Streptococcal Infections in Marine Mammals
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Evidence for Niche Adaptation in the Genome of The
University of Warwick institutional repository: http://go.warwick.ac.uk/wrap This paper is made available online in accordance with publisher policies. Please scroll down to view the document itself. Please refer to the repository record for this item and our policy information available from the repository home page for further information. To see the final version of this paper please visit the publisher’s website. Access to the published version may require a subscription. Author(s): Philip N Ward, Matthew TG Holden, James A Leigh, Nicola Lennard, Alexandra Bignell, Andy Barron, Louise Clark, Michael A Quail, John Woodward, Bart G Barrell, Sharon A Egan, Terence R Field, Duncan Maskell, Michael Kehoe, Christopher G Dowson, Neil Chanter, Adrian M Whatmore, Stephen D Bentley and Julian Parkhill Article Title: Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis Year of publication: 2009 Link to published version: http://dx.doi.org/ doi: doi:10.1186/1471-2164- 10-54 Publisher statement: None BMC Genomics BioMed Central Research article Open Access Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis Philip N Ward1, Matthew TG Holden*2, James A Leigh3, Nicola Lennard2, Alexandra Bignell2, Andy Barron2, Louise Clark2, Michael A Quail2, John Woodward2, Bart G Barrell2, Sharon A Egan3, Terence R Field4, Duncan Maskell5, Michael Kehoe6, Christopher G Dowson7, Neil Chanter8, Adrian M Whatmore7,9, Stephen D Bentley2 and Julian Parkhill2 Address: 1Nuffield Department of Clinical Laboratory Sciences, Oxford University, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK, 2The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK, 3The School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK, 4Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berks, RG20 7NN, UK, 5Dept. -
Mobile Genetic Elements in Streptococci
Curr. Issues Mol. Biol. (2019) 32: 123-166. DOI: https://dx.doi.org/10.21775/cimb.032.123 Mobile Genetic Elements in Streptococci Miao Lu#, Tao Gong#, Anqi Zhang, Boyu Tang, Jiamin Chen, Zhong Zhang, Yuqing Li*, Xuedong Zhou* State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China. #Miao Lu and Tao Gong contributed equally to this work. *Address correspondence to: [email protected], [email protected] Abstract Streptococci are a group of Gram-positive bacteria belonging to the family Streptococcaceae, which are responsible of multiple diseases. Some of these species can cause invasive infection that may result in life-threatening illness. Moreover, antibiotic-resistant bacteria are considerably increasing, thus imposing a global consideration. One of the main causes of this resistance is the horizontal gene transfer (HGT), associated to gene transfer agents including transposons, integrons, plasmids and bacteriophages. These agents, which are called mobile genetic elements (MGEs), encode proteins able to mediate DNA movements. This review briefly describes MGEs in streptococci, focusing on their structure and properties related to HGT and antibiotic resistance. caister.com/cimb 123 Curr. Issues Mol. Biol. (2019) Vol. 32 Mobile Genetic Elements Lu et al Introduction Streptococci are a group of Gram-positive bacteria widely distributed across human and animals. Unlike the Staphylococcus species, streptococci are catalase negative and are subclassified into the three subspecies alpha, beta and gamma according to the partial, complete or absent hemolysis induced, respectively. The beta hemolytic streptococci species are further classified by the cell wall carbohydrate composition (Lancefield, 1933) and according to human diseases in Lancefield groups A, B, C and G. -
Validation of the Asaim Framework and Its Workflows on HMP Mock Community Samples
