Cq values as an indicator for COVID-19 outcomes: A study of the correlation between laboratory parameters.

OBJECTIVE: The ongoing outbreak of the respiratory disease coronavirus disease 2019 (COVID-19) is currently presenting a major global health threat. This pandemic is unprecedented in recent human history. The objective of this study was to examine the relationship between cycle quantitation (Cq) and laboratory parameters in COVID-19 patients, aiming to determine if Cq levels can provide valuable insights into the COVID-19 disease. METHODS: This study involved 234 participants who were divided into case and control groups. Real-time PCR tests were used to diagnose COVID-19 cases in the study participants. Blood tests, including complete blood count, C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), lactate dehydrogenase (LDH), D-dimer, IgG, and IgM, were also conducted. Statistical analysis was performed using SPSS 22 software. RESULTS: The findings showed that COVID-19-positive cases had significantly higher levels of the neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), D-dimer, ESR, CRP, and LDH compared to normal cases. Additionally, the case group had significantly lower lymphocyte and platelet counts. There was a statistically significant positive correlation between Cq levels and lymphocyte count (r = .124, p = .014). Conversely, there was a statistically significant inverse correlation between Cq levels and NLR (r = -.208, p = .017). Furthermore, the evaluation of hematological, inflammatory, and biochemical indexes in COVID-19 patients using the receiver-operating characteristics curve demonstrated statistically appropriate sensitivity and specificity. CONCLUSION: Our outcomes indicated a significant association between Cq levels and PLR, NLR, D-dimer, CRP, and ESR in COVID-19 patients. Consequently, including the report of laboratory parameters alongside Cq values offers a promising prognosis.

Characterization of carbapenem-resistant Escherichia coli and Klebsiella: a role for AmpC-producing isolates.

Aim: This study aimed to investigate the role of AmpC enzymes in carbapenem resistance among AmpC/extended-spectrum ß-lactamase (ESBL)-producing clinical isolates of Escherichia coli and Klebsiella spp. Methods: Fifty-six bacterial strains that were AmpC producers were examined. The antibiotic susceptibility test was performed by the disk diffusion and E-test. The prevalence of the plasmid carbapenemase was determined using PCR. Results: The resistance to meropenem in the AmpC+/ESBL+ group was 64%, higher than that reported for the AmpC-/ESBL+ group. Ten isolates of the carbapenem-resistant AmpC producers were negative for carbapenemase-encoding genes. Conclusion: Carbapenem resistance among AmpC-producing isolates with negative results for carbapenemase-encoding genes potentially demonstrates the role of AmpC enzymes among these isolates.

A Comparative Study on Visual Detection of Mycobacterium tuberculosis by Closed Tube Loop-Mediated Isothermal Amplification: Shedding Light on the Use of Eriochrome Black T.

Loop-mediated isothermal amplification is a promising candidate for the rapid detection of Mycobacterium tuberculosis. However, the high potential for carry-over contamination is the main obstacle to its routine use. Here, a closed tube LAMP was intended for the visual detection of Mtb to compare turbidimetric and two more favorable colorimetric methods using calcein and hydroxy naphthol blue (HNB). Additionally, a less studied dye (i.e., eriochrome black T (EBT)) was optimized in detail in the reaction for the first time. Mtb purified DNA and 30 clinical specimens were used to respectively determine the analytical and diagnostic sensitivities of each method. The turbidimetric method resulted in the best analytical sensitivity (100 fg DNA/reaction), diagnostic sensitivity and specificity (100%), and time-to-positivity of the test (15 min). However, this method is highly prone to subjective error in reading the results. Moreover, HNB-, calcein-, and EBT-LAMP could respectively detect 100 fg, 1 pg, and 1 pg DNA/reaction (the analytical sensitivities) in 30, 15, and 30 min, while the diagnostic sensitivity and specificity were respectively 93.3% and 100% for them all. Interestingly, EBT-LAMP showed the lowest potential for subjective error in reading the results. This report helps judiciously choose the most appropriate visual method, taking a step forward toward the field applicability of LAMP for the detection of Mtb, particularly in resource-limited settings.

