DOCSLIB.ORG

Emergence of Carbapenem-Resistant Pseudomonas Aeruginosa and Acinetobacter Baumannii Clinical Isolates Collected from Some Libyan Hospitals

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Emergence of Carbapenem-Resistant Pseudomonas Aeruginosa and Acinetobacter Baumannii Clinical Isolates Collected from Some Libyan Hospitals UNIVERSITE DE TUNIS EL MANAR Ecole Doctorale des Sciences Biologiques et AIX-MARSEILLE UNIVERSITE Ecole Doctorale des Sciences de la Vie et de la Santé THESE DE DOCTORAT EN COTUTELLE En Vue de l’obtention de grade de Docteur de l’Université de Tunis et d’Aix-Marseille Université Spécialités: Microbiologie / Pathologie humaine et maladies infectieuses Déterminisme du support moléculaire et de l’épidémiologie de la résistance aux ȕ-lactamines chez des bacilles à Gram négatif isolés dans des hôpitaux tunisiens et libyens Présentée par: Najla MATHLOUTHI Composition du Jury: Pr. Imane ZOUARI Université Tunis el Manar Président de Jury Dr. Marie KEMPF Université d’Angers Rapporteur Dr. Taoufik GHRAIRI Université Tunis el Manar Rapporteur Pr. Philippe COLSON Université d’Aix-Marseille Examinateur Pr. Mr. Jean-Marc ROLAIN Université d’Aix-Marseille Directeur de Thèse Dr. Chedly CHOUCHANI Université de Carthage Directeur de Thèse (8 Avril 2017) SOMMAIRE AVANT PROPOS ...................................................................... 3 RESUME .................................................................................... 4 SUMMARY ................................................................................ 5 INTRODUCTION ..................................................................... 7 CHAPITRE I: Revue: L’émergence et la dissémination des carbapénèmases produites par les bacilles à Gram négatifs dans les pays du bassin méditerranéen ............................................... 15 Article 1: Prevalence and emergence of carbapenemases producing Gram-negative bacteria in Mediterranean basin ..... 17 CHAPITRE II: Etude du déterminisme génétique et de l’épidémiologie moléculaire de la résistance aux β-lactamines chez des souches d’Esherichia coli et de Klebsiella pneumonaie isolées dans des hôpitaux tunisiens et libyens ........................... 39 Article 2: Characteristics of Carbapenemase-and Extended- Spectrum β-Lactamase-producing Enterobacteriaceae isolated from Tunisian and Libyan Hospitals ......................................... 49 CHAPITRE III: Etude du déterminisme génétique et de l’épidémiologie moléculaire de la résistance aux β-lactamines chez des souches d’Acinetobacter baumannii et de Pseudomonas aeruginosa isolées dans des hôpitaux tunisiens et libyens ........ 61 1 Article 3: Emergence of Carbapenem-Resistant Pseudomonas aeruginosa and Acinetobacter baumannii Clinical Isolates Collected from Some Libyan Hospitals ..................................... 77 Article4: Early detection of metallo--lactamase NDM-1 and OXA-23 carbapenemase-producing Acinetobacter baumannii in Libyan hospitals ......................................................................... 87 Article 5: Incidence of OXA-23 and OXA-58 carbapenemases co-expressed in clinical isolates of Acinetobacter baumannii in Tunisia ....................................................................................... 95 Chapitre VI (Annexe): Travaux sur la description et le séquençage des génomes de nouvelles espèces ....................... 123 Article 6: Genome sequence and description of Mobilicoccus massiliensis sp. nov. isolated from the stool of a Nigerien male suffering from a severe form of acute malnutrition ‘‘kwashiorkor’’ ........................................................................ 127 Article 7: Genome sequence and description of Paenibacillus ihuae strain GD6 sp. nov. isolated from the stool of a 62-year-old man, France ............................................................................. 157 CONCLUSION ET PERSPECTIVES ................................. 185 REMERCIEMENTS ............................................................ 