Isolation and Identification of Klebsiella Aerogenes from Bee
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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. -
Carbapenem-Resistant Enterobcteriace Report
Laboratory-based surveillance for Carbapenem-resistant Enterobacterales (CRE) Center for Public Health Practice Oregon Public Health Division Published: August 2021 Figure1: CRE reported by Oregon laboratories, by year, 2010 – June 2021 180 160 140 120 100 80 60 40 20 0 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 Year 1 About carbapenem-resistant Enterobacterales (CRE): For more information about CRE The carbapenems are broad-spectrum antibiotics frequently used to surveillance in Oregon including treat severe infections caused by Gram-negative bacteria. the specifics of our definition, see Carbapenem resistance in the Enterobacterales order emerged as a http://public.health.oregon.gov/Di public health concern over the past decade, as few treatment options seasesConditions/DiseasesAZ/P remain for some severely ill patients. ages/disease.aspx?did=108 CRE Resistance. Carbapenem resistance emerges through various mechanisms, including impaired membrane permeability and the production of carbapenemases (enzymes that break down the carbapenems). Carbapenemase-producing CRE (CP-CRE) are associated with rapid spread and require the most aggressive infection control response; however, all CRE call for certain infection control measures, including contact precautions, and should be considered a public health and infection prevention priority. CRE Infection. CRE can cause pneumonia, bloodstream infections, surgical site infections, urinary tract infections, and other conditions, frequently affecting hospitalized patients and persons with compromised immune systems. Infections with CRE often require the use of very expensive antibiotics that may have toxic side effects. While CP-CRE have spread rapidly throughout the United States, they are still not endemic in Oregon. We hope we can delay or prevent their spread through surveillance and infection control. -
Pathogenic Significance of Klebsiella Oxytoca in Acute Respiratory Tract Infection
Thorax 1983;38:205-208 Thorax: first published as 10.1136/thx.38.3.205 on 1 March 1983. Downloaded from Pathogenic significance of Klebsiella oxytoca in acute respiratory tract infection JOAN T POWER, MARGARET-A CALDER From the Department ofRespiratory Medicine and the Bacteriology Laboratory, City Hospital, Edinburgh ABSTRACT A retrospective study of all Klebsiella isolations from patients admitted to hospital with acute respiratory tract infections over a 27-month period was carried out. Ten of the Klebsiella isolations from sputum and one from a blood culture were identified as Klebsiella oxytoca. The clinical and radiological features of six patients are described. Four of these patients had lobar pneumonia, one bronchopneumonia, and one acute respiratory tract infection superimposed on cryptogenic fibrosing alveolitis. One of the patients with lobar pneumonia had a small-cell carcinoma of the bronchus. We concluded that Klebsiella oxytoca was of definite pathogenic significance in these six patients and of uncertain significance in the remaining five patients. Klebsiella oxytoca has not previously been described as a specific pathogen in the respiratory tract. Close co-operation between clinicians and microbiologists in the management of patients with respiratory infections associated with the Enterobacteriaceae is desirable. Klebsiella oxytoca has not previously been described agar plate was inoculated and incubated for 18 copyright. as a specific respiratory pathogen. Bacillus oxytoca hours. The API 20E system (Analytal Product Inc) was first isolated by Flugge from a specimen of sour was used to identify the biochemical reactions. The milk in 1886.' 2 It was not until 1963 that the organ- two biochemical reactions which differentiate Kleb- ism was accepted as a member of the genus Kleb- siella oxytoca from the Klebsiella pneumoniae organ- siella and then only with reluctance on the part of ism are its ability to liquify gelatin and its indole http://thorax.bmj.com/ some authorities.3 To define more clearly the role of positivity. -
