Microarray long oligo probe designing for Escherichia coli: an in-silico DNA marker extraction.

105 Central European Journal of Urology URINARY TRACT INFECTIONS ORIGINAL PAPER Microarray long oligo probe designing for Escherichia coli: an in-silico DNA marker extraction Payam Behzadi1, Ali Najafi1, Elham Behzadi2, Reza Ranjbar1 Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran Department of Microbiology, College of Basic Sciences, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran 1 2 Citation: Behzadi P, Najafi A, Behzadi E, Ranjbar R. Microarray long oligo probe designing for Escherichia coli: an in-silico DNA marker extraction. Cent European J Urol. 2016; 69: 105-111. Article history Submitted: June 24, 2015 Accepted: Dec. 21, 2015 Published online: Jan. 18, 2016 Corresponding author Reza Ranjbar Molecular Biology Research Center Baqiyatallah University of Medical Sciences Tehran, Iran phone: +98 218 803 98 83 Introduction Urinary tract infections are predominant diseases which may be caused by different pathogenic microorganisms, particularly Escherichia coli (E.coli). DNA microarray technology is an accurate, rapid, sensitive, and specific diagnostic tool which may lead to definite diagnosis and treatment of several infectious diseases. DNA microarray is a multi-process method in which probe designing plays an important. Therefore, the authors of the present study have tried to design a range of effective and proper long oligo microarray probes for detection and identification of different strains of pathogenic E.coli and in particular, uropathogenic E.coli (UPEC). Material and methods E.coli O26 H11 11368 uid41021 was selected as the standard strain for probe designing. This strain encompasses the largest nucleotide sequence and the most number of genes among other pathogenic strains of E.coli. For performing this in silico survey, NCBI database, GReview Server, PanSeq Server, Oligoanalyzer tool, and AlleleID 7.7 were used to design accurate, appropriate, effective, and flexible long oligo microarray probes. Moreover, the genome of E.coli and its closely related microorganisms were compared. Results In this study, 15 long oligo microarray probes were designed for detecting and identifying different strains of E.coli such as UPEC. These probes possessed the best physico-chemical characteristics. The functional and structural properties of the designed probes were recognized by practical tools and softwares. Conclusions The use of reliable advanced technologies and methodologies for probe designing guarentees the high quality of microarray probes and makes DNA microarray technology more flexible and an effective diagnostic technique. Key Words: urinary tract infection ‹› E.coli ‹› microarray ‹› probe designing INTRODUCTION Escherichia coli (E.coli) is a potential uropathogenic bacterium which may cause a wide range of urinary tract infections (UTIs) including asymptomatic and/or symptomatic bacteriuria, cystis, and pyelonephritis both in children and adults. UTIs caused by UPEC are the most spread infections in the world. According to previous surveys, community acquired UTIs caused by UPEC ranks first in comparison with other pathogenic agents Cent European J Urol. 2016; 69: 105-111 and UPEC related nosocomial UTIs are in second place, worldwide [1–8]. The presence of several virulence factors enables UPEC to cause different types of UTIs in human hosts. Adhesins, different types of fimbrial and afimbrial structures, haemolysins, and cytotoxic necrotizing factors are the most important and well-known virulence factors in UPEC strains. Although identification of virulence factor genes is possible through Polymerase Chain Reaction (PCR) based molecular techniques in simple levels, for fine detection and doi: 10.5173/ceju.2016.654 106 Central European Journal of Urology Table 1. 