Validation of the ASaiM framework and its workflows on HMP mock community samples The ASaiM framework and its workflows have been tested and validated on two mock metagenomic data of an artificial community (with 22 known microbial strains). The datasets are available on EBI metagenomics database (project accession number: SRP004311). First we checked that the targeted abundances (based on number of PCR product) from both mock datasets were similar to the effective abundance (by mapping reads on reference genomes). Second, taxonomic and functional results produced by the ASaiM framework have been extensively analyzed and compared to expectations and to results obtained with the EBI metagenomics pipeline (S. Hunter et al. 2014). For these datasets, the ASaiM framework produces accurate and precise taxonomic assignations, different functional results (gene families, pathways, GO slim terms) and results combining taxonomic and functional information. Despite almost 1.4 million of raw metagenomic sequences, these analyses were executed in less than 6h on a commodity computer. Hence, the ASaiM framework and its workflows are proven to be relevant for the analysis of microbiota datasets. 1Data On EBI metagenomics database, two mock community samples for Human Microbiome Project (HMP) are available. Both samples contain a genomic mixture of 22 known microbial strains. Relative abundance of each strain has been targeted using the number of PCR product of their respective 16S sequences (Table 1). In first sample (SRR072232), the targeted 16S copies of the strains vary by up to four orders of magnitude between the strains (Table 1), whereas in second sample (SRR072233) the same 16S copy number is targeted for each strain (Table 1). -
Appendix III: OTU's Found to Be Differentially Abundant Between CD and Control Patients Via Metagenomeseq Analysis
Appendix III: OTU's found to be differentially abundant between CD and control patients via metagenomeSeq analysis OTU Log2 (FC CD / FDR Adjusted Phylum Class Order Family Genus Species Number Control) p value 518372 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.16 5.69E-08 194497 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.15 8.93E-06 175761 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 5.74 1.99E-05 193709 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 2.40 2.14E-05 4464079 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides NA 7.79 0.000123188 20421 Firmicutes Clostridia Clostridiales Lachnospiraceae Coprococcus NA 1.19 0.00013719 3044876 Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus] gnavus -4.32 0.000194983 184000 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.81 0.000306032 4392484 Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides NA 5.53 0.000339948 528715 Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium prausnitzii 2.17 0.000722263 186707 Firmicutes Clostridia Clostridiales NA NA NA 2.28 0.001028539 193101 Firmicutes Clostridia Clostridiales Ruminococcaceae NA NA 1.90 0.001230738 339685 Firmicutes Clostridia Clostridiales Peptococcaceae Peptococcus NA 3.52 0.001382447 101237 Firmicutes Clostridia Clostridiales NA NA NA 2.64 0.001415109 347690 Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira NA 3.18 0.00152075 2110315 Firmicutes Clostridia -
Canine Streptococcal Toxic Shock Syndrome Associated with Necrotizing Fasciitis: an Overview
Vet. World, 2012, Vol.5(5):311-319 REVIEW Canine Streptococcal Toxic Shock Syndrome associated with Necrotizing Fasciitis: An Overview Barkha Sharma*1 , Mukesh Kumar Srivastava2 , Ashish Srivastava2 and Rashmi Singh1 1.Department of Epidemiology and Veterinary Preventive Medicine, 2.Department of Veterinary Medicine, Pandit deen Dayal Upadhyay Pashuchikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU) Mathura, UP, 281001, India * Corresponding author email: [email protected] Received: 18-09-2011, Accepted: 23-10-2011, Published Online: 21-01-2012 doi: 10.5455/vetworld.2012.311-319 Abstract Canine Toxic Shock Syndrome (CSTSS) is a serious often fatal disease syndrome seen in dogs caused as a result of an infection caused by gram positive cocci of the family Streptococci. The main bacterium involved in the etiology of Canine Streptococcal Toxic Shock Syndrome is Streptoccoccus canis, which was discovered by Deveriese in 1986 and implicated as a cause of this disease syndrome in 1996 by Miller and Prescott. The clinical findings in this syndrome are very much similar to those seen in