Microorganisms最新文献

The atmospheric environment is formed under the influence of local and distant sources as a result of horizontal and vertical transport. In the present work, microbiological analysis of 604 samples of atmospheric aerosol collected in the period from September 2020 to September 2023 at four sites differing in anthropogenic load, located in Novosibirsk and the region, was carried out. Day and night aerosol samples were collected during 12 h every two weeks by filtration using Sartorius reinforced Teflon membranes, then sown on a set of nutrient media. The taxonomic affiliation of the isolated microbial isolates was determined based on phenotypic characteristics and analysis of 16S rRNA gene nucleotide sequences. Changes in the composition and concentration of culturable microorganisms depending on the season, time of day, and site of aerosol sampling were observed. In winter, lower fungi and bacteria of the genera Bacillus, Staphylococcus, Micrococcus dominated with an average concentration from zero to 12.5 CFU/m³ of aerosol. In the warm period, the concentration and diversity of cocci, spore-forming and non-spore-forming bacteria, actinomycetes, and fungi (up to 1970 CFU/m³), among which pathogenic microorganisms were found, increased sharply in aerosols. The use of 16S metabarcoding techniques has greatly expanded the range of aerosols' microbial diversity detectable.

Background: The aim of this study was to see if the CHA₂DS₂-VASc score (Cardiac failure or dysfunction, Hypertension, Age ≥ 75 [Doubled], Diabetes, Stroke [Doubled]-Vascular disease, Age 65-74 and Sex category [Female] score) could have potential clinical relevance in predicting the outcome of hospitalization time, need for ICU hospitalization, survival time, in-hospital mortality, and mortality at 3 and 6 months after discharge home.

Materials: A retrospective analysis of 2183 patients with COVID-19 hospitalized at the COVID-19 Centre of the University Hospital in Wrocław, Poland, between February 2020 and June 2021, was performed. All medical records were collected as part of the COronavirus in LOwer Silesia-the COLOS registry project. The CHA₂DS₂-VASc score was applied for all subjects, and the patients were observed from admission to hospital until the day of discharge or death. Further information on patient deaths was prospectively collected following the 90 and 180 days after admission. The new risk stratification derived from differences in survival curves and long-term follow-up of our patients was obtained. Primary outcomes measured included in-hospital mortality and 3-month and 6-month all-cause mortality, whereas secondary outcomes included termination of hospitalization from causes other than death (home discharges/transfer to another facility or deterioration/referral to rehabilitation) and non-fatal adverse events during hospitalization.

Results: It was shown that gender had no effect on mortality. Significantly shorter hospitalization time was observed in the group of patients with low CHA₂DS₂-VASc scores. Among secondary outcomes, CHA₂DS₂-VASc score revealed predictive value in both genders for cardiogenic (5.79% vs. 0.69%; p < 0.0001), stroke/TIA (0.48% vs. 9.92%; p < 0.0001), acute heart failure (0.97% vs. 18.18%; p < 0.0001), pneumonia (43% vs. 63.64%; p < 0.0001), and acute renal failure (7.04% vs. 23.97%; p < 0.0001). This study points at the usefulness of the CHA₂DS₂-VASc score in predicting the severity of the course of COVID-19.

Conclusions: Routine use of this scale in clinical practice may suggest the legitimacy of extending its application to the assessment of not only the risk of thromboembolic events in the COVID-19 cohort.

Clostridioides difficile infection (CDI) is generally treated with vancomycin, metronidazole or fidaxomicin, although fecal microbiota transplantation (FMT) represents a promising therapeutic option for antibiotic-resistant recurrent C. difficile infections (rCDIs) in adults. In pediatric cystic fibrosis (CF) patients, CDIs are generally asymptomatic and respond to treatment. Here, we present the case of an 8-year-old female, initially diagnosed as "CFTR-related metabolic syndrome/cystic fibrosis screen positive, inconclusive diagnosis" (CMRS/CFSPID), who then progressed to CF at 12 months. In the absence of CF-related symptoms, she presented multiple and disabling episodes of bloody diarrhoea with positive tests for C. difficile antigen and A/B toxin. After conventional treatments failed and several CDI relapses, FMT was proposed. Donor screening and GM donor-receiver matching identified her mother as a donor. Metataxonomy and targeted metabolomics provided, through a pre- and post-FMT time course, gut microbiota (GM) profiling to assess GM engraftment. At first, the GM map revealed severe dysbiosis, with a prevalence of Bacteroidetes and Proteobacteria (i.e., Klebsiella spp., Escherichia coli), a reduction in Firmicutes, a GM nearly entirely composed of Enterococcaceae (i.e., Enterococcus) and an almost complete depletion of Verrucomicrobia and Actinobacteria, mostly represented by Veillonella dispar. Post FMT, an increment in Bifidobacterium spp. and Collinsella spp. with a decrease in V. dispar restored intestinal eubiosis. Consistently, four weeks after FMT treatment, the child's gut symptoms cleared, without CDI recurrence.

