Molecular characterization of multidrug-resistant Gram-negative pathogens in three tertiary hospitals in Cairo, Egypt.

High rates of antimicrobial resistance (AMR) among Gram-negative pathogens (GNP) have been reported in Egypt. Antimicrobial surveillance and identifying the genetic basis of AMR provide important information to optimize patient care. In this study, we aimed to identify the beta-lactam resistance phenotypes and genotypes of multidrug-resistant (MDR) non-repetitive GNP from 3 tertiary hospitals in Egypt. WZe studied 495 non-repetitive MDR Gram-negative isolates from patients with complicated intra-abdominal infections (cIAI), complicated urinary tract infection (cUTI), and lower respiratory tract infection (LRTI), collected as part of the "Study for Monitoring Antimicrobial Resistance Trends" (SMART) conducted in 3 tertiary hospitals in Cairo, Egypt, from 2015 to 2016. Identification and susceptibility testing of GNP to antimicrobials were tested in each hospital laboratory and confirmed in a reference laboratory (International Health Management Associates (IHMA), Inc., Schaumburg, IL, USA). Molecular identification of extended-spectrum beta-lactamases (ESΒLs), AmpC, and carbapenem resistance genes was conducted in IHMA. Among the 495 MDR isolates, Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E. coli) were the most common (52.7% and 44.2%). K. pneumoniae was most susceptible to colistin, amikacin, ertapenem, and imipenem (92.7%, 72.7%, 69.3%, and 64%, respectively). E. coli was most susceptible to colistin (100%), amikacin (94.1%), imipenem (90.4%), and ertapenem (83.6%). ESBL was detected in 96.2% and ESBL genotypes included blaCTX-M-15 (70.1%), blaTEM-OSBL (48.5%), blaSHV-OSBL (27.9%), and blaCTX-M-14 (10.7%). AmpC resistance genes were identified in 9.7% of the isolates, dominated by blaCMY-2 (5.7%). Carbapenem resistance genes were detected in 45.3% of the isolates. In K. pneumoniae, blaOXA-48 dominated (40.6%), followed by blaNDM-1 (23.7%) and blaOXA-232 (4.5%). In E. coli, the most frequent genes were blaNDM-5 (9.6%), blaOXA-181 (5.5%), blaOXA-244 (3.7%), and blaNDM-1 (3.7%). blaKPC-2 was identified in 0.4% of isolates. Notably, 32.3% of isolates carried more than one resistance gene. Our findings emphasize the continued need for molecular surveillance of MDR pathogens, implementation of strict infection control measures, and antimicrobial stewardship policies in our hospitals.

Accurate and reliable surface-enhanced Raman spectroscopy assay for early detection of SARS-CoV-2 RNA with exceptional sensitivity.

This research proposes a highly sensitive and simple surface-enhanced Raman spectroscopy (SERS) assay for the detection of SARS-CoV-2 RNA using suitably designed probes specific for RdRp and N viral genes attached to a Raman marker. The sensitivity of the assay was optimized through precise adjustments to the conditions of immobilization and hybridization processes of the target RNA, including modifications to factors such as time and temperature. The assay achieved a remarkable sensitivity down to 58.39 copies/mL, comparable to or lower than the sensitivities reported for commercial fluorescent polymerase chain reaction (PCR) based methods. It has good selectivity in discriminating SARS-CoV-2 RNA against other respiratory viruses, respiratory syncytial virus (RSV), and influenza A virus. The reliability of the assay was validated by testing 24 clinical samples, including 12 positive samples with varying cycle threshold (Ct) values and 12 negative samples previously tested using real-time PCR. The assay consistently predicted true results that were in line with the PCR results for all samples. Furthermore, the assay demonstrated a notable limit of detection (LOD) of Ct (38 for RdRp gene and 37.5 for N-gene), indicating its capability to detect low concentrations of the target analyte and potentially facilitating early detection of the pathogen.