the infamous 'Toxic Shock 'caused by staphylococcal toxins in humans, especially females. Like in humans, the reason for emergence/reemergence of Canine Streptococcal Toxic Shock Syndrome (CSTSS) is unclear and very little is known about its transmission and prevention. The disease is characterized by multi systemic organ failure and a shock like condition in seemingly healthy dog often following an injury. In absence of proper and prompt diagnosis and subsequent treatment by injectable antibiotics and aggressive shock therapy, dog often succumbs to the disease within a few hours. The dog may have some rigidity and muscle spasms or convulsions and a deep unproductive cough followed by haemorrhage from nasal and mouth along with melena. -
Streptococcaceae
STREPTOCOCCACEAE Instructor Dr. Maytham Ihsan Ph.D Vet Microbiology 1 STREPTOCOCCACEAE Genus: Streptococcus and Enterocccus Streptococcus and Enterocccus genera, are Gram‐positive ovoid (lanceolate) cocci, approximately 1 μm in diameter, that tend to occur in singles, pairs & chains (rosary‐like) may be long or short. Streptococcus species occur as commensals on skin, upper & lower respiratory tract and mucous membranes; some may act as opportunistic pathogens causing pyogenic infections. Enteroccci spp. are enteric opportunistic & can be found in the intestinal tract of many animlas & humans. Growth & Culture Characteristics • Most streptococci are facultative anaerobes and catalase‐negative. • They are non‐motile and oxidase‐negative and do not form spores & susceptible to desiccation. • They are fastidious bacteria and require the addition of blood or serum to culture media. They grow at temperature ranging from 37°C to 42°C. Group D (Enterocooci), are considered thermophilic & can gorw at 45°C or even higher. • Colonies are small about 1 mm in size, smooth, translucent & may be greyish. • Streptococcus pneumoniae (pneumococcus or diplococcus) occurs as slightly pear‐shaped cocci in pairs. Pathogenic strains have thick capsules and produce mucoid colonies or flat colonies with smooth borders & a central concavity “draughtsman colonies” aer 48‐72 hrs on blood agar. These bacteria cause pneumonia in humans and rats. 2 • Some of streptococci grow on MacConkey like: Enterococcus faecalis, Strept. bovis, Sterpt. uberis & strept. lactis producing very tiny colonies like pin‐point appearance aer 48 hrs of incubaon at 37°C. • Streptococci genera grow slowly in broth media, sometimes forming faint opacity; whereas others with a fluffy deposit adherent to the side of the tube. -
Development of Bacterial Communities in Biological Soil Crusts Along
1 Development of bacterial communities in biological soil crusts along 2 a revegetation chronosequence in the Tengger Desert, northwest 3 China 4 5 Author names and affiliations: 6 Lichao Liu1, Yubing Liu1, 2 *, Peng Zhang1, Guang Song1, Rong Hui1, Zengru Wang1, Jin Wang1, 2 7 1Shapotou Desert Research & Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese 8 Academy of Sciences, Lanzhou, 730000, China 9 2Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Northwest Institute 10 of Eco–Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China 11 12 * Corresponding author: Yubing Liu 13 Address: Donggang West Road 320, Lanzhou 730000, P. R. China. 14 Tel: +86 0931 4967202. 15 E-mail address: [email protected] 16 17 Abstract. Knowledge of structure and function of microbial communities in different 18 successional stages of biological soil crusts (BSCs) is still scarce for desert areas. In this study, 19 Illumina MiSeq sequencing was used to assess the composition changes of bacterial communities 20 in different ages of BSCs in the revegetation of Shapotou in the Tengger Desert. The most dominant 21 phyla of bacterial communities shifted with the changed types of BSCs in the successional stages, 22 from Firmicutes in mobile sand and physical crusts to Actinobacteria and Proteobacteria in BSCs, 23 and the most dominant genera shifted from Bacillus, Enterococcus and Lactococcus to 24 RB41_norank and JG34-KF-361_norank. Alpha diversity and quantitative real-time PCR analysis 25 indicated that bacteria richness and abundance reached their highest levels after 15 years of BSC 26 development. -
