Public Health Aspects of Yersinia Pseudotuberculosis in Deer and Venison
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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. -
Supplementary Information
doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION METAGENOMIC AND FUNCTIONAL ANALYSIS OF HINDGUT MICROBIOTA OF A WOOD FEEDING HIGHER TERMITE TABLE OF CONTENTS MATERIALS AND METHODS 2 • Glycoside hydrolase catalytic domains and carbohydrate binding modules used in searches that are not represented by Pfam HMMs 5 SUPPLEMENTARY TABLES • Table S1. Non-parametric diversity estimators 8 • Table S2. Estimates of gross community structure based on sequence composition binning, and conserved single copy gene phylogenies 8 • Table S3. Summary of numbers glycosyl hydrolases (GHs) and carbon-binding modules (CBMs) discovered in the P3 luminal microbiota 9 • Table S4. Summary of glycosyl hydrolases, their binning information, and activity screening results 13 • Table S5. Comparison of abundance of glycosyl hydrolases in different single organism genomes and metagenome datasets 17 • Table S6. Comparison of abundance of glycosyl hydrolases in different single organism genomes (continued) 20 • Table S7. Phylogenetic characterization of the termite gut metagenome sequence dataset, based on compositional phylogenetic analysis 23 • Table S8. Counts of genes classified to COGs corresponding to different hydrogenase families 24 • Table S9. Fe-only hydrogenases (COG4624, large subunit, C-terminal domain) identified in the P3 luminal microbiota. 25 • Table S10. Gene clusters overrepresented in termite P3 luminal microbiota versus soil, ocean and human gut metagenome datasets. 29 • Table S11. Operational taxonomic unit (OTU) representatives of 16S rRNA sequences obtained from the P3 luminal fluid of Nasutitermes spp. 30 SUPPLEMENTARY FIGURES • Fig. S1. Phylogenetic identification of termite host species 38 • Fig. S2. Accumulation curves of 16S rRNA genes obtained from the P3 luminal microbiota 39 • Fig. S3. Phylogenetic diversity of P3 luminal microbiota within the phylum Spirocheates 40 • Fig. -
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. -
Yersinia Enterocolitica Infections in People and Other Animals
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. YERSINIA ENTEROCOLITICA INFECTIONS IN PEOPLE AND OTHER ANIMALS )- fl· .L +- � l""'-' A NEW ZEALAND STUDY STANLEY GORDON FENWICK A thesis presented in partial fulfilment of the requirements fo r the degree of Doctor of Philosophy in Veterinary Microbiology Massey University July 1997 MASSEY UNIVERSITY LIBRARY THESIS COPYRIGHT FORM I Title of Thesis: / I ffoflL I I V I PIease delete section not applicable. ( ) (a) I give permission for my thesis to be made available to readers in Massey University Library under conditions determined by the Librarian. (b) I do not wish my thesis t a e available to readers without my written consent for ... ( ) (a) I agree that my thesis, or a copy, may be sent to another institution under conditions determined by the Librarian. (b) I do not wish my thesis, or a "nr,u--f?'I e sent to another institution without my written consent for onths. (a) I agree that my thesis may be copied for Library use. (b) copied for Library use for _ months. Signed: Date: ****************************************************************************** he copyright of this thesis belongs to the author. Readers must sign their name in the space elow to show that they recognise this. They are asked to add their permanent address. AME and ADDRESS DATE ; I .. :1 ABSTRACT During the past three decades, Yersinia enterocolitica has risen to worldwide prominence from an obscure and taxonomically undefmed organism to a common zoonotic pathogen, capable of causing a wide range of clinical syndromes in both animals and people. -
Laborergebnisse Und Auswertung Der 'Hähnchenstudie', Aug-Sep. 2020
