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In Escherichia Coli: Experimental and Bioinformatics Analyses Radwa N Morgan et al. Gut Pathog (2019) 11:22 https://doi.org/10.1186/s13099-019-0304-y Gut Pathogens RESEARCH Open Access Prevalence and pathologic efects of colibactin and cytotoxic necrotizing factor-1 (Cnf 1) in Escherichia coli: experimental and bioinformatics analyses Radwa N. Morgan1, Sarra E. Saleh2, Hala A. Farrag1 and Mohammad M. Aboulwafa2* Abstract Background: The colibactin and cytotoxic necrotizing factor 1 (Cnf 1) are toxins with cell cycle modulating efects that contribute to tumorgenesis and hyperproliferation. This study aimed to investigate the prevalence and patho- logic efects of Cnf 1 and colibactin among hemolytic uropathogenic Escherichia coli (UPEC). The bioinformatics approach incorporated in this study aimed to expand the domain of the in vitro study and explore the prevalence of both toxins among other bacterial species. A total of 125 E. coli isolates were recovered from UTIs patients. The isolates were tested for their hemolytic activity, subjected to tissue culture and PCR assays to detect the phenotypic and genotypic features of both toxins. A rat ascending UTI in vivo model was conducted using isolates expressing or non- expressing Cnf 1 and colibactin (ClbA and ClbQ). The bioinformatics analyses were inferred by Maximum likelihood method and the evolutionary relatedness was deduced by MEGA X. Results: Only 21 (16.8%) out of 125 isolates were hemolytic and 10 of these (47.62%) harbored the toxins encod- ing genes (cnf 1+, clbA+ and clbQ+). The phenotypic features of both toxins were exhibited by only 7 of the (cnf 1+clbA+clbQ+) harboring isolates. The severest infections, hyperplastic and genotoxic changes in kidneys and blad- ders were observed in rats infected with the cnf 1+clbA+clbQ+ isolates. Conclusion: Only 33.3% of the hemolytic UPEC isolates exhibited the phenotypic and genotypic features of Cnf 1 and Colibactin. The in vivo animal model results gives an evidence of active Cnf 1 and Colibactin expression and indicates the risks associated with recurrent and chronic UTIs caused by UPEC. The bioinformatics analyses confrmed the predominance of colibactin pks island among Enterobacteriaceae family (92.86%), with the highest occurrence among Escherichia species (53.57%), followed by Klebsiella (28.57%), Citrobacter (7.14%), and Enterobacter species (3.57%). The Cnf 1 is predominant among Escherichia coli (94.05%) and sporadically found among Shigella species (1.08%), Salmonella enterica (0.54%), Yersinia pseudotuberculosis (1.08%), Photobacterium (1.08%), Moritella viscosa (0.54%), and Carnobacterium maltaromaticum (0.54%). A close relatedness was observed between the 54-kb pks island of Escherichia coli, the probiotic Escherichia coli Nissle 1917, Klebsiella aerogenes, Klebsiella pneumoniae and Citrobacter koseri. Keywords: Uropathogenic E. coli (UPEC), Cytotoxic necrotizing factor-1 (Cnf 1), Colibactin (pks island), Rat ascending UTI model, Bioinformatics *Correspondence: [email protected]; [email protected]. edu.eg 2 Microbiology and Immunology Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Abbassia, Cairo 11566, Egypt Full list of author information is available at the end of the article © The Author(s) 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat iveco mmons .org/licen ses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/ publi cdoma in/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Morgan et al. Gut Pathog (2019) 11:22 Page 2 of 18 Background to the bacterial cell suspension of ExPEC and commen- Cyclomodulins are cell cycle modulating toxins that sal E. coli Nissle strain 1917 [7]. Tis cytopathic efect contribute to tumorgenesis. Tese toxins are commonly difered from the efect induced by CDT, Cif or alpha- produced by Gram negative bacteria and four of which hemolysin since it was only contact dependent and lost [cytolethal distending toxin (CDT), cytotoxic necrotizing upon bacterial fltration [5, 7]. Transcriptional analysis of factors (Cnfs), cycle inhibiting factor (Cif) and colibactin] the pks island reveals its division into 7 large transcripts are produced by Escherichia coli species [1–3]. Te func- units, 2 of which covers the majority of the island; the tions of the cyclomodulins are still not completely under- frst includes 6 genes from clbI to clbN (23.3 kb) and the stood. However, their cellular modulating efects suggest second includes 5 genes from clbC to clbG (6.2 kb) [18]. that they attribute in the bacterial persistence, internali- Five Clbs encoded by these transcripts are essential for zation and the development of chronic infections [3, 4]. the colibactin activity being involved in tailoring and Colibactin and Cnf 1 (subset of the Cnfs toxins group) are transporting it to its site of action, these are Clb A, M, Q, prevalent virulence determinants and almost exclusively L and P [19]. On the other hand, the cytotoxic