No abstract

Implementation of a sustainable surveillance system in a resource-limited country was possible following a stepwise approach with continuous evaluation. Enhancing infection prevention and control programs should be an infection control priority in Egypt.

In March 2020, the SARS-CoV-2 virus outbreak was declared as a world pandemic by the World Health Organization (WHO). The only measures for controlling the outbreak are testing and isolation of infected cases. Molecular real-time polymerase chain reaction (PCR) assays are very sensitive but require highly equipped laboratories and well-trained personnel. In this study, a rapid point-of-need detection method was developed to detect the RNA-dependent RNA polymerase (RdRP), envelope protein (E), and nucleocapsid protein (N) genes of SARS-CoV-2 based on the reverse transcription recombinase polymerase amplification (RT-RPA) assay. RdRP, E, and N RT-RPA assays required approximately 15 min to amplify 2, 15, and 15 RNA molecules of molecular standard/reaction, respectively. RdRP and E RT-RPA assays detected SARS-CoV-1 and 2 genomic RNA, whereas the N RT-RPA assay identified only SARS-CoV-2 RNA. All established assays did not cross-react with nucleic acids of other respiratory pathogens. The RT-RPA assay’s clinical sensitivity and specificity in comparison to real-time RT-PCR (n = 36) were 94 and 100% for RdRP; 65 and 77% for E; and 83 and 94% for the N RT-RPA assay. The assays were deployed to the field, where the RdRP RT-RPA assays confirmed to produce the most accurate results in three different laboratories in Africa (n = 89). The RPA assays were run in a mobile suitcase laboratory to facilitate the deployment at point of need. The assays can contribute to speed up the control measures as well as assist in the detection of COVID-19 cases in low-resource settings.

Inappropriate antibiotic use leads to increased risk of antibiotic resistance and other adverse outcomes. The objectives of the study were to determine the prevalence and characteristics of antibiotic use in Egyptian hospitals to identify opportunities for quality improvement. A point prevalence survey was conducted in 18 hospitals in March 2011. A total of 3408 patients were included and 59% received at least one antibiotic, with the most significant use among persons <12 years and intensive care unit patients (p < 0.05). Third generation cephalosporin were the most commonly prescribed antibiotics (28.7% of prescriptions). Reasons for antibiotic use included treatment of community—(27%) and healthcare-associated infections (11%) and surgical (39%) and medical (23%) prophylaxis. Among surgical prophylaxis recipients, only 28% of evaluable cases received the first dose within two hours before incision and only 25% of cases received surgical prophylaxis for <24 h. The prevalence of antibiotic use in Egyptian hospitals was high with obvious targets for antimicrobial stewardship activities including provision of antibiotic prescription guidelines and optimization of surgical and medical prophylaxis practices.

An AMS program focusing on education supported by auditing and feedback can have a significant impact on optimizing antibiotic use in surgical prophylaxis practices.

Objective To report type and rates of healthcare-associated infections (HAI) as well as pathogen distribution and antimicrobial resistance patterns from a pilot HAI surveillance system in Egypt. Methods Prospective surveillance was conducted from April 2011–March 2012 in 46 intensive care units (ICUs) in Egypt. Definitions were adapted from the CDC’s National Healthcare Safety Network. Trained healthcare workers identified HAIs and recorded data on clinical symptoms and up to four pathogens. A convenience sample of clinical isolates was tested for antimicrobial resistance at a central reference laboratory. Multidrug resistance was defined by international consensus criteria. Results ICUs from 11 hospitals collected 90,515 patient-days of surveillance data. Of 472 HAIs identified, 47% were pneumonia, 22% were bloodstream infections, and 15% were urinary tract infections; case fatality among HAI case-patients was 43%. The highest rate of device-associated infections was reported for ventilator-associated pneumonia (pooled mean rate: 7.47 VAP/1,000 ventilator-days). The most common pathogens reported were Acinetobacter spp. (21.8%) and Klebsiella spp. (18.4%). All Acinetobacter spp. isolates tested (31/31) were multidrug-resistant, and 71% (17/24) of Klebsiella pneumoniae isolates were extended spectrum beta-lactamase producers. Conclusions Infection control priorities in Egypt should include preventing pneumonia and preventing infections due to antimicrobial-resistant pathogens.

Background. Methicillin-resistant Staphylococcus aureus (MRSA) has created significant epidemiological, infection-control, and therapeutic management challenges during the past three decades. Aim. To analyze the pattern of resistance of healthcare- and community-associated MRSA in Egypt and the trend of resistance of HA-MRSA over time (2005–2013). Methods. MRSA isolates were recovered from healthcare-associated (HA) and community-associated (CA) Staphylococcus aureus (S. aureus) infections. They were tested against 11 antimicrobial discs and the minimal inhibitory concentration (MIC) of vancomycin was determined. Inducible clindamycin resistance (iMLSB) was also screened using D-test. Findings. Of 631 S. aureus, MRSA was identified in 343 (76.6%) and 21 (11.5%) of HA and CA S. aureus isolates, respectively. The proportion of HA-MRSA increased significantly from 48.6% in 2005 to 86.8% in 2013 (p value < 0.001). Multidrug resistance (MDR) was observed in 85.8% of HA-MRSA and 48.6% of CA-MRSA. Vancomycin intermediate resistant S. aureus (VISA) was detected in 1.2% of HA-MRSA and none was detected in CA-MRSA. Among HA-MRSA strains, 5.3% showed iMLSB compared to 9.5% among CA-MRSA. Conclusion. The upsurge of the prevalence rates of HA-MRSA over time is alarming and urges for an effective infection control strategy and continuous monitoring of antimicrobial use.

Objective To describe the epidemiology of carbapenem-resistant Enterobacteriaceae (CRE) healthcare-associated infections (HAI) in Egyptian hospitals reporting to the national HAI surveillance system. Methods Design: Descriptive analysis of CRE HAIs and retrospective observational cohort study using national HAI surveillance data. Setting: Egyptian hospitals participating in the HAI surveillance system. The patient population included patients admitted to the intensive care unit (ICU) in participating hospitals. Enterobacteriaceae HAI cases were Klebsiella, Escherichia coli, and Enterobacter isolates from blood, urine, wound or respiratory specimen collected on or after day 3 of ICU admission. CRE HAI cases were those resistant to at least one carbapenem. For CRE HAI cases reported during 2011–2017, a hospital-level and patient-level analysis were conducted using only the first CRE isolate by pathogen and specimen type for each patient. For facility, microbiology, and clinical characteristics, frequencies and means were calculated among CRE HAI cases and compared with carbapenem-susceptible Enterobacteriaceae HAI cases through univariate and multivariate logistic regression using STATA 13. Results There were 1598 Enterobacteriaceae HAI cases, of which 871 (54.1%) were carbapenem resistant. The multivariate regression analysis demonstrated that carbapenem resistance was associated with specimen type, pathogen, location prior to admission, and length of ICU stay. Between 2011 and 2017, there was an increase in the proportion of Enterobacteriaceae HAI cases due to CRE (p-value = 0.003) and the incidence of CRE HAIs (p-value = 0.09). Conclusions This analysis demonstrated a high and increasing burden of CRE in Egyptian hospitals, highlighting the importance of enhancing infection prevention and control (IPC) programs and antimicrobial stewardship activities and guiding the implementation of targeted IPC measures to contain CRE in Egyptian ICU’s .