Date of Award

5-2019

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Medical Education

First Advisor

Dr. Agnes Sonnevend

Second Advisor

Tahir Rizvi

Third Advisor

Dr. Zahir Babiker

Abstract

Resistance to carbapenems, the ultimate beta-lactam antibiotics used to treat life-threatening Gram-negative infections associates with very high mortality. Consequently, carbapenem-resistant Enterobacteriaceae (CRE), which are usually multi- or extremely drug-resistant, is considered a critical pathogen. To help to control their spread, we investigated the molecular epidemiology of CRE in the United Arab Emirates (UAE) and its neighboring countries. CRE isolated in the UAE were screened for IncX3 incompatibility type plasmids carrying carbapenemases. The complete sequence of the IncX3 plasmids identified was established. Thirty CRE carried blaNDM-1, blaNDM-4, blaNDM-5, blaNDM-7, blaOXA-181, and blaKPC-2 on IncX3 plasmids. This CRE belonged to 16 sequence types of five different species. Phylogenetic analysis of the conserved regions of local IncX3 plasmids and those described globally clustered them according to the carbapenemase genes carried, suggesting that they do not evolve locally, rather, are imported from other regions. Furthermore, we investigated members of the Klebsiella pneumonia ST14 clone, which was found to be significantly associated with NDM- and OXA-48-like double carbapenemase production, with extreme drug resistance, and with being isolated from Emirati patients in Dubai. To gain a deeper insight into the molecular features of this clone, 39 CRKP-ST14 selected from five cities of the UAE, Bahrain, and Saudi Arabia were subjected to whole-genome sequencing, and their resistome, virulome, and core genome MLST was assessed. cgMLST revealed three clusters of 16 isolates from five UAE cities (C1), 11 isolates from three UAE cities and Bahrain (C2) and, the 5 isolates from Saudi Arabia (C3), respectively, and seven singletons. Resistance gene profile and carbapenemase carrying plasmid types were variable in both C1 and C2 clusters. Cluster 2 exhibited a capsular switch from K2 to K64. The successful dissemination of the CRKP-14 clone could be explained by the genetic flexibility demonstrated. Our data show that the emergence of CRE in the United Arab Emirates is a complex phenomenon of likely international transfer of successful plasmids, and also of countrywide clonal transmission of a genetically flexible high-risk Klebsiella pneumonia clone.

Comments

الغرامNegative Gram , ترتبط بمعدل وفيات مرتفع. ولذلك، تعتبر بكتريا المكورات المعوية المقاومة للكاربابينيم CRE , والتي تكون مقاومة بشدة للأدوية، مسبب اساسي للأمراض. وللمساعدة في السيطرة على انتشارها، قمنا بدراسة مستفيضة لهذه البكتيريا باستخدام علم الأوبئة الجزيئي في دولة الإمارات العربية المتحدة والدول المجاورة. تم فحص مجموعات من CRE والتي تحتوي على بلازمي IncX3 الحامل لجينات ال carbapenemases والتسلسل الكامل لبلازميدات IncX3 وجدنا ثلاثين CRE حمل جينات ال1 blaNDM- , ،blaNDM-4 ،blaNDM-5 , blaNDM-7, blaOXA-181 و blakPc-2 على بلازميدات IncX3 . وتنتمي مجموعات ال CRE إلى 16 نوع تسلسلي (ST) لخمسة أنواع بكتيرية .التحليل النسجي للمناطق المحفوظة من بلازميدات IncX3 المحلية ومقارنتها بتلك التي تم وصفها عالميا من حيث جينات ال carbapenemases التي تحملها، اشارت إلى أنها لا تتطور محليًا، بل يتم جلبها من مناطق أخرى.

لقد قمنا ايضا بدراسة نوع معين من بكتيريا الكلبسية الرئوية Klebsiella pneumoniae ST14 , والذي وجد أنه يرتبط بإنتاج ثنائي ال carbapenemases NDM و OXA- 48 , مع مقاومة شديدة للأدوية، وقد تم عزل العينات من المرضى الإماراتيين في مستشفيات دبي. وللحصول على نظرة أعمق للسمات الجزيئية ل 14 ST , تم إخضاع 39 عينة من هذا النوع تم اختيارها من خمس مدن في الإمارات، من البحرين ومن السعودية، إلى فحص ، تسلسلي كامل للجينوم الخاص بهذا النوع، وتم تقييم مقاومتها virulome و .MLST كشفت تقنية cgMLST عن ثلاث مجموعات، تتكون الاولى من 16 عينة من خمس مدن إماراتية (C1) , والثانية من 11 عينة من ثلاث مدن اماراتية بالإضافة الى البحرين (C2) , اما الثالثة فتتكون من 5 عينات من السعودية (C3) , على التوالي وسبعة عينات فردية.

لقد كان التوصيف الجيني لمقاومة المضادات وانواع البلازميدات التي تحمل جينات ال carbapenemase متغيرين في كلا المجموعتين 1 Cو 2 Cولكن نوع ال K2 capsular و64 K كانا مرتبطان بشكل واضح مع 1C و2C على التوالي .هذه المرونة الجينية في –CRKP 14 ST قد تعزز من سرعة انتشار هذا النوع. تشير بياناتنا إلى أن ظهور ال CRE في دولة الإمارات هو ظاهرة معقدة تتمثل في احتمال انتقال دولي للبلازميدات، وإلى انتقال على نطاق الدولة لبكتيريا ال Klebsiella pneumonia عالية الخطورة والمرنةوراثيا.

Acknowledgments

I would like to express my sincere gratitude to my advisor Dr. AgnesSonnevend for her continuous support throughout my Ph.D. study, for her motivation, patience, and immense knowledge. I will always be grateful for the opportunities she kept giving me to grow as a scientist and gain knowledge in microbiology and microbial genetics. Her guidance truly helped me at all the time of research and writing of this thesis.

I would like to thank my co-advisor Prof. Tibor Pal for his encouragement, insightful comments, and discussions which indeed helped me to widen my horizon; I would like to thank also Dr. Farah Mustafa for being a member of my advisor committee and for her support and valuable comments that helped in my research.

My sincere appreciation and gratitude go to Dr. Youssef Idaghdour and Dr. Paul G Higgins for their help in WGS and many thanks to Mame Massar Diengfor his technical assistance.

My heartfelt thanks also go to Dr. Akela Ghazawi, for teaching me everything I get to learn in the lab work, for her support in overcoming numerous obstacles, and for being generous with her time and knowledge. My gratitude extends to my fellow lab members, Mr. Mohamed Elhaj, Dania Darwish, and Greeshma for their continuous help and support

My gratitude goes to the United Arab Emirates University for providing me the fellowship and financial assistance to pursue my Ph.D.

Last but not the least; I would like to thank my family; my dear great father, my dear mother, and my brother for their enormous encouragement and love.

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