necrotiz- confned to E. coli phylogroup B2 that includes the extra- ing factor one (Cnf 1) catalyzes the deamination of Rho intestinal pathogenic E. coli (ExPEC) and the probiotic family proteins in cultured eukaryotic cells inducing E. coli Nissle strain 1917 [3, 5–7]. Extraintestinal patho- multinucleation [20–22]. Tis cytopathic efect is a char- genic E. coli (ExPEC) are the commonest causative agent acteristic phenotypic feature for the Cnfs and had been of urinary tract infections and highly frequent among diferentiated from the hemolytic activity of the UPEC neonatal meningitis and sepsis [6–8]. Molecular analysis since E. coli hemolysins cytotoxic efect was confned to of uropathogenic E. coli (UPEC) genome revealed that it a lytic efect [23, 24]. Recently, many studies have been harbors pathogenicity islands that are prevalent among focused on exploring the prevalence and impact of coli- Escherichia coli species causing diarrheal diseases and bactin and Cnf 1 after afrming that E. coli producing colonizing the gut [9]. Te pks island and pathogenicity both toxins contributes in tumorgenesis and promotes island II (PAI II) that harbors the hlyCABD operon and invasive carcinomas [25, 26]. It was also noted that Cnf cytotoxic necrotizing factor 1 are the most prevalent 1 and colibactin were overexpressed in the colon of the PAIs among UPEC species causing cystitis in females, CRC than in the normal patients [12, 27]. Tis works prostatitis, pyelonephritis and urosepsis [2, 10, 11]. Tese aimed to investigate the prevalence of colibactin and pathogenicity islands are also prevalent among micro- Cnf 1 among the hemolytic UPEC recovered from uri- biota E. coli that colonizes colon of colorectal carcinoma nary tract infected patients in Egypt. Additionally, an patients (CRC) [12] and healthy newborn children in in vivo animal model was applied to give an insight to Sweden and France acquired from their mothers dur- the possible pathologic efects associated with the pres- ing birth [13, 14]. Moreover, the pks island was prevalent ence of these virulence determinants. Te bioinformat- among members of the Enterobacteriaceae family includ- ics approach aimed to expand the domain of the in vitro ing Klebsiella pneumoniae, Enterobacter aerogenes and model exploring the prevalence of pks island and Cnf 1 Citrobacter Koseri and among Yersinia species while it among diferent related and unrelated bacterial species. was entirely absent in enteroinvasive, enteropathogenic, enterohemorrhagic, enterotoxigenic, and enteroaggrega- Materials and methods tive E. coli species [3, 6, 8]. Such predominance of the pks Reference E. coli strains and clinical E. coli isolates island among the Enterobacteriaceae family suggested Tree reference E. coli strains were used in this study. the spread of this PAI via horizontal gene transfer [5]. Te frst strain was uropathogenic E. coli ATCC 700336 Interestingly, a strong association was noticed between J96 serotype O4:K6 which harbors PAI II (pathogenicity the production of colibactin by ExPEC and other viru- island II) genes that encode hemolysin A and cytotoxic lence determinants including the adhesions determi- necrotizing factor-1 toxins. Te second strain was E. coli nants, production of hemolysin (β-hemolytic activity), 28C serotype O75:K95 isolated from porcine septicemia cytotoxins such as the Cnfs and siderophores such as kindly provided by Professor Dr. Eric Oswald, university Yersiniabactin [2, 6, 15–17]. In 2017, the prevalence and of Toulouse, UPS, faculty of medicine, France. Tis strain association between the β-hemolytic activity, Cnf 1 and harbors hlyA, cnf 1 and clbA, clbQ, clbK, and clbJ genes. colibactin production among E. coli strains phylogroup Te third strain was E. coli ATCC 25299 and it was used B2 that colonize the macaques has reached 100%, 97.7% in the antimicrobial sensitivity testing. and 100%, respectively [17]. Te Colibactin was frst A total of 125 uropathogenic E. coli isolates were discovered in 2006 when cultured Hela cells appeared obtained as grown cells on nutrient agar plates from the megalocytosised (enlarged cells with giant nuclei) with Clinical Pathology lab, Faculty of Medicine, Cairo Uni- accumulated dsDNA breaks following transient exposure versity. Te isolates were recovered from urinary tract Morgan et al. Gut Pathog (2019) 11:22 Page 3 of 18 3 infected patients (in and out patients) with their consent cell suspension was adjusted to 5 × 10 cells/ml. Tereaf- for diagnostic uses and treatment. Te collected isolates ter, 1 ml and 0.1 ml aliquots of the cell suspension were were checked for their identity by growth on MacCo- dispensed into 24 and 96 wells microtiter plates, respec- nkey and EMB agar as well as by partial sequencing of tively. Te plates were re-incubated until the confuent the 16SrRNA amplifed gene which was conducted on 3 monolayers were produced. For the 24 wells plate, 1 ml selected isolates.
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