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Article
Sequencing-based phylogenetic-study of Babesia spp detected in tick tissues in Al-Diwaniyah province, Iraq
دراسة تعاقبية للقواعد النتروجينية ونسلية للـ Babesia spp المحددة في انسجة القراد في مدينة الديوانية، العراق

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Abstract

Our study purpose was to investigate the evolution of Babesia spp isolated from tissues of ticks that were found on 150 cows in Al-Diwaniyah province, Iraq. To fulfill the required purpose, sampling of 10 ticks was performed from each infested cow. These obtained ticks were morphologically recognized first, and then they were introduced to Lab investigation that was started with crushing the tick tissues to extract the genomic DNA of the Babesia spp. The DNA was then applied to polymerase chain reaction (PCR) method to recognize the amplification of the region that is related to the 18S rRNA gene. The resulted-amplified products were sequenced for the purpose of confirming and doing the phylogenetic analyses. Here, our study has demonstrated 2 different species according to the results of the sequencing and the phylogenetic analyses of the tested Babesisa species. These 2 species are SP1 and SP2. When the phylogenetic tree was built up, the results showed that SP1 and SP2 are closely related to Babesia bovis (HQ264126.1), an isolate from Texas, USA. Our study indicates interesting and valued data that could be used to study various aspects of the tick, Babesia species, and their control in Al-Diwaniyah City, Iraq.

هدفت دراستنا التحري عن تطور الـ Babesia spp المعزولة من أنسجة القراد الذي وجد على 150 بقرة في مدينة الديوانية، العراق. لغرض تحقيق ذلك تم اخذ 10 قرادات من كل بقرة مصابة. تم تمييز هذه القرادات مظهريا في بادئ الأمر، وبعد ذلك تم معاملة هذه القرادات مختبريا والتي بدأت بسحق أنسجة تلك القرادات لاستخلاص الـ DNA للـ Babesia spp. عرض الـ DNA بعد ذلك لطريقة تفاعل أنزيم البلمرة المتسلسل (PCR) لتميز تضخيم المنطقة العائدة للجين 18S rRNA. درس المنتوج المضخم تعاقبيا بالنسبة للقواعد النتروجينية لتاكيد التشخيص وعمل التحليلات النسلية. هنا، دراستنا عرضت نوعين اعتمادا على النتائج الخاصة بالتعاقب والتحليلات النسلية لانواع Babesia المفحوصة. هذه الانواع هي SP1 و SP2. عندما بنيت الشجرة النسلية، أظهرت النتائج أن SP1 و SP2 قريبة جدا من Babesia bovis (HQ264126.1)، عزلة من ولاية تكساس، الولايات المتحدة الأمريكية. تشير دراستنا إلى بيانات قيمة ومثيرة للاهتمام والتي ممكن استخدامها لدراسة جوانب مختلفة من القرادة، أنواع الـ Babesia، والسيطرة عليهما في مدينة الديوانية، العراق.

Keywords

PCR --- phylogeny --- Babesia --- tick


Article
Genotyping of Klebsiella spp. isolated from different clinical sources
التنميط الجيني لبكتريا Klebsiella spp المعزولة من مصادر سريرية مختلفة

Authors: Dalal S. Al- Rubaye دلال صالح الربيعي --- Heba Mohammed Hamza هبة محمد حمزة --- Thanaa R. Abdulrahman ثناء رشيد عبد الرحمن
Journal: Iraqi Journal of Science المجلة العراقية للعلوم ISSN: 00672904/23121637 Year: 2016 Volume: 57 Issue: 3B Pages: 1937-1951
Publisher: Baghdad University جامعة بغداد

