Identification by 16S Ribosomal RNA Gene Sequencing of Arcobacter
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Rapid NH System Rapid Spot Indole Reagent (R8309002, Supplied Separately) • When Using the 1-Hour Procedure, Only Selective Notes: (15 Ml/Bottle) Agars Can Be Used
n,n-Dimethyl-1-naphthylamine ..................................... 6.0 g Selective Media: Thayer-Martin Agar; Martin-Lewis 6. Return the panel to a level position. If necessary, gently Glacial Acetic Acid ................................................... 280.0 ml Agar; New York City Agar. tap the panel on the bench top to remove any air Demineralized Water ............................................... 720.0 ml Notes: trapped in the cavities. RapID NH System RapID Spot Indole Reagent (R8309002, supplied separately) • When using the 1-hour procedure, only selective Notes: (15 ml/Bottle) agars can be used. • Examine the test cavities which should appear R8311001 .................................................20 Tests/Kit ρ-Dimethylaminocinnamaldehyde .............................. 10.0 g • Cultures used for inoculum preparation should bubble-free and uniformly filled. Slight irregularities 1. INTENDED USE Hydrochloric Acid .................................................... 100.0 ml preferably be 18-24 hours old. Slow-growing isolates in test cavity fills are acceptable and will not affect Remel RapID™ NH System is a qualitative micromethod Demineralized Water ............................................... 900.0 ml may be tested using 48-hour cultures. test performance. If the panel is grossly misfilled, employing conventional and chromogenic substrates for the *Adjusted as required to meet performance standards. a new panel should be inoculated and the misfilled • The use of media other than those recommended panel discarded. identification of medically important species of Neisseria, 5. PRECAUTIONS may compromise test performance. Haemophilus, and other bacteria isolated from human • Complete the inoculation of each panel receiving in vitro clinical specimens. A complete listing of the organisms This product is for diagnostic use and should be used 3. Using a cotton swab or inoculating loop, suspend inoculation fluid before inoculating additional addressed by RapID NH System is provided in the RapID NH by properly trained individuals. -
Identification of 16S Rrna and Virulence-Associated Genes Of
pathogens Article Identification of 16S rRNA and Virulence-Associated Genes of Arcobacter in Water Samples in the Kathmandu Valley, Nepal Rajani Ghaju Shrestha 1,2 , Yasuhiro Tanaka 3, Jeevan B. Sherchand 4 and Eiji Haramoto 2,* 1 Division of Sustainable Energy and Environmental Engineering, Osaka University, Suita, Osaka 565-0871, Japan 2 Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan 3 Department of Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan 4 Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu 1524, Nepal * Correspondence: [email protected]; Tel.: +81-55-220-8725 Received: 8 July 2019; Accepted: 25 July 2019; Published: 26 July 2019 Abstract: This study aimed to determine the prevalence of Arcobacter and five associated virulence genes (cadF, ciaB, mviN, pldA, and tlyA) in water samples in the Kathmandu Valley, Nepal. A total of 286 samples were collected from deep tube wells (n = 30), rivers (n = 14), a pond (n = 1), shallow dug wells (n = 166), shallow tube wells (n = 33), springs (n = 21), and stone spouts (n = 21) in February and March (dry season) and August (wet season), 2016. Bacterial DNA was extracted from the water samples and subjected to SYBR Green-based quantitative PCR for 16S rRNA and virulence genes of Arcobacter. The 16S rRNA gene of Arcobacter was detected in 36% (40/112) of samples collected in the dry season, at concentrations ranging from 5.7 to 10.2 log copies/100 mL, and 34% (59/174) of samples collected in the wet season, at concentrations of 5.4–10.8 log copies/100 mL. -
