Polish Journal of Microbiology最新文献

Leaf-associated microbiota is vital in plant-environment interactions and is the basis for micro-ecological regulation. However, there are no studies on the direct differences in microbial community composition between disease-susceptible and healthy walnut leaves. This study collected five samples of healthy and infected leaves (all leaves with abnormal spots were considered diseased leaves) from May to October 2018. Differences in fungal diversity (Chao1 index, Shannon index, and Simpson index) and community structure were observed by sequencing and analyzing diseased and healthy leaf microbial communities by Illumina HiSeq sequencing technology. The main fungal phyla of walnut leaf-associated were Ascomycota, Basidiomycota, and Glomeromycota. Diversity indices (Shannon and Chao1 index values) of healthy leaves differed significantly in the late stages of disease onset. The results showed that the fungal species that differed considerably between the healthy and infected groups differed, and the fungal species that differed significantly between the healthy and infected groups changed with the development of the leaf disease. Critical control time points were determined by analyzing the population dynamics of pathogenic fungi. Leaf-associated microorganisms are abundant and diverse, and fungal identification and diversity studies are helpful for developing more appropriate walnut management strategies.

Daptomycin is a cyclolipopeptide antibiotic produced by Streptomyces roseosporus. It is widely used to treat drug-resistant bacterial infections; however, daptomycin yield in wild strains is very low. To improve the daptomycin production by the strain BNCC 342432, a modified method of ribosome engineering with superposition of streptomycin resistance was adopted in this study. The highest-yield mutant strain SR-2620 was obtained by increasing streptomycin resistance of BNCC 342432, and achieved daptomycin production of 38.5 mg/l in shake-flask fermentation, 1.79-fold higher than the parent strain and its heredity stability was stable. The morphological characteristics of the two strains were significantly different, and the 440^th base G of the rpsL gene in the mutant strain was deleted, which resulted in a frameshift mutation. Our results demonstrate that gradually increasing strain resistance to streptomycin was an effective breeding method to improve daptomycin yield in S. roseosporus.

Research on the susceptibility of the spores of anaerobic bacteria such as Clostridium sporogenes or Clostridioides difficile is vital for assessing the sporicidal activity of disinfectants. The diverse susceptibility of anaerobic bacteria spores may lead to different disinfection parameters being determined by laboratories that prepare spore suspensions to test sporicidal effectiveness. The tests were performed using the suspension method according to PN-EN 13704:2018-09. In order to assess the susceptibility of the C. sporogenes spores, the criterion established for the C. difficile ribotype 027 spores was used in accordance with PN‑EN 17126:2019-01. The susceptibility of the C. sporogenes spores to glutardialdehyde corresponded to the susceptibility ranges established for the C. difficile ribotype 027 spores. The C. sporogenes spore suspension was susceptible to low concentrations of peracetic acid (0.01%). A disinfectant containing peracetic acid as the active substance showed high sporicidal activity at a low concentration (1%), a short contact time (15 minutes), and a high organic load (3.0 g/l bovine albumin + 3.0 ml/l sheep erythrocytes), as compared to a disinfectant with glutardialdehyde, which was sporicidal at a higher concentration (2.5%), at a longer contact time (60 minutes) and lower organic conditions (3.0 g/l bovine albumin). There is a need to define the minimum susceptibility criteria for the C. sporogenes spores to the reference substances most often found in disinfectants with sporicidal activity. Excessive susceptibility of the C. sporogenes spores to reference substances may result in low-performance parameters of disinfection products with sporicidal activity and lead to ineffective disinfection in practice.

