Development of a PCR-Based Method for Detection of Pathogenic Yersinia Enterocolitica in Pork
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Metabolic and Genetic Basis for Auxotrophies in Gram-Negative Species
Metabolic and genetic basis for auxotrophies in Gram-negative species Yara Seifa,1 , Kumari Sonal Choudharya,1 , Ying Hefnera, Amitesh Ananda , Laurence Yanga,b , and Bernhard O. Palssona,c,2 aSystems Biology Research Group, Department of Bioengineering, University of California San Diego, CA 92122; bDepartment of Chemical Engineering, Queen’s University, Kingston, ON K7L 3N6, Canada; and cNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark Edited by Ralph R. Isberg, Tufts University School of Medicine, Boston, MA, and approved February 5, 2020 (received for review June 18, 2019) Auxotrophies constrain the interactions of bacteria with their exist in most free-living microorganisms, indicating that they rely environment, but are often difficult to identify. Here, we develop on cross-feeding (25). However, it has been demonstrated that an algorithm (AuxoFind) using genome-scale metabolic recon- amino acid auxotrophies are predicted incorrectly as a result struction to predict auxotrophies and apply it to a series of the insufficient number of known gene paralogs (26). Addi- of available genome sequences of over 1,300 Gram-negative tionally, these methods rely on the identification of pathway strains. We identify 54 auxotrophs, along with the corre- completeness, with a 50% cutoff used to determine auxotrophy sponding metabolic and genetic basis, using a pangenome (25). A mechanistic approach is expected to be more appropriate approach, and highlight auxotrophies conferring a fitness advan- and can be achieved using genome-scale models of metabolism tage in vivo. We show that the metabolic basis of auxotro- (GEMs). For example, requirements can arise by means of a sin- phy is species-dependent and varies with 1) pathway structure, gle deleterious mutation in a conditionally essential gene (CEG), 2) enzyme promiscuity, and 3) network redundancy. -
Public Health Aspects of Yersinia Pseudotuberculosis in Deer and Venison
Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. PUBLIC HEALTH ASPECTS OF YERSINIA PSEUDOTUBERCULOSIS IN DEER AND VENISON A THESIS PRESENTED IN PARTIAL FULFlLMENT (75%) OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF PHILOSOPHY IN VETERINARY PUBLIC HEALTH AT MASSEY UNIVERSITY EDWIN BOSI September, 1992 DEDICATED TO MY PARENTS (MR. RICHARD BOSI AND MRS. VICTORIA CHUAN) MY WIFE (EVELYN DEL ROZARIO) AND MY CHILDREN (AMELIA, DON AND JACQUELINE) i Abstract A study was conducted to determine the possible carriage of Yersinia pseudotuberculosisand related species from faeces of farmed Red deer presented/or slaughter and the contamination of deer carcase meat and venison products with these organisms. Experiments were conducted to study the growth patternsof !.pseudotuberculosis in vacuum packed venison storedat chilling andfreezing temperatures. The serological status of slaughtered deer in regards to l..oseudotubercu/osis serogroups 1, 2 and 3 was assessed by Microp late Agglutination Tests. Forty sera were examined comprising 19 from positive and 20 from negative intestinal carriers. Included in this study was one serum from an animal that yielded carcase meat from which l..pseudotuberculosiswas isolated. Caecal contents were collected from 360 animals, and cold-enriched for 3 weeks before being subjected to bacteriological examination for Yersinia spp. A total of 345 and 321 carcases surface samples for bacteriological examination for Yersiniae were collected at the Deer Slaughter Premises (DSP) and meat Packing House respectively. -
A Case Series of Diarrheal Diseases Associated with Yersinia Frederiksenii
