DOCSLIB.ORG

Whole Genome Sequencing and Comparative Analysis of Novel Pathogen Elizbethkingia Anophelis Against Oxidative Stress

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Whole Genome Sequencing and Comparative Analysis of Novel Pathogen Elizbethkingia Anophelis Against Oxidative Stress This document is downloaded from DR‑NTU (https://dr.ntu.edu.sg) Nanyang Technological University, Singapore. Whole genome sequencing and comparative analysis of novel pathogen elizbethkingia anophelis against oxidative stress Li, Yingying 2017 Li, Y. (2017). Whole genome sequencing and comparative analysis of novel pathogen elizbethkingia anophelis against oxidative stress. Doctoral thesis, Nanyang Technological University, Singapore. http://hdl.handle.net/10356/70627 https://doi.org/10.32657/10356/70627 Downloaded on 30 Sep 2021 13:23:09 SGT WHOLE GENOME SEQUENCING AND COMPARATIVE ANALYSIS OF NOVEL PATHOGEN ELIZABETHKINGIA ANOPHELIS AGAINST OXIDATIVE STRESS LI YINGYING School of Biological Sciences 2017 WHOLE GENOME SEQUENCING AND COMPARATIVE ANALYSIS OF NOVEL PATHOGEN ELIZABETHKINGIA ANOPHELIS AGAINST OXIDATIVE STRESS LI YINGYING School of Biological Sciences A thesis submitted to the Nanyang Technological University in fulfillment of the requirement for the degree of Doctor of Philosophy 2017 ACKNOWLEDGEMENT I would like to take this opportunity to express my sincere gratitude to my supervisor Prof Yang Liang and Prof Michael Givskov for giving me an opportunity to work in NTU and for their mentorship and guidance throughout my Ph.D study. I am very grateful that they always gave me the freedom to explore concepts and hypotheses during my study. Their encouragement and enthusiasms for my work have inspired me to work towards the various goals of my project. I would also like to thank Dr. Jeanette Teo for offering me the strain Elizabethkingia anophelis to study with; Dr. Liu Yang and Dr. Martin Tay for their help and guidance in transcriptomics works and sequencing analysis; Ms. Chen Yicai for her guidance in lab skills and data analysis; Mr. Ding Yichen for helping me in data analysis; Dr. Chew Su Chuen and Mr. Yam Kuok Hoong Joey for helping me in imaging study and data analysis; all other group members and all my colleagues in Singapore Centre for Environmental Life Sciences Engineering (SCELSE) for their assistance and help throughout the years. Heartful thanks to my family members especially my dad and mum for always being there giving me support and encouragement. It would not have been possible for me to make it this far in my education without their encouragement and support. Special thanks to my husband Mr. Mao Xianwei, for his patient accompany and consolation at all the difficult times. Last but nut not least, I would like to acknowledge the financial support from National Research Foundation and Ministry of Education Singapore under its Research Centre of Excellence Program, and Nanyang research scholarship for the year 2013-2016. I | P a g e TABLE OF CONTENTS ACKNOWLEDGEMENT ................................................................................................ I TABLE OF CONTENTS ................................................................................................. II LIST OF FIGURES ........................................................................................................ IV LIST OF TABLES ......................................................................................................... VII LIST OF ABBREVIATIONS ..................................................................................... VIII LIST OF PUBLICATIONS ............................................................................................. X ABSTRACT .................................................................................................................. XI CHAPTER 1: Introduction .............................................................................................. 1 1.1 BACKGROUND ................................................................................................... 1 1.2 KNOWLEDGE GAP AND CHALLENGES ........................................................ 2 1.3 OBJECTIVE .......................................................................................................... 3 CHAPTER 2 Literature Review ...................................................................................... 4 2.1 THE GENUS ELIZABETHKINGIA ...................................................................... 4 2.1.1 Identification ................................................................................................. 4 2.1.2 Characteristics of the genus Elizabethkingia ................................................ 5 2.1.3 Elizabethkingia spp. as pathogens................................................................. 6 2.2 BIOFILM ............................................................................................................... 