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Abstract

A total of 172 clinical were obtained over 6 months. Klebsiella spp. was detected in 58 (33.7%) samples with a high percentage 29 (50%) in urine in female and low percentage 1(1.7%) in pus and burn swabs in male, and the vaginal swab was 1(1.7%). The female to male ratio was 3.1:1. PCR detection showed that 51(87.93%) out of 58 produce 108 bp. product with rpoB specific primer that represented K. pneumonia. Whereas 7(12.07%) showed PCR product with 343 bp by K. oxytoca specific primer (peh X), furthermore, the sequences of two selected isolates showed that the species related to K. oxytoca strain CAV1335, and to K. oxytoca strain CAV1374. Five selected isolates were re-tested by the gyr A primer, all were showed specific band product with 441bp. Sequencing blast analysis for these isolates showed that one was related to K. pneumoniae subsp. pneumoniae strain RJF999, two isolates related to K. pneumoniae strain 17265 GyrA, one related to K. oxytoca strain 7102 GyrA and one related to K. pneumonia isolate 103 GyrA gene. Phylogenetic tree analysis showed the relation of 3 K. pneumoniae isolates to USA and UK strains and one with the Asian strains, and 2 K. oxytoca isolates have a relation within the Iranian strains and one has a genetic variation.

جمعت 172 عينة سريرية على مدى اكثر من ستة أشهر، وتم الكشف عن الكليبسيلا في 58 (33.7%) عينة وكانت اعلى نسبة 29 (50%) في عينات الادرار في النساء, واقل نسبة 1 (1.7%) من مسحات القيح والجروح في الدكور وبنفس النسبة في مسحات المهبل. وأشارت النتائج إلى أن نسبة عزلات الكليبسيلا في الإناث إلى الذكور هي 1:3.1. اظهر فحص انزيم البلمرة المتسلسل أن نسبة 51 (87.98%) من اصل 58 باستخدام بادئ rpo B قطعه بحجم 108 والتي تشير الى pneumoniae K. . بينما اظهرت 7(12.07%) قطعة بحجم 343 بأستخدام بادئ pehx الخاص ببكتيريا K.oxytoca وكان تطابق تسلسل القواعد النتروجينية لعزلتين منتخبتين منها الى انها ترجع الى K. oxytoca strain CAV1374و K. oxytoca strain CAV1335 تم اختبار خمس عزلات منتخبة باستخدام بادئ gyra واظهرت قطعة بحجم 441 باستخدام طريقة انزيم البلمرة المتسلسل للقواعد النتروجينة الى ان واحدة تعود الى K. pneumoniae subsp. Pneumonia strain RJF999 واثنين الى K. pneumonia strain 17265 GyrA وواحدة K.oxytoca strain 7102 GyrA وواحدة الى K.pneumonia isolate 103 . اظهر فحص شجرة العائلة الى ان ثلاث عزلات من K.pneumoniaقريبة بصفاتها من العزلات الامريكية والبريطانية وواحدة قريبة من صفات العزلات الاسيوية بينما كانت عزلتين K.oxytoca قريبة بصفاتها من العزلات الايرانية وعزلة واحدة مغايرة وذات صفات جينية بعيدة.

Keywords

K.oxytoca --- PCR --- sequencing --- phylogeny


Article
MOLECULAR IDENTIFICATION AND PHYLOGENETIC-TREE ANALYSIS OF MONIEZIA SPECIES FROM SHEEP IN AL-DIWANIYAH CITY

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Abstract

The present study was performed to detect the molecular and the phylogenetic identification of species that belonging to the genus of Moniezia Blanchard, 1891 which affected intestines of sheep in Al-Diwaniyah city, Iraq; fifty intestine samples were sought for the infestation of Moniezia spp. from the city slaughterhouse from 1 October to 30 November 2017, this tapeworm was found to infest the intestines of 13 sheep. For morphological identify the genus of this tapeworm, eggs from one gravid proglottid of the thirteen worms were examined, polymerase chain reaction (PCR) and the PCR-product-based sequencing were applied on 4 Moniezia tapeworms targeting a specific region of the 18S rRNA gene. The sequencing has shown 2 species of Moniezia, SP1 and SP2 ,these two species revealed close matching on the phylogenetic tree to an according to the current study findings, Moniezia spp. affect on sheep in the city of Al-Diwaniyah, Iraq, these findings give interesting information about the evolution history of this worm in the studied city.

