhibiting respiratory distress (55.6%). Significant risk factors included prolonged labor (> 18 hours, p = 0.030) and premature rupture of membranes (p = 0.039) in mothers, preterm birth (p = 0.013), and neonatal resuscitation (p = 0.028) in neonates. The study highlights a substantial burden of S. pyogenes infections and increasing antibiotic resistance. Enhanced surveillance, antibiotic stewardship, and targeted infection control strategies are crucial to mitigating morbidity and mortality in these high-risk groups.

In recent years, several modern therapies in orthopedics have been introduced, and these have been significantly influenced by the development of innovative medical devices made from various biomaterials. All orthopedic procedures involving the use of medical devices can lead to the occurrence of postoperative infectious complications, generally referred to as biomaterial-associated infections (BAIs). Currently, the classical antimicrobial treatment of BAIs consists mainly of systemic antibiotic therapy, which does not provide adequate clinical efficacy and is associated with the risk of many adverse effects. Therefore, numerous studies have been conducted to develop various methods to limit BAIs locally. Most of them involve the development of bioactive coatings or modified surfaces of biomaterials capable of releasing various antimicrobial substances. Applying such solutions in bone surgery is primarily related to the anti-infective protection of bone scaffolds, which is currently one of the most advanced and promising techniques in regenerative medicine. Using scaffolds in the damaged tissue provides an artificial structure that supports cell growth in the appropriate spatial configuration and restores the mechanical properties of the damaged bone in a short time. Therefore, the long-term protection of bone scaffolds against infection is crucial for achieving complete therapeutic success and currently represents one of the most significant challenges in bone surgery. This article presents selected strategies for modifying bone scaffolds that have been developed to reduce the risk of BAI.

Pneumonia is a leading cause of mortality in children. While metagenomic next-generation sequencing (mNGS) has the potential to detect all the microorganisms in pneumonia patients, the relationship between these microorganisms and the patients' clinical characteristics remains to be established. Fifty-five children, diagnosed with severe pneumonia and undergoing tracheal aspirate (TA) mNGS for pathogen detection at The Heilongjiang Hospital of Beijing Children's Hospital between July 2021 and November 2022, were included in this study. The clinical characteristics, pathogen distribution, and microbiome features of these children were analyzed. Results showed that the rate of mixed infections was notably high (80%, 44/55), with bacterial-viral infections being the most common. Streptococcus pneumoniae, Mycoplasma pneumoniae (MP), Candida albicans, and Respiratory syncytial virus (RSV) were the most common pathogens in this cohort. Furthermore, RSV and S. pneumoniae were the most prevalent pathogens in children younger than 12 months (infants), while MP and Haemophilus influenzae were more commonly identified in children between 12 and 144 months. Increased richness and diversity of the microbiota were observed in the TA of the older children. Linear discriminant analysis (LDA) effect size (LEfSe) analysis identified that RSV and Streptococcus mitis were the specific species associated with infants. In contrast, Human bocaparvovirus 1 and Prevotella histicola were significantly enriched in the older children. In addition, the top 20 most abundant species exhibited correlations with neutrophil count and C-reactive protein. This study emphasizes the significance of employing mNGS to understand better the clinical characteristics and microbial diversity in pediatric patients with severe pneumonia.

