International Journal of Microbiology最新文献

Background: Candida albicans complex species are the main cause of candidiasis. Objectives: The purpose of this study was to report the prevalence and genetic diversity of C. albicans complex using hyphal wall protein 1 (HWP1) gene size polymorphism, as well as the susceptibility patterns to fluconazole and voriconazole. Methods: A total of 170 yeast isolates were obtained from vulvovaginal samples, and phenotypic and proteomic identification was performed. Results: Most clinical isolates were C. albicans complex (n = 153) followed by C. glabrata (n = 13), C. parapsilosis complex (n = 2), and Pichia kudriavzevii (n = 2). Among C. albicans complexes, all isolates were C. albicans sensu stricto and 2.61% and 4.58% were resistant to fluconazole and voriconazole, respectively. Conclusions: The presence of different alleles was confirmed, heterozygosity was more common than homozygosity (71.03% vs. 28.97%), and some isolates showed a homozygosis pattern not previously described. Despite these genetic diversities, no specific genotype was linked to azole resistance.

Enterococcus faecalis is a commensal and opportunistic pathogen increasingly recognized for its antimicrobial resistance (AMR) and zoonotic potential. This study employs whole-genome sequencing (WGS) to characterize E. faecalis isolates from retail meat samples, focusing on antimicrobial resistance genes (ARGs), virulence determinants, mobile genetic elements, and phylogenomic relationships. Fifty raw meat samples, including chicken (n = 18), beef (n = 17), and turkey (n = 15), were collected from retail markets in Akungba-Akoko, Nigeria. Confirmed isolates underwent antimicrobial susceptibility testing and WGS-based genomic analysis. Ten E. faecalis isolates were recovered, predominantly from chicken. All exhibited resistance to clindamycin, erythromycin, and tetracycline. Dominant AMR genes included aac(6⁣')-aph(2⁣^″), ant(6)-Ia, lsa(A), erm(B), tet(M), and tet(L). Plasmid replicons rep9c and repUS43 were associated with sequence types ST477 and ST16, respectively. MGEs such as IS3, IS6, IS256, and IS1380 colocalized with resistance and virulence genes. Phylogenomic analysis revealed two major lineages (ST477 and ST16) and indicated geographic clustering across African isolates. The co-occurrence of multidrug resistance, virulence factors, and MGEs in foodborne E. faecalis poses a public health concern due to the risk of horizontal gene transfer and zoonotic spread. These findings support the need for strengthened genomic surveillance and AMR control strategies in food systems, particularly within low- and middle-income countries.

Research investigating the microbial community of an ecosystem or animal can involve a range of methodologies, including sequencing technology, bioinformatic software and taxonomy database. Researchers may utilise short-read sequencing on Illumina MiSeq or long-read sequencing on platforms like Oxford Nanopore to obtain different research outcomes, for example, enhanced identification of microbes at species or strain level with Nanopore. However, replicability across these techniques is not well studied, while the technique used to process reads into microbial taxa may also result in different taxonomy assignments. In this study, we analyse an existing, real-world dataset which had low genus-level identification with Illumina sequencing and analysis with the SILVA database and compare sequencing with Nanopore on the same samples. We pair this with multiple bioinformatic approaches and taxonomy databases for each sequencing technique to compare phylum- and genus-level assignments and use mock communities to identify which combination of sequencing technique, bioinformatic approach and taxonomy database provides the most accurate taxonomy. We found that Nanopore reads processed with either utilised bioinformatic approach or taxonomy database provided higher accuracy in the assignment of a mock community than any technique combination with Illumina. We also found that the Top 10 genera assigned to a real-world database were substantially different across technique combinations and varied more by taxonomy database than either bioinformatic approach or sequencing technology.

