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Molecular microbiology

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https://www.readbyqxmd.com/read/28636666/molecular-and-microbiological-report-of-a-hospital-outbreak-of-ndm-1-carrying-enterobacteriaceae-in-mexico
#1
Paola Bocanegra-Ibarias, Elvira Garza-González, Rayo Morfín-Otero, Humberto Barrios, Licet Villarreal-Treviño, Eduardo Rodríguez-Noriega, Ulises Garza-Ramos, Santiago Petersen-Morfin, Jesus Silva-Sanchez
OBJECTIVES: To characterize the microbiological, molecular and epidemiological data of an outbreak of carbapenem-resistant Enterobacteriaceae (CRE) in a tertiary-care hospital in Mexico. METHODS: From September 2014 to July 2015, all CRE clinical isolates recovered during an outbreak in the Hospital Civil "Fray Antonio Alcalde" in Jalisco, Mexico were screened for antimicrobial susceptibility, carbapenemase production, carbapenemase-encoding genes, and plasmid profiles...
2017: PloS One
https://www.readbyqxmd.com/read/28631909/-characterization-of-microbial-flora-in-patients-suspected-of-having-urogenital-tuberculosis
#2
A G Cherednichenko, E V Kulchavenya
INTRODUCTION: In the structure of tuberculosis morbidity, urogenital tuberculosis (UGT) ranks second or third only to pulmonary tuberculosis. Every fourth patient has the stage of cavern formation at first presentation. Seventy five percent of nephrotuberculosis cases co-occur with nonspecific pyelonephritis, which excludes "sterile pyuria". We aimed to determine the microbial spectrum of urine and gonadal appendages in patients with suspected UGT and to investigate the susceptibility of the isolated microorganisms to the main antibacterial drugs...
June 2017: Urologii︠a︡
https://www.readbyqxmd.com/read/28631591/comparative-evaluation-of-veriflow-%C3%A2-listeria-species-to-usda-culture-based-method-for-the-detection-of-listeria-spp-in-food-and-environmental-samples
#3
Adam C Joelsson, Shawn P Terkhorn, Ashley S Brown, Amrita Puri, Benjamin J Pascal, Zara E Gaudioso, Nicholas A Siciliano
Veriflow(®)Listeria species (Veriflow LS) isa molecular-based assay for the presumptive detection of Listeria spp. from environmental surfaces (stainless steel, sealed concrete, plastic, and ceramic tile) and ready-to-eat (RTE) food matrixes (hot dogs and deli meat). The assay utilizes a PCR detection method coupled with a rapid, visual, flow-based assay that develops in 3 min post-PCR amplification and requires only a 24 h enrichment for maximum sensitivity. The Veriflow LS system eliminates the need for sample purification, gel electrophoresis, or fluorophore-based detection of target amplification and does not require complex data analysis...
June 20, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28631590/comparative-evaluation-of-veriflow-%C3%A2-salmonella-species-to-usda-and-fda-culture-based-methods-for-the-detection-of-salmonella-spp-in-food-and-environmental-samples
#4
Amrita Puri, Adam C Joelsson, Shawn P Terkhorn, Ashley S Brown, Zara E Gaudioso, Nicholas A Siciliano
Veriflow(®)Salmonella species (Veriflow SS)is a molecular-based assay for the presumptive detection of Salmonella spp. from environmental surfaces (stainless steel, sealed concrete, plastic, and ceramic tile), dairy (2% milk), raw meat (20% fat ground beef), chicken carcasses, and ready-to-eat (RTE) food (hot dogs). The assay utilizes a PCR detection method coupled with a rapid, visual, flow-based assay that develops in 3 min post-PCR amplification and requires only an 18 h enrichment for maximum sensitivity...
June 20, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28620877/pathogenesis-and-persistence-of-cryptoglandular-anal-fistula-a-systematic-review
#5
REVIEW
Jeremy Sugrue, Johan Nordenstam, Herand Abcarian, Amelia Bartholomew, Joel L Schwartz, Anders Mellgren, Philip J Tozer
Anal fistulas continue to be a problem for patients and surgeons alike despite scientific advances. While patient and anatomical characteristics are important to surgeons who are evaluating patients with anal fistulas, their development and persistence likely involves a multifaceted interaction of histological, microbiological, and molecular factors. Histological studies have shown that anal fistulas are variably epithelialized and are surrounded by dense collagen tissue with pockets of inflammatory cells. Yet, it remains unknown if or how histological differences impact fistula healing...
