International Journal of Microbiology最新文献

Background: Real-time polymerase chain reaction (PCR), the gold standard for viral diagnostics in children, is a sensitive but resource-intensive method. Viral antigen tests are cheaper and more rapid but have lower sensitivity. The clinical relevance of PCR positivity has been questioned because of its high sensitivity and detection in asymptomatic individuals. Thus, we hypothesized that antigen test positivity might be more indicative of active infection than PCR positivity. The aim of this study was to evaluate the antigen test mariPOC Respi test for the detection of 10 respiratory viruses versus PCR in relation to viral load, days of illness, and immunological viral response.

Methods: Children 1-59 months old with lower respiratory infections were prospectively enrolled at the emergency department, Sachs' Children and Youth Hospital, Stockholm, Sweden, between 2017 and 2019. Nasopharyngeal samples were collected from all cases (n = 314). The sensitivity and specificity of the mariPOC Respi test were assessed in children with and without an immunological viral response (defined as a blood myxovirus resistance Protein A level > 430 μg/L), using PCR as the reference standard.

Results: The highest sensitivity for mariPOC Respi test was attained for respiratory syncytial virus (68%; 95% confidence interval: 63-73). Restricting the analysis to cases with a viral immunological response did not alter the results considerably.

Conclusion: These findings do not support the idea that mariPOC Respi test positivity to a higher degree than PCR correlates with clinical relevance, as indicated by an immunological viral response. The role of antigen tests in current clinical practice requires further discussion, particularly in the post-pandemic era.

Trial registration: ClinicalTrials.gov identifier: NCT03233516.

Cheka is a grain- and vegetable-based traditionally fermented beverage usually consumed in southwest Ethiopia, mainly in Konso and Derashe. Conventionally, it is made by spontaneous fermentation and therefore mostly relies on the actions of autochthonous microorganisms. Due to the lack of scientifically documented information on the microbiology of the Cheka fermentation process, we undertook this study to explore the microbial profiles and physicochemical properties involved in Cheka fermentation. Cheka is traditionally prepared in the laboratory using aseptic procedures with locally sourced ingredients from Arba Minch. The physicochemical properties and dominant and spoilage organisms at various stages of fermentation and in the final products were analyzed. The pH reduced from 4.10 to 2.88, while the titratable acidity changed from 0.06% to 1.60% lactic acid during 0 to 48 h of fermentation. Protein content increased from 1.57 ± 0.04 to 3.62 ± 0.09 and from 1.67 ± 0.08 to 3.91 ± 0.06 at 0 h and 48 h for Cheka and Madhota. A significant increase in carbohydrate content was observed in Cheka and Madhota from 21.14 ± 1.95 to 51.51 ± 3.00 g/100 g and from 12.11 ± 1.95 to 51.58 ± 2.95 g/100 g, respectively. The analysis of microbial counts in Cheka showed that the total viable count (TVC) increased from 8.72 to 9.4 log during 0-48 h of fermentation. Yeast and mold counts increased from 6.71 to 8.80 log (CFU/mL). Clostridium was removed within 48 h of fermentation, and Enterobacteriaceae showed a significant (p < 0.05) reduction from 4.90 to 1.77 ± 0.20 and from 4.60 ± 0.30 to 1.34 log (CFU/mL) in both Cheka and Madhota products. The alcohol content of Cheka increased from 3.00% to 16.00% (v/v) between 0 and 48 h of fermentation. The findings of this study provide a comprehensive understanding of the relationship between physicochemical parameters and the microbial characteristics of Cheka during fermentation. This understanding will aid in ensuring the safe production and enhancing the quality of Cheka and similar products in the future.

Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a significant global public health concern, including in Iraq. This study investigated the epidemiology, molecular characteristics, and rifampicin resistance-associated mutations of pulmonary TB in Sulaymaniyah, Iraq, from May 2024 to May 2025. A total of 77 confirmed pulmonary TB cases were identified, yielding an incidence rate of 9.09 per 100,000 inhabitants. This rate is notably lower than those reported in other Iraqi cities and may reflect a regional, and possibly national, decline in TB burden. Contrary to global trends, females comprised the majority of cases (n = 47, 61%). The highest prevalence of TB was observed among individuals aged ≥ 60 years, which may be attributed to immunosenescence and waning protection from the BCG vaccine. Monthly case distribution indicated seasonal variation, peaking between October and March. Molecular genotyping of 50 clinical samples revealed predominantly non-Beijing strains (98%), with the first molecular evidence of Beijing lineage in Iraq, indicating potential cross-border transmission. Analysis of the rifampicin resistance-determining region (RRDR) of the rpoB gene in 22 samples revealed no resistance-associated mutations, but detected several synonymous and novel nonsynonymous mutations outside the canonical RRDR. These genetic variations may represent early evolutionary adaptations without current resistance implications. Limitations in surveillance and diagnostic capacity may contribute to underreporting and obscure the true TB burden. This study highlights the evolving molecular epidemiology of TB in Sulaymaniyah, emphasizing the importance of ongoing molecular surveillance to inform public health strategies and control efforts.

Brucellosis is an endemic zoonotic disease in Africa and Tunisia, severely affecting both human and animal health, particularly ruminants. In livestock, brucellosis causes reproductive failure, including abortions, leading to substantial economic losses. Despite surveillance and vaccination efforts in Tunisia, brucellosis remains widespread. This study is aimed at assessing the presence of Brucella infection in aborted animals (sheep, goats, and cattle) using an IS711-based real-time PCR assay, determining the circulating species (Brucella melitensis and Brucella abortus) by differential qPCR, and identifying the most suitable sample type for detection between 2020 and 2022. Samples including vaginal swabs, blood, placenta, and fetal organs (liver, spleen, stomach, and cotyledons) were collected from farms selected based on abortion reports from farm owners. A total of 272 samples were analyzed, of which 24.26% tested positive for Brucella spp., with 25.71% in sheep, 13.33% in goats, and 8.33% in cattle. The detection rate of Brucella spp. was estimated at 24% (60/250) in aborted females and 27.27% (6/22) in aborted fetal materials. Vaginal swabs exhibited a notable positivity rate of 31.13%, 28.57% in organs and 5.71% in blood. B. melitensis and B. abortus were detected in 46.96% and 19.69% of positive samples, respectively. Interestingly, one sample showed a coinfection with both species; however, neither B. abortus nor B. melitensis was detected in 21 positive samples. This study highlights the presence of Brucella spp. in aborted ruminants and the circulation of B. melitensis and B. abortus, underlining the importance of molecular tools for the reliable diagnosis of brucellosis, and their usefulness in mitigating the spread of this infection on farms by applying appropriate control measures.

Burn wounds are debilitating injuries that contribute significantly to global morbidity and mortality. The disruption of skin integrity elevates the risk of infection, which can impede healing and potentially lead to sepsis. Furthermore, antibiotic resistance, primarily driven by biofilm formation, poses a major challenge to effective treatment. This study is aimed at evaluating the potential of positively charged carbon dots (CDs) in inhibiting biofilm formation, with possible applications in wound care. Specifically, carbon nanodots (CDs-NH₂) were tested in vitro against both planktonic cells and biofilms formed by a range of pathogens, including the Gram-positive bacterium Staphylococcus aureus, the Gram-negative bacterium Escherichia coli, the yeast Candida albicans, and the mold Aspergillus brasiliensis. Additionally, the activity of CDs-NH₂ was assessed against polymicrobial biofilms composed of S. aureus and C. albicans. The in vivo efficacy of CDs-NH₂ was evaluated using the Galleria mellonella burn wound infection model for both monomicrobial and polymicrobial infections. The ability of CDs-NH₂ to penetrate fungal cells was demonstrated by fluorescence microscopy analysis. Biomass quantification showed that CDs-NH₂ reduced biofilm formation by over 50% for C. albicans, E. coli, and A. brasiliensis, as well as for C. albicans-S. aureus cocultures, at concentrations below 62.5 μg/mL. The in vivo studies further confirmed the antimicrobial activity of CDs-NH₂ against all tested strains in burn wound infections. Strategies that target biofilm-forming microorganisms at wound sites may enhance infection control and promote wound healing.

