Hasil untuk "Microbiology"

V. Gürtler, V. Stanisich

A. Zehnder

G. Muyzer

G. Drusano

R. Amann, B. Fuchs

Padma Shrestha, Bijay Bajracharya, Deena Shrestha et al.

Abstract Background Antimicrobial resistance (AMR) has emerged as a critical global health challenge and is currently addressed through a “One Health” approach that investigates its occurrence in humans, animals, and the environment, as well as the transmission pathways linking these reservoirs. In commercial poultry farms, antibiotics are routinely used to treat bacterial infections that are economically significant as well as to promote weight gain. However, data on AMR in Staphylococcus aureus (S. aureus) of poultry origin remain scarce in Nepal. Antimicrobial resistance in S aureus, particularly the emergence of methicillin-resistant (MRSA) and vancomycin-resistant (VRSA) strains in both humans and poultry, poses a significant public health threat worldwide requiring immediate attention. This study aimed to detect the prevalence of multidrug-resistant S. aureus and the distribution of tetA, tetB, ermA, ermB, and ermC genes among S. aureus from litter and soil of poultry farms of Kathmandu Valley. Methods Litter and soil samples were processed using serial dilution and spread plate techniques to isolate S. aureus. Antibiotic susceptibility testing was assessed by a modified Kirby-Bauer disc diffusion method. DNA was extracted from the isolates, and polymerase chain reaction (PCR) was performed to detect resistance genes (tetA, tetB, ermA, ermB, and ermC). Results A total of 32 S. aureus were obtained, comprising 20 isolates from litter and 12 isolates from the soil of poultry farms. A total of 59.3% (19/32) of S. aureus isolates were multidrug-resistant (MDR); from which 65% (13/20) were from litter and 50% (6/12) from soil. A Chi-square test revealed no statistically significant association between MDR isolates and the source (litter vs. soil) (p > 0.05). The antibiotic susceptibility results showed high degree of resistance towards erythromycin (68.8%) followed by tetracycline (59.4%). In PCR analysis, the majority of isolates (96.8%) showed the tetA gene, while none of the isolates showed the tetB gene. Only 15 and 11 isolates out of 32 showed the ermB (46.8%) and ermC (34.3%) genes, respectively, while all isolates tested negative for ermA. Additionally, 5 S. aureus isolates carried both ermB and ermC genes. Chi-square analysis showed no significant association between AMR gene occurrence and the source of S. aureus isolates. Conclusion The high incidence of multidrug-resistant S. aureus and detection of antibiotic resistance genes in poultry litter and soil highlight a significant risk of transmission to farm workers, butchers, and consumers, as well as possible environmental contamination through manure application. These findings underscore the urgent need for strict antimicrobial stewardship, improved biosecurity, and policy measures to prevent the spread of resistant S. aureus from poultry farms to the wider community.

Eric Lyimo, Neema B. Kulaya, Lembris Njotto et al.

Abstract Background Malaria, which affects over half of the world’s population, is controlled through clinical interventions and vector control strategies. However, these efforts are threatened by resistance to anti-malarial drugs and insecticides, as well as affected by environmental, ecological, and climatic changes. This study examined changes in malaria prevalence and related factors based on data from 18 cross-sectional surveys conducted in two villages in northeastern Tanzania. Methods From 2003 to 2021, annual cross-sectional malariometric surveys were conducted in two study villages, Mkokola (lowland) and Kwamasimba (highland), samples collected to determine Plasmodium falciparum infection and human exposure to malaria vector Anopheles. Pearson's chi-squared test was used for comparing proportions, logistic and linear regressions test were used analyse associations. Generalized Estimating Equations (GEE) was used to analyse the relationship between malaria prevalence and climatic variables. Results Malaria prevalence in Kwamasimba and Mkokola dropped from ~ 25% and ~ 80% to 0% and 1%, respectively, between 2003 and 2011, reaching 0% in both villages by 2014. This decline was associated with increased bed net use and reduced exposure to Anopheles bites. However, between 2018 and 2021, prevalence resurged, with Kwamasimba reaching 2003–2004 levels despite high bed net use. Between 2003 and 2021 there was an increasing trend in average monthly maximum temperatures (R2 = 0.1253 and 0.2005), and precipitation (R2 = 0.125 and 0.110) as well as minimum relative humidity (R2 = 0.141 and 0.1162) in Kwamasimba and Mkokola villages, respectively, while maximum relative humidity slightly decreased. Furthermore, during 2003–2011, malaria prevalence was positively associated with temperature, maximum temperature, and relative humidity, while precipitation showed a negative association (Estimate:− 0.0005, p < 0.001). Between 2012–2021, all climatic factors, including temperature (Estimate: 0.0256, p < 0.001), maximum temperature (Estimate: 0.0121, p < 0.001), relative humidity (Estimate: 0.00829, p < 0.001), and precipitation (Estimate: 0.000105, p < 0.001), showed positive associations. Conclusion From 2003 to 2014, malaria prevalence declined in two Tanzanian villages but resurged after 2018, particularly in highland Kwamasimba. Most likely, vector dynamics affected by changing climatic conditions drove this resurgence, emphasizing the need for adaptive, climate-informed malaria control strategies.

