Frequency of rifampicin-resistant mycobacterium tuberculosis by GeneXpert MTB/RIF assay and its correlates among 2605 probable tuberculosis patients in upper Egypt.

RATIONALE: GeneXpert MTB/RIF (Mycobacterium tuberculosis/rifampicin) assay is a method for detecting rifampicin resistance (RR-MTB) in suspected samples in less than 2 hours with high sensitivity and specificity yield. This study aimed to use the GeneXpert MTB/RIF assay to determine the frequency of RR-MTB and to study the possible influencing correlates associated with positive results. SUBJECTS AND METHODS: This is a retrospective cross-sectional study of patients who visited TB clinic in 5 years (2016-2021). According to the data sheet of the patients, all the collected specimens were divided into 2 parts one for diagnosis by Ziehl-Neelsen stain and the other part for GeneXpert analysis. GeneXpert was also used to look for evidence of RR. RESULTS: Out of the 2605 total samples screened, 718 (27.6%) tested positive for MTB on GeneXpert assay; of them 633 (88.4%) were sensitive to Rifampicin, 83 (11.6%) were resistant to Rifampicin and 2 cases were undetermined. Factors contributing to RR-MTB were: smoker/ex-smoker, with 2.5 times more risk (p = 0.013.0, p = 0.001); recurrence cases had a 4-fold increased risk (p < 0.001); patients with very low M. tuberculosis detected on the GeneXpert MTB/RIF test were 8 times more likely to have RR-TB (P = 0.004). CONCLUSION: This study disclosed a high-rate MTB in Egyptian probable TB cases. Smoking, recurrence and cases with a very low M. tuberculosis burden noticed on the GeneXpert MTB/RIF test had augmented risk of RR-TB.

Effectiveness and Safety of Inactivated SARS-CoV-2 Vaccine (BBIBP-CorV) among Healthcare Workers: A Seven-Month Follow-Up Study at Fifteen Central Hospitals.

BACKGROUND: During a pandemic, healthcare workers are at high risk of contracting COVID-19. To protect these important individuals, it is highly recommended that they receive the COVID-19 vaccine. Our study focused on evaluating the safety and efficacy of Egypt's first approved vaccine, the Sinopharm vaccine (BBIBP-CorV), and comparing these findings with other vaccines. METHODS: An observational study was conducted in fifteen triage and isolation hospitals, from the 1st of March until the end of September 2021. The study included fully vaccinated and unvaccinated participants, and we measured vaccine effectiveness (using 1-aHR), the incidence rate of severely to critically ill hospitalized cases, COVID-19-related work absenteeism, and the safety of the vaccine as outcomes. RESULTS: Of the 1364 healthcare workers who were interviewed, 1228 agreed to participate. After taking the hazard ratio into account, the vaccine effectiveness was found to be 67% (95% CI, 80-43%) for symptomatic PCR-confirmed cases. The incidence rate ratio for hospitalization was 0.45 (95% CI, 0.15-1.31) in the vaccinated group compared to the unvaccinated group, and there was a significant reduction in absenteeism among the vaccinated group (p < 0.007). Most adverse events were mild and well tolerated. Vaccinated pregnant and lactating mothers did not experience any sentinel adverse events. CONCLUSION: Our study found that the BBIBP-CorV vaccine was effective in protecting healthcare workers from COVID-19.

Over prescription of antibiotics in children with acute upper respiratory tract infections: A study on the knowledge, attitude and practices of non-specialized physicians in Egypt.

