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https://www.readbyqxmd.com/read/29774245/evaluation-of-phylogenetic-reconstruction-methods-using-bacterial-whole-genomes-a-simulation-based-study
#1
John A Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D Bentley, Simon R Harris
Background : Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods : We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29773945/predictive-factors-in-the-treatment-of-streptococcal-endophthalmitis
#2
Yosanan Yospaiboon, Kidakarn Meethongkam, Suthasinee Sinawat, Wipada Laovirojjanakul, Tanapat Ratanapakorn, Thuss Sanguansak, Chavakij Bhoomibunchoo
Objective: To evaluate visual outcomes and possible predictive factors in the treatment of infectious endophthalmitis caused by Streptococcus species during 2012-2016 at a large referral eye center in northeastern Thailand. Methods: A retrospective medical record chart review of patients with culture-positive endophthalmitis caused by Streptococcus species was conducted. Demographic data including age, gender, occupation, duration of symptoms, time to surgery, surgical procedures, initial visual acuity at presentation, and final visual acuity after treatment were collected and analyzed...
2018: Clinical Ophthalmology
https://www.readbyqxmd.com/read/29771255/return-of-the-tetracyclines-omadacycline-a-novel-aminomethylcycline-antimicrobial
#3
J C Cho, L M Childs-Kean, M T Zmarlicka, M P Crotty
Omadacycline is a novel aminomethylcycline antimicrobial agent that is available in both oral and intravenous formulations. The distinguishing structural characteristics of omadacycline from other tetracyclines allow for its continued antimicrobial activity in the presence of traditional tetracycline resistance mechanisms (efflux pumps and ribosomal protection proteins). Omadacycline has been found to have potent activity against antibiotic-resistant pathogens including methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus, extended spectrum beta-lactamase-producing Escherichia coli and multidrug-resistant Streptococcus pneumoniae...
March 2018: Drugs of Today
https://www.readbyqxmd.com/read/29769380/pneumococcal-metabolic-adaptation-and-colonization-are-regulated-by-the-two-component-regulatory-system-08
#4
Alejandro Gómez-Mejia, Gustavo Gámez, Stephanie Hirschmann, Viktor Kluger, Hermann Rath, Sebastian Böhm, Franziska Voss, Niamatullah Kakar, Lothar Petruschka, Uwe Völker, Reinhold Brückner, Ulrike Mäder, Sven Hammerschmidt
Streptococcus pneumoniae two-component regulatory systems (TCS) enable adaptation and ensure its maintenance in host environments. This study deciphers the impact of TCS08 on pneumococcal gene expression and its role in metabolic and pathophysiological processes. Transcriptome analysis and real-time PCR demonstrated a regulatory effect of TCS08 on genes involved mainly in environmental information processing, intermediary metabolism, and colonization by S. pneumoniae D39 and TIGR4. Striking examples are genes for fatty acid biosynthesis, genes of the arginine deiminase system, and the psa operon encoding the manganese ABC transport system...
June 27, 2018: MSphere
https://www.readbyqxmd.com/read/29769163/dauricine-combined-with-clindamycin-inhibits-severe-pneumonia-co-infected-by-influenza-virus-h5n1-and-streptococcus-pneumoniae-in-vitro-and-in-vivo-through-nf-%C3%AE%C2%BAb-signaling-pathway
#5
Hui Li, Xin Chen, Shu-Jun Zhou
Dauricine, isolated from Menispermum dauricum, has been widely used for treatment of various diseases, including cardiac ischemia and inflammation-related diseases. However, little is known regarding to the effect of dauricine on severe pneumonia. Therefore, the aim was to investigate the effect of dauricine on severe pneumonia and its mechanism during progress. Herein, H5N1 and Streptococcus pneumoniae (D39) were conducted to induce severe pneumonia in both BEAS-2B cells and mice. In vitro, dauricine reversed the protein and mRNA expressions of TNF-α, IL-6 and IL-1β, examined by ELISA and qRT-PCR assay, respectively...