Article A Case Series of Diarrheal Diseases Associated with Yersinia frederiksenii Eugene Y. H. Yeung Department of Medical Microbiology, The Ottawa Hospital General Campus, The University of Ottawa, Ottawa, ON K1H 8L6, Canada; [email protected] Abstract: To date, Yersinia pestis, Yersinia enterocolitica, and Yersinia pseudotuberculosis are the three Yersinia species generally agreed to be pathogenic in humans. However, there are a limited number of studies that suggest some of the “non-pathogenic” Yersinia species may also cause infections. For instance, Yersinia frederiksenii used to be known as an atypical Y. enterocolitica strain until rhamnose biochemical testing was found to distinguish between these two species in the 1980s. From our regional microbiology laboratory records of 18 hospitals in Eastern Ontario, Canada from 1 May 2018 to 1 May 2021, we identified two patients with Y. frederiksenii isolates in their stool cultures, along with their clinical presentation and antimicrobial management. Both patients presented with diarrhea, abdominal pain, and vomiting for 5 days before presentation to hospital. One patient received a 10-day course of sulfamethoxazole-trimethoprim; his Y. frederiksenii isolate was shown to be susceptible to amoxicillin-clavulanate, ceftriaxone, ciprofloxacin, and sulfamethoxazole- trimethoprim, but resistant to ampicillin. The other patient was sent home from the emergency department and did not require antimicrobials and additional medical attention. This case series illustrated that diarrheal disease could be associated with Y. frederiksenii; the need for antimicrobial treatment should be determined on a case-by-case basis. Keywords: Yersinia frederiksenii; Yersinia enterocolitica; yersiniosis; diarrhea; microbial sensitivity tests; Citation: Yeung, E.Y.H. A Case stool culture; sulfamethoxazole-trimethoprim; gastroenteritis Series of Diarrheal Diseases Associated with Yersinia frederiksenii. -
Two Copies of the Ail Gene Found in Yersinia Enterocolitica and Yersinia
1 Two copies of the ail gene found in Yersinia enterocolitica and Yersinia 2 kristensenii 3 4 Suvi Joutsena,b, Per Johanssona, Riikka Laukkanen-Niniosa,c, Johanna Björkrotha and Maria 5 Fredriksson-Ahomaaa 6 7 aDepartment of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, 8 P.O.Box 66 (Agnes Sjöbergin katu 2), 00014 University of Helsinki, Finland 9 bRisk Assessment Unit, Finnish Food Authority, Helsinki, Finland 10 cFood Safety Unit, Finnish Food Authority, Helsinki, Finland 11 12 Corresponding author: 13 E-mail address: [email protected] 1 14 Abstract 15 16 Yersinia enterocolitica is the most common Yersinia species causing foodborne infections in 17 humans. Pathogenic strains carry the chromosomal ail gene, which is essential for bacterial 18 attachment to and invasion into host cells and for serum resistance. This gene is commonly 19 amplified in several PCR assays detecting pathogenic Y. enterocolitica in food samples and 20 discriminating pathogenic isolates from non-pathogenic ones. We have isolated several non- 21 pathogenic ail-positive Yersinia strains from various sources in Finland. For this study, we 22 selected 16 ail-positive Yersinia strains, which were phenotypically and genotypically 23 characterised. Eleven strains were confirmed to belong to Y. enterocolitica and five strains to 24 Yersinia kristensenii using whole-genome alignment, Parsnp and the SNP phylogenetic tree. 25 All Y. enterocolitica strains belonged to non-pathogenic biotype 1A. We found two copies of 26 the ail gene (ail1 and ail2) in all five Y. kristensenii strains and in one Y. enterocolitica 27 biotype 1A strain. All 16 Yersinia strains carried the ail1 gene consisting of three different 28 sequence patterns (A6-A8), which were highly similar with the ail gene found in high- 29 pathogenic Y. -
Use of Vectorette and Subvectorette PCR to Isolate Transgene Flanking DNA
Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Use of Vectorette and Subvectorette PCR to Isolate Transgene Flanking DNA Maxine J. Allen, Andrew Collick, and Alec J. Jeffreys Department of Genetics, University of Leicester, Leicester LE1 7RH, UK Vectorette PCR permits the specific PCR allows specific amplification of structures and in the recovery of un- amplification of DNA segments flank- DNA fragments between two regions of known bacterial sequences. ~4-6~ In this ing a known DNA sequence. It en- known sequence to which primers can paper we detail its use in the systematic ables the application of the PCR be directed. Often, however, molecular isolation of 5'- and 3'-flanking junction where sequence information is only biological techniques require the isola- sequences around mouse transgenes of available for one primer site. We now tion and subsequent sequence analysis the minisatellite MS32. MS32 is a hu- show that vectorette PCR can be used of unknown regions of DNA. PCR can be man minisatellite composed of a tan- for the systematic mapping and re- used to retrieve this unknown sequence dem array of 29-bp repeat-unit sequence trieval of transgene flanking DNA. if it is flanking a region of known se- variants. The interspersion of these We also show that the sequence of quence. In this case, a primer can be de- sequence variants can be assayed in large vectorette PCR fragments can signed in either orientation from the the minisatellite variant repeat (MVR)- be obtained without cloning, by the known sequence. -
