Co-Existence of Certain ESBLs, MBLs and Plasmid Mediated Quinolone Resistance Genes among MDR E. coli Isolated from Different Clinical Specimens in Egypt.

The emergence of multi-drug resistant (MDR) strains and even pan drug resistant (PDR) strains is alarming. In this study, we studied the resistance pattern of E. coli pathogens recovered from patients with different infections in different hospitals in Minia, Egypt and the co-existence of different resistance determinants. E. coli was the most prevalent among patients suffering from urinary tract infections (62%), while they were the least isolated from eye infections (10%). High prevalence of MDR isolates was found (73%) associated with high ESBLs and MBLs production (89.4% and 64.8%, respectively). blaTEM (80%) and blaNDM (43%) were the most frequent ESBL and MBL, respectively. None of the isolates harbored blaKPC and blaOXA-48 carbapenemase like genes. Also, the fluoroquinolone modifying enzyme gene aac-(6')-Ib-cr was detected in 25.2% of the isolates. More than one gene was found in 81% of the isolates. Azithromycin was one of the most effective antibiotics against MDR E. coli pathogens. The high MAR index of the isolates and the high prevalence of resistance genes, indicates an important public health concern and high-risk communities where antibiotics are abused.

Distribution of naturally -occurring NS5B resistance-associated substitutions in Egyptian patients with chronic Hepatitis C.

BACKGROUND: NS5B polymerase inhibitors represent the cornerstone of the present treatment of Hepatitis C virus infection (HCV). Naturally occurring substitution mutations to NS5B inhibitors have been recorded. The current study intended to demonstrate possible natural direct acting antiviral (DAA)-mutations of the HCV NS5B region in HCV patients in Minia governorate, Egypt. METHODS: Samples were collected from 27 treatment-naïve HCV patients and 8 non-responders. Out of 27 treatment-naïve patients, 17 NS5B sequences (amino acids 221-345) from treatment-naïve patients and one sample of non-responders were successfully amplified. Nucleotide sequences have been aligned, translated into amino acids, and compared to drug resistance mutations reported in the literature. RESULTS: NS5B amino acid sequence analysis ensures several novel NS5B mutations existence (more than 40 substitution mutations) that have not been previously documented to be correlated with a resistant phenotype. It was found that K304R (82.4%), E327D and P300T (76.5% each) substitutions were the most distributed in the tested samples, respectively. S282T, the major resistance mutation that induces high sofosbuvir-resistance level in addition to other reported mutations (L320F/C) and (C316Y/N) were not recognized. Q309R mutation is a ribavirin-associated resistance, which was recognized in one strain (5.9%) of genotype 1g sequences. Besides, one substitution mutation (E237G) was identified in the successfully amplified non-responder sample. CONCLUSION: Our study showed various combinations of mutations in the analyzed NS5B genes which could enhance the possibility of therapy failure in patients administered regimens including multiple DAA.

Prevalence of some virulence factors and genotyping of hospital-acquired uropathogenic Escherichia coli isolates recovered from cancer patients.

OBJECTIVES: This study aimed to determine the prevalence of virulence factors among uropathogenic Escherichia coli (UPEC) isolates from cancer patients and to investigate their genetic diversity using ERIC-PCR. METHODS: A total of 42 E. coli were recovered from urine samples from cancer patients admitted to Assiut University Hospital. PCR was used to detect the presence of three virulence genes (papC, iutA and cnf1). Genetic diversity of the isolates was determined using the ERIC-PCR fingerprinting method, and amplified products were separated by agarose gel electrophoresis. Gel electrophoresis banding patterns were used for dendrogram generation using NTSYSpc software. RESULTS: Among the 42 UPEC isolates, papC was the most common virulence gene (55% of isolates), followed by iutA (38%) and cnf1 (2%). ERIC-PCR successfully produced multiple amplicons (range 2-11 bands) in each strain, with molecular weights ranging from 285 to 3000 bp. Some UPEC isolates had identical ERIC-PCR profiles (identical banding patterns), whilst 22 UPEC isolates had different ERIC-PCR profiles. The phylogenetic dendrogram of ERIC-PCR showed that the 42 isolates can be differentiated into three major clusters (I, II and III), with cluster I representing 76% of isolates, cluster II representing 19% and cluster III representing 5%. CONCLUSIONS: The results of this study suggest that both papC and iutA genes may have an important role in the pathogenesis of overt urinary tract infection. Dendrogram analysis of the ERIC-PCR profiles revealed that all UPEC isolates were assigned into three main clusters, indicating the spread of distinct clonal groups that are responsible for hospital-acquired infections.