Complete Genome Sequence of Arcobacter Nitrofigilis Type Strain (CIT)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Arcobacter nitrofigilis type strain (CI). Permalink https://escholarship.org/uc/item/4kk473v4 Journal Standards in genomic sciences, 2(3) ISSN 1944-3277 Authors Pati, Amrita Gronow, Sabine Lapidus, Alla et al. Publication Date 2010-06-15 DOI 10.4056/sigs.912121 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 2:300-308 DOI:10.4056/sigs.912121 Complete genome sequence of Arcobacter nitrofigilis type strain (CIT) Amrita Pati1, Sabine Gronow3, Alla Lapidus1, Alex Copeland1, Tijana Glavina Del Rio1, Matt Nolan1, Susan Lucas1, Hope Tice1, Jan-Fang Cheng1, Cliff Han1,2, Olga Chertkov1,2, David Bruce1,2, Roxanne Tapia1,2, Lynne Goodwin1,2, Sam Pitluck1, Konstantinos Liolios1, Natalia Ivanova1, Konstantinos Mavromatis1, Amy Chen4, Krishna Palaniappan4, Miriam Land1,5, Loren Hauser1,5, Yun-Juan Chang1,5, Cynthia D. Jeffries1,5, John C. Detter1,2, Manfred Rohde6, Markus Göker3, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz4, Philip Hugenholtz1, Hans-Peter Klenk3, and Nikos C. Kyrpides1* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 3 DSMZ – German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Nikos C. Kyrpides Keywords: symbiotic, Spartina alterniflora Loisel, nitrogen fixation, micro-anaerophilic, mo- tile, Campylobacteraceae, GEBA Arcobacter nitrofigilis (McClung et al. -
The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment
life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment. -
Aliarcobacter Butzleri from Water Poultry: Insights Into Antimicrobial Resistance, Virulence and Heavy Metal Resistance
G C A T T A C G G C A T genes Article Aliarcobacter butzleri from Water Poultry: Insights into Antimicrobial Resistance, Virulence and Heavy Metal Resistance Eva Müller, Mostafa Y. Abdel-Glil * , Helmut Hotzel, Ingrid Hänel and Herbert Tomaso Institute of Bacterial Infections and Zoonoses (IBIZ), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 07743 Jena, Germany; Eva.Mueller@fli.de (E.M.); Helmut.Hotzel@fli.de (H.H.); [email protected] (I.H.); Herbert.Tomaso@fli.de (H.T.) * Correspondence: Mostafa.AbdelGlil@fli.de Received: 28 July 2020; Accepted: 16 September 2020; Published: 21 September 2020 Abstract: Aliarcobacter butzleri is the most prevalent Aliarcobacter species and has been isolated from a wide variety of sources. This species is an emerging foodborne and zoonotic pathogen because the bacteria can be transmitted by contaminated food or water and can cause acute enteritis in humans. Currently, there is no database to identify antimicrobial/heavy metal resistance and virulence-associated genes specific for A. butzleri. The aim of this study was to investigate the antimicrobial susceptibility and resistance profile of two A. butzleri isolates from Muscovy ducks (Cairina moschata) reared on a water poultry farm in Thuringia, Germany, and to create a database to fill this capability gap. The taxonomic classification revealed that the isolates belong to the Aliarcobacter gen. nov. as A. butzleri comb. nov. The antibiotic susceptibility was determined using the gradient strip method. While one of the isolates was resistant to five antibiotics, the other isolate was resistant to only two antibiotics. The presence of antimicrobial/heavy metal resistance genes and virulence determinants was determined using two custom-made databases. -
Bacterial Diversity Within the Human Subgingival Crevice