April 19, 2018: Journal of Pharmacological Sciences
https://www.readbyqxmd.com/read/29765775/potential-impact-of-introducing-the-pneumococcal-conjugate-vaccine-into-national-immunisation-programmes-an-economic-epidemiological-analysis-using-data-from-india
#6
Itamar Megiddo, Eili Klein, Ramanan Laxminarayan
Pneumococcal pneumonia causes an estimated 105 000 child deaths in India annually. The planned introduction of the serotype-based pneumococcal conjugate vaccine (PCV) is expected to avert child deaths, but the high cost of PCV relative to current vaccines provided under the Universal Immunization Programme has been a concern. Cost-effectiveness studies from high-income countries are not readily comparable because of differences in the distribution of prevalent serotypes, population and health systems. We extended IndiaSim, our agent-based simulation model representative of the Indian population and health system, to model the dynamics of Streptococcus pneumoniae ...
2018: BMJ Global Health
https://www.readbyqxmd.com/read/29765237/comparative-genomic-analysis-of-multidrug-resistant-streptococcus-pneumoniae-isolates
#7
Fen Pan, Hong Zhang, Xiaoyan Dong, Weixing Ye, Ping He, Shulin Zhang, Jeff Xianchao Zhu, Nanbert Zhong
Introduction: Multidrug resistance in Streptococcus pneumoniae has emerged as a serious problem to public health. A further understanding of the genetic diversity in antibiotic-resistant S. pneumoniae isolates is needed. Methods: We conducted whole-genome resequencing for 25 pneumococcal strains isolated from children with different antimicrobial resistance profiles. Comparative analysis focus on detection of single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) was conducted...
2018: Infection and Drug Resistance
https://www.readbyqxmd.com/read/29765094/the-cell-wall-hydrolase-pmp23-is-important-for-assembly-and-stability-of-the-division-ring-in-streptococcus-pneumoniae
#8
Maxime Jacq, Christopher Arthaud, Sylvie Manuse, Chryslène Mercy, Laure Bellard, Katharina Peters, Benoit Gallet, Jennifer Galindo, Thierry Doan, Waldemar Vollmer, Yves V Brun, Michael S VanNieuwenhze, Anne Marie Di Guilmi, Thierry Vernet, Christophe Grangeasse, Cecile Morlot
Bacterial division is intimately linked to synthesis and remodeling of the peptidoglycan, a cage-like polymer that surrounds the bacterial cell, providing shape and mechanical resistance. The bacterial division machinery, which is scaffolded by the cytoskeleton protein FtsZ, includes proteins with enzymatic, structural or regulatory functions. These proteins establish a complex network of transient functional and/or physical interactions which preserve cell shape and cell integrity. Cell wall hydrolases required for peptidoglycan remodeling are major contributors to this mechanism...
May 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29764945/a-mechanism-of-unidirectional-transformation-leading-to-antibiotic-resistance-occurs-within-nasopharyngeal-pneumococcal-biofilm-consortia
#9
Santiago M Lattar, Xueqing Wu, Jennifer Brophy, Fuminori Sakai, Keith P Klugman, Jorge E Vidal
Streptococcus pneumoniae acquires genes for resistance to antibiotics such as streptomycin (Str) or trimethoprim (Tmp) by recombination via transformation of DNA released by other pneumococci and closely related species. Using naturally transformable pneumococci, including strain D39 serotype 2 (S2) and TIGR4 (S4), we studied whether pneumococcal nasopharyngeal transformation was symmetrical, asymmetrical, or unidirectional. Incubation of S2Tet and S4Str in a bioreactor simulating the human nasopharynx led to the generation of SpnTet/Str recombinants...
May 15, 2018: MBio
https://www.readbyqxmd.com/read/29764936/attachment-of-phosphorylcholine-residues-to-pneumococcal-teichoic-acids-and-modification-of-substitution-patterns-by-the-phosphorylcholine-esterase
#10
Franziska Waldow, Thomas P Kohler, Nathalie Heß, Dominik Schwudke, Sven Hammerschmidt, Nicolas Gisch
The bacterial lung pathogen Streptococcus pneumoniae has a unique nutritional requirement for exogenous choline and attaches phosphorylcholine ( P -Cho) residues to the Gal pN Ac moieties of its teichoic acids (TAs) in its cell wall. Two phosphorylcholine transferases, LicD1 and LicD2, mediate the attachment of P -Cho to the O -6 positions of the two Gal pN Ac residues present in each repeating unit of pneumococcal TAs (pnTAs), of which only LicD1 has been determined to be essential. At the molecular level, the specificity of the P -Cho attachment to pnTAs by LicD1 and LicD2 remains still elusive...