Klebsiella Pneumoniae Ar-Bank#0453
KLEBSIELLA PNEUMONIAE AR-BANK#0453 Key RESISTANCE: KPC MIC (µg/ml) RESULTS AND INTERPRETATION PROPAGATION DRUG MIC INT DRUG MIC INT MEDIUM Amikacin 32 I Colistin 0.5 --- Ampicillin >32 R Doripenem >8 R Medium: Trypticase Soy Agar with 5% Sheep Blood (BAP) Ampicillin/sulbactam1 >32 R Ertapenem >8 R GROWTH CONDITIONS Aztreonam >64 R Gentamicin 1 S Temperature: 35⁰C Cefazolin >8 R Imipenem >64 R Atmosphere: Aerobic 2 Cefepime >32 R Imipenem+chelators >32 --- PROPAGATION Levofloxacin PROCEDURE Cefotaxime >64 R >8 R Cefotaxime/clavulanic 1 >32 --- Meropenem >8 R Remove the sample vial to a acid container with dry ice or a Cefoxitin >16 R Piperacillin/tazobactam1 >128 R freezer block. Keep vial on ice Ceftazidime >128 R Polymyxin B 0.5 --- or block. (Do not let vial content thaw) Ceftazidime/avibactam1 16 R3 Tetracycline 8 I Ceftazidime/clavulanic >64 --- Tigecycline 1 S3 Open vial aseptically to avoid acid1 contamination Ceftriaxone >32 R Tobramycin 16 R 1 Using a sterile loop, remove a Ciprofloxacin >8 R Trimethoprim/sulfamethoxazole >8 R small amount of frozen isolate from the top of the vial S – I –R Interpretation (INT) derived from CLSI 2016 M100 S26 1 Reflects MIC of first component Aseptically transfer the loop 2 Screen for metallo-beta-lactamase production to BAP [Rasheed et al. Emerging Infectious Diseases. 2013. 19(6):870-878] 3 Based on FDA break points Use streak plate method to isolate single colonies Incubate inverted plate at 35⁰C for 18-24 hrs. [email protected] http://www.cdc.gov/drugresistance/resistance-bank/ BIOSAFETY LEVEL 2 Appropriate safety procedures should always be used with this material. -
Klebsiella Pneumoniae: Virulence, Biofilm and Antimicrobial Resistance
Divya Bharathi PIDJ ESPID REPORTS AND REVIEWS PIDJ-217-384 CONTENTS Klebsiella pneumoniae Vitulence, Biofilm and Resistance in Klebsiella EDITORIAL BOARD Piperaki et al Editor: Delane Shingadia Board Members David Burgner (Melbourne, Cristiana Nascimento-Carvalho George Syrogiannopoulos XXX Australia) (Bahia, Brazil) (Larissa, Greece) Kow-Tong Chen (Tainan,Taiwan) Ville Peltola (Turku, Finland) Tobias Tenenbaum (Mannhein, Germany) Luisa Galli (Florence, Italy) Emmanuel Roilides (Thessaloniki, Marc Tebruegge (Southampton, UK) Steve Graham (Melbourne, Pediatr Infect Dis J Greece) Marceline Tutu van Furth (Amsterdam, Australia) Ira Shah (Mumbai, India) The Netherlands) Lippincott Williams & Wilkins Klebsiella pneumoniae: Virulence, Biofilm and Antimicrobial Hagerstown, MD Resistance Evangelia-Theophano Piperaki, MD, PhD,* George A. Syrogiannopoulos, MD, PhD,† Leonidas S. Tzouvelekis, MD, PhD,* and George L. Daikos, MD, PhD‡ Key Words: Klebsiella pneumoniae, virulence, ingitis in premature neonates and infants as the immune response through cytokine and biofilm, resistance well as serious infections in immunocompro- chemokine production (Fig. 1). Among the mised and malnourished children, whereas effector cells that are recruited first to the in the community, K. pneumoniae is a com- infection site are the neutrophils. Impor- mon cause of urinary tract infections among tant mediators involved in this process are lebsiella pneumoniae is a ubiquitous immunocompetent children. interleukin (IL)-8 and IL-23, which induces K Gram-negative encapsulated bacterium In recent years, most K. pneumoniae production of IL-17 that promotes granu- that resides in the mucosal surfaces of mam- infections are caused by strains termed “clas- lopoietic response.6-7 IL-12 also amplifies the mals and the environment (soil, water, etc.). sic” K. pneumoniae (cKp). -
Rapid Identification and Phylogenetic Classification of Diverse Bacterial
