This study aimed to establish an accurate and sensitive polymerase chain reaction (PCR) technique for the diagnosis of active human brucellosis in Egypt. We failed to extract Brucella DNA with a commercial kit, but an extraction kit designed in-house using 2 sets of primers [B4/B5 (223 bp) and JPF/JPR (193 bp)] was successful and more economical. The technique showed high sensitivity, specificity and accuracy. The PCR positivity increased significantly with increasing seropositivity titres by the standard tube agglutination test and showed 100% positivity in patients with positive blood cultures. We recommend using PCR as an alternative to culture for diagnosis of brucellosis.

BackgroundAtypical pathogen infections played an important role in community-acquired pneumonia (CAP) in children. Pathogen-specific clinical symptoms are often lacking, and it is difficult to detect atypical pathogens by culture methods. The use of multiplex polymerase chain reaction (PCR) methods enables testing for many pathogens simultaneously in a single analysis.AimTo determine the role of atypical pathogens in children hospitalized with CAP.Patients and methodsThis cross-sectional study was conducted throughout a 2-year period from August 2015 to September 2017. It included 400 Egyptian children hospitalized with clinical diagnosis of CAP at a tertiary hospital in Cairo, Egypt. Sputum samples were collected from lower respiratory tract of all enrolled patients by mucus trap catheter for identification of Bordetella pertussis, Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella pneumophilia by using multiplex real-time PCR.ResultsAmong the 400 CAP patients enrolled in this study, atypical pathogens were detected in 12/400 (3%) patients. Bordetella pertussis was detected in 2% of cases, and it was responsible for CAP in 8/104 (7.69%) infants in the age stratum ≤ 4 months; compared with pertussis-negative cases, pertussis-positive cases were younger and incompletely vaccinated (P values were 0.001 and 0.007, respectively). Mycoplasma pneumoniae was detected in 1% of cases, all were among the age stratum > 4 months ≤ 59 months in 4/272 (1.47%) children.ConclusionIn early infancy, Bordetella pertussis causes a significant proportion of hospitalized CAP cases; all were ≤ 4 months old and incompletely vaccinated. This finding could suggest the role of maternal immunization in developing countries.

Background: The rate of admissions to hospital with bronchiolitis has increased over the past years. The reasons for this are likely to be multifactorial including improved survival of preterm infants. Aim: To assess the severity of viral bronchiolitis in preterm compared to term infants admitted at a tertiary hospital in Cairo, Egypt, based on the outcome. Patients and methods: This prospective study was conducted throughout a 3-year period from September 2011 to October 2014. It included 153 infants, 74 healthy preterm, and 79 healthy term infants admitted with clinical diagnosis of bronchiolitis at a tertiary hospital in Cairo, Egypt. Bronchiolitis severity score (BSS) was recorded, and nasopharyngeal swabs were obtained from each patient at the time of presentation. Viruses were identified using reverse transcription polymerase chain reaction (RT-PCR). The clinical course and patient's outcome were recorded. Results: This study recorded a significantly more severe BSS for preterm compared to term infants. The preterm group had an increased mean length of hospital stay and oxygen therapy and was more likely to need intensive care unit admission and mechanical ventilation (MV) compared to the term group. The mean (± SD) BSS for infections with h-MPV, RSV, and para-influenza 3 was more significantly severe in preterm compared to term infants. Bacterial co-infection was significantly correlated with severity scoring in both groups. Conclusion: Prematurity significantly affects the severity of bronchiolitis, and this underscores the importance of early categorization as a high-risk group on their first visit. The physician should be aware that their illness runs a more severe course, even if they have no underlying disorders.

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BackgroundThe spreading of E. coli and A. baumannii in hospitals is a growing concern due to increased resistance to carbapenems and Fluoroquinolones. The present study aimed to specifically evaluate the presence of mutations in the gyrA and parC genes in Egyptian ICU and their correlation with carbapenem-resistant genes E. coli and A. baumannii isolates from patients in 4 tertiary care hospital in Egypt.MethodsA total of 120 A. baumannii and E. coli clinical isolates were isolated from ICU patients in 4 tertiary hospitals in Egypt. The bacterial isolates were identified by VITEK-2 (Bio Merieux, France). Antimicrobial susceptibility testing was performed according to CLSI guidelines. Phenotypic detection of carbapenemase activity was done by carba-NP test, followed by molecular identification of carbapenemase encoding genes blaNDM, blaOXA-48 and blaKPC by multiplex PCR. The quinolone resistance-determining regions (QRDRs) of gyrA and parC genes were amplified by singleplex PCR followed by reverse and forward sequencing to detect the gene mutation. The DNA sequences were compared with the sequences of wild type of these genes available in GenBank database. Then, the obtained DNA sequences and their amino acid sequences were analyzed using bioinformatics tools.Results All isolates showed a high level of resistance among tested antimicrobial agents (cephalosporins, aminoglycosides, carbapenems, penicillins) that ranged from 36% to 100%. Carba-NP detected 43.59% of the carbapenem-resistant isolates. Multiplex PCR detected that 17.95%, 46.15% and 2.56% of isolates were harboring blaKPC, blaNDM and blaOXA-48 respectively. PCR and sequencing technique showed combined gene mutation in 8 carbapenem-resistant E. coli and A. baumannii isolates. The specific substitutions observed in gyrA were Cys173Arg, Cys174 Gly, Asp80Val, Tyr178ASP, Tyr84Gly, Glu85Lys, Ser172Leu and Asp176Asn. While, the specific substitutions observed in parC were point mutation 62 Arg, Phe60Leu, Ils66Val, Gln76Lys. Point mutation 62 Arg was observed in two A. baumannii isolates, whereas Ser172Leu mutation was observed in two E. coli isolates.ConclusionThe presence of carbapenem resistance genes in combination with single and multiple mutations in QRDR causes the presence of highly resistant E. coli and A. baumannii isolates in the Egyptian hospitals.Disclosures All authors: No reported disclosures.