Bacterial Serotyping Guide for Salmonella Minimizing Risk the Monitoring of Veterinary Diseases and Quality Control of Industrial Products Are Public Health Issues
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“Isolation of Antibiotic Producing Actinomycetes from Soil”
© 2020 JETIR May 2020, Volume 7, Issue 5 www.jetir.org (ISSN-2349-5162) “ISOLATION OF ANTIBIOTIC PRODUCING ACTINOMYCETES FROM SOIL” *Sneha khadse1Priyanka Titirmare2 1) Project assistant at CSIR NEERI Nagpur, 2) Kamla Nehru Mahavidyalaya, Nagpur. ABSTRACT The present study deals with the isolation, production, purification and optimization of antibiotics from soil. The soil samples were collected from various places. Actinomycetes strains were isolated in specific medium using starch casein agar medium. The actinomycetes were screened with regard to potential against gram positive and gram negative bacteria. The purified actinomycetes strains were performed in biochemical tests. Gram staining, sugars fermentation, HS production, urease production, MR-VP test, indole production, citrate 2 utilization. Fermentation was carried out with starch casein broth and identified strain of actinomyces as inoculums. Antimicrobial activity of antibiotics was detected on Mueller Hinton Agar Media against E.coli. The purification of antibiotics was done with the help of activated charcoal. During the experiment a modified fermentation medium was formulated and activity of antibiotic produced in this medium was detected against E.coli. The isolated bacteria such as actinomycetesobtained from the soil. INTRODUCTION Antibiotics are complex chemical secondary metabolites, which are produced by microorganisms & act against other microorganisms. The term antibiotics had its origin from Greek word anti-against+biotikos =”fit for life”. Antibiotics are the best known products of actinomycetes. The best known genus of actinomycetes; Streptomyces (Order Actinomycetales, family Streptomycetaceae are gram-positive, filamentous bacteria that are ubiquitous in soil and produce the majority (>70%) of known antibiotics (Tanaka and Omura, 1990). The isolation & characterization of Actinomycetes were performed in different biochemical methods. -
Extracting Structured Genotype Information from Free-Text HLA
J Korean Med Sci. 2020 Mar 30;35(12):e78 https://doi.org/10.3346/jkms.2020.35.e78 eISSN 1598-6357·pISSN 1011-8934 Original Article Extracting Structured Genotype Medical Informatics Information from Free-Text HLA Reports Using a Rule-Based Approach Kye Hwa Lee ,1 Hyo Jung Kim ,2 Yi-Jun Kim ,1 Ju Han Kim ,2 and Eun Young Song 3 1Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea 2Division of Biomedical Informatics, Seoul National University Biomedical Informatics and Systems Biomedical Informatics Research Center, Seoul National University College of Medicine, Seoul, Korea 3Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea Received: May 16, 2019 ABSTRACT Accepted: Jan 29, 2020 Address for Correspondence: Background: Human leukocyte antigen (HLA) typing is important for transplant patients to Eun Young Song, MD, PhD prevent a severe mismatch reaction, and the result can also support the diagnosis of various Division of Biomedical Informatics, Seoul disease or prediction of drug side effects. However, such secondary applications of HLA National University Biomedical Informatics (SNUBI) and Systems Biomedical Informatics typing results are limited because they are typically provided in free-text format or PDFs on Research Center, Seoul National University electronic medical records. We here propose a method to convert HLA genotype information College of Medicine, 103 Daehak-ro, stored in an unstructured format into a reusable structured format by extracting serotype/ Jongno-gu, Seoul 03080, Korea. allele information. E-mail: [email protected] Methods: We queried HLA typing reports from the clinical data warehouse of Seoul National Kye Hwa Lee, MD, PhD University Hospital (SUPPREME) from 2000 to 2018 as a rule-development data set (64,024 Center for Precision Medicine, Seoul National reports) and from the most recent year (6,181 reports) as a test set. -
Biochemical Media Casitone Broth-White Cap with Black Circle. Loop Transfer