Microbial diversity plays a crucial role within the plant rhizosphere ecosystem, serving as a pivotal indicator of plant health and stability. In order to explore the correlation between the growth of mycorrhizal seedlings and the nutrition and microbial diversity of the ectomycorrhizosphere, the soil of the ectomycorrhizosphere with different growth conditions was used as the research object, and the ITS1 region and 16S rRNA high-throughput sequencing technology were used to explore the inter-relationship. The findings indicated that the primary phyla within the rhizosphere soil microbial communities of various mycorrhizal seedlings were comparable, although their relative abundances varied. The relative abundance of Tuberaceae in good-growing mycorrhizal seedlings (CHTG) was 17.87% and 15.58% higher than in medium-growing (CHTM) and bad-growing (CHTB), respectively. Comparing the diversity indexes Chao1, Shannon and Simpson, it was found that CHTG had the lowest richness. Redundancy analysis (RDA)/canonical correspondence analysis (CCA) analysis revealed that Tuber was positively correlated with soil pH and negatively correlated with available nitrogen, organic matter, total nitrogen, total phosphorus, total potassium, available potassium, and available phosphorus. Rhizosphere core species analysis showed that symbiotic Ascomycota dominated the rhizosphere soil fungi, and the bacterial community was composed mainly of Proteobacteria. There was a positive correlation between most genera of bacteria and fungi. This study proved that in the bionic cultivation of Tuber himalayense-Corylus heterophylla, the growth of mycorrhizal seedlings can be promoted by adjusting the pH to weakly alkaline and enhancing the advantages of Plectosphaerella in the soil flora, without adding other nutrients, which provides a theoretical basis for the establishment of truffle plantations, soil improvement and ecosystem stability.

Clostridioides difficile infection (CDI), is the most common healthcare problem primarily involving the colon of individuals who's gut microbiota has been disrupted. Proteobacteria (officially updated and recognized as Pseudomonadota), a minor gut-associated microbial community within a healthy host, could serve as a metric for CDI. However, the alterations of specific members of Proteobacteria in the context of CDI are not thoroughly understood. Based on the summary data of microbiome from 7,738 participants in the Dutch cohort, linkage disequilibrium score regression (LDSC) was used to explore the causal effect of 207 gut microbiome on CDI. Secondly, we performed a Mendelian randomization analysis to investigate the causal relationship between 31 microbiota taxa affiliated with Proteobacteria and CDI. Finally, three significant taxa (p < 0.05, OR > 1) were utilized to conduct the mediation analysis of 1,400 metabolites based on a two-step Mendelian randomization study (two-step MR). The inverse-variance weighted method was conducted as a primary analysis to estimate the causal effect, and the robustness of the results was tested via sensitivity analysis using multiple methods. Bivariate LDSC analysis identified a strong correlation between four populations affiliated with Proteobacteria (Pasteurellaceae, Haemophilus, Pasteurellales and Haemophilus parainfluenzae) and CDI. In two-step MR, Burkholderiales order exerted detrimental effects on CDI by decreasing the levels of 3-hydroxylaurate (OR 0.896; 95%CI, 0.803-0.998; p = 0.047), indicating that metabolite did act as mediator between gut microbiota and CDI. We conducted a study to assess the relations between genetically predicted gut microbiota and metabolite levels with CDI. These results highlight the potential of targeting Burkholderiales and 3-hydroxylaurate as a new antimicrobial strategy against CDI.

The Qinghai-Tibetan Plateau (QTP) provides a home to diverse flora and fauna, and its ecosystems are unique worldwide. The study focused on the bharal, an endemic species found in the QTP and adjacent regions. We applied viral metagenomics technology to extract samples from the feces of 10 wild bharal. Viral nucleic acids were isolated, enriched, and sequenced from these samples, revealing the presence of a novel strain of Astroviridae virus. Phylogenetic analysis and sequence comparison identified this virus as part of the Mamastro-virus, forming a cluster with other Mamastrovirus species. Recombination analysis confirmed a multiple recombination event, suggesting that the new strain may be a potential recombinant. Additionally, nearly complete genome sequences of viruses belonging to the family Circoviridae were characterized, and a phylogenetic tree was constructed based on genotyping and predicted amino acid sequence analysis of the rep protein. Overall, this study helps us better understand the viral communities in the gut microbiome of the rare bharal. Moreover, the new recombinant discovered in this study will provide insights into the origin, genetic diversity, and evolution of bharal from the QTP and play a crucial role in future research on its presence in the intestinal ecology of sheep.