Some members of the lactic acid bacteria (LAB) have been used as probiotics. Ethiopian honey wine, Tej, may be a useful source of potential probiotic bacteria. However, LABs from this source have not yet been evaluated for their probiotic properties. This study was conducted to evaluate the in vitro probiotic properties of LAB isolated from Ethiopian honey wine, Tej. For this purpose, 30 samples were collected from Southwest Ethiopia. LAB isolates were first tested for their antimicrobial activity and those with this property were evaluated for probiotic properties, such as tolerance to acid, salt, and bile, adherence properties, anticholesterol activity, antioxidant activity, and antibiotic susceptibility. The antibacterial activity of the LAB isolates against test organisms was assessed by the agar well diffusion method. Acid, salt, and bile tolerance were evaluated by the plate count method. Adhesion properties were assessed by the determination of bacterial hydrophobicity to the nonpolar solvent p-xylene. Anticholesterol was determined by measuring the remaining cholesterol in the spent broth. The antioxidant capacity was assessed by the 1,1-diphenyl-2-picrylhydrazyl free radical-scavenging capacity, and the antibiotic susceptibility of isolates was tested by the disk diffusion method. A total of 143 LABs were isolated from Tej samples. The LAB count was ranged between 7.4 and 6.5 log cfu/mL. Of the 143 LAB isolates, 37 exhibited different levels of antimicrobial activity. Eight of these were identified to species level by 16S ribosomal genes sequence analysis. The greatest inhibition was against Shigella boydii ATCC 25931 with 19 ± 4.2 mm, and the least inhibitory activity was against Escherichia coli ATTC 25922 and Staphylococcus aureus ATTC 25913 with 8.0 ± 1.4. All except two isolates survived at pH 2 and pH 3 (18.4%-89.6%). Then, 37 isolates survived in more than 50% bile and 54%-67% adhesion capacity. The cholesterol-lowering and 1,1-diphenyl-2-picrylhydrazyl free radical-scavenging capacities ranged from 8% to 54% and 13% to 33%, respectively. Most isolates were susceptible to antibiotics, except for one isolate that resisted all tested antibiotics. This study shows that many LABs isolated from Ethiopian honey wine, Tej have probiotic properties and they can be considered as probiotic candidates. We recommend evaluation of in vivo probiotic properties of the LAB isolates to provide strong supporting evidence.

Introduction: Bacterial infection is a considerable problem in hospitals. Thus, this study was executed to appraise the rampancy of bacterial infections, antimicrobial susceptibility patterns, and molecular characterization of isolates among patients in Bafgh Hospital in Yazd, Iran, in 2020. Methods: In the current study, we surveyed 103 isolates of 400 clinical specimens from early March 2020 to September 2020 in Bafgh Hospital. We assessed phenotypic traits and antibiotic resistance with standard microbiological methods. Phenotypic methods were also performed to identify extended-spectrum beta-lactamases (ESBLs) in Gram-negative bacilli, inducible clindamycin resistance, and methicillin resistance in Staphylococcus according to CLSI guidelines. Molecular identification of isolates was done by conventional PCR 16S rRNA gene sequencing. Furthermore, we investigated the prevalence of resistant genes including bla _TEM, bla _PER-2, bla _CTX-M, bla _SHV, and bla _VEB-1 in Gram-negative bacteria and the mecA gene in staphylococcal species. Results: From 400 different clinical specimens, 103 isolates of Gram-positive and Gram-negative bacteria were isolated. Based on phenotypic and molecular methods, most common isolates were Escherichia coli (53 isolates), followed by Klebsiella spp. (18 isolates), and Staphylococcus aureus (16 isolates). The highest resistance was found in Gram-positive bacteria to erythromycin (66.67%) and penicillin (55.56%), while considering Gram-negative bacteria, the most resistant was cefixime (49.41%) and trimethoprim-sulfamethoxazole (47.05%). In addition, out of 16 S. aureus isolates, 62.5% and 17.65% were resistant to methicillin and clindamycin, respectively. Among 83 Gram-negative isolates, 22.89% were ESBL-positive. The prevalence of bla _SHV, bla _PER2, bla _TEM, bla _CTX-M, and bla _VEB-1 genes was 78.31%, 59.03%, 40.96%, 30.12%, and 0%, respectively. Conclusions: The outbreak of bacterial infections is relatively high in hospitals. Recognizing risk agents for bacterial infections and restricting the administration of multidrug-resistant antibiotics is a substantial measure that must be taken to prevent patient mortality.