Improved efficacy of probiotics can be achieved by using different strategies, including the optimization of production parameters. The impact of fermentation parameters on bacterial physiology is a frequently investigated topic, but what happens during the formulation, i.e., the step where the lyoprotectants are added prior to freeze-drying, is less studied. In addition to this, the focus of process optimization has often been yield and stability, while effects on bioactivity have received less attention. In this work, we investigated different metabolic activities of the probiotic strain Limosilactobacillus reuteri DSM 17938 during formulation with the freeze-drying protectant sucrose. We discovered that the strain consumed large quantities of the added sucrose and produced an exopolysaccharide (EPS). Using NMR, we discovered that the produced EPS was a glucan with α-1,4 and α-1,6 glycosidic bonds, but also that other metabolites were produced. The conversion of the lyoprotectant is hereafter designated lyoconversion. By also analyzing the samples with GCMS, additional potential bioactive compounds could be detected. Among these were tryptamine, a ligand for the aryl hydrocarbon receptor, and glycerol, a precursor for the antimicrobial compound reuterin (3-hydroxypropionaldehyde). To exemplify the bioactivity potential of lyoconversion, lyoconverted samples as well as purified EPS were tested in a model for immunomodulation. Both lyoconverted samples and purified EPS induced higher expression levels of IL-10 (2 times) and IL-6 (4-6 times) in peripheral blood mononuclear cells than non-converted control samples. We further found that the initial cultivation of DSM 17938 with sucrose as a sugar substrate, instead of glucose, improved the ability to convert sucrose in the lyoprotectant into EPS and other metabolites. Lyoconversion did not affect the viability of the bacteria but was detrimental to freeze-drying survival, an issue that needs to be addressed in the future. In conclusion, we show that the metabolic activities of the bacteria during the formulation step can be used as a tool to alter the activity of the bacteria and thereby potentially improve probiotic efficacy.

Capnocytophaga canimorsus is a gram-negative bacterium commonly found in the saliva of dogs and cats. Despite the frequency of animal bites, infection with Capnocytophaga species is rare, and severe infections are usually associated with underlying risk factors, such as alcohol use disorder, asplenia, or immunosuppression. We describe a case of a man who presented with a purpuric rash, lower extremity edema, and acute renal failure and was found to have tricuspid valve endocarditis and infection-associated glomerulonephritis due to C. canimorsus. Despite treatment with cefepime, the vegetation increased in size and valvular function worsened. He was readmitted with an inferior wall myocardial infarction, heart failure, and pulmonary embolism. He underwent an urgent tricuspid valve replacement with a bioprosthetic valve. A 16S ribosomal RNA amplicon sequencing performed on the resected valve tissue verified involvement of C. canimorsus. Post-operatively, he had several episodes of gastrointestinal hemorrhage requiring multiple endoscopic interventions and arterial embolization. The recurrent gastrointestinal hemorrhage combined with his severe functional decline ultimately led to his death. This patient had an uncommon presentation with leukocytoclastic vasculitis and infection-associated glomerulonephritis, which revealed an underlying diagnosis of infective endocarditis due to C. canimorsus, a rare gram-negative bacterial etiology of infective endocarditis.

Influenza A virus (IAV) causes highly contagious respiratory disease worldwide, so prevention and control of IAV is extremely important. However, overuse of neuraminidase inhibitor (NAI) drugs leads to drug resistance. To explore the up-to-date geographical distribution and evolution of drug-resistant mutations (DRMs) in the NA protein of IAV, 81,492 near full-length NA sequences downloaded from NCBI and GISAID databases, including 34,481 H1N1 and 46,622 H3N2, were processed and analyzed. Our results showed the annual number of NA sequences from 2011 to 2019 continuously increased. Meanwhile, almost 85% of sequences were from developed countries in North America, Europe and Asia. Clustering analysis demonstrated H3N2 varied more than H1N1. Notably, H3N2 exhibited a higher frequency of DRMs than H1N1, with prevailing DRMs mainly located at non-active sites within the NA protein. Phylogenetic analyses showed NA harboring DRMs collected in the same year and from the same location clustered together, which may be related to the local economic level, clinical monitoring of DRMs and research level. Consequently, it is imperative to enhance global surveillance targeting drug resistance in IAV infections which can mitigate the transmission of drug-resistant strains. In summary, our research provides valuable insights for clinical medication while establishing a robust scientific basis for IAV prevention and treatment strategies to improve overall efficacy.