Priya Koundal, Sunita Manhas, Shakeel Ahmed Mohammed et al.

Aspergillus fumigatus is a pathogenic fungus that causes fatal infectious human disease known as aspergillosis. Fungus A. fumigatus is capable of causing infections in various body parts of humans, but it primarily infects the lungs and causes pulmonary infections known as allergic bronchopulmonary aspergillosis (ABPA). Subsequent dissemination of A. fumigatus into the deeper body parts may also contribute to the development of invasive infections in other vital organs. Therefore, the complexity and spectrum of aspergillosis majorly include allergic and invasive infections. To dominate the human body and escape the human immune system, A. fumigatus produces a number of virulence factors as well as pathogenicity determinants to establish disease. These pathogenic moieties of A. fumigatus includes allergens, toxins, hydrophobins, integrins, mannans/galactomannans, lectins, adherins and many other proteins with unknown functions. Combinatorially, these components make A. fumigatus a successful pathogen for humans, although, additionally the A. fumigatus pathogenicity has also been influenced by the metabolism of nitrogen/amino acids, folate synthesis, metal ions, cell wall biosynthesis as well as protein degradation mechanisms. A number of tools and techniques are being used to provide an accurate and timely laboratory diagnosis of aspergillosis. Such comprehensive tools include microscopic examination, culture, and antigen detection methods, serological assays and molecular techniques (DNA probes and molecular typing), G-test and D-mannitol detection and others. However, identifying fungi and assessing antifungal susceptibility by detecting galactomannans and Aspergillus-DNA are also useful. However, certain limitations exist in determining the circulating biomarkers that can be addressed via upcoming approaches such as lateral flow devices and next-generation sequencing. According to current understandings, the biology and clinical impact of A. fumigatus have been complex; therefore, updated information about virulence mechanisms, clinical manifestations, and diagnosis intricacies is essentially required for effective and better management and treatment of Aspergillus-induced infections.

Yan Cheng, Qi Cheng, Rong Zhang et al.