Antibacterial activity of Mangifera indica seed extracts combined with common antibiotics against multidrug-resistant Pseudomonas aeruginosa and Acinetobacter baumannii isolates

In this project, we employed ethanolic (EMI) and aqueous (AMI) extracts of mango (Mangifera indica L., Anacardiaceae) fruit seeds as a modulator of antibiotic resistance against multidrug-resistant (MDR) Pseudomonas aeruginosa and Acinetobacter baumannii to evaluate natural compounds isolated from by-products or waste of edible plants. We also investigated the effect of these extracts alone and in combination with standard classes of antibiotics in the desired strains. M. indica seeds were processed and exploited using ethanol and water. The minimum inhibitory concentrations (MICs) of clinical isolates were examined against EMI and AMI extracts, followed by seven antibiotics of ceftazidime, ciprofloxacin, penicillin, amikacin, meropenem, ampicillin, and colistin. The checkerboard method evaluated the synergistic action between mango kernel extract (EMI) and seven antibiotics. EMI extract significantly revealed antimicrobial properties against MDR A. baumannii and P. aeruginosa with synergistic effects with the applied antibiotics. The considerable antibacterial efficacy of ethanolic extract of M. indica seeds can have great curative value as antibacterial drugs against infections caused by MDR P.aeruginosa and A. baumannii.

Allylphenols as a new class of human 15-lipoxygenase-1 inhibitors.

In this study, a series of mono- and diallylphenol derivative were designed, synthesized, and evaluated as potential human 15-lipoxygenase-1 (15-hLOX-1) inhibitors. Radical scavenging potency of the synthetic allylphenol derivatives was assessed and the results were in accordance with lipoxygenase (LOX) inhibition potency. It was found that the electronic natures of allyl moiety and para substituents play the main role in radical scavenging activity and subsequently LOX inhibition potency of the synthetic inhibitors. Among the synthetic compounds, 2,6-diallyl-4-(hexyloxy)phenol (42) and 2,6-diallyl-4-aminophenol (47) showed the best results for LOX inhibition (IC50 = 0.88 and 0.80 µM, respectively).

High prevalence of blaCMY AmpC beta-lactamase in ESBL co-producing Escherichia coli and Klebsiella spp. clinical isolates in the northeast of Iran.

OBJECTIVE: The production of ß-lactamase enzymes such as AmpC ß-lactamases and extended-spectrum ß-lactamases (ESBLs) is among the main mechanisms for resistance to expanded-spectrum cephalosporins. The present study was conducted to investigate the prevalence and molecular epidemiology of plasmid-mediated AmpC beta (ß)-lactamase in ESBL co-producing Escherichia coli (E. coli) and Klebsiella spp. (Klebsiella pneumoniae and Klebsiella oxytoca) clinical isolates in the northeast of Iran. METHODS: A total of 602 E. coli and Klebsiella spp. clinical isolates were collected from three hospitals in Mashhad (northeast of Iran). A combination disk test (CDT) was performed for the phenotypic detection of ESBLs. Screening for the detection of AmpC ß-lactamases was performed by a susceptibility test to a cefoxitin disc among ESBL producing isolates. A confirmatory test for AmpC ß-lactamases was performed using the Mast® D68C test. Identification of plasmid-mediated AmpC cluster genes was done by multiplex polymerase chain reaction (PCR). RESULTS: Among 336 ESBL-producing strains, 230 (68.4%) isolates were resistant to cefoxitin. Results of the Mast® D68C test showed that 30% (69/230) of cefoxitin-resistant isolates simultaneously exhibited ESBL and AmpC activity and 22% (51/230) of isolates probably showed multi-drug resistant (MDR) phenotype. Results of multiplex PCR among ESBL-positive isolates showed that, 16.7% (56/336) of isolates were positive for plasmid-borneampC cluster genes, and CMY (38%) was the most frequent genotype of plasmid mediated AmpC. CONCLUSION: Findings of the study revealed that an increase in the prevalence of ESBL and AmpC co-producer in E. coli and Klebsiella spp. strains may become an important public health issue. Therefore, there is a vital need for surveillance of spread of these clinical isolates.

Designing and Construction Pcdna3.1 Vector Encoding Cfp10 Gene of Mycobacterium tuberculosis.