191 2 AVANT PROPOS Le format de présentation de cette thèse correspond à une recommandation à la spécialité Pathologie Humaine et Maladies infectieuses, à l’intérieur du Master des Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter les règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe et qui permet un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de commencer le plus tôt possible une bibliographie sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté, ou soumis associé d’un bref commentaire donnant le sens général du travail. Cette forme de présentation a paru plus en adéquation avec les exigences de la compétition internationale et permet de se concentrer sur des travaux qui bénéficieront d’une diffusion internationale. Professeur Didier RAOULT 3 RESUME L’augmentation et la dissémination de la résistance aux β-lactamines chez les bacilles à Gram négatif, particulièrement les Entérobactéries, les bactéries du genre Pseudomonas et Acinetobacter, représentent un problème majeur de santé publique. Les infections nosocomiales causées par ces bactéries multi-résistantes (BMR) ont conduit à une augmentation de la mortalité, de la morbidité et du coût de traitement. L’utilisation abusive et non contrôlée de ces antibiotiques a grandement contribué à la large diffusion de cette résistance. Ainsi, face à cette préoccupation mondiale et suite à de nombreuses recommandations, plusieurs études épidémiologiques et moléculaires ont été rapportées afin de contrôler et de surveiller la diffusion et la dissémination des BMR. Contrairement à de nombreuses régions dans le monde, il existe peu d’informations concernant la caractérisation moléculaire des gènes de résistance aux β-lactamines des bacilles à Gram négatif isolés en Tunisie et surtout en Libye. C’est dans cette optique que ce projet de Thèse de Doctorat s’articule avec comme objectifs: (i) mettre en évidence la prévalence des bacilles à Gram négatifs multi-résistants isolés aux niveaux des hôpitaux tunisiens et libyens (ii) identifier le support génétique de la résistance aux β-lactamines de ces souches cliniques (iii) étudier la diversité clonale des souches multi-résistantes par typage moléculaire (iiii) étudier l’épidémiologie moléculaire de ces BMR en Tunisie et en Libye ainsi que dans le bassin méditerranéen afin de maîtriser le processus décisionnel du traitement et de limiter la dissémination des épidémies. Mots clés: bacilles à Gram-négatif, bassin méditerranéen, isolats cliniques multi-résistants aux β-lactamines, études moléculaires des mécanismes de résistance aux β-lactamines, études épidémiologiques. 4 SUMMARY The increase and spread of β-lactam resistance in gram negative bacteria especially Enterobacteriaceae, Pseudomonas and Acinetobacter (E.P.A) species have become a major concern worldwide. The hospital-acquired infections caused by MDR bacteria have led to an increase in mortality, morbidity and cost of treatment. The frequent misuse of antibiotic drug has greatly contributed to worldwide dissemination of antibiotics resistance. Front of this worldwide concern, and various recommendations, several epidemiological and molecular studies have been reported in order to control the spread and the dissemination of these MDR. Unlike many parts of the world, there is little information concerning the molecular characterization of the β-lactam resistance genes of Gram-negative bacilli isolated in Tunisia and especially in Libya. Therefore, it is in this context that the project of this thesis was conducted with essential objectives: (i) highlight the prevalence of multi-resistant Gram negative bacilli isolated in Tunisian and Libyan hospitals (ii) identify the genetic support of resistance to β-lactams of these clinical strains (iii) study the molecular epidemiology of these BMR in Tunisia and Libya as well as in the Mediterranean basin in order to control the decision-making process and to limit the spread of epidemics. Keywords: Gram-negative bacilli, mediterranean basin, clinical isolates multi-resistant to β-lactams, molecular studies of the mechanisms of β-lactam resistance, epidemiological studies. 