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https://www.readbyqxmd.com/read/27933038/computing-and-applying-atomic-regulons-to-understand-gene-expression-and-regulation
#1
José P Faria, James J Davis, Janaka N Edirisinghe, Ronald C Taylor, Pamela Weisenhorn, Robert D Olson, Rick L Stevens, Miguel Rocha, Isabel Rocha, Aaron A Best, Matthew DeJongh, Nathan L Tintle, Bruce Parrello, Ross Overbeek, Christopher S Henry
Understanding gene function and regulation is essential for the interpretation, prediction, and ultimate design of cell responses to changes in the environment. An important step toward meeting the challenge of understanding gene function and regulation is the identification of sets of genes that are always co-expressed. These gene sets, Atomic Regulons (ARs), represent fundamental units of function within a cell and could be used to associate genes of unknown function with cellular processes and to enable rational genetic engineering of cellular systems...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27930826/a-molecular-epidemiological-study-of-methicillin-resistant-staphylococci-environmental-contamination-in-railway-stations-and-coach-stations-in-guangzhou-of-china
#2
J L Lin, Y Peng, Q T Ou, D L Lin, Y Li, X H Ye, J L Zhou, Z J Yao
Methicillin-resistant Staphylococcus aureus (MRSA) has caused a series of public health problems since it was first found in 1961. However, there are few research studies on the MRSA environmental contamination in railway stations and coach stations. Therefore, the aim of this study was to determine MRSA environmental contamination in public transport stations. Between December 2013 and January 2014, 380 surface samples from three railway stations (180) and four coach stations (200) in Guangzhou were collected to isolate and determine the prevalence and characteristics of Staphylococci strains...
December 8, 2016: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/27916561/finding-srna-associated-phenotypes-by-competition-assays-an-example-with-staphylococcus-aureus
#3
Thao Nguyen Le Lam, Claire Morvan, Wenfeng Liu, Chantal Bohn, Yan Jaszczyszyn, Philippe Bouloc
Bacteria optimize their fitness in response to a changing environment by tight regulation of gene expression. Regulation can be controlled at both transcriptional and post-transcriptional levels via key players such as sigma factors, regulatory proteins and regulatory RNAs. The identification of phenotypes associated with gene deletions is the established method for finding gene functions but may require testing many conditions for each studied mutant. As regulatory RNAs often contribute to fine-tuning gene expression, phenotypes associated with their inactivation are often weak and difficult to detect...
December 1, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/27915412/formation-of-indigoidine-derived-pigments-contributes-to-the-adaptation-of-vogesella-sp-strain-eb-to-cold-aquatic-iron-oxidizing-environments
#4
Paula Arrúa Day, María S Villalba, O Marisa Herrero, Luz Alejandra Arancibia, Héctor M Alvarez
We investigated previously under explored cold aquatic environments of Andean Patagonia, Argentina. Oily sheens similar to an oil spill are frequently observed at the surface of water in creeks and small ponds in these places. Chemical analysis of a water sample revealed the occurrence of high concentrations of iron and the presence of a free insoluble indigoidine-derived pigment. A blue pigment-producing bacterium (strain EB) was isolated from the water sample and identified as Vogesella sp. by molecular analysis...
December 3, 2016: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/27912981/examining-the-association-between-surface-bioburden-and-frequently-touched-sites-in-intensive-care
#5
C E Adams, J Smith, V Watson, C Robertson, S J Dancer
BACKGROUND: Critical care patients are at increased risk of infection. Near-patient surfaces act as reservoirs of microbial soil, which may contain pathogens. AIM: To correlate soil levels with hand-touch frequency of near-patient sites in an intensive care unit (ICU). METHODS: Five sites around each bed in a 10-bed ICU were screened for total microbial soil (cfu/cm(2)) and Staphylococcus aureus every month for 10 months. Selected sites were infusion pump and cardiac monitor, left and right bedrails, and bed table...