Investigation of a COVID-19 outbreak in a University Cardio-Thoracic Hospital in Cairo: exploration of the risk to healthcare workers and patients.

Background: Corona virus Disease 2019 (COVID-19) pandemic has posed a challenge to health sectors all over the world. The pandemic arrived in Egypt a few weeks after Europe and Asia, with rapidly rising numbers. Health care workers (HCWs) are front liners sustaining a major risk of acquiring the infection. Aim: In this work, we analyse an outbreak of COVID-19 in a University hospital in Cairo involving HCWs of different categories, patients and patients' accompanying relatives. Methods: Following the reporting of the first COVID-19 confirmed case; a 55-year-old nurse at the hospital, a total of 645 healthcare workers, patients and patients' accompanying relatives were tested for SARS-CoV-2 by real-time reverse transcription polymerase chain reaction (rRT-PCR) assay. Results: Twenty-four out of 589 HCWs, 3 out of 42 patient and 4 out of 14 patients' accompanying relatives tested positive for COVID-19. No physicians, pharmacists or technicians were infected. Nursing staff and housekeeping staff were the most at risk of contracting the infection with a risk ratio of 4.99 (95% CI: 1.4-17.6) and 5.08 (95% CI: 1.4-18.4) respectively. Clustering of infected HCWs was observed in paediatrics' ICU and in the 6th floor of the hospital. Conclusions: Nursing and housekeeping staff sustain a significantly higher risk of COVID-19 infection compared to other staff categories. The nature of their duties and the frequent unprotected contact between members of these categories may play a role in increasing their risk.

Hepatitis C virus infection and risk factors among patients and health-care workers of Ain Shams University hospitals, Cairo, Egypt.

BACKGROUND: Hospitals are suspected of playing a key role in HCV epidemic dynamics in Egypt. This work aimed at assessing HCV prevalence and associated risk factors in patients and health-care workers (HCWs) of Ain Shams University (ASU) hospitals in Cairo. METHODS: We included 500 patients admitted to the internal medicine or surgery hospital from February to July, 2017, as well as 50 HCWs working in these same hospitals. Participants were screened for anti-HCV antibodies and HCV RNA. A questionnaire was administered to collect data on demographic characteristics and medical/surgical history. For HCWs, questions on occupational exposures and infection control practices were also included. RESULTS: The overall prevalence of anti-HCV antibodies was 19.80% (95% CI: 16.54-23.52) among participating patients, and 8.00% (95% CI: 0.48-15.52) among participating HCWs. In HCWs, the only risk factors significantly associated with anti-HCV antibodies were age and profession, with higher prevalence in older HCWs and those working as cleaners or porters. In patients, in a multivariate logistic regression, age over 50 (aOR: 3.4 [1.9-5.8]), living outside Cairo (aOR: 2.1 [1.2-3.4]), admission for liver or gastro-intestinal complaints (aOR: 4.2 [1.8-9.9]), and history of receiving parenteral anti-schistosomiasis treatment (aOR: 2.7 [1.2-5.9]) were found associated with anti-HCV antibodies. CONCLUSIONS: While HCV prevalence among patients has decreased since the last survey performed within ASU hospitals in 2008, it is still significantly higher than in the general population. These results may help better control further HCV spread within healthcare settings in Egypt by identifying at-risk patient profiles upon admission.

Consensus Meeting Report "Technology Enhanced Assessment" in Covid-19 Time, MENA Regional Experiences and Reflections.

