Cultivation of Microorganisms from Basaltic Rock
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Uncommon Pathogens Causing Hospital-Acquired Infections in Postoperative Cardiac Surgical Patients
Published online: 2020-03-06 THIEME Review Article 89 Uncommon Pathogens Causing Hospital-Acquired Infections in Postoperative Cardiac Surgical Patients Manoj Kumar Sahu1 Netto George2 Neha Rastogi2 Chalatti Bipin1 Sarvesh Pal Singh1 1Department of Cardiothoracic and Vascular Surgery, CN Centre, All Address for correspondence Manoj K Sahu, MD, DNB, Department India Institute of Medical Sciences, Ansari Nagar, New Delhi, India of Cardiothoracic and Vascular Surgery, CTVS office, 7th floor, CN 2Infectious Disease, Department of Medicine, All India Institute of Centre, All India Institute of Medical Sciences, New Delhi-110029, Medical Sciences, Ansari Nagar, New Delhi, India India (e-mail: [email protected]). J Card Crit Care 2020;3:89–96 Abstract Bacterial infections are common causes of sepsis in the intensive care units. However, usually a finite number of Gram-negative bacteria cause sepsis (mostly according to the hospital flora). Some organisms such as Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus are relatively common. Others such as Stenotrophomonas maltophilia, Chryseobacterium indologenes, Shewanella putrefaciens, Ralstonia pickettii, Providencia, Morganella species, Nocardia, Elizabethkingia, Proteus, and Burkholderia are rare but of immense importance to public health, in view of the high mortality rates these are associated with. Being aware of these organisms, as the cause of hospital-acquired infections, helps in the prevention, Keywords treatment, and control of sepsis in the high-risk cardiac surgical patients including in ► uncommon pathogens heart transplants. Therefore, a basic understanding of when to suspect these organ- ► hospital-acquired isms is important for clinical diagnosis and initiating therapeutic options. This review infection discusses some rarely appearing pathogens in our intensive care unit with respect to ► cardiac surgical the spectrum of infections, and various antibiotics that were effective in managing intensive care unit these bacteria. -
Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample
geosciences Article Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample Andrey A. Belov 1,*, Vladimir S. Cheptsov 1,2 , Elena A. Vorobyova 1,2, Natalia A. Manucharova 1 and Zakhar S. Ezhelev 1 1 Soil Science Faculty, Lomonosov Moscow State University, Moscow 119991, Russia; [email protected] (V.S.C.); [email protected] (E.A.V.); [email protected] (N.A.M.); [email protected] (Z.S.E.) 2 Space Research Institute, Russian Academy of Sciences, Moscow 119991, Russia * Correspondence: [email protected]; Tel.: +7-917-584-44-07 Received: 28 February 2019; Accepted: 8 April 2019; Published: 10 April 2019 Abstract: The arid Mojave Desert is one of the most significant terrestrial analogue objects for astrobiological research due to its genesis, mineralogy, and climate. However, the knowledge of culturable bacterial communities found in this extreme ecotope’s soil is yet insufficient. Therefore, our research has been aimed to fulfil this lack of knowledge and improve the understanding of functioning of edaphic bacterial communities of the Central Mojave Desert soil. We characterized aerobic heterotrophic soil bacterial communities of the central region of the Mojave Desert. A high total number of prokaryotic cells and a high proportion of culturable forms in the soil studied were observed. Prevalence of Actinobacteria, Proteobacteria, and Firmicutes was discovered. The dominance of pigmented strains in culturable communities and high proportion of thermotolerant and pH-tolerant bacteria were detected. Resistance to a number of salts, including the ones found in Martian regolith, as well as antibiotic resistance, were also estimated. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Sonication Contribution to Identifying Prosthetic Joint Infection With