BACKGROUND: Antimicrobial resistance (AMR) is currently one of the global public health threats. Increased antibiotic consumption in humans, animals, and agriculture has contributed directly to the spread of AMR. Upper respiratory tract infections (URIs) are one of the most common conditions treated by antibiotics, even if unnecessary as in cases of viral infections and self-limited conditions which represent the most cases of URIs. Investigating physicians' knowledge, attitudes, and practice regarding antibiotic prescriptions in children with acute URIs may reflect the problem of antibiotic over prescription. This study aims to assess the problem in our community and provide information for further planning of appropriate interventions to optimize antibiotic prescriptions. METHODS: This is a cross-sectional study for all non-specialized physicians dealing with acute upper respiratory tract infections (URIs) in pediatrics sittings in Assiut district, Egypt. We used a self-administered questionnaire to assess physicians' knowledge, attitudes, and practice. In addition, four clinical vignettes addressing different URI scenarios were included in the questionnaire to assess the patterns of antibiotic prescriptions in common cases. RESULTS: Our study included 153 physicians whose mean age was 32.2 ± 8.7, most of whom were pediatric residents in different health institutes in Assiut district. They had good knowledge as out of the 17 knowledge questions,the mean number of correct answers was 12.4 ± 2.9. Regarding their attitudes, mean attitude scores for inappropriate antibiotic prescribing were low. However, of those scores, the responsibility of others had the highest score (3.8 ± 0.61). Prescribing practice in special conditions of URIs showed that 80% of participants prescribed antibiotics if fever continued for more than five days and 61.4% if the child had a yellowish or greenish nasal discharge. Among 612 clinical vignettes, 326 contained antibiotic prescriptions (53.3%), and appropriate antibiotic prescriptions represented only 8.3% overall. CONCLUSIONS: Physicians dealing with acute URIs in outpatients' clinics in the Assiut district have good knowledge about antibiotic use and resistance and demonstrate a good attitude toward appropriate antibiotic use. Although the percentage of inappropriate prescriptions in clinical vignettes in high, more research is required to investigate the factors of antibiotic inappropriate prescribing practice and non-adherence to guidelines. Also, it is essential to set up a national antibiotic stewardship program to improve antibiotic prescribing and contain antimicrobial resistance problems.

Amoebicidal effect of Allium cepa against Allovahlkampfia spelaea: A keratitis model.

Allovahlkampfia spelaea (A. spelaea) is a free-living amoeba, proved to cause Acanthamoeba-like keratitis with quite difficult treatment. This study aimed to evaluate the amoebicidal effect of Allium cepa (A. cepa) on A. spelaea trophozoites and cysts both in vitro and in vivo using Chinchilla rabbits as an experimental model of this type of keratitis. Chemical constituents of the aqueous extract of A. cepa were identified using Liquid Chromatography-mass Spectrometry (LC-MS). In vitro, A. cepa showed a significant inhibitory effect on trophozoites and cysts compared to the reference drug, chlorhexidine (CHX) as well as the non-treated control (P < 0.05) with statistically different effectiveness in terms of treatment durations and concentrations. No cytotoxic effect of A. cepa on corneal cell line was found even at high concentrations (32 mg/ml) using agar diffusion method. The in vivo results confirmed the efficacy of A. cepa where the extract enhanced keratitis healing with complete resolution of corneal ulcers in 80% of the infected animals by day 14 (post infection)pi compared to 70% recovery with CHX after 20 treatment days. The therapeutic effect was also approved at histological, immune-histochemical, and parasitological levels. Our findings support the potential use of A. cepa as an effective agent against A. spelaea keratitis.

Impact of Geographical Location on the Gut Microbiota Profile in Egyptian Children with Type 1 Diabetes Mellitus: A Pilot Study.