Download At: Amplification May Be Performed During Library Con- Fenyolab/Tipseqhunter (See Table 6)
Steranka et al. Mobile DNA (2019) 10:8 https://doi.org/10.1186/s13100-019-0148-5 METHODOLOGY Open Access Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome Jared P. Steranka1,2, Zuojian Tang3,4, Mark Grivainis3,4, Cheng Ran Lisa Huang2, Lindsay M. Payer1, Fernanda O. R. Rego5, Thiago Luiz Araujo Miller5,6, Pedro A. F. Galante5, Sitharam Ramaswami7, Adriana Heguy7, David Fenyö3,4, Jef D. Boeke4* and Kathleen H. Burns1,2* Abstract Background: Transposable elements make up a significant portion of the human genome. Accurately locating these mobile DNAs is vital to understand their role as a source of structural variation and somatic mutation. To this end, laboratories have developed strategies to selectively amplify or otherwise enrich transposable element insertion sites in genomic DNA. Results: Here we describe a technique, Transposon Insertion Profiling by sequencing (TIPseq), to map Long INterspersed Element 1 (LINE-1, L1) retrotransposon insertions in the human genome. This method uses vectorette PCR to amplify species-specific L1 (L1PA1) insertion sites followed by paired-end Illumina sequencing. In addition to providing a step-by-step molecular biology protocol, we offer users a guide to our pipeline for data analysis, TIPseqHunter. Our recent studies in pancreatic and ovarian cancer demonstrate the ability of TIPseq to identify invariant (fixed), polymorphic (inherited variants),aswellassomatically-acquiredL1insertionsthat distinguish cancer genomes from a patient’s constitutional make-up. Conclusions: TIPseq provides an approach for amplifying evolutionarily young, active transposable element insertion sites from genomic DNA. Our rationale and variations on this protocol may be useful to those mapping L1 and other mobile elements in complex genomes. -
Loop-Mediated Isothermal Amplification (LAMP)
cells Review Loop-Mediated Isothermal Amplification (LAMP): The Better Sibling of PCR? Marianna Soroka, Barbara Wasowicz * and Anna Rymaszewska Department of Genetics and Genomics, Institute of Biology, University of Szczecin, 3c Felczaka St., 71-412 Szczecin, Poland; [email protected] (M.S.); [email protected] (A.R.) * Correspondence: [email protected] Abstract: In 1998, when the PCR technique was already popular, a Japanese company called Eiken Chemical Co., Ltd. designed a method known as the loop-mediated isothermal amplification of DNA (LAMP). The method can produce up to 109 copies of the amplified DNA within less than an hour. It is also highly specific due to the use of two to three pairs of primers (internal, external, and loop), which recognise up to eight specific locations on the DNA or RNA targets. Furthermore, the Bst DNA polymerase most used in LAMP shows a high strand displacement activity, which eliminates the DNA denaturation stage. One of the most significant advantages of LAMP is that it can be conducted at a stable temperature, for instance, in a dry block heater or an incubator. The products of LAMP can be detected much faster than in standard techniques, sometimes only requiring analysis with the naked eye. The following overview highlights the usefulness of LAMP and its effectiveness in various fields; it also considers the superiority of LAMP over PCR and presents RT-LAMP as a rapid diagnostic tool for SARS-CoV-2. Keywords: LAMP method; isothermal amplification; SARS-CoV-2 detection Citation: Soroka, M.; Wasowicz, B.; Rymaszewska, A. -
And White-Tailed Deer