Listeriosis is a dangerous zoonosis caused by bacteria of the genus Listeria, with Listeria monocytogenes (LM) being the most pathogenic species. Listeria monocytogenes has been detected in various animal species and in humans, and its ability to evolve from an environmental saprophyte to a powerful intracellular pathogen is driven by the invasion mechanisms and virulence factors that enable cell invasion, replication and cell-to-cell spread. Key regulatory systems, including positive regulatory factor A (PrfA) and the stress-responsive sigma factor σ^B, control the expression of virulence genes and facilitate invasion of host cells. Listeriosis poses a significant threat to cattle, sheep and goat herds, leading to abortions, septicemia and meningoencephalitis, and ruminants are important reservoirs for Listeria, facilitating transmission to humans. Other Listeria species such as Listeria ivanovii and Listeria innocua can also cause disease in ruminants. Resilience of LM in food processing environments makes it an important foodborne pathogen that is frequently transmitted through contaminated meat and dairy products, with contamination often occurring along the food production chain. In humans, listeriosis primarily affects immunocompromised individuals, pregnant women and the elderly and leads to severe conditions, such as meningitis, septicemia and spontaneous abortion. Possible treatment requires antibiotics that penetrate the blood-brain barrier. Despite the relatively low antimicrobial resistance, multidrug-resistant LM strains have been detected in animals, food and the environment. Controlling and monitoring the disease at the herd level, along with adopting a One Health approach, are crucial to protect human and animal health and to minimize the potential negative impacts on the environment.

Carbapenem-resistant Acinetobacter baumannii is one of the major problems among hospitalized patients. The presence of multiple virulence factors results in bacteria persistence in the hospital environment. It facilitates bacterial transmission between patients, causing various types of infections, mostly ventilator-associated pneumonia and wound and bloodstream infections. A. baumannii has a variable number of resistance mechanisms, but the most commonly produced are carbapenem-hydrolyzing class D β-lactamases (CHDLs). In our study, the presence of bla_OXA-23, bla_OXA-40 and bla_OXA-51 genes was investigated among 88 clinical isolates of A. baumannii, including 53 (60.2%) strains resistant to both carbapenems (meropenem and imipenem) and 35 (39.8%) strains susceptible to at least meropenem. Among these bacteria, all the isolates carried the bla_OXA-51 gene. The bla_OXA-23 and bla_OXA-40 genes were detected in two (5.7%) and three (8.6%) strains, respectively. Among the OXA-23 carbapenemase-producing A. baumannii strains (n = 55), insertion sequences (ISAba1) were detected upstream of the bla_OXA-23 gene in fifty-two (94.5%) carbapenem-resistant and two (3.6%) meropenem-susceptible isolates. A. baumannii clinical strains from Poland have a similar antimicrobial resistance profile as those worldwide, with the presence of ISAba1 among bla_OXA-23-positive isolates also being quite common. Carbapenem resistance among A. baumannii strains is associated with the presence of CHDLs, especially when insertion sequences are present.

The species of Purpureocillium are cosmopolitan and multitrophic fungi that can infect a wide range of invertebrate hosts. This study reports the mitogenome of P. atypicola, a specialized spider pathogenic fungus. The 112,465 bp mitogenome encoded genes typically found in fungal mitogenomes, and a total of 52 introns inserted into seven genes. A comparison with three other Purpureocillium species revealed significant differences in length and intron number, primarily due to intron variation; however, there was no dynamic variation in the introns of the cox1 gene within the same species of the Purpureocillium genus. Different mitochondrial protein-coding genes showed variable degrees of genetic differentiation among these species, but they were all under purifying selection. Additionally, frequent intron loss or gain events were detected to have occurred during the evolution of the Ophiocordycipitaceae mitogenomes, yet the gene arrangement remains conserved. A phylogenetic analysis of the combined mitochondrial gene set gave identical and well-supported tree topologies. The estimated age of the crown of Ophiocordycipitaceae and Purpureocillium were around the Early Cretaceous period (127 Mya) and Late Cretaceous period (83 Mya), respectively. The results of this study advance our understanding of the genomics, evolution, and taxonomy of this important fungal group.

Cystic fibrosis (CF) is a life-threatening genetic disease characterised by chronic lung infections sustained by opportunistic pathogens such as Pseudomonas aeruginosa. During the chronic long-lasting lung infections, P. aeruginosa adapts to the host environment. Hypermutability, mainly due to defects in the DNA repair system, resulting in an increased spontaneous mutation rate, represents a way to boost the rapid adaptation frequently encountered in CF P. aeruginosa isolates. We selected 609 isolates from 51 patients with CF chronically colonised by P. aeruginosa to study, by full-length genome sequencing, the longitudinal evolution of the bacterium. We recovered at least one hypermutable (mutator) isolate in 57% of patients. By combining genomic information and phenotypic analyses, we followed the evolutionary pathways of the P. aeruginosa mutator strains, identifying their contribution to multi-drug resistance and the emergence of new sub-lineages. By implementing patient clinical data, we observed that mutators preferentially follow a specific evolutionary trajectory in patients with a negative clinical outcome and that maintenance antibiotic polytherapy, based on alternating molecules, apparently reduces the occurrence of hypermutability. Finally, we draw attention to the possibility that modulator-induced changes in the pulmonary environment may be associated with the onset of hypermutability.