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Background: Tuberculosis (TB) is one of the significant health concerns in Egypt, necessitating rapid, affordable, and accurate diagnosis to aid in its control. This study presents data collected over five years (2017-2021) to explore different diagnostic TB methods in our lab. Methods: A total of 33700 non-repetitive samples were subjected to different diagnostic methods; 30000 were stained by Ziehl–Neelsen (ZN), of which 2819 were cultured on Löwenstein-Janssen (LJ) media, and 456 were analyzed by GeneXpert; 3700 samples were tested by interferon-gamma release assay (IGRA) Quantiferon. Moreover, 3650 patients underwent the tuberculin skin test (TST). Results: GeneXpert displayed the highest positivity (23.9%), while ZN smear microscopy was the lowest (4.8%). The detection capability between pulmonary and extrapulmonary samples was not statistically significant using LJ culture but significant using GeneXpert MTB/RIF. Rifampicin resistance was 17.4% among the GeneXpert Mycobacterium tuberculosis (MTB)-positive samples. Conclusions: GeneXpert MTB/RIF assay is a user-friendly, rapid, and efficient method for identifying pulmonary and extrapulmonary TB with the simultaneous detection of rifampicin-resistant strains. However, culture and smear microscopy remain the most dominant diagnostic methods in developing countries due to their low cost and relatively acceptable specificity.

Background: Ochrobactrum anthropi ( O. anthropi) is a Gram-negative, nonfermenting bacillus, which has been recovered from clinical samples worldwide. However, it has never been reported from any clinical sample in Egypt. To the best of our knowledge, we report for the first time, the isolation of O. anthropi from bloodstream infection of a 75-year-old female patient. Ochrobactrum anthropi identification was performed using Vitek-2 system (BioMérieux, Marcy l’Etoile, France), and confirmed using 16S rRNA sequencing. The organism was further classified as O. anthropi subclade I, using recA sequence analysis. Susceptibility testing was carried out using broth microdilution method, and the isolate was found to be resistant to both ceftazidime and cefepime. Molecular investigation of genes conferring resistance to the third and fourth generation cephalosporins, showed that the isolate harbored blaOCH-6 gene, and that blaTEM, blaSHV and blaCTX-M were not present. This work highlights the first isolation of O. anthropi from bloodstream infection in Alexandria, Egypt.

Background:This study aimed at analyzing the microbiological profile of neonatal sepsis in Egypt and to determine the antibiotic susceptibility patterns of the isolated microorganisms. Methods: Two thousand and four hundred blood samples were collected from neonates showing symptoms suggestive of septicemia, inoculated into BACT/ALERT culture bottles. Positive blood culture samples were identified and tested for antimicrobial susceptibility. Results: Among the neonates included in our study, 457 (19%) neonates were positively diagnosed with sepsis. early onset neonatal sepsis (EOS) was detected in 181 (39.6%), while late-onset neonatal sepsis (LOS) in 276 (60.4%) cases. Klebsiella pneumoniae was the most commonly isolated microorganism. Staphylococcus aureus and Enterococcus spp. were the most common isolated Gram-positive bacteria. Candida spp. was more encountered in LOS.An alarming feature of the present study is the high incidence of multidrug resistant microorganisms (65%). Among Gram negative isolates (56%) of were extended spectrum beta-lactamase (ESBL) producers and (70.5%) were carbapenem resistant. In Gram positive bacteria, resistance to methicillin in S. aureus and coagulase negative staphylococci were detected in (50%) and (41%) of isolates respectively. Additionally, 17% of Enterococcus isolates were vancomycin resistant. Coclusion: Our bacteriological profile of neonatal sepsis showed that Gram negative bacteria represented the majority of isolates. Klebsiella pneumoniae was the predominant isolate. In our study, both EOS & LOS share a nosocomial infection profile, as high antimicrobial resistance was observed among our isolates. The susceptibility profiles of the isolates may urge for the change of the current used empirical therapies.