Biochemical Media Casitone Broth-white cap with black circle. Loop transfer. (Use care tops may be very loose) (Do not put caps on the wrong tubes during the inoculation procedures). Can the organism split tryptophan into indole, pyruvic acid and ammonia? Test for the presence of indole (unique to this process) by adding 5 drops of Kovacs Test Reagent. If indole is present, a ruby red color will form at the top of the test tube. The media name for casitone comes from the word casein. Casein is a milk protein rich in the amino acid tryptophan. Result sheet recorded with a “pos” or “neg” Phenol Red Carbohydrate Fermentation Broths (Phenol Reds) Red capped broth with durham tube-Phenol Red with Lactose Clear capped broth with durham tube-Phenol Red with Glucose Yellow capped broth with durham tube-Phenol Red with Sucrose Blue capped broth with durham tube-Phenol Red with Maltose Green capped broth with durham tube-Phenol Red with Mannitol All tubes are inoculated with loop transfers. Can the organism ferment the carbohydrates listed above? Each comes with a separate sugar, a durham tube for gas collection and the acid-base indicator called phenolphthalein. Fermentation will produce acidity and sometimes gas. Gas alone is not produced by the fermentation process. Phenolphthalein will turn yellow in the presence of acid, red in an alkaline environment. Gas production can be observed by the presence of air bubbles captured in the durham tube. For each result both an acid and gas response should be indicated. For a large amount of acid (yellow) use “A”. -
Cluster-Specific Gene Markers Enhance Shigella and Enteroinvasive Escherichia Coli in Silico Serotyping Xiaomei Zhang1, Michael
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.30.428723; this version posted February 1, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Cluster-specific gene markers enhance Shigella and Enteroinvasive Escherichia coli in 2 silico serotyping 3 4 Xiaomei Zhang1, Michael Payne1, Thanh Nguyen1, Sandeep Kaur1, Ruiting Lan1* 5 6 1School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 7 New South Wales, Australia 8 9 10 11 *Corresponding Author 12 Email: [email protected] 13 Phone: 61-2-9385 2095 14 Fax: 61-2-9385 1483 15 16 Keywords: Phylogenetic clusters, cluster-specific gene markers, Shigella/EIEC serotyping 17 Running title: Shigella EIEC Cluster Enhanced Serotyping 18 Repositories: Raw sequence data are available from NCBI under the BioProject number 19 PRJNA692536. 20 21 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.30.428723; this version posted February 1, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 23 Abstract 24 Shigella and enteroinvasive Escherichia coli (EIEC) cause human bacillary dysentery with 25 similar invasion mechanisms and share similar physiological, biochemical and genetic 26 characteristics. The ability to differentiate Shigella and EIEC from each other is important for 27 clinical diagnostic and epidemiologic investigations. The existing genetic signatures may not 28 discriminate between Shigella and EIEC. However, phylogenetically, Shigella and EIEC 29 strains are composed of multiple clusters and are different forms of E. -
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Research Article For reprint orders, please contact: [email protected] Association of the HLA-B alleles with carbamazepine-induced Stevens–Johnson syndrome/toxic epidermal necrolysis in the Javanese and Sundanese population of Indonesia: the important role of the HLA-B75 serotype Rika Yuliwulandari*,1,2,3, Erna Kristin3,4, Kinasih Prayuni2, Qomariyah Sachrowardi5, Franciscus D Suyatna3,6, Sri Linuwih Menaldi7, Nuanjun Wichukchinda8, Surakameth Mahasirimongkol8 & Larisa H Cavallari9 1Department of Pharmacology, Faculty of Medicine, YARSI University, Cempaka Putih, Jakarta Pusat, DKI Jakarta, Indonesia 2Genomic Medicine Research Centre, YARSI Research Institute, YARSI University, Cempaka Putih, Jakarta Pusat, DKI Jakarta, Indonesia 3The Indonesian Pharmacogenomics Working Group, DKI Jakarta, Indonesia 4Department of Pharmacology & Therapy, Faculty of Medicine, Gadjah Mada University, Yogyakarta, Indonesia 5Department of Physiology, Faculty