الفهرس 
Introduction and aim of the workOnly 14 pages are availabe for public view
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Abstract
Urinary tract infections caused by uropathogenic Escherichia coli strains are one of the most common bacterial infections that affect immunocompromised cancer patients. The management of infections caused by UPEC is complicated due to the increasing resistance to antimicrobial agents. Extended-spectrum β-lactamase (ESBL) production is a common mechanism of resistance in E.coli to β-lactam antimicrobial agents containing an oxyimino-group including third- generation cephalosporins as well as monobactam (aztreonam).
The aim of this study was to detect the prevalence of ESBL producers among uropathogenic E.coli isolates from cancer patients and to characterize detected ESBL producing isolates by detection of some ESBL genes(CTX- M, TEM, SHV) then sequencing of amplified products for these genes by sanger sequencing method. Also, this study investigated the prevalence of antimicrobial resistance, virulence genes, and its relationship with phylogenetic groups among ESBL producing uropathogenic E.coli isolate. Also, our study was proposed to characterize the genetic diversity of UPEC isolates using ERIC-PCR method.
In the present study, a total number of 110 (72.4%) urine samples were positive for E. coli (UPEC ) recovered from 152 cancer patients suffering from UTIs admitted at Assuit University Hospital.
UPEC isolates were the most prevalent among patients with bladder cancer 90.14%, followed by patients with uterus cancer 84.00%, patients with breast cancer 75.00%, patients with lung cancer 57.14%, patients with Acute myeloid leukemia cancer 45.45%, patients with Esophageal cancer 21.43%, finally patients with stomach cancer 12.50%.
The disk diffusion susceptibility method was performed to determine drug resistance. It was found that UPEC isolates exhibited maximal resistance to ceftriaxone 81.82%, followed by sulfamethoxazole
/trimethoprim 80%, cefotaxime 78.18%, ceftazidime 74.55%, aztreonam
and cefepime each 70.91%, ciprofloxacin 60.00%, levofloxacin 45.45%, gentamicin 42.73%, moderate resistance to amikacin 29%, nitrofurantoin 25.45% and the lowest rate of resistance was to imipenem 21.82%.
A total of 51 UPEC isolates (46.63%) which showed resistance to one or more of ceftazidime, aztreonam, cefotaxime, or ceftriaxone were found as potential ESBL producers. Double Disk Synergy Test confirmed 42 (38.18%) of UPEC isolates as ESBL producers.
In our study, the resistance level to ceftriaxone, ceftazidime, cefotaxime, and aztreonam was highly significant in ESBL producing UPEC isolates in comparison with non-ESBL producing isolates. Also, it was observed that ESBL-producing isolates exhibited higher resistant rates to the non-β lactam drugs, ciprofloxacin, and nitrofurantoin compared to non-ESBL producing isolates.
All ESBL producing UPEC isolates were analyzed by PCR for the detection of ESBL genes. It was found that CTX-M (52.38%) was the main type of ESBLs; TEM was the second (40.48%), then SHV (16.67%).
In our study, Sequencing analysis for the PCR products of ESBL genes was done by the Sanger sequencing method to identify allele types for (CTX-M, TEM, and SHV) genes. DNA sequence analysis of the CTX- M gene showed that the blaCTX-M-15 allele type(6/8) was the most predominant CTX-M variant followed by the blaCTX-M-14 allele type(2/8).
Sequence analysis of the TEM gene showed that the bla-TEM-1 allele was the only detected allele type 100%, while the SHV gene showed that SHV 12 allele was the only detected allele type100%.
In the current study, phylogenetic grouping was carried out for EP- UPEC isolates according to the method described by Clermont et al., 2000. Phylogenetic typing revealed that the majority of UPEC isolates belonged to phylogenetic group B2 (42.86%) followed by group D (35.71%), groups A (19.05%), and group B1 (2.38%).
Regarding the correlation between phylogenetic groups and drug resistance. It was observed that group B2 includes the most resistant UPEC isolates to antimicrobial agents. Also, we observed a significant difference between phylogenetic groups and resistance to different groups of antibiotics.
Our phylogenetic analysis of the isolates revealed that strains harboring the CTX-M gene mostly belonged to the phylogenetic group D and there is a significant difference in the frequency of CTX-M type between the phylogenetic groups.
The frequencies of the studied virulence genes were reported in our study. Out of 42 UPEC isolates, the papC gene was the most common virulence gene and was detected in 55% of isolates followed by the iutA gene detected in 38% of isolates and cnf1 gene detected in 2% of isolates. Carriage of virulence factors was significantly more frequent in the phylogenetic groups B2 and D, compared to groups A and B1.
The ERIC PCR was successfully producing multiple amplicons ranging from (2-11bands) in each strain with different molecular weights ranging from 3000- 285bp. Identical ERIC PCR profiles (identical banding patterns) were shown in some EP −UPEC isolates while 22 isolates show different banding patterns.
The phylogenetic dendrogram of ERIC-PCR showed that the 42 isolates can be differentiated into three major clusters (Cluster I, II, and III). Cluster I represented 76.19%, Cluster II represented 19 %, and cluster III representing 4.76%.