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Arxiv:1903.01048V1 [Stat.AP] 4 Mar 2019 Author Summary
Early Detection of Influenza outbreaks in the United States Kai Liu1,3*, Ravi Srinivasan2, Lauren Ancel Meyers1,4 1 Departments of Integrative Biology and Statistics & Data Sciences, The University of Texas at Austin, Austin, TX, US 2 Applied Research Laboratories, The University of Texas at Austin, Austin, TX, US 3 Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, US 4 Santa Fe Institute, Santa Fe, NM, US * [email protected] Abstract Public health surveillance systems often fail to detect emerging infectious diseases, particularly in resource limited settings. By integrating relevant clinical and internet-source data, we can close critical gaps in coverage and accelerate outbreak detection. Here, we present a multivariate algorithm that uses freely available online data to provide early warning of emerging influenza epidemics in the US. We evaluated 240 candidate predictors and found that the most predictive combination does not include surveillance or electronic health records data, but instead consists of eight Google search and Wikipedia pageview time series reflecting changing levels of interest in influenza-related topics. In cross validation on 2010-2016 data, this algorithm sounds alarms an average of 16.4 weeks prior to influenza activity reaching the Center for Disease Control and Prevention (CDC) threshold for declaring the start of the season. In an out-of-sample test on data from the rapidly-emerging fall wave of the 2009 H1N1 pandemic, it recognized the threat five weeks in advance of this surveillance threshold. Simpler algorithms, including fixed week-of-the-year triggers, lag the optimized alarms by only a few weeks when detecting seasonal influenza, but fail to provide early warning in the 2009 pandemic scenario. -
Feline Calicivirus Ulcer on Tongue Unilateral Conjunctivitis Typical of Early Chlamydophila Felis Infection Feline Chronic Lymphocytic Plasmacytic Gingivostomatitis
£5.00, $9.00, €7.50 Melchizedek publications www.catvirus.com If you print this book out – please do so on recycled paper! Cover photos – feline calicivirus ulcer on tongue unilateral conjunctivitis typical of early Chlamydophila felis infection feline chronic lymphocytic plasmacytic gingivostomatitis © Diane D. Addie PhD BVMS MRCVS Sep 2006 2 Contents Page Introduction ………………………………………………………………………. 4 Feline calicivirus………………………………………………………………….. 4 Feline chronic gingivostomatitis ………………………………………….. .….. 7 Feline herpesvirus (viral rhinotracheitis)……………………………………….. 10 Chlamydophila felis……………………………………………………………….. 13 Bordetella bronchiseptica ……………………………………………………….. 16 Avian influenza virus H5N1 …………………………………………………….. 17 Poxvirus …………………………………………………………………………… 19 Feline coronavirus ……………………………………………………………….. 19 Haemophilus felis ………………………………………………………………… 19 Aelurostrongylus abstrusus …………………………………………………….. 19 Mycoplasma felis ………………………………………………………………… 20 Corynebacterium spp ……………………………………………………………. 20 Cryptococcus spp ……………………………..…………………………………. 20 Capillaria aerophila ………………………………………………………………. 21 Cuterebra larval migrans ………………………………………………………… 21 Differential diagnoses …………………………………………………………… 22 acute oral ulceration …………………………………… 22 chronic gingivostomatitis……………………………….. 22 chronic rhinitis ………………………………………….. 22 conjunctivitis ……………………………………………. 23 coughing ………………………………………………… 23 fading kittens ……………………………………………. 23 bronchopneumonia of kittens …………………………. 24 Preventing respiratory infection 25 hygiene ………………………………………. 25 barrier nursing -
Ohio Department of Health, Bureau of Infectious Diseases Disease Name Class A, Requires Immediate Phone Call to Local Health