5 INTRODUCTION La découverte des antibiotiques, notamment la pénicilline en 1928 a sans doute été l’une des avancées thérapeutiques les plus importantes du vingtième siècle. L’utilisation de ces agents anti- infectieux depuis les années 1940 a considérablement réduit le taux de morbidité et de mortalité liés aux maladies infectieuses [1]. Cependant, leur utilisation à grande échelle a également conduit à l’émergence de la résistance aux antibiotiques. Les premières bactéries résistantes ont été identifiées dès les années 1940, avec notamment l’émergence des Staphylococcus aureus résistants à la pénicilline dès 1947, soit seulement quatre années après l’utilisation à grande échelle de cet antibiotique [2]. A partir des années 1950, de nombreux antibiotiques ont été découverts ou synthétisés et le développement de chaque nouvelle classe a été suivi par l’apparition de l’émergence de nouveaux mécanismes de résistance entraînant la diffusion de bactéries pathogènes de plus en plus difficiles à traiter, comme ce fut le cas pour la méticilline G qui a été mise sur le marché en 1961 et suivie de la découverte de S. aureus résistant en 1962, pareillement pour l’ampicilline G qui a été mise sur le marché en 1962 et suivie de l’émergence d’Entérobactéries résistantes en 1964 puis des céphalosporines mis sur le marché en 1980 et suivis de l’émergence
Load more

Recommended publications
  • THE LAKE VOSTOK Ferran Romero Blanch
    MICROBIOLOGY OF A SUBGLACIAL LAKE: THE LAKE VOSTOK Ferran Romero Blanch OBJECTIVES INTRODUCTION: Lake Vostok is the largest and deepest The aim of the present review is to describe subglacial body of water in Antarctica. It has the communities present in a subglacial lake an area of 14000Km2 and a volume of (the Lake Vostok). 5600Km3. Nowadays, it is accepted that it has been buried under glacial ice for 14-15 millions It is also objective of this review to describe of years (Figure 1). Discovered between 1950 the use of ice-binding proteins as a and 1960, it has been recently reported that it method to survive in extremely cold forms a complex ecosystem with both environments. prokaryotic and eukaryotic microorganisms1,2. The living forms here have evolved to survive in an extremely oligotrophic, Main characteristics of Lake Vostok hyperbaric, cold and dark Temperature: -2°C environment. Pressure: 350atm (as it is covered by a 4- kilometer-thick layer of glacial ice) Nutrient availability: very slow Figure 1. Location of lake Vostok under Antarctic glacial ice1. Light: absent The ice above Lake Vostok freezes forming a 220m layer of accreted ice. It is generally accepted that this 220m layer of accreted ice reflects the contents into the lake and, because of this, it has been under study during the last 30 years. Ice accreting near the embayment has higher concentrations of ions, biomass and solid inclusions and it is known as type I accretion ice. The ice that forms over open water contains lower concentrations of biomass and ions and has been termed type II accretion ice3 (Figure 2).
    [Show full text]
  • Downloaded from the NCBI Database
    marine drugs Article Isolation, Phylogenetic and Gephyromycin Metabolites Characterization of New Exopolysaccharides-Bearing Antarctic Actinobacterium from Feces of Emperor Penguin Hui-Min Gao 1, Peng-Fei Xie 1,2, Xiao-Ling Zhang 1,2,* and Qiao Yang 1,2,3,* 1 College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China; [email protected] (H.-M.G.); [email protected] (P.-F.X.) 2 ABI Group, Zhejiang Ocean University, Zhoushan 316022, China 3 Department of Environment Science and Engineering, Zhejiang Ocean University, Zhoushan 316022, China * Correspondence: [email protected] (X.-L.Z.); [email protected] (Q.Y.) Abstract: A new versatile actinobacterium designated as strain NJES-13 was isolated from the feces of the Antarctic emperor penguin. This new isolate was found to produce two active gephyromycin analogues and bioflocculanting exopolysaccharides (EPS) metabolites. Phylogenetic analysis based on pairwise comparison of 16S rRNA gene sequences showed that strain NJES-13 was closely related to Mobilicoccus pelagius Aji5-31T with a gene similarity of 95.9%, which was lower than the threshold value (98.65%) for novel species delineation. Additional phylogenomic calculations of the average Citation: Gao, H.-M.; Xie, P.-F.; nucleotide identity (ANI, 75.9–79.1%), average amino acid identity (AAI, 52.4–66.9%) and digital Zhang, X.-L.; Yang, Q. Isolation, DNA–DNA hybridization (dDDH, 18.6–21.9%), along with the constructed phylogenomic tree based Phylogenetic and Gephyromycin on the up-to-date bacterial core gene (UBCG) set from the bacterial genomes, unequivocally separated Metabolites Characterization of New strain NJES-13 from its close relatives within the family Dermatophilaceae.