of Medicine, YARSI University, Cempaka Putih, Jakarta Pusat, DKI Jakarta, Indonesia 6Department of Pharmacology & Therapeutic, Faculty of Medicine, University of Indonesia, Salemba, Jakarta Pusat, DKI Jakarta, Indonesia 7Department of Dermatology Clinic, Faculty of Medicine, University of Indonesia, Salemba, Jakarta Pusat, DKI Jakarta, Indonesia 8Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand 9College of Pharmacy, University of Florida, Gainesville, FL 32603, USA * Author for correspondence: Tel.: +62 21 4206675; Fax: +62 21 4243171; [email protected] Carbamazepine (CBZ) is a common cause of life-threatening cutaneous adverse drug reactions such as Stevens–Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). Previous studies have reported a strong association between the HLA genotype and CBZ-induced SJS/TEN. We investigated the association between the HLA genotype and CBZ-induced SJS/TEN in Javanese and Sundanese patients in Indonesia. -
Association of an HLA-DQ Allele with Clinical Tuberculosis
Brief Report Association of an HLA-DQ Allele With Clinical Tuberculosis Anne E. Goldfeld, MD; Julio C. Delgado, MD; Sok Thim; M. Viviana Bozon, MD; Adele M. Uglialoro; David Turbay, MD; Carol Cohen; Edmond J. Yunis, MD Context.—Although tuberculosis (TB) is the leading worldwide cause of death clinical TB, we performed a 2-stage study due to an infectious disease, the extent to which progressive clinical disease is as- of molecular typing of HLA class I and sociated with genetic host factors remains undefined. class II alleles and also tested for the pres- α Objective.—To determine the distribution of HLA antigens and the frequency of ence of 2 TNF- alleles in Cambodian pa- 2 alleles of the tumor necrosis factor a (TNF-a) gene in unrelated individuals with tients with clinical TB and in control indi- viduals who did not have a history of TB. clinical TB (cases) compared with individuals with no history of clinical TB (controls) in a population with a high prevalence of TB exposure. Methods Design.—A 2-stage, case-control molecular typing study conducted in 1995-1996. The study subjects were unrelated Cam- Setting.—Three district hospitals in Svay Rieng Province in rural Cambodia. bodian patients recruited from a TB treat- Patients.—A total of 78 patients with clinical TB and 49 controls were included ment program in eastern rural Cambodia. in the first stage and 48 patients with TB and 39 controls from the same area and Two different groups of patients and con- socioeconomic status were included in the second stage. -
Canada 57-2 Fisheries Peches L+I and Oceans Et Oceans STANDARD PROCEDURES PROCEDURES POUR for BACTERIOLOGICAL ANALYSES ANALYSIS BACTERIOLOGIQUES
/0.58:29 Fisheries Peches l+I and Oceans et Oceans Inspection Services de Services )'inspection Standard Procedures pour Procedures for analyses Bacteriological bacteriologiques Analysis ( /v/fJ,rJ Ul.LS IX 54.3 Canada 57-2 Fisheries Peches l+I and Oceans et Oceans STANDARD PROCEDURES PROCEDURES POUR FOR BACTERIOLOGICAL ANALYSES ANALYSIS BACTERIOLOGIQUES Record of Amendments amend. no chapter date of amend. inserted by insertion date 1 5 +Qn1"' E 31 - ns- X'S C? c l~ Le.Lle.J/ gs - Dtc C; ··7 ~ />f» c ~ e:. ~.J J-~ \ s .. o sfft8 /vf:-l~ fb. ~-o 1~1r . Government Gouvernement of Canada du Canada IDate ••• Canadian Food Agence canadienne 1 15£05£98 Inspection Agency d'inspection des aliments STANDARD PROCEDURES PROCEDURES POUR FOR BACTERIOLOGICAL ANALYSES ANALYSIS BACTERIOLOGIQUES Bulletin TO: All Holders of the Standard Procedures for Bacteriological Analysis Manual SUBJECT: MODIFICATIONS TO THE PROCEDURES Attached are modifications to various Chapters and Appendices of the Bacteriological Analysis manual. The changes have been incorporated in this bulletin format in order to provide the updates to manual holders as quickly as possible and also due to the uncertainty as to whether the manual will continue to be used as a bacteriological procedures reference by the Agency. The changes to the respective sections have been incorporated on separate pages so the pertinent page(s) may be inserted with the relevant chapter/appendix. If required, these modifications will be incorporated in the manual at a later date. Cam Prince Director Fish, -