PURPOSE: Majority of the assessments, appraisals and placements have been disturbed, with some being cancelled, postponed, or modified in design. New approaches for assessment should be well-thought-out. This work attempts at capturing the collective wisdom of educators in the Middle East and North Africa region (MENA), providing an understanding of the online assessment conceptual framework in the era of COVID-19 that tells the story rather than determining cause and effect, and identifying the biggest gaps that derail the digital transformation. METHODS: A qualitative inductive study using the grounded theory approach was implemented following a synchronous virtual online meeting, a summary of the reflections as well as experiences of medical education experts was prepared. Data for this qualitative study were collected from the meeting. The meeting was video-recorded and transcribed by the researchers. Thematic analysis was performed by three separate researcher coders. The authors then discussed together until they reached a consensus. RESULTS: Three main thematic areas were identified: 1) feasibility, 2) exam fairness/equity and 3) acceptable graduate attributes, society/community acceptance. CONCLUSION: The COVID-19 era necessitated revisiting of our assessment strategies to cope with new changes within the available context. Rapid adaptation is required.

SARS-CoV-2 PCR positivity rate and seroprevalence of related antibodies among a sample of patients in Cairo: Pre-wave 2 results of a screening program in a university hospital.

BACKGROUND: Research has revealed that asymptomatic and pre-symptomatic infections are important contributors to the transmission of SARS-CoV-2 in populations. In Egypt, the true prevalence of infections is veiled due to the low number of screening tests. The aim of this study was to determine the SARS-CoV-2 PCR positivity rate as well the seroprevalence of the SARS-CoV-2 antibodies before the ultimate development of a second wave of the epidemic in Cairo, Egypt. METHODS: Our study was carried out between May 5 and the end of October 2020. It included all patients requiring admission to Ain Shams University hospitals. An interview questionnaire was used to collect demographic and clinical data. Laboratory tests for all participants included RT-PCR and total antibody assay for SARS-CoV-2. RESULTS: A total of 4,313 subjects were enrolled in our study, with females representing 56% of the sample. Adults and middle-aged individuals represented around 60% of the study sample. The positivity rate of SARS-CoV-2 PCR was 3.84% (95% CI 3.29-4.48), and the SARS-CoV-2 antibody seroprevalence was 29.82% (95% CI: 28.16-31.51). Males showed a higher risk for getting the COVID-19 infection, while middle-age group had significantly higher antibody seroprevalence rates. CONCLUSION: SARS-CoV-2 infection imposes a high burden on the community as detected by high seroprevalence rates.

Epidemiology of Carbapenem-resistant Enterobacteriaceae in Egyptian intensive care units using National Healthcare-associated Infections Surveillance Data, 2011-2017.

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 .

Antimicrobial stewardship to optimize the use of antimicrobials for surgical prophylaxis in Egypt: A multicenter pilot intervention study.

OBJECTIVE: To measure the impact of an antimicrobial stewardship (AMS) program on the use of antibiotics for surgical prophylaxis at acute care hospitals in Egypt. METHODS: This was a before-and-after intervention study conducted in 5 tertiary, acute-care surgical hospitals. The baseline, intervention, and follow-up periods were 3, 6, and 3 months, respectively. The impact of the intervention was measured by preintervention and postintervention surveys for surgical patients with clean and clean-contaminated wounds. Information was collected on demographic characteristics and antibiotic use. The intervention focused mainly on educating surgical staff on the optimal timing and duration of antibiotics used for surgical prophylaxis. Only 3 hospitals identified a surgeon to audit antibiotic surgical prescriptions. The primary outcome measures were the percentages of surgical patients receiving optimal timing and duration of surgical prophylaxis. RESULTS: Data were collected for 745 patients before the intervention and for 558 patients after the intervention. The optimal timing of the first dose improved significantly in 3 hospitals, increasing from 6.7% to 38.7% (P < .01), from 2.6% to 15.2% (P < .01), and from 0% to 11% (P < .01). All hospitals showed a significant rise in the optimal duration of surgical prophylaxis, with an overall increase of 3%-28% (P < .01). Days of therapy per 1000 patient-days were decreased significantly in hospitals A, B, C, and D, with no change in hospital E. CONCLUSIONS: An AMS program focusing on education supported by auditing and feedback can have a significant impact on optimizing antibiotic use in surgical prophylaxis practices.