Purpose: To investigate the compositional and functional characteristics of T1DM-associated gut microbiota in two Egyptian cities and to study the geographical locality effects. Patients and Methods: This case-control study included 32 children with controlled T1DM and 16 controls, selected from two different regions of Egypt. The gut microbiota of both diabetic and control children was analyzed through 16S rRNA gene sequencing; this was done using the Illumina MiSeq platform. Results: Consistent findings among the diabetic children included significantly lower alpha diversity than the control children, as well as a lower mean Firmicutes/Bacteroidetes (F/B) ratio, and reduced proportions of Firmicutes and the genera Prevotella and Ruminococcus. In the diabetic children, there were also significantly enriched representations of Actinobacteria, Bacteroidetes, and Proteobacteria and the genera Lactobacilli, Bacteroides, and Faecalibacterium. When comparing the two diabetic groups, the Ismailia group (IsDM) was found to have a significantly higher F/B ratio and diversity indices, with resultant differences at the functional level. Conclusion: There are a number of consistent changes in the microbiota profile characterizing the diabetic groups irrespective of the geographical location including significantly lower alpha diversity, mean Firmicutes/ Bacteroidetes (F/B) ratio, and reduced proportions of Firmicutes and genera Prevotella and Ruminococcus. There are also significantly enriched representations of Actinobacteria, Bacteroidetes, and Proteobacteria and genera Lactobacilli, Bacteroides, and Faecalibacterium pointing to the greater driving power of the disease.

Thymus vulgaris, Mentha piperita and Elettaria cardamomum against Trypanosoma evansi in vitro and in an animal model with new insights for the treatment of trypanosomosis.

Trypanosomosis is a worldwide disease that affects human and livestock populations with limited availability and high cost of trypanocides. The study aims to evaluate the possible in vitro and in vivo anti-trypanosomal activity of Thymus vulgaris (thyme), Mentha piperita (mint) and Elettaria cardamomum (cardamom) aqueous extracts against Trypanosoma evansi in experimentally infected rats using Intropar as a reference drug. The crude extracts of the selected plants were used in three concentrations (2500, 2000, and 1000 µg/ml). The in vitro trypanocidal activities were assessed regarding parasite motility, count, and infectivity. The in vivo susceptibility of T. evansi was evaluated by assessing the level of parasitemia in the experimental rats. The packed cell volume (PCV) was also monitored. Both the in vitro and in vivo experiments showed trypanocidal activity, of all the tested extracts, higher than that of Intropar. The in vitro trypanocidal effects were dose-dependent and represented by a significant reduction of the parasite count together with immobilizing effect within 3 hours incubation period, compared to the negative and positive controls (p< 0.05). The in vivo trypanocidal effects of the different concentrations of all the tested extracts were represented by the significantly lowered levels of parasitemia, compared to the negative control (NC) group with varying degrees; in a dose-dependent manner concerning the time. They exhibited also a significantly higher level in PCV recovery compared to the NC group (p < 0.05). This study initially confirmed the potent in vitro and in vivo trypanocidal effect of the three extracts, with a potentially promising future for the treatment of trypanosomosis.

Autoimmune Hepatitis: Shifts in Gut Microbiota and Metabolic Pathways among Egyptian Patients.

Autoimmune hepatitis (AIH) is a chronic inflammatory disorder with complex immunopathogenesis. Dysbiosis has been linked to many autoimmune diseases, but its detailed role in autoimmune hepatitis (AIH) still needs rigorous evaluation, especially in Egypt. We aimed to identify the shift in the gut microbiota profile and resultant metabolic pathways in AIH Egyptian patients compared to healthy individuals. Stool samples were collected from 15 AIH-naive patients and from 10 healthy individuals. The V3-V4 hyper-variable regions in16S rRNA gene was amplified and sequenced using Illumina MiSeq platform. Significantly lower bacterial diversity in AIH patients was found compared to the controls. A phylum-level analysis showed the overrepresentation of Firmicutes, Bacteroides, and Proteobacteria. At the genus level, AIH-associated enrichment of Faecalibacterium, Blautia, Streptococcus, Haemophilus, Bacteroides, Veillonella, Eubacterium, Lachnospiraceae and Butyricicoccus was reported in contrast to Prevotella, Parabacteroides and Dilaster, which were significantly retracted in such patients. Overall, the predicted metabolic pathways associated with dysbiosis in AIH patients could orchestrate the potential pathogenic roles of gut microbiota in autoimmune disease, though not in a disease-specific manner, calling for future large-scale studies.