7 2.3 ANTIMICROBIAL RESISTANCE .................................................................... 11 2.4 OXIDATIVE RESISTANCE IN BACTERIUM ................................................ 16 2.5 IRON AND HEME UTILIZATION BY BACTERIUM .................................... 22 CHAPTER 3 Genome Sequencing and Comparative Genomic Analysis of E. anophelis NUHP1 ..................................................................................... 24 3.1 INTRODUCTION ............................................................................................... 24 3.2 MATERIALS AND METHODS ......................................................................... 25 3.2.1 Bacterial strains ........................................................................................... 25 3.2.2 Growth medium and conditions .................................................................. 25 3.2.3 MIC of different antibiotics to E. anophelis NUHP1 ................................. 25 3.2.4 Sample preparation for complete genome sequencing ................................ 26 3.2.5 Comparative genomic analysis ................................................................... 26 3.3 RESULTS AND DISCUSSION .......................................................................... 27 3.3.1 Genome characterization ............................................................................. 27 3.3.2 Antibiotic resistance .................................................................................... 30 3.3.3 Virulence mechanisms revealed by genome analysis ................................. 32 3.3.4 Comparative genomic analysis ................................................................... 36 Genome comparison between NUHP1 and E. anophelis assembly from mosquito ......................................................................................................... 36 II | P a g e Core genome-based phylogenetic structure of 16 E. anophelis isolates from NUH ................................................................................................................ 37 CHAPTER 4 Biofilm Formation of E. anophelis NUHP1 and Transcriptomic Analysis of Stress Response of NUHP1 to Hydrogen Peroxide ........... 39 4.1 INTRODUCTION ............................................................................................... 39 4.2 MATERIALS AND METHODS ......................................................................... 40 4.2.1 Bacterial strains ........................................................................................... 40 4.2.2 Growth medium and conditions .................................................................. 40 4.2.2 Biofilm formation assay .............................................................................. 41 4.2.2.1 Static biofilm ....................................................................................... 41 4.2.2.2 Flow cell biofilm ................................................................................. 41 4.2.4 CAS Liquid Assay....................................................................................... 43 4.2 RESULTS AND DISCUSSION .......................................................................... 43 4.2.3 Biofilm formation........................................................................................ 43 Biofilm formation under static conditions ...................................................... 43 Biofilm formation in flow cell system ............................................................. 45 4.2.1 Transcriptomic analysis of stress response of E. anophelis to hydrogen peroxide ................................................................................................................ 48 4.2.2 RT-PCR analysis of stress response of E. anophelis to hydrogen peroxide50 4.2.3 Siderophore production is enhanced by oxidative stress in E. anophelis ... 51 CHAPTER 5 Transcriptomic Analysis of E. anophelis in Response to Blood and Comparative Transcriptome Analysis of E. anophelis in Response to Blood and Hydrogen Peroxide ................................................................ 54 5.1 INTRODUCTION ............................................................................................... 54 5.2 MATERIALS AND METHODS ......................................................................... 55 5.2.1 Sample harvest, RNA extraction and transcriptomic analysis of E. anophelis in response to mouse blood .................................................................................. 55 5.2.2 Time-Kill assay ........................................................................................... 56 5.2.3 Biofilm assay ............................................................................................... 56 5.3 RESULTS AND DISCUSSION .........................................................................