Abstract Background Klebsiella pneumoniae (KP) is the second most prevalent Gram-negative bacterium causing bloodstream infections (BSIs). In recent years, the management of BSIs caused by KP has become increasingly complex due to the emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP). Although numerous studies have explored the risk factors for the development of CRKP-BSIs, the mortality of patients with KP-BSIs, and the molecular epidemiological characteristics of CRKP, the variability in data across different populations, countries, and hospitals has led to inconsistent conclusions. In this single-center retrospective observational study, we utilized logistic regression analyses to identify independent risk factors for CRKP-BSIs and factors associated with mortality in KP-BSI patients. Furthermore, a risk factor-based prediction model was developed. CRKP isolates underwent whole-genome sequencing (WGS), followed by an evaluation of microbiological characteristics, including antimicrobial resistance and virulence genes, as well as epidemiological characteristics and phylogenetic analysis. Results Our study included a total of 134 patients with KP-BSIs, comprising 50 individuals infected with CRKP and 84 with carbapenem-susceptible Klebsiella pneumoniae (CSKP). The independent risk factors for CRKP-BSIs were identified as gastric catheterization (OR = 9.143; CI = 1.357–61.618; P = 0.023), prior ICU hospitalization (OR = 4.642; CI = 1.312–16.422; P = 0.017), and detection of CRKP in non-blood sites (OR = 8.112; CI = 2.130-30.894; P = 0.002). Multivariate analysis revealed that microbiologic eradication after 6 days (OR = 3.569; CI = 1.119–11.387; P = 0.032), high Pitt bacteremia score (OR = 1.609; CI = 1.226–2.111; P = 0.001), and inappropriate empirical treatment after BSIs (OR = 6.756; CI = 1.922–23.753; P = 0.003) were independent risk factors for the 28-day mortality in KP-BSIs. The prediction model confirmed that microbiologic eradication after 6.5 days and a Pitt bacteremia score of 4.5 or higher were significant predictors of the 28-day mortality. Bioinformatics analysis identified ST11 as the predominant CRKP sequence type, with bla KPC−2 as the most prevalent gene variant. CRKP stains carried multiple plasmid-mediated resistance genes along with some virulence genes. Phylogenetic analysis indicated the presence of nosocomial transmission of ST11 CRKP within the ICU. Conclusions The analysis of risk factors for developing CRKP-BSIs and the association between KP-BSIs and 28-day mortality, along with the development of a risk factor-based prediction model and the characterization of CRKP strains, enhances clinicians’ understanding of the pathogens responsible for BSIs. This understanding may help in the timely administration of antibiotic therapy for patients with suspected KP-BSIs, potentially improving outcomes.

Mahsa Rostami, Abozar Ghorbani, Samira Shahbazi

Gamma radiation-induced mutations in microorganisms can enhance their properties for the biological control of plant diseases. Mutant strains of Bacillus subtilis were found to have improved antifungal properties against Aspergillus flavus and increased production of biosurfactants and biofilms. Furthermore, combining gamma radiation with antagonists was more effective in controlling Penicillium expansum postharvest than either treatment alone. A major focus of this research was on Trichoderma species, which have shown an enhanced ability to control plant diseases through increased production of antifungal metabolites such as hydrolytic enzymes, antibiotics, and total phenols. The mechanism by which gamma radiation alters the genotype of microorganisms is the destruction of double-stranded and single-stranded DNA, resulting in changes in the genome or nucleic acid molecule, altering the antagonistic properties of microorganisms. Sensitivity to radiation is determined by the size of an organism's chromosomes, and the effect on microorganisms is primarily based on DNA or RNA disruption. Molecular analysis of gamma radiation mutants has been used to understand changes in genome composition, including downregulated genes related to secondary metabolism, cytochrome P450 s, carbohydrate-active enzymes, peptidases, and hydrophobins. Gamma radiation thus offers a promising method to induce beneficial genetic changes in microorganisms, enhancing their efficacy in the biological control of plant diseases.

Vladimir K. Chebotar, Maria S. Gancheva, Elena P. Chizhevskaya et al.

Some strains of <i>Bacillus vallismortis</i> have been reported to be efficient biocontrol agents against tomato pathogens. The aim of our study was to assess the biocontrol ability of the endophytic strain BL01 <i>Bacillus vallismortis</i> through in vitro and field trials, as well as to verify its plant colonization ability and analyze the bacterial genome in order to find genes responsible for the biocontrol activity. We demonstrated in a gnotobiotic system and by confocal laser microscopy that the endophytic strain BL01 was able to colonize the endosphere and rhizosphere of tomato, winter wheat and oilseed rape. In vitro experiments demonstrated the inhibition activity of BL01 against a wide range of phytopathogenic fungi and bacteria. BL01 showed biological efficacy in two-year field experiments with tomato plants against black bacterial spotting by 40–70.8% and against late blight by 47.1% and increased tomato harvest by 24.9% or 10.9 tons per hectare compared to the control. Genome analysis revealed the presence of genes that are responsible for the synthesis of biologically active secondary metabolites, which could be responsible for the biocontrol action. Strain BL01 <i>B. vallismortis</i> can be considered an effective biocontrol agent to control both fungal and bacterial diseases in tomato plants.