Antigen HLA-A*0201 MHC Class I Clone OP67 Product Code 9467
International Blood Group Reference Laboratory 500 North Bristol Park Antigen HLA-A*0201 MHC class I Northway Filton Clone OP67 Bristol BS34 7QH Product Code 9467 Protein Development and Production Unit Immunoglobulin Class Mouse IgG1 kappa light chain Tel: +44 (0)117 921 7500 Fax: +44 (0)117 912 5796 Website: http://ibgrl.blood.co.uk Email: [email protected] Antigen Description and Distribution The major histocompatibility complex (MHC) is the most polygenic and polymorphic region in the human genome. Human leukocyte antigens (HLA) Class I include HLA-A, -B and -C loci. HLA-A are encoded by the HLA-A locus on human chromosome 6p. The HLA genes constitute a large subset of the MHC of humans. HLA-A is a component of certain MHC class I cell surface receptor glycoproteins that resides on the surface of all nucleated cells and platelets. Class I MHC molecules bind peptides generated mainly from degradation of cytosolic proteins by the proteasome and display intracellular proteins to cytotoxic T cells. However, class I MHC can also present peptides generated from exogenous proteins, in a process known as cross-presentation. Alternatively, class I MHC itself can serve as an inhibitory ligand for natural killer cells (NKs). Reduction in the normal levels of surface class I MHC, a mechanism employed by some viruses during immune evasion or in certain tumors, will activate NK cell killing. MHC class I molecules consist of two polypeptide chains, α and β2-microglobulin (b2m). The two chains are linked noncovalently via interaction of b2m and the α3 domain. -
Laboratory Methods for the Diagnosis of Epidemic Dysentery and Cholera Centers for Disease Control and Prevention Atlanta, Georgia 1999 WHO/CDS/CSR/EDC/99.8
WHO/CDS/CSR/EDC/99.8 Laboratory Methods for the Diagnosis of Epidemic Dysentery and Cholera Centers for Disease Control and Prevention Atlanta, Georgia 1999 WHO/CDS/CSR/EDC/99.8 Laboratory Methods for the Diagnosis of Epidemic Dysentery and Cholera Centers for Disease Control and Prevention Atlanta, Georgia 1999 This manual was prepared by the National Center for Infectious Diseases (NCID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA, in cooperation with the World Health Organization Regional Office for Africa, (WHO/AFRO) Harare, Zimbabwe. Jeffrey P. Koplan, M.D., M.P.H., Director, CDC James M. Hughes, M.D., Director, NCID, CDC Mitchell L. Cohen, M.D., Director, Division of Bacterial and Mycotic Diseases, NCID, CDC Ebrahim Malek Samba, M.B.,B.S., Regional Director, WHO/AFRO Antoine Bonaventure Kabore, M.D., M.P.H., Director Division for Prevention and Control of Communicable Diseases, WHO/AFRO The following CDC staff members prepared this report: Cheryl A. Bopp, M.S. Allen A. Ries, M.D., M.P.H. Joy G. Wells, M.S. Production: J. Kevin Burlison, Graphics James D. Gathany, Photography Lynne McIntyre, M.A.L.S., Editor Cover: From top, Escherichia co//O157:H7 on sorbitol MacConkey agar, Vibrio cholerae O1 on TCBS agar, and Shige/la flexneri on xylose lysine desoxycholate agar. Acknowledgments Funding for the development of this manual was provided by the U.S. Agency for International Development, Bureau for Africa, Office of Sustainable Development. This manual was developed as a result of a joint effort by the World Health Organization Regional Office for Africa, WHO Headquarters, and the Centers for Disease Control and Prevention as part of the activities of the WHO Global Task Force on Cholera Control. -
Protocol for Non-Typhoidal Salmonella in Drinking and Surface Water - USEPA