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln U.S. Department of Veterans Affairs Staff Publications U.S. Department of Veterans Affairs 12-7-1999 Bacterial diversity within the human subgingival crevice Ian Kroes Stanford University School of Medicine Paul W. Lepp Stanford University School of Medicine, [email protected] David A. Relman Stanford University School of Medicine, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/veterans Kroes, Ian; Lepp, Paul W.; and Relman, David A., "Bacterial diversity within the human subgingival crevice" (1999). U.S. Department of Veterans Affairs Staff Publications. 18. https://digitalcommons.unl.edu/veterans/18 This Article is brought to you for free and open access by the U.S. Department of Veterans Affairs at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in U.S. Department of Veterans Affairs Staff Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Bacterialdiversity within the human subgingivalcrevice Ian Kroes, Paul W. Lepp, and David A. Relman* Departmentsof Microbiologyand Immunology,and Medicine,Stanford University School of Medicine,Stanford, CA 94305, and VeteransAffairs Palo Alto HealthCare System, Palo Alto,CA 94304 Editedby Stanley Falkow, Stanford University, Stanford, CA, and approvedOctober 15, 1999(received for review August 2, 1999) Molecular, sequence-based environmental surveys of microorgan- associated with disease (9-11). However, a directcomparison isms have revealed a large degree of previously uncharacterized between cultivation-dependentand -independentmethods has diversity. However, nearly all studies of the human endogenous not been described. In this study,we characterizedbacterial bacterial flora have relied on cultivation and biochemical charac- diversitywithin a specimenfrom the humansubgingival crevice terization of the resident organisms. -
Fate of Arcobacter Spp. Upon Exposure to Environmental
FATE OF ARCOBACTER SPP. UPON EXPOSURE TO ENVIRONMENTAL STRESSES AND PREDICTIVE MODEL DEVELOPMENT by ELAINE M. D’SA (Under the direction of Dr. Mark A. Harrison) ABSTRACT Growth and survival characteristics of two species of the ‘emerging’ pathogenic genus Arcobacter were determined. The optimal pH growth range of most A. butzleri (4 strains) and A. cryaerophilus (2 strains) was 6.0-7.0 and 7.0-7.5 respectively. The optimal NaCl growth range was 0.09-0.5 % (A. butzleri) and 0.5-1.0% (A. cryaerophilus), while growth limits were 0.09-3.5% and 0.09-3.0% for A. butzleri and A. cryaerophilus, respectively. A. butzleri 3556, 3539 and A. cryaerophilus 1B were able to survive at NaCl concentrations of up to 5% for 48 h at 25°C, but the survival limit dropped to 3.5-4.0% NaCl after 96 h. Thermal tolerance studies on three strains of A. butzleri determined that the D-values at pH 7.3 had a range of 0.07-0.12 min (60°C), 0.38-0.76 min (55°C) and 5.12-5.81 min (50°C). At pH 5.5, thermotolerance decreased under the synergistic effects of heat and acidity. D-values decreased for strains 3556 and 3257 by 26-50% and 21- 66%, respectively, while the reduction for strain 3494 was lower: 0-28%. Actual D- values of the three strains at pH 5.5 had a range of 0.03-0.11 (60°C), 0.30-0.42 (55°C) and 1.97-4.42 (50°C). -
Comparative Analysis of Four Campylobacterales
REVIEWS COMPARATIVE ANALYSIS OF FOUR CAMPYLOBACTERALES Mark Eppinger*§,Claudia Baar*§,Guenter Raddatz*, Daniel H. Huson‡ and Stephan C. Schuster* Abstract | Comparative genome analysis can be used to identify species-specific genes and gene clusters, and analysis of these genes can give an insight into the mechanisms involved in a specific bacteria–host interaction. Comparative analysis can also provide important information on the genome dynamics and degree of recombination in a particular species. This article describes the comparative genomic analysis of representatives of four different Campylobacterales species — two pathogens of humans, Helicobacter pylori and Campylobacter jejuni, as well as Helicobacter hepaticus, which is associated with liver cancer in rodents and the non-pathogenic commensal species, Wolinella succinogenes. ε CHEMOLITHOTROPHIC The -subdivision of the Proteobacteria is a large group infection can lead to gastric cancer in