May 15, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29764747/correlation-between-clinical-features-high-resolution-computed-tomography-findings-and-a-visual-scoring-system-in-patients-with-pneumonia-due-to-mycoplasma-pneumoniae
#11
Takeshi Saraya, Kosuke Ohkuma, Yayoi Tsukahara, Takayasu Watanabe, Daisuke Kurai, Haruyuki Ishii, Hirokazu Kimura, Hajime Goto, Hajime Takizawa
BACKGROUND: Mycoplasma pneumoniae (MP) is the primary cause of community-acquired pneumonia. We aimed to evaluate the correlation between clinical features, with special reference to hypoxemia and the total affected area obtained using high-resolution computed tomography (HRCT). METHODS: Medical records of MP pneumonia patients > 15 years of age at Kyorin University Hospital between January 2006 and November 2013 were reviewed retrospectively and compared to patients with Streptococcus pneumoniae pneumonia, diagnosed between January 2013 and September 2014...
April 4, 2018: Respiratory Investigation
https://www.readbyqxmd.com/read/29759089/thrombocytopenia-in-bacteraemia-and-association-with-bacterial-species
#12
D Johansson, M Rasmussen, M Inghammar
Thrombocytopenia is common in patients with invasive bacterial infections. Bacteria can activate platelets, but it is unclear if this affects platelet count. The aim of this study was to examine whether bacteraemia with Staphylococcus aureus, which readily activate human platelets, was more likely to be complicated by thrombocytopenia than bacteraemia with Escherichia coli or Streptococcus pneumoniae with different abilities to activate platelets.We compared information from 600 adult patients with community-acquired bacteraemia with S...
May 15, 2018: Epidemiology and Infection
https://www.readbyqxmd.com/read/29757699/current-status-and-future-directions-of-invasive-pneumococcal-diseases-and-prophylactic-approaches-to-control-them
#13
Paeton L Wantuch, Fikri Y Avci
Streptococcus pneumoniae is a major human bacterial pathogen responsible for millions of deaths each year and significantly more illnesses worldwide. With over 90 different serotypes, providing effective vaccine programs has been a continuing challenge. Since 1983, the world has been introduced to four different pneumococcal vaccines (PPSV23, PCV7, PCV10, and PCV13) each with their own complications and successes. Since vaccination programs began, a decrease in the overall rate of pneumococcal pneumonia and associated diseases has been observed, notably in higher risk populations...
May 14, 2018: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/29755958/gut-microbiota-contributes-to-resistance-against-pneumococcal-pneumonia-in-immunodeficient-rag-mice
#14
Krysta M Felix, Ivan A Jaimez, Thuy-Vi V Nguyen, Heqing Ma, Walid A Raslan, Christina N Klinger, Kristian P Doyle, Hsin-Jung J Wu
Streptococcus pneumoniae causes infection-related mortality worldwide. Immunocompromised individuals, including young children, the elderly, and those with immunodeficiency, are especially vulnerable, yet little is known regarding S. pneumoniae- related pathogenesis and protection in immunocompromised hosts. Recently, strong interest has emerged in the gut microbiota's impact on lung diseases, or the "gut-lung axis." However, the mechanisms of gut microbiota protection against gut-distal lung diseases like pneumonia remain unclear...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29755803/acute-mastoiditis-complicated-with-concomitant-bezold-s-abscess-and-lateral-sinus-thrombosis
#15
Aziz Mustafa, Burhan Toçi, Hajdin Thaçi, Bujar Gjikolli, Nehat Baftiu
Bezold's abscess is a very rare extracranial complication of acute mastoiditis. Lateral sinus thrombosis is another intracranial complication of acute mastoiditis that can occur, but there are only few reports of concomitant ispilateral Bezold's abscess and lateral sinus thrombosis with favorable outcome. We diagnosed and treated successfully a 14-year-old girl suffering from Streptococcus pneumoniae acute mastoiditis complicated with Bezold's abscess and lateral sinus thrombosis. Surgical treatment included myringotomy, cortical mastoidectomy, and Bezold's abscess incision and drainage...