Marcelino Campos, Juan Carlos Galán, Mario Rodríguez-Domínguez et al.

ABSTRACTThe epidemiology of sexually transmitted infections (STIs) is complex due to the coexistence of various pathogens, the variety of transmission modes derived from sexual orientations and behaviors at different ages and genders, and sexual contact hotspots resulting in network transmission. There is also a growing proportion of recreational drug users engaged in high-risk sexual activities, as well as pharmacological self-protection routines fostering non-condom practices. The frequency of asymptomatic patients makes it difficult to develop a comprehensive approach to STI epidemiology. Modeling approaches are required to deal with such complexity. Membrane computing is a natural computing methodology for the virtual reproduction of epidemics under the influence of deterministic and stochastic events with an unprecedented level of granularity. The application of the LOIMOS program to STI epidemiology illustrates the possibility of using it to shape appropriate interventions. Under the conditions of our basic landscape, including sexual hotspots of individuals with various risk behaviors, an increase in condom use reduces STIs in a larger proportion of heterosexuals than in same-gender sexual contacts and is much more efficient for reducing Neisseria gonorrhoeae than Chlamydia and lymphogranuloma venereum infections. Amelioration from diagnostic STI screening could be instrumental in reducing N. gonorrhoeae infections, particularly in men having sex with men (MSM), and Chlamydia trachomatis infections in the heterosexual population; however, screening was less effective in decreasing lymphogranuloma venereum infections in MSM. The influence of STI epidemiology of sexual contacts between different age groups (<35 and ≥35 years) and in bisexual populations was also submitted for simulation.IMPORTANCEThe epidemiology of sexually transmitted infections (STIs) is complex and significantly influences sexual and reproductive health worldwide. Gender, age, sexual orientation, sexual behavior (including recreational drug use and physical and pharmacological protection practices), the structure of sexual contact networks, and the limited application or efficiency of diagnostic screening procedures create variable landscapes in different countries. Modeling techniques are required to deal with such complexity. We propose the use of a simulation technology based on membrane computing, mimicking in silico STI epidemics under various local conditions with an unprecedented level of detail. This approach allows us to evaluate the relative weight of the various epidemic drivers in various populations at risk and the possible outcomes of interventions in particular epidemiological landscapes.

Carmen Bracke, Cristina Miranda, Sandra González et al.

Background. Prophylactic vaccination has proven to be the most effective strategy to fight the COVID-19 pandemic. Methods. This was a prospective observational cohort study involving 30 predominantly antibody deficiency disorders (ADD)-afflicted adult patients on immunoglobulin replacement therapy vaccinated with three doses of the mRNA-1273 COVID-19 vaccine, and 10 healthy controls. Anti-RBD IgG antibodies were determined in plasma samples collected just before the first dose of mRNA-based COVID-19 vaccine and on weeks 4, 8, 24, and 28 following the first vaccination. Patients were categorized based on the levels of anti-RBD antibodies determined on w8 as non-, low-, and responders. Chi-square and Kruskal–Wallis tests were used to see if any variables correlated with humoral response levels. Any adverse effects of the mRNA-based vaccine were also noted. Results. The COVID-19 vaccine was safe and well-tolerated. The humoral response elicited at w8 after vaccination depended on the type of ADD, the type of immunoglobulin deficiency, the presence of granulomatous lymphocytic interstitial lung disease, recent use of immunosuppressive drugs, and the switched memory B cells counts. The third vaccine dose boosted humoral response in previous responders to second dose but seldom in non-responders. Conclusions: The humoral response of patients with predominant ADD depends mostly on the type of immunodeficiency and on the frequency of B and T cell populations.

Juan Carbonero-Pacheco, Jaime Moreno-García, Juan Moreno et al.

