Jundishapur Journal of Microbiology
Volume:16 Issue: 11, Nov 2023

The coronavirus disease 2019 (COVID-19) poses a threat to the global economy and public health. Mutations in the spike protein of the virus can impact the functional characteristics and effectiveness of vaccines.

This study aimed to analyze mutations in three key regions of the spike protein, investigate clinical presentations, and assess protective immune levels in healthcare workers (HCWs) who had received full vaccine doses but were re-infected.

In this cross-sectional study, 49 breakthrough-infected HCWs were included from November 2021 to May 2022. After confirming COVID-19 reinfection, the SARS-CoV-2 genome was extracted using the ROJE extraction kit, and genetic variation analysis was performed through Sanger sequencing. Blood samples were collected with prior consent, and ELISA tests were performed to determine antibody levels. Clinical presentations were recorded, and independent t-tests revealed no significant gender-based differences in the C-terminal point mutation.

In this study, 75.5% (37/49) of the included HCWs were female (P-value < 0.05), and 25 were qualified for PCR and gene sequencing. Mutations were observed in 25, 10, and 1 sequence(s) of the C-terminal domain, N-terminal domain, and RBD regions of the S1 gene, respectively. The mutations had no significant correlation with the patient’s gender, age, or occupation, but they were significantly more prevalent in those with underlying diseases. 63.3% (31/49) of patients had high or very high IgG levels, and none had undetectable antibody levels at the time of reinfection. Loss of the sense of smell (69.4% - 34/49), sore throat (65.3% - 32/49), headache (59.2% - 29/49), and cough (57.1% - 28/49) were the most prevalent clinical manifestations (P > 0.05) in breakthrough-infected HCWs, aligning with the pattern of symptoms seen in the Omicron wave. However, the loss of the sense of taste showed significant results concerning clinical manifestation (P < 0.05). The examination of mutations revealed the presence of the Omicron variant in the majority of individuals. Point mutations in the C-terminal region did not significantly vary based on age, gender, or vaccine type. No significant difference was observed between vaccine types and clinical symptoms.

In conclusion, this study identified spike protein mutations in reinfections among vaccinated healthcare workers. While mutations were prevalent, no significant correlations were found with demographics or vaccine types. Symptoms resembled the Omicron variant, notably with the loss of the sense of taste as a significant marker. Detectable antibody levels post-reinfection suggest that vaccine-induced immunity remains robust. Continuous monitoring of virus variants is crucial for optimizing vaccination strategies in the face of evolving strains.

 Pseudomonas aeruginosa is one of the most important opportunistic pathogens causing hospital infections.

 This study aimed to investigate the abundance of integrons and the pattern of resistance to carbapenems (metallo-β-lactamases including Spm, Imp, and Vim) and its relationship with the presence of integrons classes I and II in P. aeruginosa isolates.

 This study was conducted on 73 samples of P. aeruginosa isolated from burn wounds of patients admitted to the burn center of Velayat Hospital, Rasht, Iran. To confirm the phenotype of P. aeruginosa, Gram staining and diagnostic biochemical tests, including oxidation-fermentation (OF), pigment production, citrate utilization, catalase activity, oxidase test, and growth at 42°C, were used. After identification and confirmation, molecular diagnosis was conducted to identify strains producing genes classes I and II using the polymerase chain reaction (PCR) method.

 In this research, the frequency of carbapenem resistance genes in clinical isolates of P. aeruginosa was found to be zero, 13.7%, and 21.9% for blaSpm, blaImp, and blaVim genes, respectively. Integrons of classes I and II were present in 53.4% of isolates of class I and 17.8% of isolates of class II. Also, 4.1% of the total integrin-positive isolates had both integron classes.

 There was a statistically significant relationship between class I integron and the blaImp gene. Importantly, the mechanisms of other integrons play a role in the development of resistance and the presence of these genes involved in this project.

It is known that the change in coagulation parameters has an effect on mortality and prognosis in COVID-19 patients. The SARS-CoV-2 virus has changed with mutations in the genome of the virus since the beginning of the pandemic, and the resulting variants have been recorded by the World Health Organization. With these variations, the clinical severity of the disease and laboratory parameters have also changed.

In this study, we examined the changes in D-dimer levels, fibrinogen levels, platelet count (PLT), and mean platelet volume (MPV) between SARS-CoV-2 Alpha (B.1.1.7), Beta (B.1.351) Delta (B.1.617.2), and Omicron (B.1.1.529) variants.

The study was conducted retrospectively on 28 195 adult patients with SARS-CoV-2 infection. At the time of application, data on age, gender, SARS-CoV-2 variant status, D-dimer levels (n = 7090), fibrinogen (n = 5709), PLT (n = 7066), and MPV (n = 8330) were collected. Patients were divided according to alpha, beta, delta, and omicron variants. The changes in variants were examined statistically.