Pathogenic Streptococcus Gallolyticus Subspecies: Genome Plasticity, Adaptation and Virulence
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Sequencing and Comparative Genome Analysis of Two Pathogenic Streptococcus gallolyticus Subspecies: Genome Plasticity, Adaptation and Virulence I-Hsuan Lin1,2., Tze-Tze Liu3., Yu-Ting Teng3, Hui-Lun Wu3, Yen-Ming Liu3, Keh-Ming Wu3, Chuan- Hsiung Chang1,4, Ming-Ta Hsu3,5* 1 Institute of BioMedical Informatics, National Yang-Ming University, Taipei, Taiwan, 2 Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, 3 VGH Yang-Ming Genome Research Center, National Yang-Ming University, Taipei, Taiwan, 4 Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan, 5 Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan Abstract Streptococcus gallolyticus infections in humans are often associated with bacteremia, infective endocarditis and colon cancers. The disease manifestations are different depending on the subspecies of S. gallolyticus causing the infection. Here, we present the complete genomes of S. gallolyticus ATCC 43143 (biotype I) and S. pasteurianus ATCC 43144 (biotype II.2). The genomic differences between the two biotypes were characterized with comparative genomic analyses. The chromosome of ATCC 43143 and ATCC 43144 are 2,36 and 2,10 Mb in length and encode 2246 and 1869 CDS respectively. The organization and genomic contents of both genomes were most similar to the recently published S. gallolyticus UCN34, where 2073 (92%) and 1607 (86%) of the ATCC 43143 and ATCC 43144 CDS were conserved in UCN34 respectively. There are around 600 CDS conserved in all Streptococcus genomes, indicating the Streptococcus genus has a small core-genome (constitute around 30% of total CDS) and substantial evolutionary plasticity. -
Common Commensals
Common Commensals Actinobacterium meyeri Aerococcus urinaeequi Arthrobacter nicotinovorans Actinomyces Aerococcus urinaehominis Arthrobacter nitroguajacolicus Actinomyces bernardiae Aerococcus viridans Arthrobacter oryzae Actinomyces bovis Alpha‐hemolytic Streptococcus, not S pneumoniae Arthrobacter oxydans Actinomyces cardiffensis Arachnia propionica Arthrobacter pascens Actinomyces dentalis Arcanobacterium Arthrobacter polychromogenes Actinomyces dentocariosus Arcanobacterium bernardiae Arthrobacter protophormiae Actinomyces DO8 Arcanobacterium haemolyticum Arthrobacter psychrolactophilus Actinomyces europaeus Arcanobacterium pluranimalium Arthrobacter psychrophenolicus Actinomyces funkei Arcanobacterium pyogenes Arthrobacter ramosus Actinomyces georgiae Arthrobacter Arthrobacter rhombi Actinomyces gerencseriae Arthrobacter agilis Arthrobacter roseus Actinomyces gerenseriae Arthrobacter albus Arthrobacter russicus Actinomyces graevenitzii Arthrobacter arilaitensis Arthrobacter scleromae Actinomyces hongkongensis Arthrobacter astrocyaneus Arthrobacter sulfonivorans Actinomyces israelii Arthrobacter atrocyaneus Arthrobacter sulfureus Actinomyces israelii serotype II Arthrobacter aurescens Arthrobacter uratoxydans Actinomyces meyeri Arthrobacter bergerei Arthrobacter ureafaciens Actinomyces naeslundii Arthrobacter chlorophenolicus Arthrobacter variabilis Actinomyces nasicola Arthrobacter citreus Arthrobacter viscosus Actinomyces neuii Arthrobacter creatinolyticus Arthrobacter woluwensis Actinomyces odontolyticus Arthrobacter crystallopoietes -
Use of the Diagnostic Bacteriology Laboratory: a Practical Review for the Clinician
148 Postgrad Med J 2001;77:148–156 REVIEWS Postgrad Med J: first published as 10.1136/pmj.77.905.148 on 1 March 2001. Downloaded from Use of the diagnostic bacteriology laboratory: a practical review for the clinician W J Steinbach, A K Shetty Lucile Salter Packard Children’s Hospital at EVective utilisation and understanding of the Stanford, Stanford Box 1: Gram stain technique University School of clinical bacteriology laboratory can greatly aid Medicine, 725 Welch in the diagnosis of infectious diseases. Al- (1) Air dry specimen and fix with Road, Palo Alto, though described more than a century ago, the methanol or heat. California, USA 94304, Gram stain remains