humans 9–11 An organism that is capable of of CHEMOLITHOTROPHIC and CHEMOORGANOTROPHIC microor- and liver cancer in rodents, respectively .The using CO, CO2 or carbonates as ganisms with diverse metabolic capabilities that colo- Campylobacter representative C. jejuni is one of the the sole source of carbon for cell nize a broad spectrum of ecological habitats. main causes of bacterial food-borne illness world- biosynthesis, and that derives Representatives of the ε-subgroup can be found in wide, causing acute gastroenteritis, and is also energy from the oxidation of reduced inorganic or organic extreme marine and terrestrial environments ranging the most common microbial antecedent of compounds. from oceanic hydrothermal vents to sulphidic cave Guillain–Barré syndrome12–15.Besides their patho- springs. Although some members are free-living, others genic potential in humans, C. -
Haemophilus] Haemoglobinophilus As Canicola Haemoglobinophilus Gen
Scotland's Rural College Reclassification of [Haemophilus] haemoglobinophilus as Canicola haemoglobinophilus gen. nov., comb. nov. including Bisgaard taxon 35 Christensen, Henrik; Kuhnert, Peter; Foster, Geoffrey; Bisgaard, Magne Published in: International Journal of Systematic and Evolutionary Microbiology DOI: 10.1099/ijsem.0.004881 First published: 15/07/2021 Document Version Peer reviewed version Link to publication Citation for pulished version (APA): Christensen, H., Kuhnert, P., Foster, G., & Bisgaard, M. (2021). Reclassification of [Haemophilus] haemoglobinophilus as Canicola haemoglobinophilus gen. nov., comb. nov. including Bisgaard taxon 35. International Journal of Systematic and Evolutionary Microbiology, 71(7), [004881]. https://doi.org/10.1099/ijsem.0.004881 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 27. Sep. 2021 1 Supplemetary material for the paper: 2 Reclassification of [Haemophilus] haemoglobinophilus as Canicola haemoglobinophilus 3 gen. nov., comb. nov. including Bisgaard taxon 35 4 By Henrik Christensen, Peter Kuhnert, Geoff Foster and Magne Bisgaard 5 1 Table S1. -
Actinomyces Naeslundii and Aggregatibacter Aphrophilus Brain Abscess in an Adolescent
Arch Clin Med Case Rep 2019; 3 (6): 409-413 DOI: 10.26502/acmcr.96550112 Case Report Actinomyces Naeslundii and Aggregatibacter Aphrophilus Brain Abscess in an Adolescent Michael Croix1, Christopher Schwarz2, Ryan Breuer3,4, Amanda B. Hassinger3,4, Kunal Chadha5, Mark Daniel Hicar4,6 1Division of Internal Medicine and Pediatrics, University at Buffalo. Buffalo, New York, USA 2Division of Emergency Medicine, University at Buffalo. Buffalo, New York, USA 3Division of Pediatric Critical Care, John R. Oishei Children’s Hospital. Buffalo, New York, USA 4Department of Pediatrics, University at Buffalo. Buffalo, New York, USA 5Division of Pediatric Emergency Medicine, University at Buffalo. Buffalo, New York, USA 6Division of Pediatric Infectious Diseases, University at Buffalo. Buffalo, New York, USA *Corresponding Authors: Dr. Mark Daniel Hicar, Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 1001 Main Street, Buffalo, NY, 14203 USA, Tel: (716) 323-0150; Fax: (716) 888-3804; E-mail: [email protected] (or) [email protected] Dr. Michael Croix, Division of Internal Medicine and Pediatrics, 300 Linwood Ave, Buffalo, NY, 14209 USA, Tel: (217) 840-5750; Fax: (716) 888-3804; E-mail: [email protected] Received: 20 July 2019; Accepted: 02 August 2019; Published: 04 November 2019 Abstract We report the case of a child with a brain abscess from which Actinomyces naeslundii and Aggregatibacter aphrophilus were isolated. The is the first case describing A. naeslundii causing a brain abscess. This case highlights the association of these two organisms which may affect antibiotic choice and therapy length. Keywords: Brain; Abscess; Actinomyces; Aggregatibacter 1. Case Report A 13 year old male with no known past medical history initially presented to the Emergency Department with one week of headache, nausea, and vomiting. -