November 13, 2016: Journal of Hospital Infection
https://www.readbyqxmd.com/read/27909431/the-microbiota-of-recreational-freshwaters-and-the-implications-for-environmental-and-public-health
#6
Chang Soo Lee, Minseok Kim, Cheonghoon Lee, Zhongtang Yu, Jiyoung Lee
The microbial communities in recreational freshwaters play important roles in both environmental and public health perspectives. In this study, the bacterial community structure and its associations with freshwater environments were investigated by analyzing the summertime microbiomes of three beach waters in Ohio (East Fork, Delaware, and Madison lakes) together with environmental and microbial water quality parameters. From the swimming season of 2009, 21 water samples were collected from the three freshwater beaches...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27906650/structure-of-the-70s-ribosome-from-human-pathogen-staphylococcus-aureus
#7
Iskander Khusainov, Quentin Vicens, Anthony Bochler, François Grosse, Alexander Myasnikov, Jean-François Ménétret, Johana Chicher, Stefano Marzi, Pascale Romby, Gulnara Yusupova, Marat Yusupov, Yaser Hashem
Comparative structural studies of ribosomes from various organisms keep offering exciting insights on how species-specific or environment-related structural features of ribosomes may impact translation specificity and its regulation. Although the importance of such features may be less obvious within more closely related organisms, their existence could account for vital yet species-specific mechanisms of translation regulation that would involve stalling, cell survival and antibiotic resistance. Here, we present the first full 70S ribosome structure from Staphylococcus aureus, a Gram-positive pathogenic bacterium, solved by cryo-electron microscopy...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27902427/phenotypic-and-genetic-characterization-of-multi-drug-resistant-staphylococcus-aureus-in-the-tropics-of-southeast-asia
#8
Siti Norayuni Mohd Zulkeflle, Yus Amira Yusaimi, Norio Sugiura, Koji Iwamoto, Masafumi Goto, Motoo Utsumi, Nor'azizi Bin Othman, Zuriati Zakaria, Hirofumi Hara
Antibiotic resistance has become a major public health problem throughout the world. The presence of antibiotic resistant bacteria such as Staphylococcus aureus (S. aureus) and antibiotic resistance genes (ARGs) in hospital wastewater is cause for great concern today. In this study, 276 S. aureus isolates were recovered from hospital wastewater samples in Malaysia. All of the isolates were screened for susceptibility to nine different classes of antibiotics: ampicillin (AMP), ciprofloxacin (CFX), gentamicin (GMN), kanamycin (KMN), erythromycin (ERM), vancomycin (VAN), trimetoprim and sulfamethaxazole (TM-SMZ), chloramphenicol (CMP), tetracycline (TET), and nalidixic acid (NAL)...
November 3, 2016: Microbiology
https://www.readbyqxmd.com/read/27894984/a-longitudinal-analysis-of-methicillin-resistant-and-sensitive-staphylococcus-aureus-incidence-in-respect-to-specimen-source-patient-location-and-temperature-variation
#9
T Delorme, A Garcia, P Nasr
OBJECTIVE: Seasonal variations in temperature exert strong selective pressure on microorganism population dynamics and should be taken into account in epidemiological studies. The objective of current study was to characterize the seasonal variation of Staphylococcal infections in respect to patient location, specimen source, month of year, and temperature variation. METHOD: A retrospective longitudinal time series analysis of methicillin-resistant and sensitive S...
November 25, 2016: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/27894856/glycopeptide-resistance-links-with-inorganic-phosphate-metabolism-and-cell-envelope-stress
#10
REVIEW
Fernando Santos-Beneit, María Ordóñez-Robles, Juan F Martín
Antimicrobial resistance is a critical health issue today. Many pathogens have become resistant to many or all available antibiotics and limited new antibiotics are in the pipeline. Glycopeptides are used as a 'last resort' antibiotic treatment for many bacterial infections, but worryingly, glycopeptide resistance has spread to very important pathogens such as Enterococcus faecium and Staphylococcus aureus. Bacteria confront multiple stresses in their natural environments, including nutritional starvation and the action of cell-wall stressing agents...
November 25, 2016: Biochemical Pharmacology
https://www.readbyqxmd.com/read/27889162/tolerance-of-clostridium-perfringens-biofilms-to-disinfectants-commonly-used-in-the-food-industry
#11
Audrey Charlebois, Mario Jacques, Martine Boulianne, Marie Archambault
Clostridium perfringens is an opportunistic pathogen that can cause food poisoning in humans and various enterotoxemia in animal species. Recently, it was shown to form mono-species biofilms, a structured community of bacterial cells enclosed in a self-produced extracellular matrix. Biofilms have been associated with tolerance to antibiotics, disinfectants, and physical and environmental stresses. Very little is known about the tolerance of C. perfringens biofilm toward disinfectants. In the present study, susceptibilities of C...
