Arcobacter Species in Humans1
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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. -
Identification by 16S Ribosomal RNA Gene Sequencing of Arcobacter
182 ORIGINAL ARTICLE Identification by 16S ribosomal RNA gene sequencing of Mol Path: first published as 10.1136/mp.55.3.182 on 1 June 2002. Downloaded from Arcobacter butzleri bacteraemia in a patient with acute gangrenous appendicitis SKPLau,PCYWoo,JLLTeng, K W Leung, K Y Yuen ............................................................................................................................. J Clin Pathol: Mol Pathol 2002;55:182–185 Aims: To identify a strain of Gram negative facultative anaerobic curved bacillus, concomitantly iso- lated with Escherichia coli and Streptococcus milleri, from the blood culture of a 69 year old woman with acute gangrenous appendicitis. The literature on arcobacter bacteraemia and arcobacter infections associated with appendicitis was reviewed. Methods: The isolate was phenotypically investigated by standard biochemical methods using conventional biochemical tests. Genotypically, the 16S ribosomal RNA (rRNA) gene of the bacterium was amplified by the polymerase chain reaction (PCR) and sequenced. The sequence of the PCR prod- uct was compared with known 16S rRNA gene sequences in the GenBank by multiple sequence align- ment. Literature review was performed by MEDLINE search (1966–2000). Results: The bacterium grew on blood agar, chocolate agar, and MacConkey agar to sizes of 1 mm in diameter after 24 hours of incubation at 37°C in 5% CO2. It grew at 15°C, 25°C, and 37°C; it also grew in a microaerophilic environment, and was cytochrome oxidase positive and motile, typically a member of the genus arcobacter. Furthermore, phenotypic testing showed that the biochemical profile See end of article for of the isolate did not fit into the pattern of any of the known arcobacter species. -
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. -
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. -
Accumulation and Expression of Horizontally Acquired Genes in Arcobacter Cryaerophilus That Thrives in Sewage
Accumulation and expression of horizontally acquired genes in Arcobacter cryaerophilus that thrives in sewage Jess A. Millar and Rahul Raghavan Biology Department, Portland State University, Portland, OR, United States ABSTRACT We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of putative antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater. We also determined that a majority of candidate ARGs was being expressed in sewage, suggestive of trace levels of antibiotics or other stresses that could act as a selective force that amplifies multidrug resistant bacteria in municipal sewage. Because all bacteria are not eliminated even after several rounds of wastewater treatment, ARGs in sewage could affect public health due to their potential to contaminate environmental water. Subjects Environmental Sciences, Genomics, Microbiology Keywords Arcobacter cryaerophilus, Sewage, Multidrug resistance INTRODUCTION Submitted 30 November 2016 Accepted 3 April 2017 Over the past few decades, based on numerous studies that examined the bacterial Published 25 April 2017 composition of wastewater during varying stages of treatment, there is growing evidence Corresponding author that sewage is an important hub for horizontal gene transfer (HGT) of antibiotic resistance Rahul Raghavan, [email protected] genes (e.g., Baquero, Martínez & Cantón, 2008; Zhang, Shao & Ye, 2012; Rizzo et al., 2013; Academic editor Pehrsson et al., 2016). -
Improved Culture Enrichment Broth for Isolation of Arcobacter-Like Species
www.nature.com/scientificreports OPEN Improved culture enrichment broth for isolation of Arcobacter‑like species from the marine environment Faiz Ur Rahman 1,2*, Karl B. Andree1, Nuria Salas‑Massó1,2, Margarita Fernandez‑Tejedor1, Anna Sanjuan1, Maria J. Figueras2 & M. Dolors Furones1 Arcobacter‑like species are found associated with many matrices, including shellfsh in marine environments. The culture media and conditions play a major role in the recovery of new Arcobacter‑ like species. This study was aimed to develop a culture media for isolation and enhanced growth of Arcobacter‑like spp. from marine and shellfsh matrices. For this purpose, 14 diferent Arcobacter‑like spp. mostly isolated from shellfsh, were grown in 24 diferent formulations of enrichment broths. The enrichment broths consisted of fve main groups based on the organic contents (fresh oyster homogenate, lyophilized oyster either alone or in combination with other standard media), combined with artifcial seawater (ASW) or 2.5% NaCl. Optical density (OD420nm) measurements after every 24 h were compared with the growth in control media (Arcobacter broth) in parallel. The mean and standard deviation were calculated for each species in each broth and statistical diferences (p < 0.05) among broths were calculated by ANOVA. The results indicated that shellfsh‑associated Arcobacter‑ like species growth was signifcantly higher in Arcobacter broth + 50% ASW and the same media supplemented with lyophilized oysters. This is the frst study to have used fresh or lyophilized oyster fesh in the enrichment broth for isolation of shellfsh‑associated Arcobacter‑like spp. Arcobacter-like species are gram negative, slightly curved, rod-shaped bacteria. -