Load more

Recommended publications
  • Structural Basis of Mammalian Mucin Processing by the Human Gut O
    ARTICLE https://doi.org/10.1038/s41467-020-18696-y OPEN Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila ✉ ✉ Beatriz Trastoy 1,4, Andreas Naegeli2,4, Itxaso Anso 1,4, Jonathan Sjögren 2 & Marcelo E. Guerin 1,3 Akkermansia muciniphila is a mucin-degrading bacterium commonly found in the human gut that promotes a beneficial effect on health, likely based on the regulation of mucus thickness 1234567890():,; and gut barrier integrity, but also on the modulation of the immune system. In this work, we focus in OgpA from A. muciniphila,anO-glycopeptidase that exclusively hydrolyzes the peptide bond N-terminal to serine or threonine residues substituted with an O-glycan. We determine the high-resolution X-ray crystal structures of the unliganded form of OgpA, the complex with the glycodrosocin O-glycopeptide substrate and its product, providing a comprehensive set of snapshots of the enzyme along the catalytic cycle. In combination with O-glycopeptide chemistry, enzyme kinetics, and computational methods we unveil the molecular mechanism of O-glycan recognition and specificity for OgpA. The data also con- tribute to understanding how A. muciniphila processes mucins in the gut, as well as analysis of post-translational O-glycosylation events in proteins. 1 Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain. 2 Genovis AB, Box 790, 22007 Lund, Sweden. 3 IKERBASQUE, Basque Foundation for Science, 48013 ✉ Bilbao, Spain. 4These authors contributed equally: Beatriz Trastoy, Andreas Naegeli, Itxaso Anso.
    [Show full text]
  • Emerging Flavobacterial Infections in Fish
    Journal of Advanced Research (2014) xxx, xxx–xxx Cairo University Journal of Advanced Research REVIEW Emerging flavobacterial infections in fish: A review Thomas P. Loch a, Mohamed Faisal a,b,* a Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, 174 Food Safety and Toxicology Building, Michigan State University, East Lansing, MI 48824, USA b Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Natural Resources Building, Room 4, Michigan State University, East Lansing, MI 48824, USA ARTICLE INFO ABSTRACT Article history: Flavobacterial diseases in fish are caused by multiple bacterial species within the family Received 12 August 2014 Flavobacteriaceae and are responsible for devastating losses in wild and farmed fish stocks Received in revised form 27 October 2014 around the world. In addition to directly imposing negative economic and ecological effects, Accepted 28 October 2014 flavobacterial disease outbreaks are also notoriously difficult to prevent and control despite Available online xxxx nearly 100 years of scientific research. The emergence of recent reports linking previously uncharacterized flavobacteria to systemic infections and mortality events in fish stocks of Keywords: Europe, South America, Asia, Africa, and North America is also of major concern and has Flavobacterium highlighted some of the difficulties surrounding the diagnosis and chemotherapeutic treatment Chryseobacterium of flavobacterial fish diseases. Herein, we provide a review of the literature that focuses on Fish disease Flavobacterium and Chryseobacterium spp. and emphasizes those associated with fish. Coldwater disease ª 2014 Production and hosting by Elsevier B.V. on behalf of Cairo University. Flavobacteriosis Mohamed Faisal D.V.M., Ph.D., is currently a Thomas P.
    [Show full text]
  • Insights from the Draft Genome Into the Pathogenicity of a Clinical Isolate of Elizabethkingia Meningoseptica Em3 Shicheng Chen1*, Marty Soehnlen2, Frances P
    Chen et al. Standards in Genomic Sciences (2017) 12:56 DOI 10.1186/s40793-017-0269-8 EXTENDED GENOME REPORT Open Access Insights from the draft genome into the pathogenicity of a clinical isolate of Elizabethkingia meningoseptica Em3 Shicheng Chen1*, Marty Soehnlen2, Frances P. Downes3 and Edward D. Walker1 Abstract Elizabethkingia meningoseptica is an emerging, healthcare-associated pathogen causing a high mortality rate in immunocompromised patients. We report the draft genome sequence of E. meningoseptica Em3, isolated from sputum from a patient with multiple underlying diseases. The genome has a length of 4,037,922 bp, a GC-content 36.4%, and 3673 predicted protein-coding sequences. Average nucleotide identity analysis (>95%) assigned the bacterium to the species E. meningoseptica. Genome analysis showed presence of the curli formation and assembly operon and a gene encoding hemagglutinins, indicating ability to form biofilm. In vitro biofilm assays demonstrated that E. meningoseptica Em3 formed more biofilm than E. anophelis Ag1 and E. miricola Emi3, both lacking the curli operon. A gene encoding thiol-activated cholesterol-dependent cytolysin in E. meningoseptica Em3 (potentially involved in lysing host immune cells) was also absent in E. anophelis Ag1 and E. miricola Emi3. Strain Em3 showed α-hemolysin activity on blood agar medium, congruent with presence of hemolysin and cytolysin genes. Furthermore, presence of heme uptake and utilization genes demonstrated adaptations for bloodstream infections. Strain Em3 contained 12 genes conferring resistance to β-lactams, including β-lactamases class A, class B, and metallo-β-lactamases. Results of comparative genomic analysis here provide insights into the evolution of E.