Flor yeast velum is a biofilm formed by certain yeast strains that distinguishes biologically aged wines such as Sherry wine from southern Spain from others. Although Saccharomyces cerevisiae is the most common species, 5.8 S-internal transcribed spacer (ITS) restriction fragment length polymorphism analyses have revealed the existence of non-Saccharomyces species. In order to uncover the flor microbiota diversity at a species level, we used ITS (internal transcribed spacer 1)-metabarcoding and matrix-assisted laser desorption/Ionization time of flight mass spectrometry techniques. Further, to enhance identification effectiveness, we performed an additional incubation stage in 1:1 wine:yeast extract peptone dextrose (YPD) before identification. Six species were identified: S. cerevisiae, Pichia manshurica, Pichia membranifaciens, Wickerhamomyces anomalus, Candida guillermondii, and Trichosporon asahii, two of which were discovered for the first time (C. guillermondii and Trichosporon ashaii) in Sherry wines. We analyzed wines where non-Saccharomyces yeasts were present or absent to see any potential link between the microbiota and the chemical profile. Only 2 significant volatile chemicals (out of 13 quantified), ethanol and ethyl lactate, and 2 enological parameters (out of 6 quantified), such as pH and titratable acidity, were found to differ in long-aged wines. Although results show a low impact where the non-Saccharomyces yeasts are present, these yeasts isolated from harsh environments (high ethanol and low nutrient availability) could have a potential industrial interest in fields such as food microbiology and biofuel production.

Jacqueline A. Labra-Muñoz, Arie de Reuver, Friso Koeleman et al.

We report on the fabrication of single-electron devices based on horse-spleen ferritin particles. At low temperatures the current vs. voltage characteristics are stable, enabling the acquisition of reproducible data that establishes the Coulomb blockade as the main transport mechanism through them. Excellent agreement between the experimental data and the Coulomb blockade theory is demonstrated. Single-electron charge transport in ferritin, thus, establishes a route for further characterization of their, e.g., magnetic, properties down to the single-particle level, with prospects for electronic and medical applications.

Ovsyannikov N.V., Bilevich O.A.

The novel coronavirus (COVID-19) pandemic announced by the World Health Organization in March 2020 assigned medical community to the new tasks that require immediate solutions. Recent studies have shown that invasive aspergillosis associated with COVID-19 often complicates a course of the disease and leads to death. This review aims to describe the diagnosis and therapy challenges due to COVID-19 associated invasive pulmonary aspergillosis.

Xiaonan Zhao, Zhengjie Liu, Yin Zhang et al.

The objective of this study was to evaluate the prevalence and characteristics of avian-origin mcr-1-harbouring Escherichia coli in Shandong Province, China. During 2017—2018, a total of 668 non-duplicate E. coli isolates were separately collected from 8eight large intensive poultry farms in Shandong Province. Antimicrobial susceptibility testing for 10 antimicrobial agents commonly used in farms was performed on all E. coli isolates by the agar dilution method; the mobile colistin resistance gene (mcr-1) gene was screened by PCR, and mcr-1 positive isolates were PCR-screened for antimicrobial resistance genes and typed by multi-locus sequence typing (MLST). Among the 668 E. coli, 102 (15.3%) harbored the mcr-1 gene; high antimicrobial resistance rates were observed for ampicillin (100/102, 98.0%), followed by amoxicillin (99/102, 97.1%) and florfenicol (97/102, 95.1%), and a low level of resistance was found for amoxicillin/clavulanic acid (24/102, 23.5%). Five ESBL genes were detected, and all isolates carried blaTEM (102/102, 100%), followed by blaCTX–M (90/102, 88.2%). Four PMQR genes were detected; aac(6)-Ib-cr (40/102, 39.2%) was the most commonly isolated PMQR gene, followed by qnrA (10/102, 9.8%). Thirty-eight different kinds of STs were identified, and the dominant ST was ST93 (19/102, 18.6%), followed by ST48 (9/102, 8.8%). In summary, E. coli from poultry in Shandong could be a reservoir for the mcr-1 gene, which could pose serious risks to human public health.