2018: Case Reports in Otolaryngology
https://www.readbyqxmd.com/read/29754466/temporal-trends-in-paediatric-bacterial-meningitis-in-a-tropical-australian-region-1992-2014
#16
Stephanie White, Hala Katf, Rob Baird, Joshua Francis
AIM: The epidemiology of community-acquired bacterial meningitis has changed following the introduction of routine immunisation against common causative organisms. Indigenous children living in the Northern Territory, Australia, have high rates of bacterial infections. This study describes changes in the epidemiology of childhood bacterial meningitis and the distribution of the burden of disease in the Top End. METHODS: A retrospective review of cases derived from hospital medical records and laboratory data was performed...
May 13, 2018: Journal of Paediatrics and Child Health
https://www.readbyqxmd.com/read/29753735/molecular-characterization-of-single-chain-antibody-variable-fragments-scfv-specific-to-pep27-from-streptococcus-pneumoniae
#17
Dongho Kim, ShinA Jang, Jihye Oh, Seungsu Han, Soobin Park, Prachetash Ghosh, Dong-Kwon Rhee, Sangho Lee
Pep27 from Streptococcus pneumoniae is reported to initiate pneumococcal autolysis, thereby constituting a major virulence factor. Although a few antisera recognizing Pep27 have been reported, no monoclonal, well-characterized antibody for Pep27 has been developed. Here we screened two single-chain antibody variable fragments (scFv) using a phage display from a large human synthetic scFv library to select clones E2 and F9. Dissociation constants (Kd ) of E2 and F9 were 1.1 μM and 0.50 μM, respectively...
May 10, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29752592/the-rate-of-endophthalmitis-after-pars-plana-vitrectomy-and-its-risk-factors
#18
Seyed Ali Tabatabaei, Mohammad Soleimani, Hadi Vakili, Morteza Naderan, Alireza Lashay, Houshang Faghihi, Mehdi Yaseri
PURPOSE: To study the incidence of endophthalmitis after pars plana vitrectomy, its causative organisms, and visual acuity outcomes. PATIENTS AND METHODS: In this retrospective, comparative study, the medical records of patients with acute-onset postoperative endophthalmitis after pars plana vitrectomy at Farabi Eye Hospital, Tehran, Iran, during a 12-year period between January 2004 and November 2015 were reviewed. To compare the endophthalmitis patients with other cases who underwent pars plana vitrectomy at the same day and also the same operating room, a control group was developed by gathering the data from surgical records...
May 11, 2018: International Ophthalmology
https://www.readbyqxmd.com/read/29751582/whole-exome-sequencing-identifies-new-host-genomic-susceptibility-factors-in-empyema-caused-by-streptococcus-pneumoniae-in-children-a-pilot-study
#19
Antonio Salas, Jacobo Pardo-Seco, Ruth Barral-Arca, Miriam Cebey-López, Alberto Gómez-Carballa, Irene Rivero-Calle, Sara Pischedda, María-José Currás-Tuala, Jorge Amigo, José Gómez-Rial, Federico Martinón-Torres
Pneumonia is the leading cause of death amongst infectious diseases. Streptococcus pneumoniae is responsible for about 25% of pneumonia cases worldwide, and it is a major cause of childhood mortality. We carried out a whole exome sequencing (WES) study in eight patients with complicated cases of pneumococcal pneumonia (empyema). An initial assessment of statistical association of WES variation with pneumonia was carried out using data from the 1000 Genomes Project (1000G) for the Iberian Peninsula (IBS) as reference controls...
May 3, 2018: Genes
https://www.readbyqxmd.com/read/29750817/ritr-is-an-archetype-for-a-novel-family-of-redox-sensors-in-the-streptococci-that-has-evolved-from-two-component-response-regulators-and-is-required-for-pneumococcal-colonization
#20
David G Glanville, Lanlan Han, Andrew F Maule, Alexandra Woodacre, Devsaagar Thanki, Iman Tajer Abdullah, Julie A Morrissey, Thomas B Clarke, Hasan Yesilkaya, Nicholas R Silvaggi, Andrew T Ulijasz
To survive diverse host environments, the human pathogen Streptococcus pneumoniae must prevent its self-produced, extremely high levels of peroxide from reacting with intracellular iron. However, the regulatory mechanism(s) by which the pneumococcus accomplishes this balance remains largely enigmatic, as this pathogen and other related streptococci lack all known redox-sensing transcription factors. Here we describe a two-component-derived response regulator, RitR, as the archetype for a novel family of redox sensors in a subset of streptococcal species...
May 11, 2018: PLoS Pathogens
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