ORIGINAL_ARTICLE
The new era for diagnostic microbiology laboratories: ‘All things are ready, if our mind be so’
Identification and characterization of micro-organisms that cause infections are crucial for successful management of patients. For several decades, routine clinical microbiological diagnostic laboratories have been equipped with a growing panel of culture-dependent and culture-independent methods to investigate the microbial etiology of infectious diseases. Considering the disadvantages of traditional methods, multiplex PCR techniques have been routinely endorsed in clinical microbiology laboratories as rapid and sensitive diagnostic and prognostic tool including many PCR panels routinely used in microbial diagnostics. The great advance in medical biotechnology has been associated with development of Matrix-Associated Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI TOF MS). The power of MALDI TOF MS correctly identified 93.2% of organisms to the species level and 5.3% to the genus level. Recently, the application of next-generation sequencing (NGS) technology and its various methodological variants makes it possible to detect different types of microorganisms present within a microbial sample simultaneously, using a culture-independent approach and in a single sequencing run. Over the next 5 to 10 years, although it is unlikely to see NGS completely replacing the conventional culture and susceptibility methods, a wealth of NGS applications will be acquired in the vast majority of diagnostic microbiology laboratories worldwide, providing enhanced diagnostic capabilities and improving the quality of patients care. In Egyptian diagnostic microbiology laboratories, we have to ask ourselves; are we ready to subsist this new era? Sure the answer is: ‘All things are ready, if our mind be so’.
https://mid.journals.ekb.eg/article_80220_8c92a1c222e5fb2d06c93a7e8055d9a7.pdf
2020-05-01
1
3
10.21608/mid.2020.25905.1001
PCR
MALDI TOF
NGS
metagenomics
Ahmed
Asaad
ahmedmoradasaad@hotmail.com
1
Medical Microbiology and Immunology Department, Faculty of Medicine, Zagazig University, Microbes and Infectious Diseases Editor-In-Chief, ZUMJ Editor-In-Chief, Egypt
LEAD_AUTHOR
ORIGINAL_ARTICLE
Continuous medical education activities; Case No. 1
A three years old male was presented, fatigued with history of fever for 4 days. He became acutely ill and vomited during lunch. Over the next 4 days he developed fever as high as 40oC that was controlled by Acetaminophen. He developed cough, rhinorrhea, and conjunctivitis. His parents reported that he was very sleepy. Over the past 2 days, he had begun to rub his eyes and complained a severe pain in it His parents noted that his eyes were puffy and sensitive to light. He had had no rashes. The patient’s lips were dried and cracked and he has a greatly reduced urinary output (To be continued...).
https://mid.journals.ekb.eg/article_80313_342b2a48c43c908672de46d76715e983.pdf
2020-05-01
4
5
10.21608/mid.2020.27073.1006
Respiratory infection
children
Fever
Said
Hamed Abbadi
saidabbadi@hotmail.com
1
Professor of Medical Microbiology and Immunology, Faculty of Medicine, Suiz University
LEAD_AUTHOR
ORIGINAL_ARTICLE
The burden of unspecified febrile syndrome in a community hospital of Cuba
Background: The Cuban health-care system recommends the hospital admissions of patients with unspecified febrile syndrome (UFS) to rule out arboviral diseases and to prevent healthcare associated adverse outcomes. Aim: Evaluate the burden of unspecified febrile syndrome in a Cuban hospital. Methods: A cross-sectional study was carried out in the Hospital Joaquín Albarrán (La Habana, Cuba) from 1 January 2017 to 31 December 2019. It was collected the admissions and patients days (total and UFS patients) and laboratory test for dengue diagnosis. Results: During the three-year period, the epidemic curve starts in April-May and decline in November, with the highest peak in August 2019. It was admitted 16964 patients with UFS representing 43% of the hospital admissions, and 43512 patients’ days were documented. In 2019 the 51.9% of the hospital admissions and 22.9% of patients’ days were related to UFS, and were performed 7492 IgM test (repeated test in 89 patients) and 46.2% were reactive. Conclusion: The hospital admission related to unspecified febrile syndrome constitute a challenge to the organization and the healthcare system to provide the best care for all and minimize its economic impact.