    [Show full text]
  • Revisiting the Taxonomy of the Genus Elizabethkingia Using Whole
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE HHS Public Access provided by CDC Stacks Author manuscript Author ManuscriptAuthor Manuscript Author Antonie Manuscript Author Van Leeuwenhoek Manuscript Author . Author manuscript; available in PMC 2019 January 01. Published in final edited form as: Antonie Van Leeuwenhoek. 2018 January ; 111(1): 55–72. doi:10.1007/s10482-017-0926-3. Revisiting the taxonomy of the genus Elizabethkingia using whole-genomesequencing, opticalmapping, andMALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov Ainsley C. Nicholson, Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA Christopher A. Gulvik, Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA Anne M. Whitney, Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA Ben W. Humrighouse, Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta,
    [Show full text]
  • Elizabethkingia Endophytica Sp. Nov., Isolated from Zea Mays and Emended Description of Elizabethkingia Anophelis Ka¨Mpfer Et Al
    International Journal of Systematic and Evolutionary Microbiology (2015), 65, 2187–2193 DOI 10.1099/ijs.0.000236 Elizabethkingia endophytica sp. nov., isolated from Zea mays and emended description of Elizabethkingia anophelis Ka¨mpfer et al. 2011 Peter Ka¨mpfer,1 Hans-Ju¨rgen Busse,2 John A. McInroy3 and Stefanie P. Glaeser1 Correspondence 1Institut fu¨r Angewandte Mikrobiologie, Universita¨t Giessen, Giessen, Germany Peter Ka¨mpfer 2Institut fu¨r Mikrobiologie, Veterina¨rmedizinische Universita¨t, A-1210 Wien, Austria peter.kaempfer@umwelt. 3 uni-giessen.de Department of Entomology and Plant Pathology, Auburn University, Alabama, 36849 USA A slightly yellow bacterial strain (JM-87T), isolated from the stem of healthy 10 day-old sweet corn (Zea mays), was studied for its taxonomic allocation. The isolate revealed Gram- stain-negative, rod-shaped cells. A comparison of the 16S rRNA gene sequence of the isolate showed 99.1, 97.8, and 97.4 % similarity to the 16S rRNA gene sequences of the type strains of Elizabethkingia anophelis, Elizabethkingia meningoseptica and Elizabethkingia miricola, respectively. The fatty acid profile of strain JM-87T consisted mainly of the major fatty acids C15:0 iso, C17:0 iso 3-OH, and C15:0 iso 2-OH/C16:1v7c/t. The quinone system of strain JM- 87T contained, exclusively, menaquinone MK-6. The major polyamine was sym-homospermidine. The polar lipid profile consisted of the major lipid phosphatidylethanolamine plus several unidentified aminolipids and other unidentified lipids. DNA–DNA hybridization experiments with E. meningoseptica CCUG 214T (5ATCC 13253T), E. miricola KCTC 12492T (5GTC 862T) and E. anophelis R26T resulted in relatedness values of 17 % (reciprocal 16 %), 30 % (reciprocal 19 %), and 51 % (reciprocal 54 %), respectively.