    [Show full text]
  • General Microbiota of the Soft Tick Ornithodoros Turicata Parasitizing the Bolson Tortoise (Gopherus flavomarginatus) in the Mapimi Biosphere Reserve, Mexico
    biology Article General Microbiota of the Soft Tick Ornithodoros turicata Parasitizing the Bolson Tortoise (Gopherus flavomarginatus) in the Mapimi Biosphere Reserve, Mexico Sergio I. Barraza-Guerrero 1,César A. Meza-Herrera 1 , Cristina García-De la Peña 2,* , Vicente H. González-Álvarez 3 , Felipe Vaca-Paniagua 4,5,6 , Clara E. Díaz-Velásquez 4, Francisco Sánchez-Tortosa 7, Verónica Ávila-Rodríguez 2, Luis M. Valenzuela-Núñez 2 and Juan C. Herrera-Salazar 2 1 Unidad Regional Universitaria de Zonas Áridas, Universidad Autónoma Chapingo, 35230 Bermejillo, Durango, Mexico; [email protected] (S.I.B.-G.); [email protected] (C.A.M.-H.) 2 Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, 35010 Gómez Palacio, Durango, Mexico; [email protected] (V.Á.-R.); [email protected] (L.M.V.-N.); [email protected] (J.C.H.-S.) 3 Facultad de Medicina Veterinaria y Zootecnia No. 2, Universidad Autónoma de Guerrero, 41940 Cuajinicuilapa, Guerrero, Mexico; [email protected] 4 Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, 54090 Tlalnepantla, Estado de México, Mexico; [email protected] (F.V.-P.); [email protected] (C.E.D.-V.) 5 Instituto Nacional de Cancerología, 14080 Ciudad de México, Mexico 6 Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, 54090 Tlalnepantla, Estado de México, Mexico 7 Departamento de Zoología, Universidad de Córdoba.Edificio C-1, Campus Rabanales, 14071 Cordoba, Spain; [email protected] * Correspondence: [email protected]; Tel.: +52-871-386-7276; Fax: +52-871-715-2077 Received: 30 July 2020; Accepted: 3 September 2020; Published: 5 September 2020 Abstract: The general bacterial microbiota of the soft tick Ornithodoros turicata found on Bolson tortoises (Gopherus flavomarginatus) were analyzed using next generation sequencing.