April 2017: Food Microbiology
https://www.readbyqxmd.com/read/27884664/bacterial-contamination-of-saline-used-for-epidural-procedures-in-an-obstetric-setting-a-randomised-comparison-of-two-drawing-up-techniques
#12
M Onofrei, M Y Wee, B Parker, N Wee, S Hill
BACKGROUND: There is little evidence to inform practice regarding the optimum aseptic technique of drawing up saline for epidural insertion. Our regional practice is to draw up saline from a non-sterile packaged plastic ampoule, therefore introducing the risk of bacterial contamination. Usually, the anaesthetist draws up saline directly from the vial held by an assistant using a needle (needle technique). Alternatively, the saline vial is emptied onto a sterile tray by an assistant and then drawn up by the anaesthetist (tray technique)...
October 8, 2016: International Journal of Obstetric Anesthesia
https://www.readbyqxmd.com/read/27870247/sparse-neural-network-models-of-antimicrobial-peptide-activity-relationships
#13
Alex T Müller, Aral C Kaymaz, Gisela Gabernet, Gernot Posselt, Silja Wessler, Jan A Hiss, Gisbert Schneider
We present an adaptive neural network model for chemical data classification. The method uses an evolutionary algorithm for optimizing the network structure by seeking sparsely connected architectures. The number of hidden layers, the number of neurons in each layer and their connectivity are free variables of the system. We used the method for predicting antimicrobial peptide activity from the amino acid sequence. Visualization of the evolved sparse network structures suggested a high charge density and a low aggregation potential in solution as beneficial for antimicrobial activity...
December 2016: Molecular Informatics
https://www.readbyqxmd.com/read/27865985/cfr-mediated-linezolid-resistant-clinical-isolates-of-methicillin-resistant-coagulase-negative-staphylococci-from-china
#14
Yunjia Song, Yuan Lv, Lanqing Cui, Yun Li, Qian Ke, Yixuan Zhao
Three linezolid-resistant coagulase-negative staphylococci (LR-CoNS), including two Staphylococcus cohnii and one Staphylococcus capitis, were isolated from 1104 clinical staphylococcal isolates across China in 2013-2014. Antibiotic susceptibilities of the bacteria were determined by the agar dilution method. PCR and DNA sequencing were performed to determine the potential molecular mechanism of linezolid resistance. The two linezolid-resistant S. cohnii isolates were subjected to pulsed-field gel electrophoresis (PFGE) to investigate their genetic relatedness...
November 5, 2016: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/27865514/coagulase-negative-staphylococcus-species-in-bulk-milk-prevalence-distribution-and-associated-subgroup-and-species-specific-risk-factors
#15
A De Visscher, S Piepers, F Haesebrouck, K Supré, S De Vliegher
Coagulase-negative staphylococci (CNS) have become the main pathogens causing bovine mastitis in recent years. A huge variation in species distribution among herds has been observed in several studies, emphasizing the need to identify subgroup- and species-specific herd-level factors to improve our understanding of the differences in ecological and epidemiological nature between species. The use of bulk milk samples enables the inclusion of a large(r) number of herds needed to identify herd-level risk factors and increases the likelihood of recovering enough isolates per species needed for conducting subgroup- and, eventually, species-specific analyses at the same time...
November 16, 2016: Journal of Dairy Science
https://www.readbyqxmd.com/read/27863959/transmission-of-staphylococcus-aureus-between-health-care-workers-the-environment-and-patients-in-an-intensive-care-unit-a-longitudinal-cohort-study-based-on-whole-genome-sequencing
#16
James R Price, Kevin Cole, Andrew Bexley, Vasiliki Kostiou, David W Eyre, Tanya Golubchik, Daniel J Wilson, Derrick W Crook, A Sarah Walker, Timothy E A Peto, Martin J Llewelyn, John Paul
BACKGROUND: Health-care workers have been implicated in nosocomial outbreaks of Staphylococcus aureus, but the dearth of evidence from non-outbreak situations means that routine health-care worker screening and S aureus eradication are controversial. We aimed to determine how often S aureus is transmitted from health-care workers or the environment to patients in an intensive care unit (ICU) and a high-dependency unit (HDU) where standard infection control measures were in place. METHODS: In this longitudinal cohort study, we systematically sampled health-care workers, the environment, and patients over 14 months at the ICU and HDU of the Royal Sussex County Hospital, Brighton, England...