https://mid.journals.ekb.eg/article_80243_df17f12651c0275e6cc452721cac5197.pdf
2020-05-01
6
14
10.21608/mid.2020.26826.1000
unspecified febrile syndrome
dengue
hospital
cost
Cuba
Humberto
Guanche Garcell
guanche@infomed.sld.cu
1
Hospital Epidemiology Department, Hospital Docente Clínico Quirúrgico, Joaquín Albarrán, Cuba
LEAD_AUTHOR
Carlos R
Pérez Díaz
direccion@albarran.sld.cu
2
Medical administration, Hospital Docente Clínico Quirúrgico, Joaquín Albarrán, Cuba
AUTHOR
Manuel
Ramirez Nodal
manuelramirez@infomed.sld.cu
3
Internal Medicine Department. Hospital Docente Clínico Quirúrgico, Joaquín Albarrán, Cuba
AUTHOR
Alfredo
Ruiz Lozano
vd.asistmedica@albarran.sld.cu
4
Medical Administration, Hospital Docente Clínico Quirúrgico, Joaquín Albarrán, Cuba
AUTHOR
Carlos
Martinez Quesada
cmartinezq@infomed.sld.cu
5
Emergency Department, Hospital Docente Clínico Quirúrgico, Joaquín Albarrán, Cuba
AUTHOR
Carlos Omar
Mitjans Fuente
comitfu@infomed.sld.cu
6
Medical Administration, Hospital Docente Clínico Quirúrgico, Joaquín Albarrán, Cuba
AUTHOR
ORIGINAL_ARTICLE
Evaluation of antibacterial activity of silver nanoparticles against multidrug-resistant Gram negative bacilli clinical isolates from Zagazig University Hospitals
Background: The growing incidence of multidrug resistant (MDR) bacterial infections has become a public health crisis. This work aims to evaluate the in-vitro activity of silver nanoparticles (AgNPs), alone and in combination with the antimicrobials amikacin and ceftazidime, against MDR Gram-negative bacilli (GNB) isolated from clinical cases in Zagazig University Hospitals. Methods: In a cross sectional study, MDR GNB were isolated from different clinical specimens and were tested to determine the minimal inhibitory concentration (MIC), minimal bactericidal concentration (MBC) and bactericidal activity of AgNPs using broth microdilution method. The effect of combining subMIC levels of AgNPs (MIC/2 and MIC/4) with amikacin and ceftazidime, was also determined by broth microdilution. Results: A total of 63 MDR GNB was obtained during the study period (22 E. coli, 17 Klebsiella, 15 Pseudomonas aeruginosa and 9 Acinetobacter isolates). AgNPs demonstrated a bactericidal effect on all tested isolates with an MBC/MIC ratio of less than 4. When combined with amikacin, a synergistic effect was demonstrated on all tested E.coli and Klebsiella isolates at AgNPs MIC/2 and on 45.4%, 40% and 77.8% of E.coli, P.aeruginosa and Acinetobacter isolates, respectively at MIC/4. In combination with ceftazidime, AgNPs exhibited a synergistic effect on 100% of E. coli and 88.2% Klebsiella at both MIC/2 and MIC/4 and on 40% of P. aeruginosa isolates at AgNPs MIC/4. Conclusions: AgNPs exert a bactericidal activity on MDR GNB as well as a synergistic effect when combined with amikacin and ceftazidime suggesting them as a new weapon in the war against MDR GNB.