www.nature.com/scientificreports OPEN Rapid identifcation and phylogenetic classifcation of diverse bacterial pathogens in a Received: 1 November 2018 Accepted: 18 February 2019 multiplexed hybridization assay Published: xx xx xxxx targeting ribosomal RNA Roby P. Bhattacharyya1,2, Mark Walker1, Rich Boykin3, Sophie S. Son1, Jamin Liu 1,4, Austin C. Hachey1,5, Peijun Ma1, Lidan Wu 1,6, Kyungyong Choi7, Kaelyn C. Cummins8,9, Maura Benson8, Jennifer Skerry10, Hyunryul Ryu 7,11, Sharon Y. Wong1, Marcia B. Goldberg2, Jongyoon Han7,12, Virginia M. Pierce10, Lisa A. Cosimi8, Noam Shoresh1, Jonathan Livny1, Joseph Beechem3 & Deborah T. Hung1,13,14 Rapid bacterial identifcation remains a critical challenge in infectious disease diagnostics. We developed a novel molecular approach to detect and identify a wide diversity of bacterial pathogens in a single, simple assay, exploiting the conservation, abundance, and rich phylogenetic content of ribosomal RNA in a rapid fuorescent hybridization assay that requires no amplifcation or enzymology. Of 117 isolates from 64 species across 4 phyla, this assay identifed bacteria with >89% accuracy at the species level and 100% accuracy at the family level, enabling all critical clinical distinctions. In pilot studies on primary clinical specimens, including sputum, blood cultures, and pus, bacteria from 5 diferent phyla were identifed. Afer long relying on decades-old culture methods and traditional biochemical assays, modern clinical micro- biology laboratories have begun to incorporate novel methods for bacterial pathogen identifcation in recent years1. Fundamentally, the challenge remains to recognize key distinguishing characteristics of a pathogen from a variety of clinical specimens as rapidly, sensitively, accurately, and inexpensively as possible. -
Carbapenem-Resistant Enterobacteriaceae a Microbiological Overview of (CRE) Carbapenem-Resistant Enterobacteriaceae
PREVENTION IN ACTION MY bugaboo Carbapenem-resistant Enterobacteriaceae A microbiological overview of (CRE) carbapenem-resistant Enterobacteriaceae. by Irena KennelEy, PhD, aPRN-BC, CIC This agar culture plate grew colonies of Enterobacter cloacae that were both characteristically rough and smooth in appearance. PHOTO COURTESY of CDC. GREETINGS, FELLOW INFECTION PREVENTIONISTS! THE SCIENCE OF infectious diseases involves hundreds of bac- (the “bug parade”). Too much information makes it difficult to teria, viruses, fungi, and protozoa. The amount of information tease out what is important and directly applicable to practice. available about microbial organisms poses a special problem This quarter’s My Bugaboo column will feature details on the CRE to infection preventionists. Obviously, the impact of microbial family of bacteria. The intention is to convey succinct information disease cannot be overstated. Traditionally the teaching of to busy infection preventionists for common etiologic agents of microbiology has been based mostly on memorization of facts healthcare-associated infections. 30 | SUMMER 2013 | Prevention MULTIDRUG-resistant GRAM-NEGative ROD ALert: After initial outbreaks in the northeastern U.S., CRE bacteria have THE CDC SAYS WE MUST ACT NOW! emerged in multiple species of Gram-negative rods worldwide. They Carbapenem-resistant Enterobacteriaceae (CRE) infections come have created significant clinical challenges for clinicians because they from bacteria normally found in a healthy person’s digestive tract. are not consistently identified by routine screening methods and are CRE bacteria have been associated with the use of medical devices highly drug-resistant, resulting in delays in effective treatment and a such as: intravenous catheters, ventilators, urinary catheters, and high rate of clinical failures. -
Klebsiella Meningitis Report of Nine Cases
Journal of Neurology, Neurosurgery, and Psychiatry, 1972, 35, 903-908 J Neurol Neurosurg Psychiatry: first published as 10.1136/jnnp.35.6.903 on 1 December 1972. Downloaded from Klebsiella meningitis report of nine cases D. J. E. PRICE' AND J. D. SLEIGH From the Institute of Neurological Sciences, Killearn Hospital, Glasgow SUMMARY During a serious epidemic of chest and urinary infections due to Klebsiella aerogenes in a neurosurgical unit, several patients developed klebsiella meningitis after trauma or surgery. Despite all attempts to control the epidemic and treat the meningitis with antibiotics, eight of the nine patients died. It was not until all antibiotics used to treat respiratory and urinary infections had been totally withdrawn that no further patients developed klebsiella meningitis. Recent advances in antibiotic therapy have re- Lancet, 1970). Such outbreaks in neurosurgical sulted in a great reduction in mortality from