Treatment of Escherichia coli infections has become increasingly challenging due to the emergence of multidrug-resistant mechanisms within the bacterial genome. Integrons play an essential role in spreading antibiotic resistance. This study is aimed at detecting the prevalence of Class 1, 2, and 3 integrons among E. coli associated with urinary tract infections (UTIs). A total of 90 E. coli strains were isolated from UTI samples and tested for antibiotic susceptibility using phenotypic methods. Biofilm formation was conducted using the microtiter plate method. Conventional PCR was used to detect the integrase genes. Overall, 48.9% of E. coli isolates (44/90) were MDR, and 58.9% (53/90) were resistant to ampicillin. A total of 60% (54/90) of E. coli isolates were biofilm producers. PCR results showed that 22.2% (20/90), 6.7% (6/90), and 3.3% (3/90) of E. coli isolates were positive for Class 1, Class 2, and both classes of integrons, respectively. However, Class 3 integron was not detected in all E. coli isolates. A significant correlation was observed between the MDR and Class 1 integron (p < 0.05). There is no statistical significance between the presence of integrons and biofilm formation among E. coli isolates. Our findings revealed that the presence of Class 1 integron among E. coli isolates was associated with antibiotic resistance.

Introduction: Klebsiella oxytoca causes antibiotic-associated hemorrhagic colitis due to the production of the enterotoxins tilimycin and tilivalline. These toxins are synthesized by enzymes encoded in the aroX and NRPS operons, which are expressed divergently. This study investigated how the nucleoid-associated proteins Fis and IHF regulate these operons and influence the production of enterotoxins.

Methods: We used reverse transcription quantitative PCR (RT-qPCR) to assess the role of Fis and IHF in the transcription of the aroX and NRPS operons. Electrophoretic mobility shift assays (EMSAs) were used to examine the binding of Fis and IHF to the regulatory region. Additionally, Caco-2 viability assays were performed using cells infected with WT, mutant, and complemented strains.

Results: RT-qPCR demonstrated that deletions of fis or ihfA/ihfB significantly reduced operon expression. EMSA confirmed that Fis and IHF bind specifically to the regulatory region between the aroX and NRPS operons. Viability assays in Caco-2 epithelial cells indicated increased host cell survival when exposed to the deletion mutants. Genetic complementation restored both transcription levels and cytotoxicity.

Conclusions: Fis and IHF are positive regulators of the aroX and NRPS operons, enhancing the production of tilimycin and tilivalline. These findings highlight the potential of targeting Fis and IHF for therapeutic intervention in antibiotic-associated hemorrhagic colitis.

The SARS-CoV-2 RNA load in different specimens has been analyzed to evaluate its correlation with disease outcomes and other factors. However, conflicting results have emerged due to variations in study design. This study examines the impact of viral load in stool and nasopharyngeal/oropharyngeal (NP) specimens on the clinical outcomes of hospitalized patients with severe COVID-19. Forty-six intensive care unit (ICU) patients with COVID-19 were enrolled between September 2020 and March 2021. NP swab and stool samples were collected at admission and at clinical outcome, and viral load was quantified using RT-qPCR. All patients had positive NP RNA at admission, with 41 (89.1%) also testing positive in stool samples. At the time of clinical outcome, 67.4% of NP samples and 45.7% of stool samples remained positive. Patients without gastrointestinal symptoms had a higher stool viral load at admission. Additionally, a greater NP viral load at admission was associated with unfavorable outcomes, whereas patients with diarrhea exhibited a more rapid decline in NP viral load. These preliminary findings suggest that diarrhea is associated with faster NP viral load reduction. Furthermore, viral load clearance was more efficient in stool samples than in respiratory specimens. These results highlight the relationship between viral load and COVID-19 severity.