Nationales Referenzzentrum für gramnegative Krankenhauserreger in der Abteilung für Medizinische Mikrobiologie Ruhr-Universität Bochum, D-44780 Bochum Nationales Referenzzentrum für gramnegative Krankenhauserreger Prof. Dr. med. Sören Gatermann Institut für Hygiene und Mikrobiologie Abteilung für Medizinische Mikrobiologie Gebäude MA 01 Süd / Fach 21 Universitätsstraße 150 / D-44780 Bochum Tel.: +49 (0)234 /32-26467 Fax.:+49 (0)234 /32-14197 Dr. med. Agnes Anders Dr. rer. nat. Niels Pfennigwerth Tel.: +49 (0)234 / 32-26938 Fax.:+49 (0)234 /32-14197 [email protected] 14. Oktober 2020 GA/LKu Auswertung der „Hähnchenstudie“ Germanwatch, Aug-Sep. 2020 Proben Die Proben wurden von Germanwatch zur Verfügung gestellt. Es handelte sich meist um originalverpackte Handelsware, hinzu kamen Proben eines Werksverkaufes. Die Proben waren entweder gekühlte Ware oder tiefgefroren. Zur Qualitätssicherung wurde ein Minimum- Maximum-Thermometer in den Transportbehälter eingebracht. Die Proben waren von Germanwatch nach einem abgesprochenen Schema nummeriert und wurden bei Ankunft im Labor auf Schäden oder Zeichen von Transportproblemen überprüft, fotografiert und ggf. aufgetaut, bevor sie verarbeitet wurden. Bearbeitung Details der Methodik finden sich am Ende dieses Textes. Die Kultivierung schloss eine semiquantitative Bestimmung der Keimbelastung ein. Die Proben wurden auf Selektivmedien (solche, die selektiv bestimmte, auch resistente Organismen nachweisen) und auf Universalnährmedien (solche, die eine große Anzahl unterschiedlicher Organismen nachweisen) -
R Graphics Output
883 | Desulfovibrio vulgaris | DvMF_2825 298701 | Desulfovibrio | DA2_3337 1121434 | Halodesulfovibrio aestuarii | AULY01000007_gene1045 207559 | Desulfovibrio alaskensis | Dde_0991 935942 | Desulfonatronum lacustre | KI912608_gene2193 159290 | Desulfonatronum | JPIK01000018_gene1259 1121448 | Desulfovibrio gigas | DGI_0655 1121445 | Desulfovibrio desulfuricans | ATUZ01000018_gene2316 525146 | Desulfovibrio desulfuricans | Ddes_0159 665942 | Desulfovibrio | HMPREF1022_02168 457398 | Desulfovibrio | HMPREF0326_00453 363253 | Lawsonia intracellularis | LI0397 882 | Desulfovibrio vulgaris | DVU_0784 1121413 | Desulfonatronovibrio hydrogenovorans | JMKT01000008_gene1463 555779 | Desulfonatronospira thiodismutans | Dthio_PD0935 690850 | Desulfovibrio africanus | Desaf_1578 643562 | Pseudodesulfovibrio aespoeensis | Daes_3115 1322246 | Pseudodesulfovibrio piezophilus | BN4_12523 641491 | Desulfovibrio desulfuricans | DND132_2573 1121440 | Desulfovibrio aminophilus | AUMA01000002_gene2198 1121456 | Desulfovibrio longus | ATVA01000018_gene290 526222 | Desulfovibrio salexigens | Desal_3460 1121451 | Desulfovibrio hydrothermalis | DESAM_21057 1121447 | Desulfovibrio frigidus | JONL01000008_gene3531 1121441 | Desulfovibrio bastinii | AUCX01000006_gene918 1121439 | Desulfovibrio alkalitolerans | dsat_0220 941449 | Desulfovibrio | dsx2_0067 1307759 | Desulfovibrio | JOMJ01000003_gene2163 1121406 | Desulfocurvus vexinensis | JAEX01000012_gene687 1304872 | Desulfovibrio magneticus | JAGC01000003_gene2904 573370 | Desulfovibrio magneticus | DMR_04750 -
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. -
Culturable Aerobic and Facultative Bacteria from the Gut of the Polyphagic Dung Beetle Thorectes Lusitanicus
Insect Science (2015) 22, 178–190, DOI 10.1111/1744-7917.12094 ORIGINAL ARTICLE Culturable aerobic and facultative bacteria from the gut of the polyphagic dung beetle Thorectes lusitanicus Noemi Hernandez´ 1,Jose´ A. Escudero1, Alvaro´ San Millan´ 1, Bruno Gonzalez-Zorn´ 1, Jorge M. Lobo2,Jose´ R. Verdu´ 3 and Monica´ Suarez´ 1 1Department Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Avenida Puerta de Hierro s/n, Madrid, CP 28040, 2Department Biogeograf´ıa y Cambio Global, Museo Nacional de Ciencias Naturales, CSIC, JoseGuti´ errez´ Abascal 2, Madrid 28006, and 3I.U.I. CIBIO (Centro Iberoamericano de la Biodiversidad), Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, Alicante 03080, Spain Abstract Unlike other dung beetles, the Iberian geotrupid, Thorectes lusitanicus, exhibits polyphagous behavior; for example, it is able to eat acorns, fungi, fruits, and carrion in addition to the dung of different mammals. This adaptation to digest a wider diet has physiological and developmental advantages and requires key changes in the composition and diversity of the beetle’s gut microbiota. In this study, we isolated aerobic, facultative anaerobic, and aerotolerant microbiota amenable to grow in culture from the gut contents of T. lusitanicus and resolved isolate identity to the species level by sequencing 16S rRNA gene fragments. Using BLAST similarity searches and maximum likelihood phylogenetic analyses, we were able to reveal that the analyzed fraction (culturable, aerobic, facultative anaerobic, and aerotolerant) of beetle gut microbiota is dominated by the phyla Pro- teobacteria, Firmicutes,andActinobacteria. Among Proteobacteria, members of the order Enterobacteriales (Gammaproteobacteria) were the most abundant. -