Mitsuo Ogura, Kazutoshi Shindo, Yu Kanesaki

Bacteria must survive harsh environmental fluctuations at times and have evolved several strategies. “Collective” behaviors have been identified due to recent progress in single-cell analysis. Since most bacteria exist as single cells, bacterial populations are often considered clonal. However, accumulated evidence suggests this is not the case. Gene expression and protein expression are often not homogeneous, resulting in phenotypic heterogeneity. In extreme cases, this leads to bistability, the existence of two stable states. In many cases, expression of key master regulators is bimodal via positive feedback loops causing bimodal expression of the target genes. We observed bimodal expression of metabolic genes for alternative carbon sources. Expression profiles of the frlBONMD-yurJ operon driven by the frlB promoter (PfrlB), which encodes degradation enzymes and a transporter for amino sugars including fructoselysine, were investigated using transcriptional lacZ and gfp, and translational fluorescence reporter mCherry fusions. Disruption effects of genes encoding CodY, FrlR, RNaseY, and nucleoid-associated protein YlxR, four known regulatory factors for PfrlB, were examined for expression of each fusion construct. Expression of PfrlB-gfp and PfrlB-mCherry, which were located at amyE and its original locus, respectively, was bimodal; and disruption of ylxR resulted in the disappearance of the clear bimodal expression pattern in flow cytometric analyses. This suggested a role for YlxR on the bimodal expression of PfrlB. The data indicated that YlxR acted on the bimodal expression of PfrlB through both transcription and translation. YlxR regulates many genes, including those related to translation, supporting the above notion. Depletion of RNaseY abolished heterogenous expression of transcriptional PfrlB-gfp but not bimodal expression of translational PfrlB-mCherry, suggesting the role of RNaseY in regulation of the operon through mRNA stability control and regulatory mechanism for PfrlB-mCherry at the translational level. Based on these results, we discuss the meaning and possible cause of bimodal PfrlB expression.

Liliana Simões-Silva, Sara Silva, Carla Santos-Araujo et al.

Peritonitis and exit-site infections are important complications in peritoneal dialysis (PD) patients that are occasionally caused by opportunistic fungi inhabiting distant body sites. In this study, the oral yeast colonization of PD patients and the antifungal susceptibility profile of the isolated yeasts were accessed and correlated with fungal infection episodes in the following 4 years. Saliva yeast colonization was accessed in 21 PD patients and 27 healthy controls by growth in CHROMagar-Candida® and 18S rRNA/ITS sequencing. PD patients presented a lower oral yeast prevalence when compared to controls, namely, Candida albicans. Other species were also isolated, Candida glabrata and Candida carpophila. The antifungal susceptibility profiles of these isolates revealed resistance to itraconazole, variable susceptibility to caspofungin, and higher MIC values of posaconazole compared to previous reports. The 4-year longitudinal evaluation of these patients revealed Candida parapsilosis and Candida zeylanoides as PD-related exit-site infectious agents, but no correlation was found with oral yeast colonization. This pilot study suggests that oral yeast colonization may represent a limited risk for fungal infection development in PD patients. Oral yeast isolates presented a variable antifungal susceptibility profile, which may suggest resistance to some second-line drugs, highlighting the importance of antifungal susceptibility assessment in the clinical practice.

Drosou Foteini, Yang Enoch, Marinea Marina et al.

Pulsed electric fields (PEF) is a non-thermal processing technology that uses instantaneous, pulses of high voltage for a short period in the range of milliseconds to microseconds; the application of high intensity electric field on toasted wood chips leads to a quick diffusion of extractable molecules. Currently most PEF studies, in the field of oenology, have been focusing on the application of PEF as a pretreatment of grape musts by examining the microbial inactivation and the enhancement of polyphenol extraction. In this study a post-treatment of wine is introduced as method to enhance the wood flavor in the wine with a green noninvasive technology. Major phenolic aldehydes that have been identified as the characteristic compounds of oak volatile compounds were selected as markers and were analyzed instrumentally to compare the influence of PEF processing to non-treated samples. PEF treated samples brought about higher concentrations of the examined oak compounds in the samples treated with PEF, which may explain the advantages of its application. The modulation of the intensity of the electric field and the period of pulses influenced the concentrations of the volatile phenols that were leached out. Differences found between the assayed treatments indicate that PEF application could be a potential practice for a rapid extraction of volatile compounds from oak.