Virulence and Antibiotic Resistance Plasticity of Arcobacter Butzleri: Insights on the Genomic Diversity
bioRxiv preprint doi: https://doi.org/10.1101/775932; this version posted September 19, 2019. 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-NC-ND 4.0 International license. Virulence and antibiotic resistance plasticity of Arcobacter butzleri: insights on the genomic diversity of an emerging human pathogen Joana Isidro1, Susana Ferreira2, Miguel Pinto1, Fernanda Domingues2, Mónica Oleastro3, João Paulo Gomes1, Vítor Borges1 1 Bioinformatics Unit, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal 2 CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal 3 National Reference Laboratory for Gastrointestinal Infections, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal Corresponding authors: Susana Ferreira Email address: [email protected] Vítor Borges Email address: [email protected] Keywords: Arcobacter butzleri; genome diversity; virulence factors; antibiotic resistance; porA; phase variation Repositories: Sequence data was deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB34441) Abstract Arcobacter butzleri is a food and waterborne bacteria and an emerging human pathogen, frequently displaying a multidrug resistant character. Still, no comprehensive genome-scale comparative analysis has been performed so far, which has limited our knowledge on A. butzleri diversification and pathogenicity. Here, we performed a deep genome analysis of A. butzleri focused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. In total, 49 A. butzleri strains (collected from human, animal, food and environmental sources) were screened. -
Biological Composition and Microbial Dynamics of Sinking Particulate Organic Matter at Abyssal Depths in the Oligotrophic Open Ocean
Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean Dominique Boeufa,1, Bethanie R. Edwardsa,1,2, John M. Eppleya,1, Sarah K. Hub,3, Kirsten E. Poffa, Anna E. Romanoa, David A. Caronb, David M. Karla, and Edward F. DeLonga,4 aDaniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI 96822; and bDepartment of Biological Sciences, University of Southern California, Los Angeles, CA 90089 Contributed by Edward F. DeLong, April 22, 2019 (sent for review February 21, 2019; reviewed by Eric E. Allen and Peter R. Girguis) Sinking particles are a critical conduit for the export of organic sample both suspended as well as slowly sinking POM. Because material from surface waters to the deep ocean. Despite their filtration methods can be biased by the volume of water filtered importance in oceanic carbon cycling and export, little is known (21), also collect suspended particles, and may under-sample about the biotic composition, origins, and variability of sinking larger, more rapidly sinking particles, it remains unclear how well particles reaching abyssal depths. Here, we analyzed particle- they represent microbial communities on sinking POM in the associated nucleic acids captured and preserved in sediment traps deep sea. Sediment-trap sampling approaches have the potential at 4,000-m depth in the North Pacific Subtropical Gyre. Over the 9- to overcome some of these difficulties because they selectively month time-series, Bacteria dominated both the rRNA-gene and capture sinking particles. rRNA pools, followed by eukaryotes (protists and animals) and trace The Hawaii Ocean Time-series Station ALOHA is an open- amounts of Archaea. -
Arcobacter Butzleri: First Isolation Report from Chicken Carcasses in Costa Rica
Brazilian Journal of Microbiology (2011) 42: 703-706 ISSN 1517-8382 ARCOBACTER BUTZLERI: FIRST ISOLATION REPORT FROM CHICKEN CARCASSES IN COSTA RICA Maria Laura Arias¹*, Adriana Cid¹, Heriberto Fernandéz² 1Faculty of Microbiology. Universidad de Costa Rica. San José. Costa Rica; 2Institute of Clinical Microbiology. Universidad Austral de Chile. Valdivia. Chile. Submitted: January 06, 2010; Returned to authors for corrections: April 23, 2010; Approved: August 23, 2010. ABSTRACT Arcobacter butzleri isolation from chicken carcasses in Costa Rica is reported for the first time. The isolated strains (P and R) were presumptively identified by their phenotypic characteristics. Definitive identification was made using a multiplex PCR assay for the simultaneous detection and identification of Arcobacter butzleri, Arcobacter cryaerophilus and Arcobacter skirrowii. These first isolations indicate the necessity of further investigation about the prevalence, distribution, ecology and interactions with human beings of this and other Arcobacter species. Key words: Arcobacter butzleri, chicken carcasses, isolation, epidemiology The genus Arcobacter, belongs to the family of animal origin, especially from poultry, carcasses and offal, Campylobacteraceae, class Proteobacteria, subclass milk, mussels, as well as from water bodies, sewage and fecal Gracillicutes and comprises polar flagellates, spirally, curved, samples of different animal species (6, 7, 12, 17, 19). Gram negative rods formerly known as aerotolerant In Latin America little information about Arcobacter Campylobacter-like organisms (4). species is available, being isolated in Chile (6, 7), Argentina The first isolates were obtained by Ellis et al. (5) from aborted (8), Brazil (3) and Mexico (18). In order to provide additional bovine fetuses. Further studies related these microorganisms information about the occurrence of A.