اجريت الدراسة للكشف عن التحديد النشوئي والجزيئي لديدان الانواع العائدة للجنس Moniezia Blanchard, 1891 التي تؤثر على امعاء الاغنام في مدينة الديوانية, العراق. تم استخراج 50 معي اغنام للبحث عن الاصابة بأنواع هذا الجنس في مجزرة المدينة، اذ وجدت هذه الديدان الشريطية في امعاء 13فرداً من الاغنام لغرض التشخيص المظهري لجنس هذه الديدان. صبغت خمسة قطع جسمية ناضجة بصبغة الكارمن مبينة الاشكال التناسلية البالغة لهذه الدودة.

Keywords

Cestoda --- Moniezia --- PCR --- Phylogeny --- Sheep


Article
Phylogenetic Analysis of Streptomyces spp. Exhibited Different Antimicrobial Activities
تحليل النسل لانواع الستربتومايسس المنتجة للمضادات الميكروبية ذات الفعاليات المختلفة

Author: Dalal S. Al-Rubaye دلال صالح الربيعي
Journal: Iraqi Journal of Science المجلة العراقية للعلوم ISSN: 00672904/23121637 Year: 2016 Volume: 57 Issue: 1B Pages: 397-403
Publisher: Baghdad University جامعة بغداد

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Abstract

Fourteen isolates were collected from a previous study and all were assigned to be Streptomyces genus, according to physiological and biochemical tests, however all the isolates varied morphologically and exhibited different antimicrobial activity. All 14 isolates were confirmed Streptomyces by 16S rRNA PCR amplification. Six isolates with high antimicrobial activities were ascertained Streptomyces spp. by sequencing and phylogenetic analysis. Two isolates among the selected 6 isolates with antimicrobial activity against E. coli and S. aureus . It recommended to make a complete sequence for 16S rRNA to detect the species that produce antimicrobial substances, also it’s very necessary to identify the natural structure of these product.

تم الحصول على 14 عزلة من دراسة سابقه والتي تم تشخيصها على انها جنس ال Streptomycesاعتمادا على الفحوصات الفسيولوجية والبايوكيميائية.اظهرت العزلات اختلاف بالشكل وبالفعالية المضادة للميكروبات. شخصت العزلات جزيئياباستخدام تقنية تفاعل انزيم البلمرة المتسلسل واكدت النتائج ان 14 عزله تابعه لجنس .Streptomycesست عزلات اثبتت انها تابعه لجنس spp. Streptomyces ذات الفعالية المضادة للميكروبات باستخدام تحليل تسلسل القواعد النتروجينيه وتحليل النسل¸ كما اظهرت عزلتان من بين الست عزل فعالية عالية ضد بكتريا ال E. coli و S. aureus.


Article
Phylogenetic tree analysis study of Lumpy skin disease virus based envelope protein P32 gene in Al-Qadisiyah Province- Iraq

Author: Khalefa Ali Mansour
Journal: Al-Qadisiyah Journal of Veterinary Medicine Sciences مجلة القادسية لعلوم الطب البيطري ISSN: 18185746 23134429 Year: 2017 Volume: 16 Issue: 1 Pages: 99-104
Publisher: Al-Qadisiyah University جامعة القادسية

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Abstract

In this study, fifty samples from nodules of skin tissue collected from cattle were clinically supposed to be infected with lumpy skin disease (LSD) from deferent area in Al-Qadisiyah province .These specimens were provided to PCR assay. The endpoint of conventional PCR assay was sent to sequence analysis. The results revealed that thirty-nine samples out of fifty were positive to lumpy skin disease virus at 752bp PCR product of p32 gene, the sequence analysis of five positive samples were done as a confirmative diagnosis to PCR assay. The sequences of these five samples can be found under the accession numbers (KR066462.1,KR066463.1,KR066464.1,KR066465.1 and KR066466.1) at NCBI-Gen Bank submission. In conclusion; the sequence analysis of five local isolate of lumpy skin disease virus was close related to NCBI-Blast reference lumpy skin disease virus isolate (KU720359.1) and Kurdistan isolates, whereas others "Turkish and Egyptian isolates" were different.