A Primary Assessment of the Endophytic Bacterial Community in a Xerophilous Moss (Grimmia Montana) Using Molecular Method and Cultivated Isolates
Brazilian Journal of Microbiology 45, 1, 163-173 (2014) Copyright © 2014, Sociedade Brasileira de Microbiologia ISSN 1678-4405 www.sbmicrobiologia.org.br Research Paper A primary assessment of the endophytic bacterial community in a xerophilous moss (Grimmia montana) using molecular method and cultivated isolates Xiao Lei Liu, Su Lin Liu, Min Liu, Bi He Kong, Lei Liu, Yan Hong Li College of Life Science, Capital Normal University, Haidian District, Beijing, China. Submitted: December 27, 2012; Approved: April 1, 2013. Abstract Investigating the endophytic bacterial community in special moss species is fundamental to under- standing the microbial-plant interactions and discovering the bacteria with stresses tolerance. Thus, the community structure of endophytic bacteria in the xerophilous moss Grimmia montana were esti- mated using a 16S rDNA library and traditional cultivation methods. In total, 212 sequences derived from the 16S rDNA library were used to assess the bacterial diversity. Sequence alignment showed that the endophytes were assigned to 54 genera in 4 phyla (Proteobacteria, Firmicutes, Actinobacteria and Cytophaga/Flexibacter/Bacteroids). Of them, the dominant phyla were Proteobacteria (45.9%) and Firmicutes (27.6%), the most abundant genera included Acinetobacter, Aeromonas, Enterobacter, Leclercia, Microvirga, Pseudomonas, Rhizobium, Planococcus, Paenisporosarcina and Planomicrobium. In addition, a total of 14 species belonging to 8 genera in 3 phyla (Proteo- bacteria, Firmicutes, Actinobacteria) were isolated, Curtobacterium, Massilia, Pseudomonas and Sphingomonas were the dominant genera. Although some of the genera isolated were inconsistent with those detected by molecular method, both of two methods proved that many different endophytic bacteria coexist in G. montana. According to the potential functional analyses of these bacteria, some species are known to have possible beneficial effects on hosts, but whether this is the case in G. -
Clinical Isolates of Yersinia Enterocolitica in Finland 117 2013 117
Leila M. Sihvonen Leila Leila M. Sihvonen Clinical isolates of Yersinia enterocolitica in Finland Leila M. Sihvonen Identification and Epidemiology Clinical isolates of Yersinia enterocolitica in Finland Identification and Epidemiology Clinical isolates of Clinical isolates Yersinia enterocolitica is a foodborne bacterium that causes gastroenteritis and post-infectious complications, such as reactive arthritis, in humans. Y. enterocolitica species is divided into six biotypes, which differ in their ability to cause illness. The Y. enterocolitica incidence in Finland has been among the highest in the EU, but there has been little information on the occurrence of different Y. enterocolitica biotypes. enterocolitica Yersinia In this thesis Y. enterocolitica strains isolated from Finnish patients were characterised and the symptoms and sources of infections were analysed RESEARCH RESEARCH in a case-control study. The majority of clinical isolates of Y. enterocolitica were found to belong to biotype 1A, the status of which as a true pathogen is controversial. Furthermore, the study investigated the microbiological identification and molecular typing methods for Y. enterocolitica. The MLVA method was found to be appropriate for investigating foodborne outbreaks. in Finland This study adds to the understanding of epidemiology of Y. enterocolitica in Finland and emphasises the importance of correct identification of Yersinia strains in order to evaluate the clinical importance of the microbiological findings. National Institute for Health and Welfare P.O. Box 30 (Mannerheimintie 166) FI-00271 Helsinki, Finland 117 Telephone: 358 29 524 6000 117 117 2013 ISBN 978-952-302-064-1 www.thl.fi RESEARCH NRO 117 2014 Leila M. Sihvonen Clinical isolates of Yersinia enterocolitica in Finland Identification and Epidemiology ACADEMIC DISSERTATION To be presented with the permission of the Faculty of Agriculture and Forestry, University of Helsinki, for public examination in Auditorium 1041, Biocenter 2, Viikinkaari 5, on 17.01.2014, at 12 noon. -