Background: Surgical site infections (SSIs) remain a critical challenge globally and are aggravated by rising antimicrobial resistance (AMR). Here, we evaluated the bacterial profile, AMR patterns, and ESβL characterization of isolates from patients diagnosed with SSI after trauma orthopedic surgery. Methods: This prospective study was carried out at Tamale Teaching Hospital from September 2023 to May 2024. Patients were asked to provide demographic data. Samples were also collected from patients suspected of SSI and cultured for bacterial isolation, identification, and AMR characterization. Results: In all, 210 patients were recruited for this study, and 14 (6.7%) out of 19 suspected cases developed SSI. Of 19 specimens, 14 (73.68%) were culture-positive, yielding 22 isolates. Monomicrobial growth were 7 (50.0%) and polymicrobial growth 7 (50.0%). Among the isolates, 3 (13.64%) were Gram-positive and 19 (86.36%) were Gram-negative bacilli. Pseudomonas aeruginosa (5, 22.73%) were the most common isolates, followed by Klebsiella spp. (4, 18.18%). ESβL-positive isolates were 3 (23.08%). PCR confirmed the expression of CTXM and SHV genes by two Klebsiella spp. and the CTXM gene by Proteus vulgaris. Conclusion: Gram-negative bacteria, particularly Pseudomonas aeruginosa, were the dominant isolates from surgical sites after trauma orthopedic surgery. Among the Gram-positives, Staphylococcus aureus was dominant. Among the Enterobacterales isolates, ESBL production was detected in three cases (23.08%), with two Klebsiella spp. harboring CTXM and SHV resistance genes, and CTXM in one Proteus vulgaris. The current study has revealed varied resistant patterns of AMR, with CTXM and SHV as common ESβL genes among the isolates. The clinical identification of CTX-M and SHV genes could guide clinicians to consider alternative treatments to optimize therapeutic outcomes and limit the spread of resistant pathogens.

Knowledge about the diversity and distribution of microorganisms in natural environments is essential for understanding the dominant microbial groups and predicting their ecological functions. This study is aimed at describing the bacteriome diversity in soils associated with bromeliads in the Brazilian Pantanal region, utilizing genomic approaches. We analyzed the 16S rRNA gene from soil environmental DNA (eDNA) samples linked to Bromelia balansae and Deuterocohnia meziana (Bromeliaceae), which inhabit ironstone outcrops in the Pantanal. The analysis revealed Ktedonobacteraceae as the most abundant bacterial group, showing a mean relative abundance of 22.8% ± 15.5% in B. balansae and 33.5% ± 18.4% in D. meziana soils. Other highly abundant families were Chthoniobacteraceae and Pyrinomonadaceae, each exceeding 14.5% mean abundance. Despite the similarities in bacteriome composition between the bromeliads, beta-diversity analysis revealed phylogenetic distinctions across localities. The São João and Vale do Paraíso Farms, which experience the highest human impact from livestock farming, showed considerable differences, with 25 and 13 exclusive taxa, respectively. The environmental stresses of ironstone outcrops, such as high insolation and thermal variation, likely favor specific taxa adapted to these conditions. Understanding the bacteriome diversity in these unique habitats is crucial for promoting sustainable use and conserving the Pantanal's biodiversity.