Keywords

LSDV --- P32 gene --- PCR --- sequence analysis --- Phylogeny


Article
Molecular and Phylogenetic study of Klebsiellaaerogenes isolated from infected burned skin
دراسة جزيئية و phylogenetic من Klebsiellaaerogenes المعزولة من الجلد المحروق المصاب

Authors: HayderNajiAyyez حيدر ناجي عايز --- Alaa Abdelkadhim Jawad علاء عبد الكاظم جواد --- Hayder Ali Muhammid حيدر علي محمد
Journal: Al-Qadisiyah Medical Journal مجلة القادسية الطبية ISSN: 18170153 Year: 2019 Volume: 15 Issue: 1 Pages: 5-8
Publisher: Al-Qadisiyah University جامعة القادسية

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Abstract

This study was intended to explore if infected burns of patients of Al-Diwaniyah City, Iraq, haveKlebsiellaaerogenes as one of the pathogenic bacteria that infect burns or wounds. For such case, traditional, Polymerase chain reaction (PCR), and DNA gyrase subunit B gene (gyrB)-partial sequencing tooling to confirm diagnosis. Primary testing of the sample using blood and MacConkey agars and certain biochemical tests alarmed that the bacterium was present in this specimen. The PCR results confirmed the occurrence of the infection by this bacterial agent. The gyrBgene-partial sequencing followed by drawing a phylogenic tree placed the bacterium in a separate cluster from other Enterobacteriaceae family members. The current study indicates that this bacterium is present in the infected burns or injuries in Al-Diwaniyahcity.Our results have been reviewed the current trends in molecular phylogenetic analysis, A computational phylogenetic study and data was approach and registered Klebsiellaaerogenes with accession number (MG560868.1).

تهدف هذه الدراسة إلى اكتشاف ما إذا كانت حروق مرضى مدينة الديوانية في العراق مصابة بالبكتريا السبيلوجينية كأحد البكتيريا المسببة للأمراض التي تصيب الحروق أو الجروح. في مثل هذه الحالة ، فإن تفاعل تسلسل البوليميريز التقليدي (PCR) ، وتسلسل جيني الدنا الوريدي وحدة فرعية (B) (gyrB) لتأكيد التشخيص. إن الاختبار الأولي للعينة باستخدام أجار الدم والماكونكي وبعض الفحوصات الكيميائية الحيوية قد أثار جزعها من وجود البكتيريا في هذه العينة. أكدت نتائج PCR حدوث العدوى بهذا العامل البكتيري. وضع التسلسل الجزئي لل gyrBgene متبوعًا برسم شجرة نشوء البكتيريا في مجموعة منفصلة عن أفراد عائلة Enterobacteriaceae. تشير الدراسة الحالية إلى أن هذه البكتيريا موجودة في الحروق أو الإصابات المصابة في الديوانية. وقد تم استعراض نتائجنا في الاتجاهات الحالية في التحليل الوراثي للتطور الجزيئي ، وكانت دراسة النشوء والبيانات الحسابية الحسابية هي المنهجية المسجلة وتم تسجيل الكليبسيلايروجينيز برقم الانضمام (MG560868). 1).