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/Ijsem.0.001485
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/ijsem.0.001485 Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Mobolaji Adeolu,† Seema Alnajar,† Sohail Naushad and Radhey S. Gupta Correspondence Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Radhey S. Gupta L8N 3Z5, Canada [email protected] Understanding of the phylogeny and interrelationships of the genera within the order ‘Enterobacteriales’ has proven difficult using the 16S rRNA gene and other single-gene or limited multi-gene approaches. In this work, we have completed comprehensive comparative genomic analyses of the members of the order ‘Enterobacteriales’ which includes phylogenetic reconstructions based on 1548 core proteins, 53 ribosomal proteins and four multilocus sequence analysis proteins, as well as examining the overall genome similarity amongst the members of this order. The results of these analyses all support the existence of seven distinct monophyletic groups of genera within the order ‘Enterobacteriales’. In parallel, our analyses of protein sequences from the ‘Enterobacteriales’ genomes have identified numerous molecular characteristics in the forms of conserved signature insertions/deletions, which are specifically shared by the members of the identified clades and independently support their monophyly and distinctness. Many of these groupings, either in part or in whole, have been recognized in previous evolutionary studies, but have not been consistently resolved as monophyletic entities in 16S rRNA gene trees. The work presented here represents the first comprehensive, genome- scale taxonomic analysis of the entirety of the order ‘Enterobacteriales’. -
Yersinia Enterocolitica Monographic Study
Tirziu E. et. al./Scientific Papers: Animal Science and Biotechnologies, 2011, 44 (2) Yersinia enterocolitica Monographic Study Emil Tirziu, Ciceronis Cumpanasoiu, Radu Valentin Gros, Monica Seres Faculty of Veterinary Medicine, 300645, Timisoara, Calea Aradului, 119, Romania Abstract Germs from Yersinia genus have a vast ecologic niche, being met at different domestic and wild animal species, but also in food, water and soil. The majority of yersinis live in the digestive tract of human and numerous animal species, especially rodents, but also in soil, plant debris, waters etc. Numerous species of Yersinia genus could produce characteristic infections in human, the main source of infections is represented by rodents and hematophagous insects or, more frequently, by water or contaminated food. In a 1999 study, Mead and coauthors established that the Yersinia enterocolitica prevalence in food, in USA, is around 90%. Foods of animal origin more frequently contaminated with Yersinia enterocolitica are: pork, poultry, beef and lamb meat, milk, ice-cream, sea fruits etc., among them pork meat and milk represents the sources of the most numerous toxi-infection outbreaks in human, in different world regions. Bacteria determine infections which interest the digestive tract in numerous animal species and human, with diarrhea, lymphadenitis, pneumonia and abortion are the most important symptoms. Yersinia enterocolitica enter the human body regularly by oral ingestion, and localize itself with predilection in the distal portion of the ileum and at the ileocaecal appendix and proximal colon level, were determine a terminal ileitis with lymphadenitis, acute enterocolitis, and secondary accompanied with nodosum erythema, poliartritis that could be complicated with septicemia, sometimes leading to death.