Deep sequencing technologies can be used to evaluate pathogens in environmental samples. The objective of this study was to use this technology to evaluate Sargassum samples that were characterized by different stranding times, one classified as short-term stranded (STS) and another classified as long-term stranded (LTS) Sargassum. Nine replicates of the STS Sargassum showed a range in Shannon diversity between 3.04 and 3.38, whereas 11 replicates of LTS showed a range between 1.17 and 1.22. Nonmetric multidimensional scaling analysis showed distinct differences between STS and LTS by about 0.5 coordinate units, while variations within replicates ranged by 0.1 coordinate units. Comparison between the two Sargassum samples showed a greater abundance of Vibrio species in STS Sargassum when compared to LTS Sargassum, with major pathogenic forms observed for Vibrio alginolyticus (11%), Vibrio parahaemolyticus (1.5%), and Vibrio vulnificus (0.29%). Additional known human pathogens were observed, including Listeria monocytogenes, Legionella pneumophila, and Staphylococcus aureus, as well as the presence of gut commensals and fecal coliforms. Overall results show that deep sequencing analysis of these environmental samples was reproducible. Given the abundance of pathogenic bacteria, more research is needed to evaluate the risk of disease transmission as Sargassum strands and decomposes on coastal beaches.

Prokaryotic organisms rely on a limited array of metabolites for survival, which varies according to their natural environment. For example, soil-borne bacteria produce diverse metabolites, such as antibiotics, to thrive in their competitive surroundings, inhibiting the growth of nearby competing bacteria. The structural diversity of these compounds offers great analytical challenges, since there is no universal acquisition setting that can be applied to achieve their comprehensive coverage. Therefore, the use of a single experimental setup inevitably hinders the comprehensive metabolite coverage, which would affect the outputs. To address this, we propose employing a design of experiment (DoE) approach through the central composite design (CCD) to enhance the metabolite detection and broaden the coverage of the data-dependent acquisition (DDA) mode of the UHPLC-qTOF-MS technique. Our study reveals that altering collision energy significantly enhances metabolite coverage compared to adjusting the DDA threshold of detection. Furthermore, the ability of global natural product social (GNPS)-based molecular network models to annotate metabolites is greatly influenced by data acquisition settings, particularly affecting MS² data. Interestingly, molecular networks constructed from averaged spectral data obtained through randomly selected DDA settings outperform those generated using customized settings through DoE modeling. This study demonstrates that in untargeted LC-MS metabolomics, both collision energy and intensity threshold independently enhance metabolite coverage in untargeted metabolomics. However, their combined use results in even greater coverage. Consequently, we recommend adopting group-based optimization over single-point optimization for more comprehensive metabolite coverage and in-depth exploration. However, caution should be taken in order to balance between robust data and redundancy.

The Brazilian savannah, Cerrado, a Brazilian phytophysiognomy, is an entire biome that contains as well as other Brazilian ecosystems, a vast biodiversity of microorganisms associated with native plants. Plant species of the Cerrado have attracted attention due to the still limited knowledge regarding their associated microbiota and the possible applications of these microorganisms. Considering that wildflowers are rich reservoirs of yeast diversity, the present study isolated 58 yeast strains from flowers of Qualea grandiflora from two areas of Cerrado sensu stricto in northern Minas Gerais, Brazil. The isolates were evaluated for producing extracellular enzymes in cellulase, amylase, xylanase, protease, tannase, and pectinase tests. We used the YNB agar diffusion method (Difco) supplemented with specific substrates for each enzyme. The strains were identified by analyzing the sequences of the D1/D2 region of the large subunit (26S) rRNA gene and compared to the sequences deposited on GenBank. Fifty-eight strains were isolated, and 14 genera were identified, of which 18 species were yeasts, two species were yeast-like fungi, and three were yeast-like strains to which it was not yet possible to assign the species they belonged to. Among the identified species, the phylum Ascomycota predominated; exceptions were the isolates of the yeast Papiliotrema laurentii and the fungus Anthracocystis heteropogonicola, both belonging to the phylum Basidiomycota. In the enzymatic tests, 44.8% of the strains tested presented an enzymatic profile in solid medium, being capable of producing at least one of the enzymes studied, with the species Coniochaeta rhopalochaeta showing the greatest cellulolytic activity.