    [Show full text]
  • Elizabethkingia Miricola As an Opportunistic Oral Pathogen Associated with Superinfectious Complications in Humoral Immunodefici
    Zdziarski et al. BMC Infectious Diseases (2017) 17:763 DOI 10.1186/s12879-017-2886-7 CASE REPORT Open Access Elizabethkingia miricola as an opportunistic oral pathogen associated with superinfectious complications in humoral immunodeficiency: a case report Przemysław Zdziarski1, Mariola Paściak2*, Klaudia Rogala2, Agnieszka Korzeniowska-Kowal2 and Andrzej Gamian2 Abstract Background: Elizabethkingia miricola is a rare Gram-negative bacterium found in water and clinical specimens. Typical culturing methods often misidentify Elizabethkingia spp. as Flavobacterium or Chryseobacterium. Although diagnosis is based on culturing samples taken from sterile sites, such as blood, a proper identification of this bacterium requires an expertise that goes beyond the capabilities of a typical clinical laboratory. Case presentation: A 35-year-old woman diagnosed with common variable immunodeficiency was admitted to our center. Previous treatment with antibiotics (amoxicillin plus clavulanate, first and third generation of cephalosporins, macrolides) and systemic corticosteroids (up to 120 mg/day of prednisolone) failed to arrest the spread of inflammation. Gingival recession was observed in her oral cavity, resulting in an apparent lengthening of her teeth. In addition to typical commensal bacteria, including streptococci and neisseriae, strains of Rothia mucilaginosa and Elizabethkingia miricola were identified upon a detailed microbiological examination using a MALDI-TOF MS Biotyper system. The presence of the latter strain correlated with severe periodontitis, lack of IgA in her saliva and serum, a very low IgG concentration (< 50 mg/dl), IgM-paraproteinemia, decreases in C3a and C5a and microvascular abnormality. High-dose immunoglobulin (to maintain IgG > 500 mg/dl) and targeted levofloxacin treatment resulted in immune system reconstitution, oral healing, and eradication of the Elizabethkingia infection.
    [Show full text]
  • Genomic Epidemiology and Global Diversity of the Emerging Bacterial
    www.nature.com/scientificreports OPEN Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis Received: 04 April 2016 Sebastien Breurec1,2,*, Alexis Criscuolo3,*, Laure Diancourt4, Olaya Rendueles5,6, Accepted: 04 July 2016 Mathias Vandenbogaert4, Virginie Passet5,6, Valérie Caro4, Eduardo P. C. Rocha5,6, Published: 27 July 2016 Marie Touchon5,6,# & Sylvain Brisse5,6,# Elizabethkingia anophelis is an emerging pathogen involved in human infections and outbreaks in distinct world regions. We investigated the phylogenetic relationships and pathogenesis-associated genomic features of two neonatal meningitis isolates isolated 5 years apart from one hospital in Central African Republic and compared them with Elizabethkingia from other regions and sources. Average nucleotide identity firmly confirmed thatE. anophelis, E. meningoseptica and E. miricola represent demarcated genomic species. A core genome multilocus sequence typing scheme, broadly applicable to Elizabethkingia species, was developed and made publicly available (http://bigsdb.pasteur.fr/ elizabethkingia). Phylogenetic analysis revealed distinct E. anophelis sublineages and demonstrated high genetic relatedness between the African isolates, compatible with persistence of the strain in the hospital environment. CRISPR spacer variation between the African isolates was mirrored by the presence of a large mobile genetic element. The pan-genome of E. anophelis comprised 6,880 gene families, underlining genomic heterogeneity of this species. African isolates carried unique resistance genes acquired by horizontal transfer. We demonstrated the presence of extensive variation of the capsular polysaccharide synthesis gene cluster in E. anophelis. Our results demonstrate the dynamic evolution of this emerging pathogen and the power of genomic approaches for Elizabethkingia identification, population biology and epidemiology. Elizabethkingia is a genus of aerobic, non-motile bacteria belonging to the family Flavobacteriaceae in the phy- lum Bacteroidetes.