units may result in patients developing menin- many infections and pyogenic meningitis is no gitis or serious wound infections which may en- exception. Klebsiella species are an uncommon danger life (Ayliffe, Lowbury, Hamilton, Small, cause of pyogenic meningitis, but this infection Asheshov, and Parker, 1965). still carries a high mortality. This paper reports Until 1971, the Glasgow Institute of Neuro- guest. Protected by copyright. nine patients in a neurosurgical unit who devel- logical Sciences was situated at Killearn Hospi- oped this form of meningitis within one year. tal, some 16 miles from Glasgow, and during Only one patient survived. the winter of 1967-68, antibiotic-resistant coli- In recent years an increasing number of hos- form organisms producing mucoid colonies, later pital epidemics due to antibiotic-resistant Gram- identified as Klebsiella aerogenes, were isolated negative bacilli have been reported (Lancet, 1966; from sputum and urine specimens in increasing numbers. -
Enteric Dysbiosis and Fecal Calprotectin Expression in Premature Infants
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Pediatr Manuscript Author Res. Author manuscript; Manuscript Author available in PMC 2019 June 10. Published in final edited form as: Pediatr Res. 2019 February ; 85(3): 361–368. doi:10.1038/s41390-018-0254-y. Enteric Dysbiosis and Fecal Calprotectin Expression in Premature Infants Thao T. B. Ho1, Maureen W. Groer1,2, Bradley Kane2, Alyson L. Yee3,4,5, Benjamin A. Torres1, Jack A. Gilbert4,5,6, and Akhil Maheshwari7,* 1Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, Florida. 2College of Nursing, University of South Florida, Tampa, Florida. 3Interdisciplinary Scientist Training Program, University of Chicago, Chicago, Illinois. 4Microbiome Center, University of Chicago, Chicago, Illinois. 5Department of Surgery, University of Chicago, Chicago, Illinois. 6Argonne National Laboratory, Chicago, Illinois. 7Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland. Abstract Background: Premature infants often develop enteric dysbiosis with a preponderance of Gammaproteobacteria, which has been related to adverse clinical outcomes. We investigated the relationship between increasing fecal Gammaproteobacteria and mucosal inflammation, measured by fecal calprotectin (FC). Methods: Stool samples were collected from very-low-birth weight (VLBW) infants at ≤2, 3, and 4 weeks’ postnatal age. Fecal microbiome was surveyed using PCR-amplification of the V4 region of 16S rRNA, and FC was measured by enzyme immunoassay. Results: We enrolled 45 VLBW infants (gestation 27.9±2.2 weeks, birth weight 1126±208 g) and obtained stool samples at 9.9±3, 20.7±4.1, and 29.4±4.9 days. FC was positively correlated with the genus Klebsiella (r = 0.207, p = 0.034) and its dominant amplicon sequence variant (r = 0.290, p = 0.003) but not with the relative abundance of total Gammaproteobacteria. -
Detection of Escherichia Coli and Harmful Enteric Bacterial Pathogens in Domestic Hand-Dug Wells in the Cuvelai Etosha Basin of Namibia
Advances in Microbiology, 2018, 8, 297-313 http://www.scirp.org/journal/aim ISSN Online: 2165-3410 ISSN Print: 2165-3402 Detection of Escherichia coli and Harmful Enteric Bacterial Pathogens in Domestic Hand-Dug Wells in the Cuvelai Etosha Basin of Namibia B. McBenedict1,2*, H. Wanke3, B. M. Hang’ombe2, P. M. Chimwamurombe4 1Department of Veterinary Medicine, University of Zambia, Lusaka, Zambia 2Department of Biological Sciences, University of Namibia, Windhoek, Namibia 3Geology Department, University of Namibia, Windhoek, Namibia 4Department of Natural and Applied Sciences, Namibia University of Science and Technology, Windhoek, Namibia How to cite this paper: McBenedict, B., Abstract Wanke, H., Hang’ombe, B.M. and Chim- wamurombe, P.M. (2018) Detection of The Cuvelai Etosha Basin of Namibia is characterised by complex aquifer sys- Escherichia coli and Harmful Enteric Bac- tems with multi-layered aquifers and various water qualities. Some parts of terial Pathogens in Domestic Hand-Dug the basin have been covered with a pipeline system that supplies purified sur- Wells in the Cuvelai Etosha Basin of Nami- bia. Advances in Microbiology, 8, 297-313. face water from the Kunene River. Locations that lack a pipeline system utilise https://doi.org/10.4236/aim.2018.84020 hand-dug wells as a source of drinking water. These wells draw water from shallow perched aquifers and are not protected from surface contamination Received: March 19, 2018 nor is the water quality monitored. Sanitised water supply is relevant for the Accepted: April 27, 2018 Published: April 30, 2018 growth and development of societies and is a priority of the United Nations Millennium Development Goals. -