Ohio Department of Health, Bureau of Infectious Diseases Reporting specifics for select diseases reportable by ELR Class A, requires immediate phone Susceptibilities specimen type Reportable test name (can change if Disease Name other specifics+ call to local health required* specifics~ state/federal case definition or department reporting requirements change) Culture independent diagnostic tests' (CIDT), like BioFire panel or BD MAX, E. histolytica Stain specimen = stool, bile results should be sent as E. histolytica DNA fluid, duodenal fluid, 260373001^DETECTED^SCT with E. histolytica Antigen Amebiasis (Entamoeba histolytica) No No tissue large intestine, disease/organism-specific DNA LOINC E. histolytica Antibody tissue small intestine codes OR a generic CIDT-LOINC code E. histolytica IgM with organism-specific DNA SNOMED E. histolytica IgG codes E. histolytica Total Antibody Ova and Parasite Anthrax Antibody Anthrax Antigen Anthrax EITB Acute Anthrax EITB Convalescent Anthrax Yes No Culture ELISA PCR Stain/microscopy Stain/spore ID Eastern Equine Encephalitis virus Antibody Eastern Equine Encephalitis virus IgG Antibody Eastern Equine Encephalitis virus IgM Arboviral neuroinvasive and non- Eastern Equine Encephalitis virus RNA neuroinvasive disease: Eastern equine California serogroup virus Antibody encephalitis virus disease; LaCrosse Equivocal results are accepted for all California serogroup virus IgG Antibody virus disease (other California arborviral diseases; California serogroup virus IgM Antibody specimen = blood, serum, serogroup -
Paradoxical Evolution of Rickettsial Genomes
Ticks and Tick-borne Diseases 10 (2019) 462–469 Contents lists available at ScienceDirect Ticks and Tick-borne Diseases journal homepage: www.elsevier.com/locate/ttbdis Paradoxical evolution of rickettsial genomes T ⁎ Awa Diopa, Didier Raoultb, Pierre-Edouard Fourniera, a UMR VITROME, Aix-Marseille University, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Uuniversitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France b UMR MEPHI, Aix-Marseille University, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Uuniversitaire Méditerranée Infection, Marseille, France ARTICLE INFO ABSTRACT Keywords: Rickettsia species are strictly intracellular bacteria that evolved approximately 150 million years ago from a Rickettsia presumably free-living common ancestor from the order Rickettsiales that followed a transition to an obligate Genomics intracellular lifestyle. Rickettsiae are best known as human pathogens vectored by various arthropods causing a Evolution range of mild to severe human diseases. As part of their obligate intracellular lifestyle, rickettsial genomes have Virulence undergone a convergent evolution that includes a strong genomic reduction resulting from progressive gene Genome rearrangement degradation, genomic rearrangements as well as a paradoxical expansion of various genetic elements, notably Non-coding DNA Gene loss small RNAs and short palindromic elements whose role remains unknown. This reductive evolutionary process is DNA repeats not unique to members of the Rickettsia genus but is common to several human pathogenic bacteria. Gene loss, gene duplication, DNA repeat duplication and horizontal gene transfer all have shaped rickettsial genome evolution. Gene loss mostly involved amino-acid, ATP, LPS and cell wall component biosynthesis and tran- scriptional regulators, but with a high preservation of toxin-antitoxin (TA) modules, recombination and DNA repair proteins. -
“Candidatus Rickettsia Kellyi,” India
was also on his palms and soles. No tick bite was noted. A “Candidatus skin biopsy was taken from a maculopapular lesion. Laboratory tests showed a leukocyte count of 15,300/mm3, Rickettsia hemoglobin level of 9.2 g/dL, and normal platelet count, and normal cerebrospinal fluid was seen by lumbar punc- kellyi,” India ture. The patient was given doxycycline syrup and cefo- taxime because the diagnosis was not definitive and the Jean-Marc Rolain,* Elizabeth Mathai,† boy was very ill. The boy responded dramatically and Hubert Lepidi,* Hosaagrahara R. Somashekar,† eventually recovered. Results of conventional culture of Leni G. Mathew,† John