the most frequently used (2) Add crystal violet stain. USA rapid diagnostic test, and in conjunction with W J Steinbach various biochemical tests is the cornerstone of (3) Rinse with water to wash unbound A K Shetty the clinical laboratory. First described by Dan- dye, add mordant (for example, iodine: 12 potassium iodide). Correspondence to: ish pathologist Christian Gram in 1884 and Dr Steinbach later slightly modified, the Gram stain easily (4) After waiting 30–60 seconds, rinse with [email protected] divides bacteria into two groups, Gram positive water. Submitted 27 March 2000 and Gram negative, on the basis of their cell (5) Add decolorising solvent (ethanol or Accepted 5 June 2000 wall and cell membrane permeability to acetone) to remove unbound dye. Growth on artificial medium Obligate intracellular (6) Counterstain with safranin. Chlamydia Legionella Gram positive bacteria stain blue Coxiella Ehrlichia Rickettsia (retained crystal violet). -
Zanieczyszcenia Mikrobiologiczne Podziemnych Magazynow Gazu I Gazociagow Agnieszka Staniszewksa, Alina Kunicka-Stycynska, Krystzof Zieminski
Zanieczyszcenia mikrobiologiczne podziemnych magazynow gazu i gazociagow Agnieszka Staniszewksa, Alina Kunicka-Stycynska, Krystzof Zieminski To cite this version: Agnieszka Staniszewksa, Alina Kunicka-Stycynska, Krystzof Zieminski. Zanieczyszcenia mikrobio- logiczne podziemnych magazynow gazu i gazociagow. Polish journal of microbiology / Polskie To- warzystwo Mikrobiologów = The Polish Society of Microbiologists, 2017, 56, pp.94. hal-02736852 HAL Id: hal-02736852 https://hal.inrae.fr/hal-02736852 Submitted on 2 Jun 2020 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. POLSKIE TOWARZYSTWO MIKROBIOLOGÓW Kwartalnik Tom 56 Zeszyt 2•2017 KWIECIE¡ – CZERWIEC CODEN: PMKMAV 56 (2) Advances in Microbiology 2017 POLSKIE TOWARZYSTWO MIKROBIOLOGÓW Kwartalnik Tom 56 Zeszyt 3•2017 LIPIEC – WRZESIE¡ CODEN: PMKMAV 56 (3) Advances in Microbiology 2017 POLSKIE TOWARZYSTWO MIKROBIOLOGÓW Kwartalnik Tom 56 Zeszyt 4•2017 PAèDZIERNIK – GRUDZIE¡ CODEN: PMKMAV 56 (4) Advances in Microbiology 2017 Index Copernicus ICV = 111,53 (2015) Impact Factor ISI = 0,311 (2016) Punktacja -
Clinical Interest of Streptococcus Bovis Isolates in Urine
Brief report Javier de Teresa-Alguacil1 Miguel Gutiérrez-Soto2 Clinical interest of Streptococcus bovis isolates in Javier Rodríguez-Granger3 Antonio Osuna-Ortega1 urine José María Navarro-Marí3 José Gutiérrez-Fernández3,4 1UGC de Nefrología, Complejo Hospitalario Universitario de Granada-ibsgranada. 2Centro de Salud “Polígono Guadalquivir”. Córdoba. 3Laboratorio de Microbiología, Complejo Hospitalario Universitario de Granada-ibsgranada. 4Departamento de Microbiología – Universidad de Granada-ibsgranada. ABSTRACT Significado clínico de los aislados de Streptococcus bovis en orina Introduction. Streptococcus bovis includes variants re- lated to colorectal cancer and non-urinary infections. Its role RESUMEN as urinary pathogen is unknown. Our objective was to assess the presence of urinary infection by S. bovis, analysing the pa- Introducción. Streptococcus bovis comprende multitud tients and subsequent clinical course. de variantes de especie relacionados con infecciones no uri- Material and Methods. Observational study, with lon- narias y cáncer colorrectal. Su papel como patógeno urinario gitudinal data collection, performed at our centre between es desconocido. Nuestro objetivo fue valorar la presencia de all the cultures requested between February and April 2015. infección urinaria por S. bovis, analizando los pacientes y su Clinical course of the patients and response to treatment were evolución clínica posterior. analysed. Material y métodos. Estudio observacional, con obten- Results. Two thousand five hundred and twenty urine ción de datos longitudinal, realizado en nuestro centro entre cultures were analysed, of which 831 (33%) had a significant todos los urocultivos solicitados durante entre los meses de microbial count. S. bovis was isolated in 8 patients (0.96%). In febrero y abril de 2015. Se analizó la evolución clínica y la 75% of these cases the urine culture was requested because of respuesta al tratamiento.