Birlutiu et al. BMC Musculoskeletal Disorders (2017) 18:311 DOI 10.1186/s12891-017-1678-y CASE REPORT Open Access Sonication contribution to identifying prosthetic joint infection with Ralstonia pickettii: a case report and review of the literature Rares Mircea Birlutiu1*, Mihai Dan Roman2, Razvan Silviu Cismasiu3, Sorin Radu Fleaca2, Crina Maria Popa4, Manuela Mihalache5 and Victoria Birlutiu6 Abstract Background: In the context of an increase number of primary and revision total hip and total knee arthroplasty performed yearly, an increased risk of complication is expected. Prosthetic joint infection (PJI) remains the most common and feared arthroplasty complication. Ralstonia pickettii is a Gram-negative bacterium, that has also been identified in biofilms. It remains an extremely rare cause of PJI. There is no report of an identification of R. pickettii on an extracted spacer loaded with antibiotic. Case presentation: We present the case of an 83-years-old Caucasian male patient, that underwent a right cemented total hip replacement surgery. The patient is diagnosed with an early PJI with no isolated microorganism. A debridement and change of mobile parts is performed. At the beginning of 2016, the patient in readmitted into the Orthopedic Department for sever, right abdominal and groin pain and elevated serum erythrocyte sedimentation rate and C-reactive protein. A joint aspiration is performed with a negative microbiological examination. A two-stage exchange with long interval management is adopted, and a preformed spacer loaded with gentamicin was implanted. In July 2016, based on the proinflammatory markers evolution, a shift a three-stage exchange strategy is decided. In September 2016, a debridement, and changing of the preformed spacer loaded with gentamicin with another was carried out. -
Phylogenetic Diversity of Gram-Positive Bacteria and Their Secondary Metabolite Genes
UC San Diego Research Theses and Dissertations Title Phylogenetic Diversity of Gram-positive Bacteria and Their Secondary Metabolite Genes Permalink https://escholarship.org/uc/item/06z0868t Author Gontang, Erin A Publication Date 2008 Peer reviewed eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Phylogenetic Diversity of Gram-positive Bacteria and Their Secondary Metabolite Genes A Dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Oceanography by Erin Ann Gontang Committee in charge: William Fenical, Chair Douglas H. Bartlett Bianca Brahamsha William Gerwick Paul R. Jensen Kit Pogliano 2008 3324374 3324374 2008 The Dissertation of Erin Ann Gontang is approved, and it is acceptable in quality and form for publication on microfilm: ____________________________________ ____________________________________ ____________________________________ ____________________________________ ____________________________________ ____________________________________ Chair University of California, San Diego 2008 iii DEDICATION To John R. Taylor, my incredible partner, my best friend and my love. ***** To my mom, Janet M. Gontang, and my dad, Austin J. Gontang. Your generous support and unconditional love has allowed me to create my future. Thank you. ***** To my sister, Allison C. Gontang, who is as proud of me as I am of her. You are a constant source of inspiration and I am so fortunate to have you in my life. iv TABLE OF CONTENTS -
Coffee Microbiota and Its Potential Use in Sustainable Crop Management. a Review Duong Benoit, Marraccini Pierre, Jean Luc Maeght, Philippe Vaast, Robin Duponnois
Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review Duong Benoit, Marraccini Pierre, Jean Luc Maeght, Philippe Vaast, Robin Duponnois To cite this version: Duong Benoit, Marraccini Pierre, Jean Luc Maeght, Philippe Vaast, Robin Duponnois. Coffee Mi- crobiota and Its Potential Use in Sustainable Crop Management. A Review. Frontiers in Sustainable Food Systems, Frontiers Media, 2020, 4, 10.3389/fsufs.2020.607935. hal-03045648 HAL Id: hal-03045648 https://hal.inrae.fr/hal-03045648 Submitted on 8 Dec 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License REVIEW published: 03 December 2020 doi: 10.3389/fsufs.2020.607935 Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review Benoit Duong 1,2, Pierre Marraccini 2,3, Jean-Luc Maeght 4,5, Philippe Vaast 6, Michel Lebrun 1,2 and Robin Duponnois 1* 1 LSTM, Univ. Montpellier, IRD, CIRAD, INRAE, SupAgro, Montpellier, France, 2 LMI RICE-2, Univ. Montpellier, IRD, CIRAD, AGI, USTH, Hanoi, Vietnam, 3 IPME, Univ. Montpellier, CIRAD, IRD, Montpellier, France, 4 AMAP, Univ. Montpellier, IRD, CIRAD, INRAE, CNRS, Montpellier, France, 5 Sorbonne Université, UPEC, CNRS, IRD, INRA, Institut d’Écologie et des Sciences de l’Environnement, IESS, Bondy, France, 6 Eco&Sols, Univ. -
Antimicrobial Susceptibility Patterns of Unusual Nonfermentative Gram
Mem Inst Oswaldo Cruz, Rio de Janeiro, Vol. 100(6): 571-577, October 2005 571 Antimicrobial susceptibility patterns of unusual nonfermentative gram-negative bacilli isolated from Latin America: report from the SENTRY Antimicrobial Surveillance Program (1997-2002) Ana C Gales/+, Ronald N Jones*, Soraya S Andrade, Helio S Sader* Disciplina de Doenças Infecciosas e Parasitárias, Departamento de Medicina, Universidade Federal de São Paulo, Rua Leandro Dupret 188, 04025-010 São Paulo, SP, Brasil *The Jones Group/JMI Laboratories, North Liberty, IA, US The antimicrobial susceptibility of 176 unusual non-fermentative gram-negative bacilli (NF-GNB) collected from Latin America region through the SENTRY Program between 1997 and 2002 was evaluated by broth microdilution according to the National Committee for Clinical Laboratory Standards (NCCLS) recommendations. Nearly 74% of the NF-BGN belonged to the following genera/species: Burkholderia spp. (83), Achromobacter spp. (25), Ralstonia pickettii (16), Alcaligenes spp. (12), and Cryseobacterium spp. (12). Generally, trimethoprim/sulfamethoxazole (MIC50, ≤ 0.5 µg/ml) was the most potent drug followed by levofloxacin (MIC50, 0.5 µg/ml), and gatifloxacin (MIC50, 1 µg/ml). The highest susceptibility rates were observed for levofloxacin (78.3%), gatifloxacin (75.6%), and meropenem (72.6%). Ceftazidime (MIC50, 4 µg/ml; 83.1% susceptible) was the most active β-lactam against B. cepacia. Against Achro- mobacter spp. isolates, meropenem (MIC50, 0.25 µg/ml; 88% susceptible) was more active than imipenem (MIC50, 2 µg/ml). Cefepime (MIC50, 2 µg/ml; 81.3% susceptible), and imipenem (MIC50, 2 µg/ml; 81.3% susceptible) were more active than ceftazidime (MIC50, >16 µg/ml; 18.8% susceptible) and meropenem (MIC50, 8 µg/ml; 50% susceptible) against Ralstonia pickettii. -
Supplementary Fig. S2. Taxonomic Classification of Two Metagenomic Samples of the Gall-Inducing Mite Fragariocoptes Seti- Ger in Kraken2
Supplementary Fig. S2. Taxonomic classification of two metagenomic samples of the gall-inducing mite Fragariocoptes seti- ger in Kraken2. There was a total of 708,046,814 and 82,009,061 classified reads in samples 1 and 2, respectively. OTUs (genera) were filtered based on a normalized abundance threshold of ≥0.0005% in either sample, resulting in 171 OTUs represented by 670,717,361 and 72,439,919 reads (sample 1 and 2, respectively). Data are given in Supplementary Table S3. Sample1 Sample2 0.000005 0.002990 Bacteria:Proteobacteria:Inhella Read % (log2) 0.000005 0.005342 Bacteria:Actinobacteria:Microbacteriaceae:Microterricola 10.00 0.000006 0.003983 Bacteria:Actinobacteria:Microbacteriaceae:Cryobacterium 5.00 0.000012 0.006576 Eukaryota:Ascomycota:Mycosphaerellaceae:Cercospora 0.00 0.000013 0.002947 Bacteria:Actinobacteria:Bifidobacteriaceae:Gardnerella 0.000017 0.003555 Eukaryota:Ascomycota:Chaetomiaceae:Thielavia -5.00 0.000014 0.004244 Bacteria:Firmicutes:Clostridiaceae:Clostridium -10.00 0.000010 0.001699 Bacteria:Proteobacteria:Caulobacteraceae:Phenylobacterium -15.00 0.000012 0.001183 Bacteria:Actinobacteria:Microbacteriaceae:Leifsonia 0.000009 0.001144 Bacteria:Proteobacteria:Desulfovibrionaceae:Desulfovibrio -20.00 0.000016 0.000777 Bacteria:Firmicutes:Leuconostocaceae:Weissella -25.00 0.000014 0.000761 Bacteria:Cyanobacteria:Oscillatoriaceae:Oscillatoria 0.000013 0.000683 Bacteria:Proteobacteria:Methylobacteriaceae:Microvirga Read % 0.000011 0.000578 Bacteria:Fusobacteria:Leptotrichiaceae:Leptotrichia 0.000009 0.000842 Bacteria:Firmicutes:Paenibacillaceae:Paenibacillus -