Food Microbiology 78 (2019) 82–88 Contents lists available at ScienceDirect Food Microbiology journal homepage: www.elsevier.com/locate/fm Microbial contamination of moose (Alces alces) and white-tailed deer T (Odocoileus virginianus) carcasses harvested by hunters ∗ Mikaela Sauvalaa, , Sauli Laaksonenb, Riikka Laukkanen-Niniosa, Katri Jalavaa,c, Roger Stephand, Maria Fredriksson-Ahomaaa a Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland b Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Finland c Department of Statistics and Mathematics, Faculty of Science, University of Helsinki, Finland d Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland ARTICLE INFO ABSTRACT Keywords: Hunting is currently a very popular activity, and interest in game meat is increasing. However, only limited Moose research is available on the bacterial quality and safety of moose (Alces alces) and white-tailed deer (Odocoileus Deer virginianus) harvested by hunters. Poor hunting hygiene can spread bacteria onto the carcasses, and inadequate Hunting hygiene chilling of the carcasses may increase the bacterial load on the carcass surface. We studied the bacterial con- Carcass tamination level on carcasses of 100 moose and 100 white-tailed deer shot in southern Finland. Hunters evis- Bacterial contamination cerated carcasses in the field and skinned them in small slaughter facilities. During the sampling, same person visited 25 facilities located in 12 municipalities of four provinces. Moose carcasses had mean mesophilic aerobic 2 bacteria (MAB), Enterobacteriaceae (EB) and Escherichia coli (EC) values of 4.2, 2.6 and 1.2 log10 cfu/cm , re- 2 spectively, while deer carcass values were 4.5, 1.5 and 0.7 log10 cfu/cm , respectively. -
Biosafety Guidelines for Contained Use of Genetically Modified Microorganisms at Pilot and Industrial Scales
Biosafety Guidelines for Contained Use of Genetically Modified Microorganisms at Pilot and Industrial Scales TECHNICAL BIOSAFETY COMMITTEE (TBC) NATIONAL CENTER FOR GENETIC ENGINEERING AND BIOTECHNOLOGY (BIOTEC) NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY (NSTDA) MINISTRY OF SCIENCE AND TECHNOLOGY (MOST) 2015 Biosafety Guidelines for Contained Use of Genetically Modified Microorganisms at Pilot and Industrial Scales TECHNICAL BIOSAFETY COMMITTEE (TBC) NATIONAL CENTER FOR GENETIC ENGINEERING AND BIOTECHNOLOGY (BIOTEC) NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY (NSTDA) MINISTRY OF SCIENCE AND TECHNOLOGY (MOST) 2015 Biosafety Guidelines for Contained Use of Genetically Modified Microorganisms at Pilot and Industrial Scales Technical Biosafety Committee National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency (NSTDA) © National Center for Genetic Engineering and Biotechnology 2015 ISBN : 978-616-12-0386-3 Tel : +66(0)2-564-6700 Fax : +66(0)2-564-6703 E-mail : [email protected] URL : http://www.biotec.or.th Printing House : P.A. Living Printing Co.,Ltd 4 Soi Sirintron 7 Road Sirintron District Bangplad Province Bangkok 10700 Tel : +66(0)2-881 9890 Fax : +66(0)2-881 9894 Preface Genetically Modified Microorganisms (GMMs) were first used in B.E. 2525 to produce insulin in industrial medicine. Currently, GMMs are used in various industries, such as the food, pharmaceutical and bioplastic industries, to manufacture a number of important consumer products. To ensure operator and environmental safety, the Technical Biosafety Committee (TBC) of the National Center for Genetic Engineering and Biotechnology (BIOTEC), the National Science and Technology Development Agency (NSTDA), has prepared guidelines for GMM work, publishing “Biosafety Guidelines for Contained Use of Genetically Modified Microorganisms at Pilot and Industrial Scales” in B.E. -
Are Molecular Tools Solving the Challenges Posed by Detection Of
Curr. Issues Mol. Biol. 11: 13-46. Molecular Tools for DetectionOnline journal of Plant at http://www.cimb.org Pathogens 13 Are Molecular Tools Solving the Challenges Posed by Detection of Plant Pathogenic Bacteria and Viruses? María M. López*, Pablo Llop, Antonio Olmos, Ester plant pathogens due to their low titre in the plants, their Marco-Noales, Mariano Cambra and Edson Bertolini uneven distribution, the existence of latent infections and the lack of validated sampling protocols. Research Centro de Protección Vegetal y Biotecnología, Instituto based on genomic advances and innovative detection Valenciano de Investigaciones Agrarias (IVIA). Carretera methods as well as better