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Abstract Background Zoonotic human tuberculosis (TB) caused by Mycobacterium bovis (M. bovis) is as vital as Mycobacterium tuberculosis, however with scarce available information. We aimed to use whole-genome sequencing (WGS) technology to take a deep insight into the circulating genotypes of human M. bovis and the genomic characteristics underlying virulence and drug resistance. Methods The study included smear positive Ziehl-Neelsen samples from patients with suspected tuberculosis. Samples were cultured on Lowenstein-Jensen media and suspected colonies of M. bovis were selected to undergo DNA extraction and WGS. Data was analysed using the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), and online bioinformatics tools. A phylogenetic tree was constructed for our sequenced strains, in addition to a set of 59 previously sequenced M. bovis genomes from different hosts and countries. Results Out of total 112 mycobacterial positive cultures, five M. bovis were isolated and underwent WGS. All sequenced strains belonged to Mycobacterium tuberculosis var bovis, spoligotype BOV_1; BOV_11. Resistance gene mutations were determined in 100% of strains to pyrazinamide (pncA and rpsA), isoniazid (KatG and ahpC), ethambutol (embB, embC, embR and ubiA), streptomycin (rpsl) and fluoroquinolones (gyrA and gyrB). Rifampin (rpoB and rpoC) and delamanid (fbiC) resistance genes were found in 80% of strains. The major represented virulence classes were the secretion system, cell surface components and regulation system. The phylogenetic analysis revealed close genetic relatedness of three sequenced M. bovis strains to previous reported cow strains from Egypt and human strains from France, as well as relatedness of one M. bovis strain to four human Algerian strains. One sequenced strain was related to one cow strain from Egypt and a human strain from South Africa. Conclusions All sequenced M. bovis isolates showed the same spoligotype, but diverse phylogeny. Resistance gene mutations were detected for anti-TB drugs including pyrazinamide, isoniazid, streptomycin, ethambutol, fluoroquinolones, cycloserine, rifampin and delamanid. The virulence profile comprised genes assigned mainly to secretion system, cell surface components and regulation system. Phylogenetic analysis revealed genetic relatedness between our isolates and previously sequenced bovine strains from Egypt as well as human strains from other nearby countries in the region.

Abstract Tuberculosis is a global public health concern. Earlier reports suggested the emergence of high rates of drug resistant tuberculosis in Egypt. This study included 102 isolates of Mycobacterium tuberculosis collected from two reference laboratories in Cairo and Alexandria. All clinical isolates were sub-cultured on Löwenstein–Jensen medium and analyzed using both BD BACTEC MGIT 960 SIRE Kit and standard diffusion disk assays to identify the antibiotic sensitivity profile. Extracted genomic DNA was subjected to whole genome sequencing (WGS) using Illumina platform. Isolates that belong to lineage 4 represented > 80%, while lineage 3 represented only 11% of the isolates. The percentage of drug resistance for the streptomycin, isoniazid, rifampicin and ethambutol were 31.0, 17.2, 19.5 and 20.7, respectively. Nearly 47.1% of the isolates were sensitive to the four anti-tuberculous drugs, while only one isolate was resistant to all four drugs. In addition, several new and known mutations were identified by WGS. High rates of drug resistance and new mutations were identified in our isolates. Tuberculosis control measures should focus on the spread of mono (S, I, R, E)- and double (S, E)-drug resistant strains present at higher rates throughout the whole Nile Delta, Egypt.

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.

Abstract Background Carbapenemase-producing Enterobacterales (CPE) show rapid global dissemination and pose a significant therapeutic challenge. This study aimed to characterize carbapenemase-producing Klebsiella spp. and Escherichia coli (E. coli) phenotypically and genotypically and evaluate the effect of ceftazidime/ avibactam plus aztreonam combination. Methods A total of 219 Klebsiella species and 390 E. coli strains were isolated from clinical samples, in which 80 Klebsiella spp. and 20 E coli isolates were resistant to tested carbapenems (imipenem, ertapenem, meropenem) by disk diffusion/broth dilution method and Vitek-2 compact system. MASTDISCS Combi Carba plus discs and real time PCR were used to determine type of carbapenemase phenotypically and genotypically, respectively. Interestingly, the synergistic effect between ceftazidime-avibactam (E-test) and aztreonam (disc) was tested against the CPE isolates. Results Out of the carbapenem-resistant isolates, 76.25% Klebsiella spp. isolates were extensively drug-resistant (XDR) while 18.75% were pan drug-resistant (PDR), and 5% were multidrug-resistant (MDR). Regarding E. coli, 5% were PDR, 20% were MDR and 75% were XDR. More than one carbapenemase gene was detected in 99% of the isolates. In comparison between MAST-Carba plus discs and PCR results, sensitivity and specificity were (85.42–97.92%) in Klebsiella spp., and (69.64–100%) in E. coli, respectively. Moreover, a strong association was detected between both test results among Klebsiella spp. (p

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.

Background: Countries are committed to the international agenda and essential to achieving sexual and reproductive health goal is their capability to integrate equity lens in structural social determinants framing of inequalities. The aim is to propose comprehensive practical methodology which can alert countries to the injustice of sexual and reproductive health inequalities and provide tool to guide evidence-based policies and actions. Method: The methodology was founded on literature review. This was followed by consultation meetings and workshops to drive scientific output. Finally, the methodology was applied on data in five Arab countries to illustrate its relevance. Results: There are five contributions made. First, integrating equity lens to conceptual framing of sexual and reproductive health inequalities. Second, operationalizing the framework by articulating comprehensive list of indicators, adding distribution of gender norms, and choosing two inequality measures (index of dissimilarity and concentration index redistribution need) to allow for assessment of magnitude and comparisons. Third, illustrating the responsiveness of the health system and its relative contribution as social determinant of health. Fourth, demonstrating unfairness of root social structures and of social configurations of sexual and reproductive health. Finally, using the decomposition analysis and six questions to identify entry points for actions and responsibilities. Conclusion: the proposed methodology provides countries clear way to assess severity and fairness of health-related conditions and not specifically sexual and reproductive inequalities. It offers an ethical urgency for addressing health inequities and guidance to main stream fairness in the full package of national policies.

Background Currently, there is no consensus on standard measure that can be routinely part of the health information systems to alert countries to inequalities in health and identify the priority health inequality conditions. Objectives To identify the health inequality measures relevant for assessing geographic and wealth inequalities; use the measures as a demonstration to what can happen in practice to recognize the geographic and wealth-related priority health inequalities within a country; and identify the geographic and wealth underprivileged populations. Method Egypt data were used as demonstration. Pearson coefficient of correlation was calculated to compare the various geographic and wealth health inequality measures. T test was used to identify significant correlations. The relevant inequality measures were used to rank geographic and wealth health inequalities and identify the underprivileged populations. Results The wealth inequalities in health measured by the concentration index provide a familiar and perform adequately in identifying economic inequalities in health. However, the geographic health inequalities identified by the index of dissimilarity appear to provide a more comprehensive profile of health inequalities within a country. Conclusion There is a need for a feasible inequality measure in the health information systems. A country’s geographic health distribution measured by the index of dissimilarity appears to provide a feasible first-step alarm to inform and guide the uptake of equity-sensitive policies.