Standard Analytical Protocol for Non-Typhoidal Salmonella in Drinking and Surface Water - USEPA Jeremy Olstadt WI State Laboratory of Hygiene, Madison, WI Background • Prolonged survival in water • 1.2 million illnesses in the US per year (CDC)- most are foodborne • Non-typhoidal Salmonella genus is comprised of Salmonella bongori and Salmonella enterica • 2500 know serotypes – all of which are potential human pathogens • Only a few serotypes cause the majority of illness • Haley (2009) Background • Salmonellosis • Symptoms: diarrhea, vomiting, abdominal cramps • Develops 12-72 hours after infection • Lasts 4-7 days Standard Analytical Procedure - Salmonella • BSL-2 Laboratory • USEPA Method 1682: Salmonella in Sewage Sludge (Biosolids) • Support of EPA Homeland Security Efforts Summary of Method • Identification of Salmonella by: Non-Selective and Selective Media Morphological characteristics Biochemical characteristics Serological characteristics Non-Selective Media – Tryptic Soy Broth XLD Plate, Triple Sugar Iron and Salmonella O antiserum agglutination XLD TSI Antibody Test Selective Media – MSRV Plate-Modified Semisolid Rappaport- Vassiliadis Agar Quantitative Sample Analysis • 15 Tube MPN (most probable number)Method 3 Rows of 5 tubes 10mL of 3X (TSB), 5ml of 3X(TSB) and 10mL of 1X(TSB) Inoculate 10mL 3X TSB tubes with 20 mL of sample Inoculate 5mL 3X TSB with 10mL of sample Inoculate 10mL of 1X TSB with 1 mL of sample Incubate at 36.0oC for 24+ 2 hours Arrangement of TSB Tubes for initial enrichment Isolation of Salmonella on -
Accepted Version
Article The cellular protein TIP47 restricts Respirovirus multiplication leading to decreased virus particle production BAMPI, Carole, et al. Abstract The cellular tail-interacting 47-kDa protein (TIP47) acts positively on HIV-1 and vaccinia virus production. We show here that TIP47, in contrast, acts as a restriction factor for Sendai virus production. This conclusion is supported by the occurrence of increased or decreased virus production upon its suppression or overexpression, respectively. Pulse-chase metabolic labeling of viral proteins under conditions of TIP47 suppression reveals an increased rate of viral protein synthesis followed by increased incorporation of viral proteins into virus particles. TIP47 is here described for the first time as a viral restriction factor that acts by limiting viral protein synthesis. Reference BAMPI, Carole, et al. The cellular protein TIP47 restricts Respirovirus multiplication leading to decreased virus particle production. Virus Research, 2013, vol. 173, no. 2, p. 354-63 DOI : 10.1016/j.virusres.2013.01.006 PMID : 23348195 Available at: http://archive-ouverte.unige.ch/unige:28890 Disclaimer: layout of this document may differ from the published version. 1 / 1 Virus Research 173 (2013) 354–363 Contents lists available at SciVerse ScienceDirect Virus Research journa l homepage: www.elsevier.com/locate/virusres The cellular protein TIP47 restricts Respirovirus multiplication leading to decreased virus particle production a a,b,1 c,d Carole Bampi , Anne-Sophie Gosselin Grenet , Grégory Caignard -
Introduction to the Peptide Binding Problem of Computational Immunology: New Results
Found Comput Math DOI 10.1007/s10208-013-9173-9 Introduction to the Peptide Binding Problem of Computational Immunology: New Results Wen-Jun Shen · Hau-San Wong · Quan-Wu Xiao · Xin Guo · Stephen Smale Received: 26 August 2012 / Revised: 5 May 2013 / Accepted: 17 July 2013 © SFoCM 2013 Abstract We attempt to establish geometrical methods for amino acid sequences. To measure the similarities of these sequences, a kernel on strings is defined using only the sequence structure and a good amino acid substitution matrix (e.g. BLOSUM62). The kernel is used in learning machines to predict binding affinities of peptides to human leukocyte antigen DR (HLA-DR) molecules. On both fixed allele (Nielsen and Lund in BMC Bioinform. 10:296, 2009) and pan-allele (Nielsen et al. in Immunome Res. 6(1):9, 2010) benchmark databases, our algorithm achieves the state-of-the-art performance. The kernel is also used to define a distance on an HLA-DR allele set Communicated by Teresa Krick. W.-J. Shen · H.-S. Wong Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong W.-J. Shen e-mail: [email protected] H.-S. Wong e-mail: [email protected] Q.-W. Xiao Microsoft Search Technology Center Asia, Beijing, China e-mail: [email protected] X. Guo Department of Statistical Science, Duke University, Durham, NC, USA e-mail: [email protected] S. Smale (B) Department of Mathematics, City University of Hong Kong, Kowloon, Hong Kong e-mail: [email protected] Found Comput Math based on which a clustering analysis precisely recovers the serotype classifications assigned by WHO (Holdsworth et al.