The frequency of opportunistic fungal infections in critically ill patients whose intensive care unit stays are prolonged due to coronavirus disease 2019 (COVID-19) is higher than in the period before COVID-19. We planned this study to improve the management of Candida infections by defining the Candida species, the etiology of infections caused by Candida species, and the antifungal susceptibility of the species. This retrospective study included patients older than 18 hospitalized in the intensive care unit (ICU) with a definitive diagnosis of COVID-19 for seven months (from March 2021 to September 2021). All study data that we recorded in a standard study form were analyzed with TURCOSA (Turcosa Analytics Ltd. Co., Turkey, www.turcosa.com.tr) statistical software. The patients were evaluated in four groups as group 1 (candidemia patients, n = 78), group 2 (candiduria patients, n = 189), group 3 (control patients, n = 57), and group 4 (patients with candidemia in urine cultures taken before Candida was detected in blood culture, n = 42). Candida species were identified using both conventional and VITEK® 2 (BioMérieux, France) methods. The antifungal susceptibility of fungi was determined using the E test method. Of the 5,583 COVID-19 patients followed during the study period, 78 developed candidemia, and 189 developed candiduria. The incidence of candidemia (per 1,000 admissions) was determined to be 1.6. As a result of statistical analysis, we found that Candida albicans was the dominant strain in candidemia and candiduria, and there was no antifungal resistance except for naturally resistant strains. Candida strains grown in blood and urine were the same in 40 of 42 patients. Mortality was 69.2% for group 1, 60.4% for group 2, and 57.8% for group 3. Antifungals were used in 34 (43.5%) patients from group 1, and 95 (50.2%) from group 2. In the candidemia group without antifungal use, mortality was quite high (77.2%). Antifungal use reduced mortality in the group 2 (p < 0.05). Length of ICU stays, comorbidity, broad-spectrum antibiotics, and corticosteroids are independent risk factors for candidemia in critically ill COVID-19 patients. Our study contributes to the knowledge of risk factors for developing COVID-19-related candida infections. The effect of candiduria on the development of candidemia in critically ill COVID-19 patients should be supported by new studies.

Nutrient stimulation is considered effective for improving biogenic coalbed methane production potential. However, our knowledge of the microbial assembly process for profuse and rare microbial communities in coals under nutrient stimulation is still limited. This study collected 16S rRNA gene data from 59 microbial communities in coals for a meta-analysis. Among these communities, 116 genera were identified as profuse taxa, and the remaining 1,637 genera were identified as rare taxa. Nutrient stimulation increased the Chao1 richness of profuse and rare genera and changed the compositions of profuse and rare genera based on nonmetric multidimensional scaling with Bray-Curtis dissimilarities. In addition, many profuse and rare genera belonging to Proteobacteria and Acidobacteria were reduced, whereas those belonging to Euryarchaeota and Firmicutes were increased under nutrient stimulation. Concomitantly, the microbial co-occurrence relationship network was also altered by nutrient addition, and many rare genera mainly belonging to Firmicutes, Bacteroides, and Euryarchaeota also comprised the key microorganisms. In addition, the compositions of most of the profuse and rare genera in communities were driven by stochastic processes, and nutrient stimulation increased the relative contribution of dispersal limitation for both profuse and rare microbial community assemblages and that of variable selection for rare microbial community assemblages. In summary, this study strengthened our knowledge regarding the mechanistic responses of coal microbial diversity and community composition to nutrient stimulation, which are of great importance for understanding the microbial ecology of coals and the sustainability of methane production stimulated by nutrients.

Lactic acid bacteria are used in various types of probiotic products. Due to the constantly growing probiotics market, new strains with pro-health properties are sought. The present study compared 39 strains of Lactobacillus, Lacticaseibacillus, and Lactiplantibacillus, isolated from probiotic products and healthy people. The current research aimed to search for new, potentially probiotic strains. For this purpose the relationship between Lactobacillaceae strains was carried out; moreover, the basic properties of probiotic microorganisms, such as survival at low pH and bile salt environment, antibiotic susceptibility, aggregation and antagonism were estimated. The properties of these isolates were also compared with the properties of probiotic strains from the ATCC collection. In comparing the genetic relationship (PFGE method) between the tested isolates, it was observed that some of them show a high degree of similarity. All tested strains tolerated an environment with a pH value of 3.0, and the addition of 0.3% bile salt; showed auto-aggregation properties and displayed antagonism against pathogenic microorganisms. In the present study, the bacteria were susceptible to tetracycline, chloramphenicol and ampicillin; the resistance to vancomycin depended on the bacteria type. All the properties were strain-depended. Most of the tested strains had properties comparable to the reference strains. Three L. acidophilus strains isolated from cervical swabs seem to be promising candidates for probiotic strains.