Multiple Drug Resistance Patterns in Various Phylogenetic Groups of Hospital-Acquired Uropathogenic E. coli Isolated from Cancer Patients.

Cancer patients are more susceptible to several bacterial infections, particularly urinary tract infections caused by uropathogenic E. coli (UPEC). The objective of this work was detection and the phylogenetic characterization of hospital-acquired isolates of uropathogenic E. coli in cancer patients and the determination of its relation with antibiotic resistance. A total of 110 uropathogenic E. coli responsible for hospital-acquired urinary tract infections in cancer patients were included in this study. A triplex PCR was employed to segregate different isolates into four different phylogenetic groups (A, B1, B2 and D). Drug resistance was evaluated by the disc diffusion method. All of the isolates were multiple drug-resistant (MDR) and 38.18% of all UPEC isolates were extended-spectrum beta-lactamase (ESBL) producers from which 52% were positive for the blaCTX-M gene, 40% for the blaTEM gene, and 17% for the blaSHVgene. Among 42 ESBL-producing uropathogenic E. coli isolates, the majority belonged to phylogenetic group B2 (43%), followed by group D (36%), group A (19%) and group B1 (2%). Our results have shown the emergence of MDR isolates among uropathogenic E. coli with the dominance of phylogenetic group B2. Groups A and B1 were relatively less common. The most effective drug in all phylogenetic groups was imipenem.

Molecular Epidemiology and Mechanisms of High-Level Resistance to Meropenem and Imipenem in Pseudomonas aeruginosa.

PURPOSE: Pseudomonas aeruginosa possesses a large number of resistance mechanisms to different antimicrobials with carbapenems being the most powerful in treating resistant P. aeruginosa. Hence, it is imperative to explore different mechanisms of carbapenems-resistance in P. aeruginosa to achieve successful treatment through the design of new drugs acting on this interaction to combat against antimicrobial resistance. STRAINS AND METHODS: A total of 634 P. aeruginosa clinical isolates were collected from various patient sources and their MIC levels were measured. Molecular evaluation of carbapenem resistance was assessed by investigating the presence of bla IMP1, bla IMP2, bla VIM1, bla VIM2, bla SPM and bla NDM genes and the gene expression of the following multi-drug efflux pump systems: MexAB-OprM, MexCD-OprJ, MexEF-OprN and MexXY-OprM and its correlation with MIC. Isolates were typed by Random Amplified Polymorphic DNA (RAPD)-typing. RESULTS: Carbapenem resistance was detected in 32 (5%) isolates, which were all imipenem resistant (of which 29 were meropenem resistant). High-level resistance (≥64mg/mL) to imipenem was found in 27 (84.3%) isolates, and to meropenem in 28 (96.5%) isolates. The carbapenemase bla VIM-1 was found in 31 isolates, while bla NDM was detected in 4 isolates. None of the isolates possessed either bla- VIM-2, bla IMP-1, bla IMP-2 or bla SPM. The majority of the isolates displayed over-expression of MexCD-OprJ (75%) followed by MexXY-OprM efflux pump (62%), while MexAB-OprM and MexEF-OprN efflux pumps were overexpressed in 21.8% and 18.7% of the isolates, respectively, with no down-regulation of oprD in any of the isolates. A strong correlation was found between CDJ efflux pump expression and meropenem, imipenem resistance (r=0.532, 0.654, p<0.001, <0.001) respectively. Four major clusters were detected by RAPD-typing: group 1(10 isolates), group 3 (9 isolates), group 2 (8 isolates) while the fourth group (4) included 4 isolates (12.5% polymorphism). CONCLUSION: High-level carbapenem resistance reported in this study was allied to multiple mechanisms including carbapenemase production and efflux-pump over-expression. Threatening cross-infection is possible inside the hospital and stringent infection control measures are crucial.