BACKGROUND: Pathogenic mycobacteria are a major cause of human morbidity and mortality. Mycobacterium tuberculosis is an etiological agent of human tuberculosis (TB). Designing new vaccines, including DNA vaccines, may be a useful strategy for preventing TB. OBJECTIVES: The purpose of this study was to design and construct an eukaryotic expression vector containing M. tuberculosis. MATERIALS AND METHODS: Genomic DNA of M. tuberculosis H37Rv cultured on Lowenstein Jensen medium was extracted, and cfp10 was amplified by PCR. After digesting the PCR product and the plasmid, the cfp10 fragment was ligated into the vector pcDNA3.1 (+). Correct insertion was confirmed by colony PCR, restriction enzyme digestion, and sequencing. RESULTS: Electrophoresis of the PCR product on gel showed a 303-bp target fragment. Colony PCR, restriction enzyme digestion, and Sequencing methods confirmed the accuracy of the gene cloning. Colony PCR and restriction enzyme digestion confirmed the cloning. CONCLUSIONS: Cloning of cfp10 of M. tuberculosis into an eukaryotic expression vector was performed successfully. We propose this recombinant plasmid for inducing immunity in animal models in future studies. This recombinant vector can also be used in the construction of fusion proteins.

Sequence Analysis of lip R: A Good Method for Molecular Epidemiology of Clinical Isolates of Mycobacterium tuberculosis.

Advances in DNA sequencing have greatly enhanced the molecular epidemiology studies. In order to assess evolutionary and phylogenetic relation of Mycobacterium tuberculosis isolates several gene targets were evaluated. In this study, appropriate fragments of 5 highly variable genes (rpsL, mprA, lipR, katG, and fgd1 genes) were sequenced. The sequence data were analyzed with neighbor-joining method using mega and Geneious software. The phylogenetic trees analyzes revealed that the discriminatory power of lipR is much stronger than that observed in the other genes. lipR could distinguish between more clinical isolates. Therefore, lipR is a promising target for sequence analyzes of M. tuberculosis.

Potent and selective inhibitors of class A ß-lactamase: 7-prenyloxy coumarins.

Class A and D ß-lactamases are the main causes of resistance against ß-lactam antibiotics, especially the penam group, in Staphylococcus aureus. On the basis of the potentiator property of ethanolic extracts of Ferula szowitsiana root on penicillin, MIC values observed for resistant S. aureus, the main naturally occurring compounds in these extracts, auraptene, umbelliprenin and galbanic acid, were evaluated for ß-lactamase inhibitory activity. Amongst them auraptene showed the most potent inhibitory activity (IC50=21±1.5 µM) toward class A ß-lactamase, whereas no inhibition was observed for class D ß-lactamase. To obtain the structure activity relationship of the mentioned compounds and rationalize the enzyme inhibitory results, docking analysis was performed for both groups of ß-lactamases. Docking analysis showed that the compounds have 100-500-fold lower bonding affinity toward the class D ß-lactamase than toward the class A enzyme.

Synthesis and SAR studies of 3-allyl-4-prenyloxyaniline amides as potent 15-lipoxygenase inhibitors.

15-Lipoxygenases are one of the nonheme iron-containing proteins with ability of unsaturated lipid peroxidation in animals and plants. The critical role of the enzymes in formation of inflammations, sensitivities and some of cancers has been demonstrated in mammalians. Importance of the 15-lipoxygenases leads to development of mechanistic studies, products analysis and synthesis of their inhibitors. In this work new series of the 3-allyl-4-allyoxyaniline amides and 3-allyl-4-prenyloxyaniline amides were designed, synthesized and their inhibitory potency against soybean 15-lipoxygenase were determined. Among the synthetic amides, 3-allyl-4-(farnesyloxy)-adamantanilide showed the most potent inhibitory activity by IC(50) value of 0.69 µM. SAR studies showed that in spite of prenyl length increases, the effects of the amide size and its electronic properties on the inhibitory potency became predominant. The SAR studies was also showed that the orientation of allyl and prenyloxy moieties toward Fe core of the SLO active site pocket is the most suitable location for enzyme inhibition.