knowledge of the pathogens’ de Moncada a Náquera km 4.5, 46113 Moncada, lifecycle, will facilitate their early and accurate detection, Valencia, Spain thus improving the sanitary status of cultivated plants in the near future. *For correspondence: [email protected] Introduction Abstract Plant pathogenic bacteria, phytoplasmas, viruses and Plant pathogenic bacteria, phytoplasmas, viruses and viroids cause harmful, widespread and economically viroids are difficult to control, and preventive measures important diseases in a very broad range of plant are essential to minimize the losses they cause each species worldwide (Agrios, 2001; Janse, 2007). Damage year in different crops. In this context, rapid and accurate is often sufficient to cause significant yield losses in methods for detection and diagnosis of these plant cultivated plants (Schaad, 1988; Scortichini, 1995; pathogens are required to apply treatments, undertake Cambra et al., 2006b). The two main effects on agronomic measures or proceed with eradication agriculture are decreased production and, in a less direct practices, particularly for quarantine pathogens. -
(12) United States Patent (10) Patent No.: US 9,546,389 B2 Li (45) Date of Patent: Jan
USOO9546,389 B2 (12) United States Patent (10) Patent No.: US 9,546,389 B2 Li (45) Date of Patent: Jan. 17, 2017 (54) METHODS AND SYSTEMS FOR NUCLEIC (56) References Cited ACIDAMPLIFICATION U.S. PATENT DOCUMENTS (71) Applicant: Coyote Bioscience Co., Ltd., Beijing 5,759,821. A * 6/1998 Teasdale .............. C12O 1/6806 (CN) 435,912 2004/0209331 A1* 10, 2004 Ririe ....................... BO1L 3,505 435,912 (72) Inventor: Xiang Li, Beijing (CN) 2008/0085541 A1 4/2008 Spangler 2012/0308990 A1* 12/2012 TeMaat ..................... BO1L, 7,52 (73) Assignee: COYOTE BIOSCIENCE CO.,LTD., 435/3 Beijing (CN) 2013/0022963 A1 1/2013 Exner et al. FOREIGN PATENT DOCUMENTS (*) Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 CN 101597652. A 12/2009 U.S.C. 154(b) by 0 days. CN 103074349 A 5, 2013 JP EP 1069 190 A2 * 1 2001 ............. C12O 1/686 WO WO-2012109604 A1 8, 2012 (21) Appl. No.: 14/963,986 OTHER PUBLICATIONS (22) Filed: Dec. 9, 2015 Callahan et al. Use of a portable real-time reverse transcriptase (65) Prior Publication Data polymerase chain reaction assay for rapid detection of foot-and mouth disease virus. JAVMA 220: 1636-1642 (2002).* US 2016/O115513 A1 Apr. 28, 2016 Gilbert et al. Typing of bovine viral diarrhea viruses directly from blood of persistently infected cattle by multiplex PCR. Journal of Clinical Microbiology 37:2020-2023 (1999).* International search report and written opinion dated Feb. 26, 2015 Related U.S. Application Data for PCT Application No. CN2014/094914. -
Aerobic Gram-Positive Bacteria
Aerobic Gram-Positive Bacteria Abiotrophia defectiva Corynebacterium xerosisB Micrococcus lylaeB Staphylococcus warneri Aerococcus sanguinicolaB Dermabacter hominisB Pediococcus acidilactici Staphylococcus xylosusB Aerococcus urinaeB Dermacoccus nishinomiyaensisB Pediococcus pentosaceusB Streptococcus agalactiae Aerococcus viridans Enterococcus avium Rothia dentocariosaB Streptococcus anginosus Alloiococcus otitisB Enterococcus casseliflavus Rothia mucilaginosa Streptococcus canisB Arthrobacter cumminsiiB Enterococcus durans Rothia aeriaB Streptococcus equiB Brevibacterium caseiB Enterococcus faecalis Staphylococcus auricularisB Streptococcus constellatus Corynebacterium accolensB Enterococcus faecium Staphylococcus aureus Streptococcus dysgalactiaeB Corynebacterium afermentans groupB Enterococcus gallinarum Staphylococcus capitis Streptococcus dysgalactiae ssp dysgalactiaeV Corynebacterium amycolatumB Enterococcus hiraeB Staphylococcus capraeB Streptococcus dysgalactiae spp equisimilisV Corynebacterium aurimucosum groupB Enterococcus mundtiiB Staphylococcus carnosusB Streptococcus gallolyticus ssp gallolyticusV Corynebacterium bovisB Enterococcus raffinosusB Staphylococcus cohniiB Streptococcus gallolyticusB Corynebacterium coyleaeB Facklamia hominisB Staphylococcus cohnii ssp cohniiV Streptococcus gordoniiB Corynebacterium diphtheriaeB Gardnerella vaginalis Staphylococcus cohnii ssp urealyticusV Streptococcus infantarius ssp coli (Str.lutetiensis)V Corynebacterium freneyiB Gemella haemolysans Staphylococcus delphiniB Streptococcus infantarius