Whole genome characterization of methicillin resistant Staphylococcus aureus in an Egyptian Tertiary Care Hospital.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is a significant healthcare-associated (HA-MRSA) pathogen due to its increased morbidity and mortality rates. There is a paucity of data regarding MRSA clones circulating in the Middle East in the literature, especially from Egypt. We aimed to identify the pattern of resistance and virulence in the propagating clones using NGS technologies for the whole genome sequence. METHODS: From an 18-month surveillance program for MRSA-positive patients, 18 MRSA isolates from surgical healthcare associated infections were selected. The Vitek2 system was used to assess antimicrobial susceptibility. The whole genome sequencing was performed using the NovaSeq6000. The reads were mapped to the reference genome (Staphylococcus_aureus_ATCC_BAA_1680), used for variant calling, screened for virulence/resistance genes, and typed using multi-locus sequence typing and spa typing. Correlation between demographic and clinical data and molecular findings were performed. RESULTS: All the MRSA isolates were highly resistant to tetracycline followed by gentamicin (61%) and highly susceptible to trimethoprim/sulfamethoxazole. Most of the isolates showed a high virulence profile. ST239 was the predominant sequence type (6/18), while t037 was the predominant spa type (7/18). Five isolates shared the same ST239 and spa t037. ST1535, an emerging MRSA strain, was the second most prevalent in our study. One isolate showed a unique pattern of a high abundance of resistance and virulence genes. CONCLUSION: WGS elucidated the resistance and virulence profiles of MRSA isolated from clinical samples of HAI patients with high-resolution tracking of clones predominant in our healthcare facility.

Molecular characterization of carbapenem-resistant Acinetobacter baumannii clinical isolates from Egyptian patients.

Acinetobacter baumannii (A. baumannii) represents a global threat owing to its ability to resist most of the currently available antimicrobial agents. Moreover, emergence of carbapenem resistant A. baumannii (CR-AB) isolates limits the available treatment options. Enzymatic degradation by variety of ß-lactamases, have been identified as the most common mechanism of carbapenem resistance in A. baumannii. The alarming increase in the prevalence of CR-AB necessitates continuous screening and molecular characterization to appreciate the problem. The present study was performed to assess the prevalence and characterize carbapenemases among 206 CR-AB isolated from various clinical specimens collected from different intensive care units at Kasr Al-Aini Hospital. All isolates were confirmed to be A. baumannii by detection of the blaOXA-51-like gene. Molecular screening of 13 common Ambler class bla carbapenemases genes in addition to insertion sequence (IS-1) upstream OXA-23 were performed by using four sets of multiplex PCR, followed by identification using gene sequencing technology. Among the investigated genes, the prevalence of blaOXA-23, and blaOXA-58 were 77.7%, and 1.9%, respectively. The ISAba1 was detected in 10% of the blaOXA-23 positive isolates. The prevalence of metallo-ß-lactamases (MBLs) studied; blaNDM-1, blaSPM, blaVIM, blaSIM-1 were 11.7%, 6.3%, 0.5%, and 0.5% respectively. One of class A; bla KPC was detected in 10.7% of the investigated isolates. blaOXA-24/40, blaIMP, blaGES, blaVEB and blaGIM were not detected in any of the studied isolates. Moreover, 18.4% of the isolates have shown to harbor two or more of the screened bla genes. We concluded that the most prevalent type of ß-lactamases genes among CR-AB isolates collected from Egyptian patients were blaOXA-23 followed by blaNDM-1 and blaKPC.

Establishment of an antimicrobial stewardship strategy on the surgical NICU at Cairo University specialized pediatric hospital.

PURPOSE: Antimicrobial resistance is a major concern that we are facing nowadays. This is due to antibiotic misuse and bacteria developing resistance to the commonly used antibiotics. This may lead to increased mortality and consumption of country resources. Implementation of an antimicrobial stewardship program [ASP] can limit the use of unnecessary antibiotics and subsequently decrease the infection rates with better patient outcome. We aimed to control antibiotic misuse, reduce infection rate, decrease drug costs, and reduce length of hospital stay in the ICU. METHODS: We conducted a prospective study on the surgical neonatal ICU [SNICU] over a period of 6 months divided into pre-implementation phase, followed by an ASP phase, in which we applied the antibiotic guidelines approved by the ASP committee. Data were collected in the two phases and analyzed for demographics, compliance with guidelines, prescribed antibiotics, lab investigations, surgical site infection [SSI], length of stay and patient outcome. RESULTS: Compliance to the guidelines was encountered in 86% and SSI rate decreased to 20%. Days of Therapy (DOT) per 1000 patient days showed a significant decrease in Ampicillin Sulbactam by 296 (p = 0.024), Imipenem by 220.34 (p = 0.024) and Vancomycin by 287.34 (p = 0.048). Drug cost showed a 1185.97 EGP decrease in the ASP period compared to the pre-implementation period (p = 0.714). Average LOS decreased in the ASP period by a mean difference of 2.5 (p = 0.027). CONCLUSION: ASP implementation can control antibiotic misuse, decrease the medical care expenses and improve patient outcome. TYPE OF STUDY: Clinical research paper. LEVEL OF EVIDENCE: Level one.

Neutrophil and monocyte receptor expression in patients with sepsis: implications for diagnosis and prognosis of sepsis.

Understanding the complex immune responses in sepsis is crucial to provide insight into the clinical syndrome. We evaluated the changes in the surface receptors of the cells of innate immunity, neutrophils and monocytes, in patients with sepsis. Since sepsis remains a clinical challenge, we aimed to assess the significance of altered receptor expression in diagnosis and prognosis. Critically ill patients with sepsis (n=31) were investigated for the expression of receptors for IgG heavy chain CD64 and CD16 on neutrophils and CD64 and the lipopolysaccharide receptor CD14 on monocytes by flow cytometry and compared to 23 patients with no sepsis. Patients with sepsis had increased expression of neutrophil CD64. Neutrophil CD64 was specific for discriminating patients with sepsis but showed weak sensitivity. When integrated in a scoring system, neutrophil CD64 in combination with C-reactive protein (CRP) and SOFA score showed a diagnostic accuracy of 0.93 for sepsis and significantly predicted increased mortality risk. While neutrophil CD16 did not discriminate for sepsis, decreased expression was associated with increased mortality risk. In contrast, monocyte CD64 and CD14 expression was unaltered in sepsis and was not associated with mortality risk. Our study demonstrates that unlike monocytes, neutrophil receptor expression is altered in patients with sepsis receiving intensive care. It is promising to apply a combination approach to diagnose sepsis especially in time-limited conditions.

Bacteremia Caused by Kocuria kristinae from Egypt: Are There More? A Case Report and Review of the Literature.

Kocuria kristinae is opportunistic Gram-positive cocci from the family Micrococcaceae. It is usually considered part of the normal flora that rarely is isolated from clinical specimens. Here, we report a case of Kocuria kristinae bacteremia; to the best of our knowledge, this is the first report from Egypt.