A.J. Prakash,† cerebrospinal fluid, skin biopsy specimens, and blood cul- and Didier Raoult* ture were negative. We report the first laboratory-confirmed human infec- With Weil-Felix agglutination assay, the serum sample tion due to a new rickettsial genotype in India, “Candidatus taken at admission was weakly positive with OX-2 antigen Rickettsia kellyi,” in a 1-year-old boy with fever and macu- (titer 40) and negative for OXK and OX-19 antigens, giv- lopapular rash. The diagnosis was made by serologic test- ing presumptive evidence of a rickettsial infection. DNA ing, polymerase chain reaction detection, and immuno- was extracted from the skin biopsy specimen and used as histochemical testing of the organism from a skin biopsy a template in 2 previously described PCR assays that tar- specimen. geted a portion of the rickettsial ompA gene as well as a portion of the rickettsial gltA gene, ompB gene, and sca4 uman rickettsioses are infections of emerging impor- genes (6,7). -
View Full Issue
Volume 31, Issue 2, December 2015 ISSN 0204-8809 ACTA MICROBIOLOGICA BULGARICA Bulgarian Society for Microbiology Union of Scientists in Bulgaria Acta Microbiologica Bulgarica The journal publishes editorials, original research works, research reports, reviews, short communications, letters to the editor, historical notes, etc from all areas of microbiology An Official Publication of the Bulgarian Society for Microbiology (Union of Scientists in Bulgaria) Volume 31 / 2 (2015) Editor-in-Chief Angel S. Galabov Press Product Line Sofia Editor-in-Chief Angel S. Galabov Editors Maria Angelova Hristo Najdenski Editorial Board I. Abrashev, Sofia S. Aydemir, Izmir, Turkey L. Boyanova, Sofia E. Carniel, Paris, France M. Da Costa, Coimbra, Portugal E. DeClercq, Leuven, Belgium S. Denev, Stara Zagora D. Fuchs, Innsbruck, Austria S. Groudev, Sofia I. Iliev, Plovdiv A. Ionescu, Bucharest, Romania L. Ivanova, Varna V. Ivanova, Plovdiv I. Mitov, Sofia I. Mokrousov, Saint-Petersburg, Russia P. Moncheva, Sofia M. Murdjeva, Plovdiv R. Peshev, Sofia M. Petrovska, Skopje, FYROM J. C. Piffaretti, Massagno, Switzerland S. Radulovic, Belgrade, Serbia P. Raspor, Ljubljana, Slovenia B. Riteau, Marseille, France J. Rommelaere, Heidelberg, Germany G. Satchanska, Sofia E. Savov, Sofia A. Stoev, Kostinbrod S. Stoitsova, Sofia T. Tcherveniakova, Sofia E. Tramontano, Cagliari, Italy A. Tsakris, Athens, Greece F. Wild, Lyon, France Vol. 31, Issue 2 December 2015 ACTA MICROBIOLOGICA BULGARICA CONTENTS Review Articles Biohydrometallurgy in Bulgaria - Achievements and -
Tick- and Flea-Borne Rickettsial Emerging Zoonoses Philippe Parola, Bernard Davoust, Didier Raoult
Tick- and flea-borne rickettsial emerging zoonoses Philippe Parola, Bernard Davoust, Didier Raoult To cite this version: Philippe Parola, Bernard Davoust, Didier Raoult. Tick- and flea-borne rickettsial emerging zoonoses. Veterinary Research, BioMed Central, 2005, 36 (3), pp.469-492. 10.1051/vetres:2005004. hal- 00902973 HAL Id: hal-00902973 https://hal.archives-ouvertes.fr/hal-00902973 Submitted on 1 Jan 2005 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. Vet. Res. 36 (2005) 469–492 469 © INRA, EDP Sciences, 2005 DOI: 10.1051/vetres:2005004 Review article Tick- and flea-borne rickettsial emerging zoonoses Philippe PAROLAa, Bernard DAVOUSTb, Didier RAOULTa* a Unité des Rickettsies, CNRS UMR 6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, 13385 Marseille Cedex 5, France b Direction Régionale du Service de Santé des Armées, BP 16, 69998 Lyon Armées, France (Received 30 March 2004; accepted 5 August 2004) Abstract – Between 1984 and 2004, nine more species or subspecies of spotted fever rickettsiae were identified as emerging agents of tick-borne rickettsioses throughout the world. Six of these species had first been isolated from ticks and later found to be pathogenic to humans. -
Using Core Genome Alignments to Assign Bacterial Species 2