    [Show full text]
  • Streptomyces Hokutonensis Sp. Nov., a Novel Actinomycete Isolated from the Strawberry Root Rhizosphere
    The Journal of Antibiotics (2014) 67, 465–470 & 2014 Japan Antibiotics Research Association All rights reserved 0021-8820/14 www.nature.com/ja ORIGINAL ARTICLE Streptomyces hokutonensis sp. nov., a novel actinomycete isolated from the strawberry root rhizosphere Hideki Yamamura1, Haruna Ashizawa1, Moriyuki Hamada2, Akira Hosoyama2, Hisayuki Komaki2, Misa Otoguro2, Tomohiko Tamura2, Yukikazu Hayashi1, Youji Nakagawa1, Takashi Ohtsuki1, Nobuyuki Fujita2, Sadaharu Ui1 and Masayuki Hayakawa1 A polyphasic approach was used to determine the taxonomic position of actinomycete strain R1-NS-10T, which was isolated from a sample of strawberry root rhizosphere obtained from Hokuto, Yamanashi, Japan. Strain R1-NS-10T was Gram-staining-positive and aerobic, and formed brownish-white aerial mycelia and grayish-brown substrate mycelia on ISP-2 medium. The strain grew in the presence of 0–5% (w/v) NaCl and optimally grew without NaCl. The strain grew at pH 5–8, and the optimum for growth was pH 7. The optimal growth temperature was 30 1C, but the strain grew at 5–37 1C. Whole-cell T hydrolysates of strain R1-NS-10 contained A2pm, galactose, mannose and rhamnose. The predominant menaquinones were MK-9(H6) and MK-9(H8). The major cellular fatty acids were anteiso-C15:0 and iso-C16:0. Comparative 16S rRNA gene sequence analysis revealed that strain R1-NS-10T was most closely related to Streptomyces prunicolor NBRC 13075T (99.4%). The draft genome sequences of both strains were determined for characterization of genome sequence-related parameters such as average nucleotide identity (ANI) and the diversity of secondary metabolite biosynthetic gene clusters.
    [Show full text]
  • T H È S E Rita Abou Abdallah
    81,9(56,7e D’AIX0$56(,//( )$&8/7e'(0e'(&,1('(0$56(,//( 7+Ê6( 6RXWHQXHSXEOLTXHPHQWOH-XLOOHW en vue de l’obtention du titre de Docteur de l’Université d’Aix0DUVHLOOH 6SpFLDOLWp0DODGLHV,QIHFWLHXVHV SDU 5LWD$ERX$EGDOODK /D*pQRPLTXH 8Q2XWLO5REXVWHHW(PHUJHQW8WLOLVp GDQVOD7D[RQRPLH%DFWpULHQQHHW O’analyse Comparative &RPSRVLWLRQGXMXU\ 3URIHVVHXU%/$6&2/$ 8QLYHUVLWp$L[0DUVHLOOH 3UpVLGHQWGX-XU\ 3URIHVVHXU00$85,1 8QLYHUVLWpGH*UHQREOH 5DSSRUWHXU 3URIHVVHXU35(1(672 8QLYHUVLWpGH*UHQREOH 5DSSRUWHXU 3URIHVVHXU3()2851,(5 Université d’Aix0DUVHLOOH 'LUHFWHXUGH7KqVH 8059,7520( $L[0DUVHLOOH8QLYHUVLWp,QVWLWXWGH5HFKHUFKHSRXUOH'pYHORSSHPHQW $VVLVWDQFH3XEOLTXH–+{SLWDX[GH0DUVHLOOH $3+0 6HUYLFHGH6DQWp GHV$UPpHV,QVWLWXW+RVSLWDOR8QLYHUVLWDLUH0pGLWHUUDQpH,QIHFWLRQ 5HPHUFLHPHQWV Je tiens à remercier Professeur Pierre-Edourad Fournier, pour son encadrement et enseignement au cours de ces dernières années. Ses conseils et encouragements ont été des éléments moteurs pour moi et déterminants pour le déroulement de cette thèse. Votre calme, respect, humanité et gentillesse envers vos étudiants sont gravés dans mon cœur. Finalement, je vous remercie pour votre support et confiance tout au long de ces trois années. Vous aurez toujours une place dans mon esprit et mon cœur. Je remercie Professeur Didier Raoult pour m’avoir accueillie au sein de l’Institut Hospitalo-Universitaire, Méditerranée-Infection. C’est dans un environnement stimulant intellectuellement que mon goût pour la recherche est né. Je remercie Professeur Bernard La Scola, d’avoir accepté de présider au sein du jury de cette Thèse. Je remercie Professeur Max Maurin et Patricia Renesto d’avoir accepté de siéger au sein du jury de cette Thèse et pour l’intérêt porté à ce travail. Je remercie ma mère et ma sœur, pour leurs supports et conseils quotidiens.