Proposed Minimal Standards for Describing New Genera and Species of the Suborder Micrococcineae
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 1823–1849 DOI 10.1099/ijs.0.012971-0 Proposed minimal standards for describing new genera and species of the suborder Micrococcineae Peter Schumann,1 Peter Ka¨mpfer,2 Hans-Ju¨rgen Busse 3 and Lyudmila I. Evtushenko4 for the Subcommittee on the Taxonomy of the Suborder Micrococcineae of the International Committee on Systematics of Prokaryotes Correspondence 1DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, P. Schumann 38124 Braunschweig, Germany [email protected] 2Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t, 35392 Giessen, Germany 3Institut fu¨r Bakteriologie, Mykologie und Hygiene, Veterina¨rmedizinische Universita¨t, A-1210 Wien, Austria 4All-Russian Collection of Microorganisms (VKM), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, RAS, Pushchino, Moscow Region 142290, Russia The Subcommittee on the Taxonomy of the Suborder Micrococcineae of the International Committee on Systematics of Prokaryotes has agreed on minimal standards for describing new genera and species of the suborder Micrococcineae. The minimal standards are intended to provide bacteriologists involved in the taxonomy of members of the suborder Micrococcineae with a set of essential requirements for the description of new taxa. In addition to sequence data comparisons of 16S rRNA genes or other appropriate conservative genes, phenotypic and genotypic criteria are compiled which are considered essential for the comprehensive characterization of new members of the suborder Micrococcineae. Additional features are recommended for the characterization and differentiation of genera and species with validly published names. INTRODUCTION Aureobacterium and Rothia/Stomatococcus) and one pair of homotypic synonyms (Pseudoclavibacter/Zimmer- The suborder Micrococcineae was established by mannella) (Table 1 and http://www.the-icsp.org/taxa/ Stackebrandt et al. -
Lacisediminihabitans Profunda Gen. Nov., Sp. Nov., a Member of the Family Microbacteriaceae Isolated from Freshwater Sediment
Antonie van Leeuwenhoek (2020) 113:365–375 https://doi.org/10.1007/s10482-019-01347-8 (0123456789().,-volV)( 0123456789().,-volV) ORIGINAL PAPER Lacisediminihabitans profunda gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from freshwater sediment Ye Zhuo . Chun-Zhi Jin . Feng-Jie Jin . Taihua Li . Dong Hyo Kang . Hee-Mock Oh . Hyung-Gwan Lee . Long Jin Received: 14 August 2019 / Accepted: 2 October 2019 / Published online: 18 October 2019 Ó The Author(s) 2019 Abstract A novel Gram-stain-positive bacterial sequence similarities to Glaciihabitans tibetensis strain, CHu50b-6-2T, was isolated from a 67-cm-long KCTC 29148T, Frigoribacterium faeni KACC sediment core collected from the Daechung Reservoir 20509T and Lysinibacter cavernae DSM 27960T, at a water depth of 17 m, Daejeon, Republic of Korea. respectively. The phylogenetic trees revealed that The cells of strain CHu50b-6-2T were aerobic non- strain CHu50b-6-2T did not show a clear affiliation to motile and formed yellow colonies on R2A agar. The any genus within the family Microbacteriaceae. The phylogenetic analysis based on 16S rRNA gene chemotaxonomic results showed B1a type pepti- sequencing indicated that the strain formed a separate doglacan containg 2, 4-diaminobutyric acid (DAB) lineage within the family Microbacteriaceae, exhibit- as the diagnostic diamino acid, MK-10 as the ing 98.0%, 97.7% and 97.6% 16S rRNA gene predominant respiratory menaquinone, diphos- phatidylglycerol, phosphatidylglycerol, and an unidentified glycolipid as the major polar lipids, Ye Zhuo and Chun-Zhi Jin have contributed equally to this work. anteiso-C15:0, iso-C16:0, and anteiso-C17:0 as the major fatty acids, and a DNA G ? C content of 67.3 mol%. -