November 15, 2016: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/27858378/label-free-3d-ag-nanoflower-based-electrochemical-immunosensor-for-the-detection-of-escherichia-coli-o157-h7-pathogens
#17
He Huang, Minghuan Liu, Xiangsheng Wang, Wenjie Zhang, Da-Peng Yang, Lianhua Cui, Xiansong Wang
It is highly desirable to develop a rapid and simple method to detect pathogens. Combining nanomaterials with electrochemical techniques is an efficient way for pathogen detection. Herein, a novel 3D Ag nanoflower was prepared via a biomineralization method by using bovine serum albumin (BSA) as a template. It was adopted as a sensing interface to construct an electrochemical bacteria immunosensor for the rapid detection of foodborne pathogens Escherichia coli (E. coli) O157:H7. Bacterial antibody was immobilized onto the surface of Ag nanoflowers through covalent conjugation...
December 2016: Nanoscale Research Letters
https://www.readbyqxmd.com/read/27854041/functional-analysis-of-plantaricin-e-and-its-mutant-by-heterologous-expression-in-escherichia-coli
#18
Fanqiang Meng, Xiaoyu Zhu, Fengxia Lu, Xiaomei Bie, Zhaoxin Lu
Plantaricins are a group of ribosomally synthesized antimicrobial peptides in Lactobacillus plantarum that exert antimicrobial activities against some foodborne pathogens. In this study, we observed that plantaricin E in L. plantarum 163 was missing 19 amino acids (plnE mutant amino acid sequence: FNRGGYNFGKSVRH, plnE amino acid sequence: FNRGGYNFGKSVRHVVDAIGSVAGIRGILKSIR). In order to study the effects of mutant plnE, plnE mutant genes with and without the signal peptide were cloned from the L. plantarum 163 genome, linked to the pET32a vector, and expressed via a fusion protein (thioredoxin) in Escherichia coli BL21 (DE3)...
November 16, 2016: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/27848063/concordance-of-renal-stone-culture-pmuc-rpuc-rsc-and-post-pcnl-sepsis-a-non-randomized-prospective-observation-cohort-study
#19
Annerleim Walton-Diaz, José Ignacio Vinay, Jaime Barahona, Pieter Daels, Mariano González, Juan Pablo Hidalgo, Cristian Palma, Pablo Díaz, Alfredo Domenech, Rodrigo Valenzuela, Fernando Marchant
INTRODUCTION: Between 5 and 10% of patients undergoing percutaneous nephrolithotomy (PCNL) develop postoperative sepsis 1, 2. Strategies to prevent infectious complications are based on information provided by preoperative midstream urine cultures (PMUC). The aim of this study is to evaluate the concordance of the microbiologic findings of PMUC, cultures of the renal stone (RSC) and urine obtained directly from the renal pelvis (RPUC) in patients undergoing PCNL. MATERIALS AND METHODS: This is a multicenter prospective study...
November 15, 2016: International Urology and Nephrology
https://www.readbyqxmd.com/read/27842515/evaluation-of-pacbio-sequencing-for-full-length-bacterial-16s-rrna-gene-classification
#20
Josef Wagner, Paul Coupland, Hilary P Browne, Trevor D Lawley, Suzanna C Francis, Julian Parkhill
BACKGROUND: Currently, bacterial 16S rRNA gene analyses are based on sequencing of individual variable regions of the 16S rRNA gene (Kozich, et al Appl Environ Microbiol 79:5112-5120, 2013).This short read approach can introduce biases. Thus, full-length bacterial 16S rRNA gene sequencing is needed to reduced biases. A new alternative for full-length bacterial 16S rRNA gene sequencing is offered by PacBio single molecule, real-time (SMRT) technology. The aim of our study was to validate PacBio P6 sequencing chemistry using three approaches: 1) sequencing the full-length bacterial 16S rRNA gene from a single bacterial species Staphylococcus aureus to analyze error modes and to optimize the bioinformatics pipeline; 2) sequencing the full-length bacterial 16S rRNA gene from a pool of 50 different bacterial colonies from human stool samples to compare with full-length bacterial 16S rRNA capillary sequence; and 3) sequencing the full-length bacterial 16S rRNA genes from 11 vaginal microbiome samples and compare with in silico selected bacterial 16S rRNA V1V2 gene region and with bacterial 16S rRNA V1V2 gene regions sequenced using the Illumina MiSeq...
November 14, 2016: BMC Microbiology
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