    [Show full text]
  • Genomic Epidemiology and Global Diversity of the Emerging Bacterial Pathogen Elizabethkingia Anophelis
    Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis Sebastien Breurec, Alexis Criscuolo, Laure Diancourt, Olaya Rendueles, Mathias Vandenbogaert, Virginie Passet, Valerie Caro, Eduardo Rocha, Marie Touchon, Sylvain Brisse To cite this version: Sebastien Breurec, Alexis Criscuolo, Laure Diancourt, Olaya Rendueles, Mathias Vandenbogaert, et al.. Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis. Scientific Reports, Nature Publishing Group, 2016, 6, pp.30379. 10.1038/srep30379. hal-02613124 HAL Id: hal-02613124 https://hal.archives-ouvertes.fr/hal-02613124 Submitted on 28 May 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License www.nature.com/scientificreports OPEN Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis Received: 04 April 2016 Sebastien Breurec1,2,*, Alexis Criscuolo3,*, Laure Diancourt4, Olaya Rendueles5,6, Accepted:
    [Show full text]
  • Elizabethkingia Intra-Abdominal Infection and Related Trimethoprim-Sulfamethoxazole Resistance: a Clinical-Genomic Study
    antibiotics Article Elizabethkingia Intra-Abdominal Infection and Related Trimethoprim-Sulfamethoxazole Resistance: A Clinical-Genomic Study Ling-Chiao Teng 1,†, Jiunn-Min Wang 2,†, Hsueh-Yin Lu 3, Yan-Chiao Mao 4,5 , Kuo-Lung Lai 6, Chien-Hao Tseng 1 , Yao-Ting Huang 3,* and Po-Yu Liu 1,7,8,* 1 Section of Infectious Disease, Taichung Veterans General Hospital, Taichung 40705, Taiwan; [email protected] (L.-C.T.); [email protected] (C.-H.T.) 2 Routine Laboratory, Taichung Veterans General Hospital, Taichung 40705, Taiwan; [email protected] 3 Department of Computer Science and Information Engineering, National Chung Cheng University, Taichung 62102, Taiwan; mrfi[email protected] 4 Department of Emergency Medicine, Division of Clinical Toxicology, Taichung Veterans General Hospital, Taichung 40705, Taiwan; [email protected] 5 National Defense Medical Center, School of Medicine, Taipei 11490, Taiwan 6 Division of Allergy, Immunology and Rheumatology, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan; [email protected] 7 Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan 8 Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan * Correspondence: [email protected] (Y.-T.H.); [email protected] (P.-Y.L.) † These authors contributed equally to this work. Citation: Teng, L.-C.; Wang, J.-M.; Abstract: (1) Background: Elizabethkingia spp. is an emerging nosocomial pathogen which causes Lu, H.-Y.; Mao, Y.-C.; Lai, K.-L.; Elizabethkingia Eliza- Tseng, C.-H.; Huang, Y.-T.; Liu, P.-Y. mostly blood stream infection and nosocomial pneumonia. Among species, Elizabethkingia Intra-Abdominal bethkingia anophelis is the major pathogen, but misidentification as Elizabethkingia meningoseptica is a Infection and Related common problem.
    [Show full text]
  • Comparative Genomics and Antimicrobial Resistance Profiling of Elizabethkingia Isolates Reveals Nosocomial Transmission and in V
    medRxiv preprint doi: https://doi.org/10.1101/2020.03.12.20032722; this version posted March 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license . 1 Comparative genomics and antimicrobial resistance profiling of Elizabethkingia isolates 2 reveals nosocomial transmission and in vitro susceptibility to fluoroquinolones, 3 tetracyclines and trimethoprim-sulfamethoxazole 4 5 Delaney Burnard1,3,4#, Letitia Gore2#, Andrew Henderson1, Ama Ranasinghe1, Haakon 6 Bergh2, Kyra Cottrell1, Derek S. Sarovich3,4, Erin P. Price3,4, David L. Paterson1, Patrick N. 7 A. Harris1,2* 8 1University of Queensland Centre for Clinical Research, Royal Brisbane and Woman’s 9 Hospital, Herston, Queensland, Australia 10 2Central Microbiology, Pathology Queensland, Herston, Queensland, Australia 11 3 Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, 12 Australia 13 4Sunshine Coast Health Institute, Birtinya, Queensland, Australia 14 #Authors contributed equally 15 *Corresponding author: Dr Patrick N. A. Harris 16 University of Queensland Centre for Clinical Research, Building 71/918 Royal Brisbane & 17 Women's Hospital Campus, Herston, QLD, 4029 18 Email: [email protected]; Tel: +61 (0) 7 3346 6081 19 Word count abstract:436, Word count text:4,493 20 Keywords: Elizabethkingia, MDR, multidrug resistance, nosocomial, MIC, minimum 21 inhibitory concentration, antimicrobial resistance, AMR, comparative genomics 1 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.