    [Show full text]
  • Genome-Based Taxonomic Classification of the Phylum
    ORIGINAL RESEARCH published: 22 August 2018 doi: 10.3389/fmicb.2018.02007 Genome-Based Taxonomic Classification of the Phylum Actinobacteria Imen Nouioui 1†, Lorena Carro 1†, Marina García-López 2†, Jan P. Meier-Kolthoff 2, Tanja Woyke 3, Nikos C. Kyrpides 3, Rüdiger Pukall 2, Hans-Peter Klenk 1, Michael Goodfellow 1 and Markus Göker 2* 1 School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom, 2 Department Edited by: of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Martin G. Klotz, Germany, 3 Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States Washington State University Tri-Cities, United States The application of phylogenetic taxonomic procedures led to improvements in the Reviewed by: Nicola Segata, classification of bacteria assigned to the phylum Actinobacteria but even so there remains University of Trento, Italy a need to further clarify relationships within a taxon that encompasses organisms of Antonio Ventosa, agricultural, biotechnological, clinical, and ecological importance. Classification of the Universidad de Sevilla, Spain David Moreira, morphologically diverse bacteria belonging to this large phylum based on a limited Centre National de la Recherche number of features has proved to be difficult, not least when taxonomic decisions Scientifique (CNRS), France rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft *Correspondence: Markus Göker genome sequences
    [Show full text]
  • Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics?
    ORIGINAL RESEARCH published: 23 May 2017 doi: 10.3389/fmicb.2017.00899 Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics? Maryam Tidjani Alou 1, 2 †, Matthieu Million 1 †, Sory I. Traore 1, 3, Donia Mouelhi 1, Saber Khelaifia 1, Dipankar Bachar 1, Aurelia Caputo 1, Jeremy Delerce 1, Souleymane Brah 4, Daouda Alhousseini 4, Cheikh Sokhna 5, Catherine Robert 1, Bouli A. Diallo 2, Aldiouma Diallo 5, Philippe Parola 1, Michael Golden 6, Jean-Christophe Lagier 1 and Didier Raoult 1* 1 URMITE, Aix Marseille Université, UM63, Centre National de la Recherche Scientifique 7278, IRD 198, Institut National de la Santé Et de la Recherche Médicale 1095, IHU—Méditerranée Infection, Marseille, France, 2 Laboratoire de Microbiologie, Département de Biologie, Université Abdou Moumouni de Niamey, Niamey, Niger, 3 Département d’Epidémiologie des Edited by: Affections Parasitaires, Faculté de Médecine, Université des Sciences, des Techniques et Technologies de Bamako, John W. A. Rossen, Bamako, Mali, 4 Service de Médecine Interne et Générale, Hôpital de Niamey, Niamey, Niger, 5 Unité de Recherche sur les University Medical Center Groningen, Maladies Infectieuses et Tropicales Emergentes IRD 198, Centre National de la Recherche Scientifique 7278, Aix-Marseille Netherlands Université, Dakar, Senegal, 6 Department of Medicine and Therapeutics, University of Aberdeen, Aberdeen, United Kingdom Reviewed by: Abelardo Margolles, Consejo Superior de Investigaciones Severe acute malnutrition is the world-leading cause of children under-five’s death. Científicas (CSIC), Spain Recent metagenomics studies have established a link between gut microbiota and severe Eleni Sibbald-Tsompanidou, acute malnutrition, describing an immaturity with a striking depletion in oxygen-sensitive University Medical Center Groningen, Netherlands prokaryotes.