Antimicrobial Resistant Phenotype Definitions
Antimicrobial-Resistant Phenotype Definitions Analysis of Antimicrobial-Resistant Organisms in NHSN Updated 06/2021 This document provides definitions for the pre-defined antimicrobial resistance patterns (phenotypes) that are used in the NHSN analytic reports located in the following analysis folder: HAI Antimicrobial Resistance (DA + PA Modules) > Antimicrobial Resistant HAIs. Phenotype Name Phenotype Code Phenotype Definition Methicillin-resistant MRSA_HAI Staphylococcus aureus that has tested Resistant (R) to at least 1 of the Staphylococcus aureus following: methicillin, oxacillin, or cefoxitin. Carbapenem-resistant CREall_HAI Any Escherichia coli, Klebsiella aerogenes, Klebsiella oxytoca, Klebsiella Enterobacteriaceae pneumoniae, or Enterobacter spp. that has tested Resistant (R) to at least 1 of the following: imipenem, meropenem, doripenem, ertapenem, meropenem/vaborbactam, or imipenem/relebactam. *NOTE: For data prior to 2021, meropenem/vaborbactam and imipenem/relebactam are not included in the CRE definition, as results for these drugs were not collected in NHSN. Carbapenem-resistant CREecoli_HAI Any Escherichia coli that has tested Resistant (R) to at least 1 of the E. coli following: imipenem, meropenem, doripenem, ertapenem, meropenem/vaborbactam, or imipenem/relebactam. *NOTE: For data prior to 2021, meropenem/vaborbactam and imipenem/relebactam are not included in the CRE definition, as results for these drugs were not collected in NHSN. Carbapenem-resistant CREenterobacter_HAI Any Enterobacter spp. that has tested Resistant -
Treatment of Urinary Tract Infections Caused by ESBL-Producing
Jayachitra PIDJ ESPID REPORTS AND REVIEWS PIDJ-219-663 CONTENTS UTI Caused by E. Coli or Klebsiella pneumoniae UTI Caused by E. coli or Klebsiella EDITORIAL BOARD Editors: Shamez N. Ladhani and Emmanuel J. Roilides Bitsori and Galanakis Board Members David Burgner (Melbourne, Cristiana Nascimento-Carvalho (Larissa, Greece) XXX Australia) (Bahia, Brazil) Tobias Tenenbaum (Mannhein, Kow-Tong Chen (Tainan,Taiwan) Ville Peltola (Turku, Finland) Germany) 11/19/2019 on BhDMf5ePHKav1zEoum1tQfN4a+kJLhEZgbsIHo4XMi0hCywCX1AWnYQp/IlQrHD3TDbD+Y6NAIGu+rtg6z5XDLNf0MN8NgKi8U6WmRZ598BTdqYKNjB+OQ== by https://journals.lww.com/pidj from Downloaded Luisa Galli (Florence, Italy) Ira Shah (Mumbai, India) Marc Tebruegge (Southampton, UK) Downloaded Steve Graham (Melbourne, George Syrogiannopoulos Pediatr Infect Dis J Australia) from https://journals.lww.com/pidj Lippincott Williams & Wilkins Treatment of Urinary Tract Infections Caused by ESBL-producing Escherichia coli or Klebsiella pneumoniae Hagerstown, MD by BhDMf5ePHKav1zEoum1tQfN4a+kJLhEZgbsIHo4XMi0hCywCX1AWnYQp/IlQrHD3TDbD+Y6NAIGu+rtg6z5XDLNf0MN8NgKi8U6WmRZ598BTdqYKNjB+OQ== Maria Bitsori, MD, PhD, and Emmanouil Galanakis, MD, PhD rinary tract infections (UTIs) are usually and classifiedβ -lactamases into 4 classes, A, 5% among community-acquired UTIs and Ucaused by Gram-negative Enterobacte- C and D serine β-lactamases and B metallo- 12% among healthcare-associated ones.5 riaceae, the most common pathogens being β-lactamases.3 A functional classification Global trends for AmpC uropathogens Escherichia coli and Klebsiella pneumo- correlated the properties of a specific enzyme are not available but surveillance programs niae.1,2 Antimicrobial resistance is increasing with the resistance profile of a clinical iso- suggest high rates in regions with high ESBL among uropathogens and the production of late and included 3 major groups, 1, 2 and 3 prevalence.4 In a multicenter study from β-lactamases is a major resistance mecha- with subgroups.3 In Table 1, we summarize China, 2% of E.