Outbreak of Ralstonia Mannitolilytica Bacteraemia in Patients Undergoing Haemodialysis at a Tertiary Hospital in Pretoria, South
Said et al. Antimicrobial Resistance and Infection Control (2020) 9:117 https://doi.org/10.1186/s13756-020-00778-7 RESEARCH Open Access Outbreak of Ralstonia mannitolilytica bacteraemia in patients undergoing haemodialysis at a tertiary hospital in Pretoria, South Africa Mohamed Said1* , Wesley van Hougenhouck-Tulleken2,3, Rashmika Naidoo1, Nontombi Mbelle1,4 and Farzana Ismail4,5 Abstract Background: Ralstonia species are Gram-negative bacilli of low virulence. These organisms are capable of causing healthcare associated infections through contaminated solutions. In this study, we aimed to determine the source of Ralstonia mannitolilytica bacteraemia in affected patients in a haemodialysis unit. Methods: Our laboratory noted an increase in cases of bacteraemia caused by Ralstonia mannitililytica between May and June 2016. All affected patients underwent haemodialysis at the haemodialysis unit of an academic hospital. The reverse osmosis filter of the haemodialysis water system was found to be dysfunctional. We collected water for culture at various points of the dialysis system to determine the source of the organism implicated. ERIC-PCR was used to determine relatedness of patient and environmental isolates. Results: Sixteen patients were found to have Ralstonia mannitolilytica bacteraemia during the outbreak period. We cultured Ralstonia spp. from water collected in the dialysis system. This isolate and patient isolates were found to have the identical molecular banding pattern. Conclusions: All patients were septic and received directed antibiotic therapy. There was 1 mortality. The source of the R. mannitolilytica infection in these patients was most likely the dialysis water as the identical organism was cultured from the dialysis water and the patients. The hospital management intervened and repaired the dialysis water system following which no further cases of R. -
Schumannella Luteola Gen. Nov., Sp. Nov., a Novel Genus of the Family Microbacteriaceae
J. Gen. Appl. Microbiol., 54, 253‒258 (2008) Full Paper Schumannella luteola gen. nov., sp. nov., a novel genus of the family Microbacteriaceae Sun-Young An*, Tian Xiao, and Akira Yokota Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113‒0032, Japan (Received February 28, 2008; Accepted June 24, 2008) An actinobacterial strain KHIAT, isolated from lichen in Tokyo, was taxonomically characterized using a polyphasic approach. The isolate is a Gram-positive, anaerobic, non-motile and rod- shaped bacterium. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the isolate is represented as an independent lineage distinctive from the Microbacteriaceae genera. The G+C content of DNA was 58.7 mol%. The chemotaxonomic characteristics of the isolate are cell wall peptidoglycan type (2,4-diaminobutyric acid), major cellular fatty acids (anteiso-C15:0 and iso-C16:0) and quinone type (MK-11 and MK-10). On the basis of the phenotypic and phyloge- netic distinctness, it is proposed that strain KHIAT represents a novel species in a new genus of the family Microbacteriaceae, Schumannella luteola gen. nov., sp. nov. The type strain is KHIAT (=JCM 23215T=TISTR 1824T). Key Words—Schumannella luteola gen. nov., sp. nov. Introduction butyric acid in the cell wall. Analyses of the 16S rRNA gene sequences from strain KHIAT showed that it was The family Microbacteriaceae currently contains 24 related to genera such as Leifsonia, Rhodoglobus, and genera, which are characterized by unsaturated major Salinibacterium of the family Microbacteriaceae. menaquinones (Collins and Jones, 1981) and B-type The aim of the present study is to elucidate the taxo- peptidoglycan (Park et al., 1993; Schleifer and Kan- nomic position of the isolate, using polyphasic taxon- dler, 1972; Stackebrandt et al., 1997).