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BACKGROUND: Several SARS-CoV-2 variants with increased transmissibility and/or potential immune escape have emerged and rapidly spread worldwide. Ongoing surveillance analyses are performed worldwide to designate new variants of concern (VOC) of coronavirus. MAIN TEXT: This report identifies the first Egyptian patient with a confirmed SARS-CoV-2 omicron variant. The patient showed positivity on reverse transcriptase-polymerase chain reaction and full genome sequencing was performed to confirm the variant. The mutations found in the variant were compared with the GISAID reference strain hCoV-19/Wuhan/WIV04/2019. Genome BLAST showed the highest similarity to omicron variants isolated in South Africa. Phylogenetic analysis revealed that the variant belongs to the 21K clade. CONCLUSIONS: The study indicates the importance of information-sharing among global public health partners. Moreover the importance of implementation of full genome sequencing to rapidly identify and track the new SARS-CoV-2 variants.
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Background and Objectives: With the increase in immunosuppressed patients and antimicrobial misuse, Bacillus species have risen as opportunistic pathogens in hospitalized patients. The present study aimed at comparing chromogenic media, automated identification cards versus MALDI-TOF as the gold standard method for identification of different Bacillus species and determining minimal inhibitory concentration (MIC) of different antibiotics by broth microdilution method (BMD) to suggest recommendations for Bacillus treatment. Materials and Methods: The study included 30 Bacillus species isolates recovered from normally sterile sites of the human body and were subjected to identification by MALDI-TOF, Vitek-2c, and HiCrome Bacillus Agar. BMD test was performed to determine the MIC of vancomycin, gentamicin, and ciprofloxacin. Results: Our study showed B. cereus was the most commonly isolated species (76.66%) followed by B. subtilis (23.33%). Regarding the different methods of identification, the highest agreement with MALDI-TOF was exhibited by HiCrome agar without polymyxin B (93.3%) followed by Vitek-2C and HiCrome agar with polymyxin with an agreement of 83.3%. Concerning the antibiogram, the tested isolates showed a susceptibility of 93.3%, 86.6%, and 83.3% towards vancomycin, gentamicin, and ciprofloxacin respectively. Conclusion: In conclusion, we spotlight that Bacillus species should no longer be considered contaminant bacteria in cultures, particularly in immunosuppressed patients. HiCrome Bacillus Agar without polymyxin B displayed the highest agreement with MALDI-TOF. Hence, it represents a good option for identification for routine laboratories where expensive instruments are unavailable. The high susceptibility towards the tested antibiotics can suggest the possibility of empirical use of vancomycin, gentamicin, and ciprofloxacin.
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BACKGROUND: Cardiovascular diseases (CVDs) are a major cause of morbidity and mortality in patients with end stage renal disease (ESRD). Circulating endotoxins may have toxic effect on myocardial functions and are speculated as pathogens of accelerated atherosclerosis and hemodialysis (HD) patients. OBJECTIVE: We aimed to assess the possible relation between circulating endotoxin levels and left ventricular functions parameters, common carotid artery intimal media thickness (CIMT) in prevalent HD patients. PATIENTS AND METHODS: Forty stable prevalent HD patients with mean age (47.97 ± 14.42) year using regular conventional hemodialysis sessions in Ain shams university hemodialysis unit, Cairo, Egypt were randomly selected. Diabetics, congestive heart failure and those with history of myocardial infarction or coronary artery disease were excluded from the study. All patients were studied by CBC and routine chemistry, as well as hs CRP, Intact PTH, lipid profile and endotoxin level by ELISA before and after the HD session, Delta change of endotoxin (pre dialysis endotoxin-post dialysis endotoxin) was calculated, resting Doppler echocardiographic and carotid duplex. RESULTS: Mean of Pre-HD session serum endotoxin level was (0.356 ± 0.090) EU/mL and the mean of post -HD endotoxin levels was (0.367 ± 0.110) EU/mL. Significant positive correlation between post dialysis endotoxin, MV E/A ratio and grades of left ventricular diastolic dysfunction (P < 0.05) and significant correlation between delta change in endotoxin and EF% (r = -0.36,P = 0.02). By stepwise linear regression analysis for determinants of MVE/A post -HD endotoxin level independently associated with MV E/A ratio (ß = 0.350, P = 0.027). We did not detect any significant correlation between CCA atherosclerosis and neither pre nor post- HD endotoxin level nor with delta change of pre and post HD endotoxin levels. CONCLUSION: Acute increase in post dialytic circulating endotoxin level in prevalent HD patients may be associated with both left ventricular systolic and diastolic dysfunction and that attempts to reduce endotoxin level may have a positive impact on cardiovascular complications in HD Patients.
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The aim of this study was identifying bacterial pathogens involved in meningitis, studying their antibiotic resistance profiles, investigating the antibiotic resistance genes as well as evaluating the use of various antibiotic combinations. Antibiotic susceptibility tests were evaluated according to CLSI guidelines. Antibiotic combinations were evaluated by calculating the Fractional Inhibitory Concentration (FIC) index. A total of 71 bacterial isolates were recovered from 68 culture positive CSF specimens. Sixty five of these isolates (91.5%) were recovered from single infection specimens, while 6 isolates (8.4%) were recovered from mixed infection specimens. Out of the 71 recovered isolates, 48 (67.6%) were Gram-positive, and 23 (32.4%) were Gram-negative. Thirty one of the Gram positive isolates were S. pneumoniae (64.6%, n = 48). Out of the recovered 71 isolates; 26 (36.6%) were multidrug-resistant (MDR) isolates of which, 18 (69.2%) were Gram-negative and 8 (30.8%) were Gram-positive. All MDR isolates (100%) showed resistance to penicillin and ampicillin, however, they showed lower resistance to meropenem (50%), levofloxacin (50%), amikacin (48%), pipercillin-tazobactam (45.8%). Most common antibiotic resistance genes were investigated including: tem (21.1%), shv (15.8%), ctx-m (15.8%) coding for TEM-, SHV, CTX-M extended-spectrum beta-lactamases (ESBLs), respectively; aac(6')-I b(26.3%) coding for aminoglycoside 6'-N-acetyltransferase type Ib ciprofloxacin resistant variant; and qnrA (5.3%) gene coding for quinolone resistance. The DNA sequences of the respective resistance genes of some selected isolates were PCR amplified, analyzed and submitted to the GenBank database under the accession numbers, KX214665, KX214664, KX214663, KX214662, respectively. The FIC values for ampicillin/sulbactam plus cefepime showed either additive or synergistic effect against ten tested Gram-negative MDR isolates, while doxycycline plus levofloxacin combination revealed synergism against two MDR Gram-positive isolates. The results indicate high prevalence of antibiotic resistance among MDR isolates. Therefore, new guidelines should be implemented in Egypt to rationalize the use and avoid the misuse and abuse of antimicrobial agents.