Introduction: The World Health Organization (WHO) recommends the administration of booster doses after completing primary vaccination. Yet, recommendations are largely based on a small set of vaccines, with little information about vaccine mixes used in low and middle-income countries. We aimed to estimate the titers of anti-protein S (RBD) IgG antibodies and neutralization in Mexican adults with a complete vaccination scheme without a booster or with one of five different booster types (heterologous or homologous) to assess immunogenic response.

Materials and methods: We included data from 2953 adults aged 18 years and older, representing 49.1 million Mexicans, from the National Health and Nutrition Survey (ENSANUT) 2022. We included five primary schemes: BNT162b2, AZD1222, Ad5-nCoV, Gam-COVID-Vac, and CoronaVac. A booster dose was defined as an additional dose beyond the primary scheme and classified as homologous or heterologous based on three vaccine platforms: mRNA, viral vector, and inactivated virus. For each primary scheme, we estimated marginal means of anti-protein S geometric mean titers (GMTs) with 95% CI in each group (no booster, heterologous booster, or homologous booster) adjusted for age, time since the last dose, and prior natural infection using anti-protein N antibodies seropositivity as a proxy using a multivariable linear regression. Then, we estimated the percentage of neutralizing antibodies for the original SARS-CoV-2 strain.

Results: We observed that the highest anti-protein S GMTs were in the group that received a heterologous booster with BNT162b2, AZD1222, Ad5-nCoV, or CoronaVac; the group without a booster showed the lowest GMTs. All groups in the primary schemes had 90% or more inhibition for the original SARS-CoV-2 strain, except in the AZD1222 and Ad5-nCoV groups without a booster.

Conclusions: Boosters increased GMTs for all people, independently of their primary vaccine scheme. Yet, our findings suggest that a heterologous booster produced higher titers against SARS-CoV-2 protein S. Efforts should be made to reach people who received AZD1222 and Ad5-nCoV as their primary scheme and did not get boosted, as neutralization in those groups was particularly low.

Paracoccidioidomycosis is a systemic fungal disease caused by Paracoccidioides spp., predominantly affecting populations in Latin America, with Brazil reporting the highest number of cases. The infection is associated with severe pulmonary and systemic manifestations. Previous studies have highlighted the role of fungal proteases in adhesion, invasion, and the modulation of host immune responses, implicating them as key virulence factors. Our group previously demonstrated that Paracoccidioides restrepiensis secretes proteases that activate protease-activated receptors (PAR-1 and PAR-2) in human lung epithelial cells, stimulating the secretion of proinflammatory cytokines, including IL-6 and IL-8. We hypothesized that P. restrepiensis secretes proteases that are capable of degrading key host cytokines, such as IL-6, thereby contributing to modulate the host immune response during infection. This study is aimed at identifying and characterizing proteases secreted by P. restrepiensis that degrade human IL-6. Proteases secreted by P. restrepiensis were isolated using a p-aminomethylbenzamidine (pABA)-Sepharose affinity column. Protease-containing fractions were incubated with recombinant human IL-6 and further analyzed by Western blot to evaluate their ability to degrade this cytokine. Fractions were submitted to liquid chromatography and mass spectrometry to characterize the proteome content, focusing on the identification of fungal proteases. The hydrolysis of IL-6 in the presence of different protease inhibitors was also analyzed to confirm the specific activity of the fungal proteases. Enzymatic assays revealed proteases that hydrolyze human IL-6, suggesting a mechanism by which P. restrepiensis modulates the host immune response. In addition, mass spectrometry analysis confirmed the presence of a serine protease in the protease activity-containing fractions. These findings indicate that Paracoccidioides proteases may modulate host immune response by degrading key cytokines involved in inflammation and host defense.