bioRxiv preprint doi: https://doi.org/10.1101/328021; this version posted May 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 Using Core Genome Alignments to Assign Bacterial Species 2 3 Matthew Chunga,b, James B. Munroa, Julie C. Dunning Hotoppa,b,c,# 4 a Institute for Genome Sciences, University of Maryland Baltimore, Baltimore, MD 21201, USA 5 b Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD 6 21201, USA 7 c Greenebaum Comprehensive Cancer Center, University of Maryland Baltimore, Baltimore, MD 21201, 8 USA 9 10 Running Title: Core Genome Alignments to Assign Bacterial Species 11 12 #Address correspondence to Julie C. Dunning Hotopp, [email protected]. 13 14 Word count Abstract: 371 words 15 Word count Text: 4,833 words 16 1 bioRxiv preprint doi: https://doi.org/10.1101/328021; this version posted May 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 17 ABSTRACT 18 With the exponential increase in the number of bacterial taxa with genome sequence data, a new 19 standardized method is needed to assign bacterial species designations using genomic data that is 20 consistent with the classically-obtained taxonomy. -
Bennett, Susan (2015) Development of Multiplex Real-Time PCR Screens for the Diagnosis of Feline and Canine Infectious Disease
Bennett, Susan (2015) Development of multiplex real-time PCR screens for the diagnosis of feline and canine infectious disease. MSc(R) thesis. http://theses.gla.ac.uk/5971/ Copyright and moral rights for this thesis are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the Author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the Author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Glasgow Theses Service http://theses.gla.ac.uk/ [email protected] Development of Multiplex Real-Time PCR Screens for the Diagnosis of Feline and Canine Infectious Disease Susan Bennett BSc (Hons) Master of Science by Research University of Glasgow College of Medical, Veterinary & Life Sciences May 2014 Copyright Statement 24th May 2014 This thesis is submitted in partial fulfilment for the degree of Master of Science by Research. I declare that it has been composed by myself, and the work described is my own research. Susan Bennett BSc (Hons) i Abstract Infectious disease is a significant cause of morbidity and mortality in cats and dogs. The diagnosis of the causative agent is essential to allow for the appropriate clinical intervention, to reduce infection spread, and also to support epidemiological studies which in turn will better the understanding of infectious disease transmission and control. -
Disease Outbreak Detection Using Search Keywords Patterns
EPiC Series in Computing Volume 69, 2020, Pages 362{371 Proceedings of 35th International Confer- ence on Computers and Their Applications Disease Outbreak Detection Using Search Keywords Patterns Izzat Alsmadi1,*, Zaid Almubaid2, and Hisham Al-Mubaid3 1Texas A&M San Antonio, San Antonio, Texas, USA 2 University of Texas, Austin, Texas, USA. 3University of Houston–Clear Lake, Houston, Texas, USA *[email protected] Abstract In the recent years, people are becoming more dependent on the Internet as their main source of information about healthcare. A number of research projects in the past few decades examined and utilized the internet data for information extraction in healthcare including disease surveillance and monitoring. In this paper, we investigate and study the potential of internet data like internet search keywords and search query patterns in the healthcare domain for disease monitoring and detection. Specifically, we investigate search keyword patterns for disease outbreak detection. Accurate prediction and detection of disease outbreaks in a timely manner can have a big positive impact on the entire health care system. Our method utilizes machine learning in identifying interesting patterns related to target disease outbreak from search keyword logs. We conducted experiments on the flu disease, which is the most searched disease in the interest of this problem. We showed examples of keywords that can be good predictors of outbreaks of the flu. Our method proved that the correlation between search queries and keyword trends are truly reliable in the sense that it can be used to predict the outbreak of the disease. Keywords: Disease outbreak detection, disease monitoring and surveillance. -