Article
Comparative Study of Molecular Phylogeny, Adhesion Genes and Antiobiogram of Escherichia Coli Clinical Isolates From High Vaginal Swabs and Urine in Women

Author: Mohanad Mohsin Ahmed
Journal: Karbala Journal of Medicine مجلة كربلاء الطبية ISSN: 19905483 Year: 2015 Volume: 8 Issue: 1 Pages: 2034-2042
Publisher: Kerbala University جامعة كربلاء

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Abstract

background: Escherichia coli is a frequent cause of urinary tract infections, however, its identity as pathogen in the cervico-vaginal area is required to be ascertained. In addition, source (s) for E.coli colonzing female vagina is needed to be confirmed, whether its fecal contamination or from urinary tract.Aim of the Study: To perform a comparative analysis of the E. coli clinical isolates from vagina versus those from urine in terms of molecular phylogeny, molecular determinants of virulence and antimicrobial susceptibility.Materials and methods: A total of 60 E. coli strains from high vaginal swabs (n=30) and urine (n=30) were analyzed. Identification of phylogenetic groups and detection of adhesive genes were conducted by 2 different multiplex PCR systems. Antibiograms for all isolates were performed by Kirby-Bauer method.Results and Discussion: Majority of vaginal E coli (VEC) isolates were belong to B2 phylogenetic group (n=20, 66.7%), whereas, majority of uro-pathogenic E. coli (UPEC) isolates were distributed between two phylogenetic groups, namely B2 12 (40%) and D 11 (36.7%). Therefore, most of the strains from both vagina and urine are belonging to pathogenic phylogenetic groups; however, they differ in prevalence of the groups. The pap gene has a higher frequency among UPEC (n= 13, 43.3%) than in VEC isolates (n=7, 23.3%). Similarly, sfa gene has a higher frequency in VEC isolates (n= 20, 66.7%) than in UPEC isolates 11 (36.4%). Consequently, adhesion genes playing roles in vaginal colonization may differ from that in urinary tract .VEC strains where highly susceptible to ciprofloxacin (100%) followed by nitrofurantoin (73.3%) and nalidixic acid (70%). Whereas UPEC strains were highly susceptible to nitrofurantoin (100%) followed by nalidixic acid. Thus, it seems that cirpofloxacin is appropriate for empirical therapy in vaginal infections, whereas nitrofurantoin is more appropriate for empirical therapy in UTI.Conclusion: Strains isolated from high vaginal swabs differ from strains isolated from urine in the prevalence of phyelogenetic groups andmolecular determinants of virulence as well as in antibiograms.

Keywords

E. coli --- pap --- sfa --- afa --- high vaginal swab --- Phylogeny


Article
Prevalence and Molecular Characterization of Fim H Gene in Escherichia Coli Isolates Recovered From Patients With Utis

Author: Narmin Saeed Merza
Journal: Medical Journal of Babylon مجلة بابل الطبية ISSN: 1812156X 23126760 Year: 2017 Volume: 14 Issue: 3 Pages: 470 -477
Publisher: Babylon University جامعة بابل

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Abstract

In this study, the prevalence of fim H gene was studied among 105 E. coli isolates obtained from urine samples of patients attended Azadi hospital in Duhok City. The intended gene was detected in94.3% of the isolates. Triplex PCR assay was applied and according to which the studied isolates were assigned into four groups namely A, B1, B2, and D groups which constituted 20.95 %, 3.8 %, 54.28 %, 20.95 %, respectively. Ten randomly selected isolates were subjected to SNPs fimH analysis with 3 reference strains of E. coli. The results revealed that 44 SNPs observed at 42 polymorphic sites accounting for 5.59%. All mutations were of substitutions and 29.5 % of mutations were transversions while transition type mutations constituted of 70.5 %. Ten SNPs accounting for 22.7 % of mutations gave rise to amino-acid changes (sense mutation) while the rest 34 (77.3 %) resulted in silent mutations. Moreover, twelve SNPs were singletons and among them five were with amino acid replacements. Amino acid replacements due to SNPs accounted for 1.27% of whole sequenced fragment of fimH.It can be concluded that there is no relationship inferred between the isolates of E.coli when the two phylotyping techniques are compared but the results of both can serve the purpose of genotypic characterization of uropathogenic E. coli.

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