The incidence of the delta variant in women was higher than the other variants, followed by alpha and omicron (P = 0.001). The Beta variant was detected at a higher rate in males. The ages of the cases with the Omicron variant were higher than the cases with Alpha, Beta, and Delta variants (P = 0.001, P = 0.001, P = 0.001, and P < 0.01, respectively). In laboratory parameters, D-dimer and fibrinogen levels were detected to be significantly higher in Delta and Omicron variants. PLT and MPV were determined to be lower in delta and omicron than in alpha and beta variants.

Examination of the changes in laboratory coagulation parameters according to variants shows that the tendency to clot increases from alpha to omicron.

Antifungal resistance is increasing, posing a challenge for treating candidiasis. Cold atmospheric plasma (CAP) is a potential alternative, but its association with traditional antifungals is poorly understood.

This study aims to evaluate the effects of dielectric barrier discharge (DBD) plasma on Candida albicans.

In this in vitro study, C. albicans strains were irradiated with DBD plasma for 5, 10, and 15 minutes, both with and without nystatin. The number of colonies was counted, and the MTT method assessed Candida’s survival. Data were analyzed with SPSS26.

This study showed that in both experimental groups, with and without nystatin, the lowest C. albicans cell viability was observed following a 10 minute DBD exposure within the groups subjected to plasma treatment (P < 0.001). The positive control group (nystatin without plasma exposure) exhibited a diminished count of viable cells in comparison to the group with 10 minute plasma irradiation without nystatin (P < 0.001). The 10 and 15 minute DBD plasma exposures, along with their positive control counterparts, demonstrated a statistically significant reduction in colony count compared to the 5 minute DBD exposure and the negative control groups (P < 0.001).

Nystatin was more effective than DBD plasma irradiation in reducing C. albicans cell viability. When used in combination, 10 minute DBD plasma irradiation with nystatin was more effective than 5 or 15 minute irradiation times in reducing the survival rate of C. albicans.

 β-lactamases (BLs) are the leading cause of antimicrobial resistance in gram-negative bacteria. Metallo-β-lactamases (MBL) play a critical role in hydrolyzing a wide range of β-lactam drugs, including carbapenems. Recent reports have highlighted an increase in Pseudomonas aeruginosa abundance during acute SARS-CoV-2 infections, potentially complicating viral treatment.

 This study aims to present the discovery of novel inhibitors targeting P. aeruginosa Verona integrin-encoded (VIM)-2 MBL using a combination of computational and experimental methods.

 A total of 61 953 natural compounds and captopril (used as a positive control) were screened as potential inhibitors. Additionally, the 3D structure of the enzyme was obtained from the Protein Data Bank (PDB). The most promising compounds were selected through molecular docking, and further analysis of conformational changes in the protein-inhibitor complex was conducted using the GROMACS molecular dynamics package. Enzyme assays were performed to validate the results obtained through molecular modeling.

 Two compounds, namely ZINC98363781 and indolebutyroyl aspartic acid (ZINC04090499), demonstrated strong inhibitory potential with docking energies of -14.1 and -12.7 kcal mol-1, respectively. Captopril exhibited a docking energy of -10.684 kcal mol-1. Molecular dynamics analysis indicated good stability and flexibility in the studied systems. According to the binding energies calculated by mechanics-Poisson Boltzmann surface area (MM-PBSA), captopril, ZINC98363781, and ZINC04090499 displayed binding energies of -29.39 ± 5.92 kcal mol-1, -79.74 ± 67.51 kcal mol-1, and -99.65 ± 26.52 kcal mol-1, respectively. Enzyme assays confirmed that the IC50 value of ZINC04090499 against VIM-2 MBL was 25 μM.

 Our findings suggest that ZINC04090499 is a promising inhibitor of VIM-2 MBL and warrant further investigation in laboratory studies.

Vibrio cholera is the primary culprit of the cholera epidemic, causing gastrointestinal diseases. Non-O1/O139 strains of V. cholera spread into food and drink, causing food poisoning. The present study aimed to investigate the identification ability of the VITEK Mass Spectrometer (VITEK MS) for V. cholera strains.

Firstly, we utilized VITEK MS and VITEK 2 Compact, in addition to the serum agglutination test and 16S rRNA gene sequencing, to identify two V. cholera strains. The VITEK MS was employed to identify two clinical strains of V. cholera, and their protein spectra were compared. The VITEK MS incorrectly identified one strain as Vibrio mimicus with a confidence level of 99.9%; nevertheless, another strain was correctly identified as V. cholera with a confidence level of 99.9%. VITEK 2 Compact identified both strains as V. cholera at a confidence level of 97.0%. Serological tests revealed that the V. cholera strains were neither in the O1 nor O139 group. The 16S rRNA sequencing results confirmed the strains as V. cholera. The protein profiles of V. cholera and V. mimicus were observed to be similar, leading to the inability of the mass spectrometer to distinguish between them.

Vibrio mimicus and V. cholera both belong to the Vibrio genus. The VITEK MS cannot completely differentiate between V. cholera and V. mimicus. For accurate identification, it is recommended to use biochemical serological tests by VITEK 2 Compact or serum.