This study aims to investigate trends in bloodstream infections and their antimicrobial susceptibility profiles over 12 years in our hospital. This retrospective study was carried out in the Bursa Uludag University Hospital, Turkey, during 2008-2019. Blood cultures from patients were performed using BACTEC System. Isolates were identified with Phoenix System until 2018 and "matrix-assisted laser desorption ionization time-of-flight mass spectrometry" (MALDI-TOF MS) in 2019. Antibiotic susceptibility testing was performed with Phoenix System. Patient data came from the BD EpiCenter™ data management system. Escherichia coli was found to be the most common Gram-negative (11.6%), and coagulase-negative staphylococci were the most common Gram-positive (10.1%) monomicrobial growth. Overall, there was a significant increase in rates of extended-spectrum β-lactamase positive E. coli (p = 0.014) and Klebsiella pneumonia (p < 0.001), carbapenem-resistant E. coli (p < 0.001), and K. pneumoniae (p < 0.001) and colistin-resistant K. pneumoniae (p < 0.001) and Acinetobacter baumannii (p < 0.001) over 12 years. Carbapenem and colistin resistance has increased dramatically in recent years. We believe that regular monitoring of the distribution of pathogens and antibiotic susceptibility profiles, especially in intensive care units, can contribute to evidence for the increase in resistant microorganisms and help prevent their spread with antimicrobial stewardship and infection control policies.

Phage P2 was isolated from failed fermentation broth carried out by Lactiplantibacillus plantarum IMAU10120. A previous study in our laboratory showed that this phage belonged to the Siphoviridae family. In this study, this phage's genomic characteristics were analyzed using whole-genome sequencing. It was revealed that phage P2 was 77.9 kb in length and had 39.28% G + C content. Its genome included 96 coding sequences (CDS) and two tRNA genes involved in the function of the structure, DNA replication, packaging, and regulation. Phage P2 had higher host specificity; many tested strains were not infected. Cell wall adsorption experiments showed that the adsorption receptor component of phage P2 might be a part of the cell wall peptidoglycan. This research might enrich the knowledge about genomic information of lactobacillus phages and provide some primary data to establish phage control measures.

In the present study, a comparative genome analysis of the novel alkaliphilic actinobacterial Nesterenkonia haasae with other members of the genus Nesterenkonia was performed. The genome size of Nesterenkonia members ranged from 2,188,008 to 3,676,111 bp. N. haasae and Nesterenkonia members of the present study encode the essential glycolysis and pentose phosphate pathway genes. In addition, some Nesterenkonia members encode the crucial genes for Entner-Doudoroff pathways. Some Nesterenkonia members possess the genes responsible for sulfate/thiosulfate transport system permease protein/ ATP-binding protein and conversion of sulfate to sulfite. Nesterenkonia members also encode the genes for assimilatory nitrate reduction, nitrite reductase, and the urea cycle. All Nesterenkonia members have the genes to overcome environmental stress and produce secondary metabolites. The present study helps to understand N. haasae and Nesterenkonia members' environmental adaptation and niches specificity based on their specific metabolic properties. Further, based on genome analysis, we propose reclassifying Nesterenkonia jeotgali as a later heterotypic synonym of Nesterenkonia sandarakina.

This study aims to evaluate associations between the immunochromatographic rapid test technique and Trichomonas vaginalis (TV) infection in patients with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) in Taiwan. All patients received post-prostate massage urine (VB3) Trichomonas rapid tests. The demographic characteristics and urogenital symptoms of CP/CPPS were recorded. Routine urinalysis of VB3 was also performed, and laboratory examination results of semen were recorded if available. A total of 29 patients with TV infection and 109 without TV infection were enrolled, which reflected that the prevalence in patients with TV infection was approximately 21%. Patients with TV infection displayed a significantly higher frequency of suprapubic/lower abdominal pain (p = 0.034), semen leukocyte > 5/high-power field (HPF) (p = 0.020), and an inflammatory type (category IIIA) (p = 0.005) than patients without TV infection. A higher prevalence of TV infection was found in patients with category IIIA (47.37%). No significant difference was found in the symptom duration and other clinical symptoms. In conclusion, the high prevalence of TV infection was revealed in CP/CPPS patients using the VB3 rapid Trichomonas test, especially in CP/CPPS patients with category IIIA. Thus, rapid TV testing might be vital for CP/CPPS patients in the hospital.