Copyrighted Material
361 Index a – PCR 224 abdominal and intestinal anthrax 14 – – virus culture and antigen testing 224 abscesses 40 – prevention 340–341 acid-fast bacilli (AFB) 151 – protection 338–339 activated partial thromboplastin time (APTT) – treatment 342 219 Argentinian hemorrhagic fever (AHF) 213, Advisory Committee on Immunization 217, 219, 220 Practices (ACIP) 203 ‘‘Army Vaccine’’ 97 African tick bite fever (ATBF) 124, 129, 142 arthropod-borne infections 124, 125, 127, agar gel immunodiffusion (AGID) 181 128, 129, 139, 142 Agrobacterium 20 avian influenza viruses (AIVs) 177, 178 Alphaproteobacteria 124 Amblyomma hebraeum 129 b Amblyomma variegatum 129 bacille Calmette–Guerin´ (BCG) 150, 153, amplified fragment length polymorphism 155 (AFLP) 159 Bacillus anthracis 5, 159 Anaplasmataceae 124, 126 – characteristics 5–6 Andes virus (ANDV) 273, 276, 277 – clinical and pathological findings anthrax. See Bacillus anthracis 13–14 antibiotic resistance 7–8 – – abdominal and intestinal anthrax 14 antigen detection 8 – – inhalation and pulmonary anthrax 14 Antiqua biovar 93 – – oropharyngeal anthrax 14 Arenaviridae 253 – clinical guidelines 297 arenaviruses 211–212 – decontamination 296 – clinical signs – diagnosis – – New World hemorrhagic fevers 214–215 – – antibiotic resistance 7–8 – – Old World hemorrhagic fevers 214 – – antigen detection 8 – decontamination 340 – – chromosome 10–11 – diagnostics COPYRIGHTED– – growth characteristics MATERIAL 6–7 – – serological tests 223 – – MLVA, SNR, and SNP typing 11 – disinfection 339–340 – – molecular identification 8–10 – epidemiology – – phage testing and biochemistry 8 – – New World 213–214 – – phenotypical identification 6 – – Old World 212–213 – – serological investigations 11 – pathogenesis 218–223 – disinfection 295, 296 – pathological signs – epidemiology 15 – – New World hemorrhagic fevers 217–218 – pathogenesis – – Old World hemorrhagic fevers 215–216 – – animals 12 BSL3 and BSL4 Agents: Epidemiology, Microbiology, and Practical Guidelines, First Edition. -
Rocky Mountain Spotted Fever
23.03.2013 CHYPRE «Emerging Rickettsioses» © by author ESCMID Online Lecture Library Didier Raoult Marseille - France [email protected] www.mediterranee-infection.com Gram negative bacterium Strictly intracellular Transmitted by arthropods: ticks, fleas, lice,© mites by author ESCMIDMosquitoes? Online Lecture Library U R 2 Louse borne disease - typhus Tick borne : the big killer - RMSF Other: less severe Flea borne - Murine typhus (Maxcy 1925 and Mooser 1921 ) Mite borne diseases - Scrub typhus (tsutsugamushi disease) Rickettsial pox (Huebner 1946© ) by author OtherESCMID rickettsia: non Online pathogenic Lecture Library Any Gram negative intracellular bacteria= Rickettsiales U R 3 NEW RICKETTSIAL DISEASES Many new diseases comparable to Arboviruses New clinical features no rash but adenopathy (R. slovaca, R. raoultii ) no rash, no inoculation eschar (R. helvetica ) others? Several species involved in a same area R. conorii and R. africae - Africa R. conorii, R. mongolotimonae© by author- France R. conorii, R. aeschlimannii - Spain, North Africa R. typhi and R. felis - USA ESCMID R. honei and R.Online australis - Australia Lecture Library R. rickettsii and R. parkeri - USA R. conorii and R. helvetica, R. slovaca - Switzerland U R 4 SITUATION DURING THE XXTH CENTURY One tick borne rickettsiosis per geographical area R. rickettsii agent of RMSF in the USA – other found in ticks: non pathogenic rickettsia (such as Coxiella burnetii or Legionella pneumophila) R. conorii alone in Europe© byand author Africa ESCMID