Bacteriology
SECTION 1 High Yield Microbiology 1 Bacteriology MORGAN A. PENCE Definitions Obligate/strict anaerobe: an organism that grows only in the absence of oxygen (e.g., Bacteroides fragilis). Spirochete Aerobe: an organism that lives and grows in the presence : spiral-shaped bacterium; neither gram-positive of oxygen. nor gram-negative. Aerotolerant anaerobe: an organism that shows signifi- cantly better growth in the absence of oxygen but may Gram Stain show limited growth in the presence of oxygen (e.g., • Principal stain used in bacteriology. Clostridium tertium, many Actinomyces spp.). • Distinguishes gram-positive bacteria from gram-negative Anaerobe : an organism that can live in the absence of oxy- bacteria. gen. Bacillus/bacilli: rod-shaped bacteria (e.g., gram-negative Method bacilli); not to be confused with the genus Bacillus. • A portion of a specimen or bacterial growth is applied to Coccus/cocci: spherical/round bacteria. a slide and dried. Coryneform: “club-shaped” or resembling Chinese letters; • Specimen is fixed to slide by methanol (preferred) or heat description of a Gram stain morphology consistent with (can distort morphology). Corynebacterium and related genera. • Crystal violet is added to the slide. Diphtheroid: clinical microbiology-speak for coryneform • Iodine is added and forms a complex with crystal violet gram-positive rods (Corynebacterium and related genera). that binds to the thick peptidoglycan layer of gram-posi- Gram-negative: bacteria that do not retain the purple color tive cell walls. of the crystal violet in the Gram stain due to the presence • Acetone-alcohol solution is added, which washes away of a thin peptidoglycan cell wall; gram-negative bacteria the crystal violet–iodine complexes in gram-negative appear pink due to the safranin counter stain. -
Phylogenomic and Molecular Demarcation of the Core Members of the Polyphyletic Pasteurellaceae Genera Actinobacillus, Haemophilus,Andpasteurella
Hindawi Publishing Corporation International Journal of Genomics Volume 2015, Article ID 198560, 15 pages http://dx.doi.org/10.1155/2015/198560 Research Article Phylogenomic and Molecular Demarcation of the Core Members of the Polyphyletic Pasteurellaceae Genera Actinobacillus, Haemophilus,andPasteurella Sohail Naushad, Mobolaji Adeolu, Nisha Goel, Bijendra Khadka, Aqeel Al-Dahwi, and Radhey S. Gupta Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada L8N 3Z5 Correspondence should be addressed to Radhey S. Gupta; [email protected] Received 5 November 2014; Revised 19 January 2015; Accepted 26 January 2015 Academic Editor: John Parkinson Copyright © 2015 Sohail Naushad et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The genera Actinobacillus, Haemophilus, and Pasteurella exhibit extensive polyphyletic branching in phylogenetic trees and do not represent coherent clusters of species. In this study, we have utilized molecular signatures identified through comparative genomic analyses in conjunction with genome based and multilocus sequence based phylogenetic analyses to clarify the phylogenetic and taxonomic boundary of these genera. We have identified large clusters of Actinobacillus, Haemophilus, and Pasteurella species which represent the “sensu stricto” members of these genera. We have identified 3, 7, and 6 conserved signature indels (CSIs), which are specifically shared by sensu stricto members of Actinobacillus, Haemophilus, and Pasteurella, respectively. We have also identified two different sets of CSIs that are unique characteristics of the pathogen containing genera Aggregatibacter and Mannheimia, respectively. It is now possible to demarcate the genera Actinobacillus sensu stricto, Haemophilus sensu stricto, and Pasteurella sensu stricto on the basis of discrete molecular signatures.