Drug resistance and genomic variations among Mycobacterium tuberculosis isolates from The Nile Delta, Egypt.

Tuberculosis is a global public health concern. Earlier reports suggested the emergence of high rates of drug resistant tuberculosis in Egypt. This study included 102 isolates of Mycobacterium tuberculosis collected from two reference laboratories in Cairo and Alexandria. All clinical isolates were sub-cultured on Löwenstein-Jensen medium and analyzed using both BD BACTEC MGIT 960 SIRE Kit and standard diffusion disk assays to identify the antibiotic sensitivity profile. Extracted genomic DNA was subjected to whole genome sequencing (WGS) using Illumina platform. Isolates that belong to lineage 4 represented > 80%, while lineage 3 represented only 11% of the isolates. The percentage of drug resistance for the streptomycin, isoniazid, rifampicin and ethambutol were 31.0, 17.2, 19.5 and 20.7, respectively. Nearly 47.1% of the isolates were sensitive to the four anti-tuberculous drugs, while only one isolate was resistant to all four drugs. In addition, several new and known mutations were identified by WGS. High rates of drug resistance and new mutations were identified in our isolates. Tuberculosis control measures should focus on the spread of mono (S, I, R, E)- and double (S, E)-drug resistant strains present at higher rates throughout the whole Nile Delta, Egypt.

High Rates of Aminoglycoside Methyltransferases Associated with Metallo-Beta-Lactamases in Multidrug-Resistant and Extensively Drug-Resistant Pseudomonas aeruginosa Clinical Isolates from a Tertiary Care Hospital in Egypt.

BACKGROUND: Multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains of Pseudomonas aeruginosa are the leading cause of healthcare-associated infections worldwide. OBJECTIVE: The aim was to identify the resistant phenotypes among P. aeruginosa and to characterize different aminoglycosides and carbapenem resistance genes as major mechanisms of resistance in these isolates, in Theodor Bilharz Research Institute (TBRI), a tertiary care hospital in Cairo, Egypt. METHODS: During a period of 11 months, 42 P. aeruginosa clinical isolates were collected from the microbiology laboratory by routine culture. Antimicrobial sensitivity testing to the aminoglycosides gentamicin and amikacin, and other classes of antibiotics, was performed by a disk diffusion method. Isolates were tested for aminoglycoside resistance genes, aac(6')-lb, aac-(3)-lla, rmtB, rmtC, armA, rmtD, and rmtF, and carbapenemase resistance genes bla NDM, bla VIM, and bla IMP, using conventional PCR. RESULTS: Thirty-three (78.5%) of the clinical P. aeruginosa isolates showed MDR and XDR phenotypes at 42.4% and 57.65%, respectively, and these were included in the study. Aminoglycoside resistance was found in 97%, whereas carbapenem resistance was found in 81% of the isolates phenotypically. Only 59.4% (19/26) of the aminoglycoside-resistant isolates harbored resistance genes; none of the amikacin-susceptible isolates harbored any of the tested aminoglycoside resistance genes. Aminoglycoside resistance genes rmtB, armA, aac(6')-lb, and rmtF were found at rates of 17/33 (51.5%), 3/33 (9%), 2/33 (6%), and 2/33 (6%), respectively, whereas rmtD, acc(3)-II, and rmtC were not detected. Only 40.7% (11/27) of the carbapenem-resistant isolates harbored resistance genes. Carbapenem resistance genes, bla NDM andbla VIM, were found at rates of 7/33 (21.2%) and 6/33 (18.1%), respectively, and bla IMP was not detected. CONCLUSION: Rates of MDR and XDR P. aeruginosa and resistance to aminoglycosides and carbapenems in our setting are high. Methyltransferases and metallo-beta-lactamases are the main mechanisms of resistance to aminoglycosides and carbapenems, respectively. The presence of bla NDM and rmtF in the strains confirms their rapid dissemination in the Egyptian environment.

Genomic Characterization of Methicillin-Resistant Staphylococcus aureus (MRSA) by High-Throughput Sequencing in a Tertiary Care Hospital.

Methicillin-resistant Staphylococcus aureus (MRSA) strains are associated with serious complications and poor clinical outcome. In Egypt, they contribute to more than 70% of S. aureus healthcare-associated infections. This study combined whole-genome sequencing, bioinformatics, and statistical analyses to identify the phylogeny, resistome, virulome and potential genotype-phenotype-clinical correlation among 18 clinical isolates of MRSA in a tertiary hospital in Cairo, Egypt. The ST1535-V MRSA clone was the most frequently isolated (16.6%), followed by ST5-VI, ST1-V and ST239-III (11.1% each). SCCmec V, VI, IV and III types were detected at frequencies of 50%, 16.6%, 11.1% and 11.1%, respectively. None of the tested virulence genes were detected in all isolates, but they ranged in distribution from 1/18 to 17/18. The Panton-Valentine leukocidin (PVL)-encoding genes were detected in only four isolates and were enriched in isolates causing non-severe cases. Phylogenetic analysis revealed relatedness between three ST1535-Vs, two ST5-VIs, two ST239-IIIs and two ST1-Vs; however, only the two genetically related ST1-V isolates were epidemiologically linked. While disease outcome and source of infection had no correlation with a particular genotypic pattern, the sequence type was the most correlated factor with phylogeny and genotypic patterns, and a few genes were associated with non-severe cases.

Prevalence of Candida blood stream infections among children in tertiary care hospital: detection of species and antifungal susceptibility.

BACKGROUND: Of all blood stream infections (BSI), candidaemia poses the greatest threat with a high fatality rate among children. There has been an increase in the number of reports of non-C. albicans species and antifungal resistance has progressively emerge. AIM: The present study aimed to demonstrate the prevalence of candidaemia among children and to characterize the involved species and their susceptibility to antifungal agents. METHODOLOGY: Microbes were isolated from blood samples and identified via standard microbiological procedures. Chromogenic media was used to characterize the Candida species. The susceptibility of the isolates to the antifungal agents; caspofungin, amphotericin, itraconazole, and fluconazole was determined with the E-test. STATISTICAL METHODS: The data were analysed with Statistical Package for the Social Science SPSS; SPSS Inc., Chicago, IL, USA) version 15 for Microsoft Windows. Comparisons between the study groups were performed using the Chi square (χ2) test. p-values less than 0.05 were considered significant. RESULTS: Candidaemia accounted for 17.3% of all BSIs. C. albicans and non-C. albicans species accounted for 36% and 64% of the cases of candidaemia, respectively. Caspofungin, amphotericin, itraconazole, and fluconazole antifungals had activities of 99%, 97%, 73% and 64%, respectively. In total, 64% of patients with candiaemia died. CONCLUSION: The prevalence of candidaemia was high, the fatality rate was alarming and non-C. albicans species were predominant. Fluconazole was the least effective of the tested antifungal agents owing to the high level of resistance.