Microbiology Department

About Department

The microbiology department represents a vital laboratory in Theodor Bilharz Research Institute. It is concerned in diagnosis of the most important infectious microbes and selection of the appropriate antimicrobial treatment for all patients attending the institute outpatient clinics in addition to inpatients. The lab clinic receives various clinical samples for the performance of culture and sensitivity tests for microbes. The lab also performs serological tests for diagnosis of hepatic viral diseases. The lab combines conventional and automated methods that allow rapid and accurate interventions to treat sepsis at early stage through culture followed by automated identification and sensitivity to isolated bacteria or fungi. In addition to reliable automated detection of important biomarkers of sepsis. It is also concerned with determining resistant infectious bacteria to various antibiotics and their resistance genes and conducting innovative scientific research addressing the global problem by using the most recent diagnostic techniques in molecular biology.

Mission

Service :The primary role of the microbiology laboratory is to identify causative agents of various infectious diseases and help and facilitate the justified use of antibiotics. This should be done in a cost-effective and timely manner that enable good and effective patient care.

Teaching :To teach appropriate use of diagnostic laboratory tests and resource utilization in the care of patients through upgrading of technical performance and scientific background of junior staff.

Research :To develop and to evaluate procedures and protocols that support, enhance and extend the ability of Microbiology lab to effectively carry out their primary service in diagnosis and combating antimicrobial resistance.

Vision

Microbiology department envisages a future where applied microbiology diagnostics and research policies contribute significantly in the community to overcome the emerging infectious diseases challenges including the uprising antimicrobial resistance crisis.

Research Fields

Detection of multi-drug resistant (MDR) bacteria
Effect of novel or old reviving therapeutic agents against MDR pathogens
Rapid diagnosis of septicemia and other life-threatening infections

Structure

The department consists of 4 research laboratories and one outpatient clinic laboratory equipped with basic facilities for microbiological tests:

A. Bacteriology Lab for Culture, Identification and Antimicrobial SusceptibilityTesting (AST)

● Routine bacterial cultures on different culture media.

● Kirby-Bauer disk diffusion method for routine AST for isolated bacterial species.

● Identification and detection of minimal inhibitory concentration (MIC) of antibiotics for Gram-positive and Gram-negative bacteria and yeasts by automated vitek 2 compact system.

● Culture for blood and other body fluids by automated Bact/Alert 3D or BACTEC 9050 systems.

B. Serology Lab

● Automated Enzyme Linked Fluorescent Assay (ELFA) technology using benchtop VIDAS immunoanalyzer.

● Serological diagnosis of Hepatitis markers by ELISA system.

● Detection of H. pylori antigen in stool.

● Latex agglutination for detection of Typhoid disease and Brucellosis.

● Detection of Procalcitonin by VIDAS immunoanalyzer.

● Detection of CRP qualitative by latex agglutination tests and quantitative by automated protein analyzer.

C. Molecular Lab

● DNA extraction by boiling methods as well as by commercialized kits.

● Detection of genes of antimicrobial resistance; ESBLs, Carbapenemases and mecA gene of MRSA by conventional PCR; singlex or multiplex.

● Typing of different infectious pathogens through Pulsed Field Gel Electrophoresis (PFGE) by Bio-Rad CHEF mapper system.

Techniques

Microbiology service is achieved through several running techniques;

● Gram/ Ziehl-Neelsen and fluorescent staining

● Urine microscopic examination

● Urine culture and sensitivity

● Sputum culture and sensitivity

● Throat swab culture and sensitivity

● Pus / discharge culture and sensitivity

● Blood culture and sensitivity

● Ascitic/ pleural fluids culture and sensitivity

● Yeast culture and sensitivity by VITEK 2 compact system.

● Anaerobic and Microaerophilic cultures on request.

● Widal and Brucella agglutination tests

● Qualitative detection of CRP by latex agglutination.

● Quantitative detection of CRP by protein analyzer.

● Hepatitis markers (HBsAg, HCV Ab) by ELISA and VIDAS system.

● Measuring of procalcitonin (PCT) sepsis biomarker by VIDAS sysrem

● Rapid detection of Helicobacter pylori antigen in stool.

Work In Progress

Current research work focuses on four main categories;

Detection of multi-drug resistant (MDR) bacteria: Hot topics include researches on carbapenem resistant Enterobacteriaceae and Acinetobacter baumannii isolates as well as resistance among Helicobacter pylori (H. pylori).
Effect of novel or old reviving therapeutic agents against MDR pathogens: Research work of fosfomycin, doripenem, tigecycline and ceftolozane/ tazobactam against ESBL-producing Enterobacteriaceae have been recently carried out. Running hot topics of colistin susceptibility in carbapenem resistant Enterobacteriaceae as well as carbapenem resistant Acinetobacter baumannii are in progress.
Rapid diagnosis of septicemia and other life-threatening infections: Comparing various sepsis biomarkers (CRP- presepsin- procalcitonin) with blood culture results as well as with clinical methodology of APACHE score for septicemia is a hot running topic.

Services

The department policy is designed to meet the needs of patients in the hospital and outpatient setting. So in- and out-patient services comprise routine identification and antimicrobial susceptibility testing of nosocomial and community-acquired clinical bacterial isolates to diagnose several infections;

● Urinary tract infections.

● Diarrheal diseases.

● Blood stream infections.

● Fever of unknown origin.

● Infections associated with medical devices and procedures.

● Post surgical infections and sepsis.

● Infections related to compromised immunity in hepatic and chronic renal patients.

● Pneumonias.

● Tuberculosis.

● Viral infections.

● Fungal infections.

Training

Training in the field of routine microbiological procedures is available periodically in the form of:

● Annual training program for local and foreign laboratory personnel working on the cutting edge of diagnosis of infectious diseases.

● Two weeks rotation program through the outpatient microbiology lab for undergraduate medical students and faculty of science candidates.

● Annual teaching of microbiology course for TBRI nursing school students.

Publications

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Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s,
Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s,
Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s,
Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s,
Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s,

Projects

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Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s,
Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s,
Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s,
Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s,