61 Reported identified Escherichia coli (E.coli) genomes via NCBI FTP site [11, 20, 21] E.coli strains E.coli 042 uid161985 E.coli 536 uid58531 E.coli 55989 uid59383 Removed from NCBI RefSeq E.coli ABU 83972 uid161975 E.coli APEC O1 uid58623 E.coli APEC O78 uid187277 E.coli ATCC 8739 uid58783 E.coli BL21 DE3 uid161947 E.coli BL21 DE3 uid161949 E.coli BW2952 uid59391 E.coli B REL606 uid58803 E.coli CFT073 uid57915 Removed from NCBI RefSeq E.coli DH1 uid161951 E.coli DH1 uid162051 E.coli E24377A uid58395 E.coli ED1a uid59379 Removed from NCBI RefSeq E.coli ETEC H10407 uid161993 E.coli HS uid58393 Removed from NCBI RefSeq E.coli IAI1 uid59377 Removed from NCBI RefSeq E.coli IAI39 uid59381 E.coli IHE3034 uid162007 E.coli JJ1886 uid226103 E.coli KO11FL uid162099 E.coli KO11FL uid52593 E.coli K 12 substr DH10B_uid58979 Removed from NCBI RefSeq E.coli K 12 substr MDS42 uid193705 E.coli K 12 substr MG1655 uid57779 E.coli K 12 substr W3110 uid161931 Removed from NCBI RefSeq E.coli LF82 uid161965 Removed from NCBI RefSeq E.coli LY180 uid219461 E.coli NA114 uid162139 E.coli O103 H2 12009 uid41013 E.coli O104 H4 2009EL 2050 uid175905 E.coli O104 H4 2009EL 2071 uid176128 E.coli O104 H4 2011C 3493 uid176127 E.coli O111 H 11128 uid41023 E.coli O127 H6 E2348 69 uid59343 Removed from NCBI RefSeq E.coli O157 H7 EC4115 uid59091 E.coli O157 H7 EDL933 uid57831 Removed from NCBI RefSeq E.coli O157 H7 TW14359 uid59235 E.coli O157 H7 uid57781 E.coli O26 H11 11368 uid41021 E.coli O55 H7 CB9615 uid46655 E.coli O55 H7 RM12579 uid162153 E.coli O7 K1 CE10 uid162115 E.coli O83 H1 NRG 857C uid161987 Complete genome/RefSeq accessio no NC_017626 NC_008253 Sequence length (bp) 5,241,977 4,938,920 Total genes 5,392 4,816 NC_011748 5,154,862 Not mentioned NC_017631 NC_008563 NC_020163 NC_010468 NC_012971 NC_012892 NC_012759 NC_012967 5,131,397 5,082,025 4,798,435 4,746,218 4,558,953 4,558,947 4,578,159 4,629,812 5,083 5,572 4,810 4,644 4,530 4,530 4,564 4,573 NC_004431 5,231,428 Not mentioned NC_017625 NC_017638 NC_009801 4,630,707 4,621,430 4,979,619 4,578 4,573 5,301 NC_011745 5,209,548 Not mentioned NC_017633 5,153,435 5,411 NC_009800 4,643,538 Not mentioned NC_011741 4,700,560 Not mentioned NC_011750 NC_017628 NC_022648 NC_017660 NC_016902 5,132,068 5,108,383 5,129,938 5,021,812 4,920,168 Not mentioned 5,132 5,397 4,963 5,037 NC_010473 4,686,137 Not mentioned NC_020518 NC_000913 3,976,195 4,641,652 3,872 Not mentioned NC_007779 4,646,332 Not mentioned NC_011993 4,773,108 Not mentioned NC_022364 NC_017644 NC_013353 NC_018650 NC_018661 NC_018658 NC_013364 4,835,601 4,971,461 5,449,314 5,253,138 5,312,586 5,273,097 5,371,077 4,789 5,039 5,689 5,529 5,475 Not mentioned 6,034 NC_011601 4,965,553 Not mentioned NC_011353 5,572,075 5,924 NC_002655 5,528,445 Not mentioned NC_013008 NC_002695 NC_013361 NC_013941 NC_017656 NC_017646 NC_017634 5,528,136 5,498,450 5,697,240 5,386,352 5,263,980 5,313,531 4,747,819 5,820 Not mentioned 6,125 5,526 5,495 5,443 Not mentioned 107 Central European Journal of Urology Table 1. 61 Reported identified Escherichia coli (E.coli) genomes via NCBI FTP site [11, 20, 21] (...truncated)