    [Show full text]
  • Subglacial Lake Vostok (Antarctica) Accretion Ice Contains a Diverse Set of Sequences from Aquatic, Marine and Sediment-Inhabiting Bacteria and Eukarya
    Subglacial Lake Vostok (Antarctica) Accretion Ice Contains a Diverse Set of Sequences from Aquatic, Marine and Sediment-Inhabiting Bacteria and Eukarya Yury M. Shtarkman., Zeynep A. Koc¸er.¤a, Robyn Edgar, Ram S. Veerapaneni¤b, Tom D’Elia¤c, Paul F. Morris, Scott O. Rogers* Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America Abstract Lake Vostok, the 7th largest (by volume) and 4th deepest lake on Earth, is covered by more than 3,700 m of ice, making it the largest subglacial lake known. The combination of cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier), limited nutrients and complete darkness presents extreme challenges to life. Here, we report metagenomic/metatranscriptomic sequence analyses from four accretion ice sections from the Vostok 5G ice core. Two sections accreted in the vicinity of an embayment on the southwestern end of the lake, and the other two represented part of the southern main basin. We obtained 3,507 unique gene sequences from concentrates of 500 ml of 0.22 mm-filtered accretion ice meltwater. Taxonomic classifications (to genus and/or species) were possible for 1,623 of the sequences. Species determinations in combination with mRNA gene sequence results allowed deduction of the metabolic pathways represented in the accretion ice and, by extension, in the lake. Approximately 94% of the sequences were from Bacteria and 6% were from Eukarya. Only two sequences were from Archaea. In general, the taxa were similar to organisms previously described from lakes, brackish water, marine environments, soil, glaciers, ice, lake sediments, deep-sea sediments, deep-sea thermal vents, animals and plants.
    [Show full text]
  • Community of Actinomycetes in 42 Species of Animal Feces
    Online International Interdisciplinary Research Journal, {Bi-Monthly}, ISSN2249-9598, Volume-IV, July 2014 Special Issue Community of actinomycetes in 42 species of animal feces Yi Jiang a*, Xiu Chen 1，2，Li Han b, Xueshi Huang b, Chenglin Jiang a,b aYunnan Institute of Microbiology, Yunnan University, 650091 Kunming, Yunnan, P. R. China. bInstitute of Microbial pharmaceuticals, College of Life and Health Science, Northeastern University, 110819 Shenyang, P. R. China Abstract The study on animal fecal actinomycete, as a source for discovering new drug laeds, is a few in the past. There is a great deal of and un-exlroited actinomycete resources in animal feces. To provide new sources for discovering new drug leads, the diversity and bioactivities of cultivable actinobacteria from animal feces have been studied. 42 species of animal fecal samples were collected from Yunnan Wild Animal Park and other habitats. The purified cultures of actinobacteria were isolated from these samples by using 5 media. 3049 pure strains were isolated. The 16S rRNA gene sequences of 1869 selected strains of them were determined, the phylogenetic analysis was carried out, and anti-microbial anti-tumor, enzyme activities as well as toxin to mice were determined. 51 genera (including a new genus, Enteractinococcus ) of actinobacteria from the 42 species of animal feces were identified. Results of this study indicate that there is a great deal of and un-exlroited actinomycete resources in animal feces. Animal fecal actinomycete is considered as a new resource for discovering drug leads, agricultural chemicals and other industry products. KEYWORDS Actinobacteria; diversity; animal feces. 1. Introduction Actinomycetes (Actinobacteria) have recently received much attention, as these bacteria produce a variety of natural drugs and other bioactive metabolites, including antibiotics, enzyme inhibitors and enzymes.