https://mid.journals.ekb.eg/article_81760_3f9a348013be5405228b758ad1c6a0c5.pdf
2020-05-01
15
23
10.21608/mid.2020.27148.1003
silver nanoparticles
multidrug resistance
Gram negative bacilli
Enas
Desouky
enasdesouky91@gmail.com
1
Medical Microbiology and Immunology Department, Faculty of Medicine, Zagazig University, Egypt
AUTHOR
Mona
Shalaby
engymm@hotmail.com
2
Medical Microbiology and Immunology Department, Faculty of Medicine, Zagazig University, Egypt
AUTHOR
Maha
Gohar
goharmaha@gmail.com
3
Medical Microbiology and Immunology Department, Faculty of Medicine, Zagazig University, Egypt
AUTHOR
Marian
Gerges
maromicro2006@yahoo.com
4
Medical Microbiology and Immunology, Faculty of Medicine, Zagazig University
LEAD_AUTHOR
ORIGINAL_ARTICLE
Detection of carbapenemase enzymes and genes among carbapenem-resistant Enterobacteriaceae isolates in Suez Canal University Hospitals in Ismailia ,Egypt.
Background: Carbapenem antibiotics are important therapeutic agents in the health care setting, they are frequently used as an empiric therapy for life-threatening infections as well as infections with multi-drug-resistant gram-negative bacilli. Carbapenemase-producing Carbapenem-Resistant Enterobacteriaceae (CRE) are a significant public health challenge worldwide. The detection of carbapenemases productions in CRE strains is performed by phenotypic and genotypic methods. The phenotypic methods target carbapenemases production but provide no guidance regarding the specific carbapenemases types, while the genotypic diagnosis has the benefit of determining the exact mechanism conferring carbapenems resistance. Aim: Improvement of the antibiotic policy and infection control strategies in Suez Canal University Hospitals in Ismailia; through adequate detection of carbapenem resistance in the hospitals. Methods: All the CRE isolates were tested by the phenotypic methods (mCIM & eCIM) test to detect carbapenemases production, and screened by the conventional PCR for the presence of five carbapenemase genes, namely blaKPC, blaIMI, blaVIM, blaNDM, blaOXA-48 Results: The study showed that (53/155) 34.1% of the Enterobacteriaceae isolates were carbapenems resistant. Carbapenemases activity was detected in (36/53) 67.9% of the examined CRE isolates using mCIM test (20/36)37.8 % showed Metallo-carbapenemases and (16/36) 30.2% showed Serine- carbapenemases by eCIM test. 60.4% (32/53) were sensitive to colistin. While by PCR all the isolates (100%) harbor one or more carbapenemases genes. (51/53) 96.2% were proved to harbor blaOXA-48 gene, (47/53) 88.7% were proved to harbor blaNDM gene, (28/53) 52.8%, were proved to harbor blaVIM,gene, the percentage of blaIMI, blaKPC isolation was (17/53) 32.1%, (4/53)7.5% respectively. Conclusion: High frequencies of carbapenemase genes among CRE isolates.
https://mid.journals.ekb.eg/article_84202_ae61aad9f4977dfffcd1f21188c44ea9.pdf
2020-04-21
24
33
10.21608/mid.2020.25702.1007
CRE
carbapenems
PCR
mCIM
Atef
Raheel
atefraheel@yahoo.com
1
Microbiology and Immunology department, faculty of medicine, Suez Canal university, Egypt
LEAD_AUTHOR
Hasnaa
Azab
hasnaa_azab@yahoo.com
2
Microbiology and Immunology department, faculty of medicine, Suez Canal university, Egypt
AUTHOR
Waheed
Hessam
w_hessam@hotmail.com
3
Microbiology and Immunology department, faculty of medicine, Suez Canal university, Egypt
AUTHOR
Said
Abbadi
saidabbadi@hotmai.com
4
microbiology department, faculty of medicine, Suez university, Egypt
AUTHOR
Abeer
Ezzat
dr.abeer.ezzat@gmail.com
5
Medical Microbiology and Immunology department, Director of IPC Suez Canal University Hospitals, Egypt
AUTHOR