    [Show full text]
  • Matyi Okstate 0664D 13328.Pdf
    COMPARISON OF MULTIPLE ANTIBIOTIC RESISTANT STAPHYLOCOCCUS AUREUS GENOMES AND THE GENOME STRUCTURE OF ELIZABETHKINGIA MENINGOSEPTICA By STEPHANIE ANN MATYI Bachelor of Science in Biology New Mexico State University Las Cruces, New Mexico 2004 Master of Science in Biology New Mexico State University Las Cruces, New Mexico 2006 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY May, 2014 COMPARISON OF MULTIPLE ANTIBIOTIC RESISTANT STAPHYLOCOCCUS AUREUS GENOMES AND THE GENOME STRUCTURE OF ELIZABETHKINGIA MENINGOSEPTICA Dissertation Approved: Dr. John E. Gustafson Dissertation Adviser Dr. Peter R. Hoyt Dr. Patricia Canaan Dr. Marianna Patrauchan ii ACKNOWLEDGEMENTS I would like to thank my advisor, Dr. John E. Gustafson, who has shown tremendous patience and support over the last four years (not to mention the years spent mentoring me for my Master’s degree). You have not only been a great advisor to me but also a great friend. I thank you for encouraging my research and allowing me to grow as a scientist. Your advice on both my research and my career path has been invaluable. Words cannot express how grateful I am for everything you have done for my family and I. Thank you to my committee members, Dr. Peter Hoyt, Dr. Patricia Canaan and Dr. Marianna Patrauchan for your guidance, support and constructive criticism in making me a better scientist. Many thanks to my fellow graduate students for all their help over the years especially Nathanial Torres and Karyn Willyerd. These two friends and co-workers have provided much needed humor and entertainment in what could have otherwise been a somewhat stressful period of my life.
    [Show full text]
  • High-Quality Genome Sequence and Description of Chryseobacterium
    NEW MICROBES IN HUMANS High-quality genome sequence and Introduction description of Chryseobacterium The family Flavobacteriaceae, which formerly belonged to the senegalense sp. nov. Cytophaga–Flexibacter–Bacteroides group, represents the most important bacterial lineage in the phylum Bacteroidetes [1]. Likewise, Chryseobacterium, Bergeyella, Ornithobacterium, Empe- C. I. Lo1, S. A. Sankar1, O. Mediannikov1, C. B. Ehounoud1, dobacter, Weeksella, Wautersiella, Elizabethkingia, Sejongia and N. Labas1, N. Faye3, D. Raoult1,2, P.-E. Fournier1 and Kaistella are the genera currently included in this family [1–3]. F. Fenollar1 However, Kaistella flava and Kaistella korensis are reclassified in 1) Unité de Recherche sur les Maladies Infectieuses et Tropicales the genus Chryseobacterium [4,5]. The genus Chryseobacterium Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo- was proposed for the first time in 1994 [2]. Currently 90 Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille species with validly published names are included in this genus Université, Marseille, France, 2) Special Infectious Agents Unit, King Fahd [6]. Members of this genus have been isolated from a variety of Medical Research Center, King Abdulaziz University, Jeddah, Saudi environments, including soil [7,8], plant rhizosphere [9], Arabia and 3) Université Cheikh Anta Diop de Dakar, Laboratoire de wastewater [10], freshwater [11], compost [12], diseased fish Parasitologie générale, Dakar, Senegal [13] and clinical samples [14,15]. Chryseobacterium FF12T strain (CSUR = P1490, DSM 100279) is the type strain of Chrys- eobacterium senegalense sp. nov. It was isolated from the mouth of a West African lungfish (Protopterus annectens). Cells are Abstract Gram negative, aeroanaerobic, nonmotile, non–spore forming and rods.
    [Show full text]