    [Show full text]
  • Agromyces Marinus Sp. Nov., a Novel Actinobacterium Isolated from Sea Sediment
    The Journal of Antibiotics (2014) 67, 703–706 & 2014 Japan Antibiotics Research Association All rights reserved 0021-8820/14 www.nature.com/ja ORIGINAL ARTICLE Agromyces marinus sp. nov., a novel actinobacterium isolated from sea sediment Moriyuki Hamada, Chiyo Shibata, Tomohiko Tamura and Ken-ichiro Suzuki Two novel Gram-stain-positive actinobacteria, designated H23-8T and H23-19, were isolated from a sea sediment sample and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that these isolates were closely related to the members of the genus Agromyces, with similarity range of T 94.5–97.4%. Strains H23-8 and H23-19 contained L-2,4-diaminobutyric acid, D-alanine, D-glutamic acid and glycine in their peptidoglycan. The predominant menaquinones were MK-13 and MK-12, and the major fatty acids were anteiso-C15:0, anteiso- C17:0 and iso-C16:0. The DNA G þ C content was 72.3–72.5 mol%. The chemotaxonomic characteristics of the isolates matched those described for members of the genus Agromyces. The results of phylogenetic analysis and DNA–DNA hybridization, along with differences in phenotypic characteristics between strains H23-8T and H23-19 and the species of the genus Agromyces with validly published names, indicated that the two isolates should be assigned to a novel species of the genus Agromyces, for which the name Agromyces marinus sp. nov. is proposed; the type strain is H23-8T ( ¼ NBRC 109019T ¼ DSM 26151T). The Journal of Antibiotics (2014) 67, 703–706; doi:10.1038/ja.2014.60; published online 14 May 2014 INTRODUCTION the genus Agromyces.
    [Show full text]
  • Metagenomic and Metatranscriptomic Analyses of Lake Vostok Accretion Ice
    METAGENOMIC AND METATRANSCRIPTOMIC ANALYSES OF LAKE VOSTOK ACCRETION ICE Yury M. Shtarkman A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2015 Committee: Scott O. Rogers, Advisor Rober W. Midden Graduate Faculty Representative Vipaporn Phuntumart Paul F. Morris Robert Michael McKay © 2015 Yury M Shtarkman All Rights Reserved iii ABSTRACT Scott O. Rogers, Advisor Lake Vostok (Antarctica) is the 4th deepest lake on Earth, the 6th largest by volume, and 16th largest by area, being similar in area to Ladoga Lake (Russia) and Lake Ontario (North America). However, it is a subglacial lake, constantly covered by more than 3,800 m of glacial ice, and has been covered for at least 15 million years. As the glacier slowly traverses the lake, water from the lake freezes (i.e., accretes) to the bottom of the glacier, such that on the far side of the lake a 230 m thick layer of accretion ice collects. This essentially samples various parts of the lake surface water as the glacier moves across the lake. As the glacier enters the lake, it passes over a shallow embayment. The embayment accretion ice is characterized by its silty inclusions and relatively high concentrations of several ions. It then passes over a peninsula (or island) and into the main basin. The main basin accretion ice is clear with almost no inclusions and low ion content. Metagenomic/metatranscriptomic analysis has been performed on two accretion ice samples; one from the shallow embayment and the other from part of the main lake basin.
    [Show full text]
  • Research Article Endophytic Actinomycetes from Tea Plants (Camellia Sinensis): Isolation, Abundance, Antimicrobial, and Plant-Growth-Promoting Activities
    Hindawi BioMed Research International Volume 2018, Article ID 1470305, 12 pages https://doi.org/10.1155/2018/1470305 Research Article Endophytic Actinomycetes from Tea Plants (Camellia sinensis): Isolation, Abundance, Antimicrobial, and Plant-Growth-Promoting Activities Wenna Shan,1,2 Ying Zhou,2,3 Huihui Liu,1,2 and Xiaomin Yu 2 College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou , China FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou , China College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou , China Correspondence should be addressed to Xiaomin Yu; [email protected] Received 27 August 2018; Accepted 11 October 2018; Published 1 November 2018 Guest Editor: Walter Chitarra Copyright © 2018 Wenna Shan et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Endophytic actinomycetes are a promising source of novel metabolites with diverse biological activities. Tea plants (Camellia sinensis) produce arsenals of phytochemicals, which are linked to a number of medicinal and nutritional properties. However, a systematic investigation into the abundance and diversity of cultivated actinomycetes residing in tea plants has not been performed. In this study, a total of 46 actinobacteria were
    [Show full text]