June 15, 2017: Techniques in Coloproctology
https://www.readbyqxmd.com/read/28619149/abortion-and-mortality-in-farm-mink-neovison-vison-associated-with-feed-born-clostridium-limosum
#6
Anne Sofie Hammer, Lars Andresen, Bent Aalbæk, Peter Damborg, Vilhelm Weiss, Mette Line Christiansen, Søren Selsing, Martin Iain Bahl
Disease in mink clinically characterized by abortion and increased mortality among pregnant female mink on 28 Danish farms was observed during April and May 2015. Most of these farms suffered extensive disease problems, including a significant increase in the number of mated females without litters. Pathological, microbiological and molecular biological methods were applied to investigate the cause of disease. Necropsies of animals found dead revealed fragile and partially dissolved (liquefying) uterine tissue, with the presence of Gram positive rod-shaped bacteria...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28619124/multiplex-tests-to-identify-gastrointestinal-bacteria-viruses-and-parasites-in-people-with-suspected-infectious-gastroenteritis-a-systematic-review-and-economic-analysis
#7
Karoline Freeman, Hema Mistry, Alexander Tsertsvadze, Pam Royle, Noel McCarthy, Sian Taylor-Phillips, Rohini Manuel, James Mason
BACKGROUND: Gastroenteritis is a common, transient disorder usually caused by infection and characterised by the acute onset of diarrhoea. Multiplex gastrointestinal pathogen panel (GPP) tests simultaneously identify common bacterial, viral and parasitic pathogens using molecular testing. By providing test results more rapidly than conventional testing methods, GPP tests might positively influence the treatment and management of patients presenting in hospital or in the community. OBJECTIVE: To systematically review the evidence for GPP tests [xTAG(®) (Luminex, Toronto, ON, Canada), FilmArray (BioFire Diagnostics, Salt Lake City, UT, USA) and Faecal Pathogens B (AusDiagnostics, Beaconsfield, NSW, Australia)] and to develop a de novo economic model to compare the cost-effectiveness of GPP tests with conventional testing in England and Wales...
April 2017: Health Technology Assessment: HTA
https://www.readbyqxmd.com/read/28618013/not-a-barrier-but-a-key-how-bacteriophages-exploit-host-s-o-antigen-as-an-essential-receptor-to-initiate-infection
#8
Nina K Broeker, Stefanie Barbirz
Tailed bacteriophages specific for Gram-negative bacteria encounter lipopolysaccharide (LPS) during the first infection steps. Yet, it is not well understood how biochemistry of these initial interactions relates to subsequent events orchestrating phage adsorption and tail rearrangements to initiate cell entry. For many phages, long O-antigen chains found on the LPS of smooth bacterial strains serve as essential receptor recognized by their tailspike proteins (TSP). Many TSP are depolymerases and O-antigen cleavage was described as necessary step for subsequent orientation towards a secondary receptor...
June 15, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28612383/a-new-player-in-bacterial-sulfide-inducible-transcriptional-regulation
#9
David P Giedroc
Although hydrogen sulfide (H2 S) is perhaps best known as a toxic gas, the electron-rich H2 S functions as an energy source and electron donor for chemolithotrophic and photosynthetic bacteria, via sulfide oxidation, and is a universal substrate for cysteine biosynthesis. These distinct harmful and beneficial roles of H2 S suggest the need to "sense" prevailing concentrations of sulfide and downstream reactive sulfur species (RSS) and regulate the expression of genes mediating sulfide homeostasis. The paper by Li et al...
June 14, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28600760/characterization-of-sinus-microbiota-by-16s-sequencing-from-swabs
#10
Thad W Vickery, Jennifer M Kofonow, Vijay R Ramakrishnan
New culture-independent microbiology methods are leading to a paradigm shift in our understanding of how the microbial community at the mucosal surface impacts sinonasal health and disease. Whereas traditional culture-based protocols were designed to identify specific pathogens in order to direct antibiotic therapies and eradicate bacteria, newer molecular techniques allow for the identification of both culturable and nonculturable bacteria in diverse communities. As a result of the recent explosion in the use of molecular techniques, we are gaining an understanding of how commensal bacteria may help modulate the host immune response and promote homeostasis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28592223/feline-leprosy-due-to-mycobacterium-lepraemurium
#11
Carolyn R O'Brien, Richard Malik, Maria Globan, George Reppas, Christina McCowan, Janet A Fyfe
OBJECTIVES: This paper, the second in a series of three on 'feline leprosy', provides a detailed description of disease referable to Mycobacterium lepraemurium, the most common cause of feline leprosy worldwide. METHODS: Cases were sourced retrospectively and prospectively for this observational study, describing clinical, geographical and molecular microbiological data for cats definitively diagnosed with M lepraemurium infection. RESULTS: A total of 145 cases of feline leprosy were scrutinised; 114 'new' cases were sourced from the Victorian Infectious Diseases Reference Laboratory records, veterinary pathology laboratories or veterinarians, and 31 cases were derived from six published studies...
July 2017: Journal of Feline Medicine and Surgery
https://www.readbyqxmd.com/read/28591662/a-loop-mediated-isothermal-amplification-lamp-assay-for-the-rapid-detection-of-enterococcus-spp-in-water
#12
Roland Martzy, Claudia Kolm, Kurt Brunner, Robert L Mach, Rudolf Krska, Hana Šinkovec, Regina Sommer, Andreas H Farnleitner, Georg H Reischer
Faecal pollution of water and the resulting potential presence of human enteric pathogens is a predominant threat to public health. Microbiological water quality can be assessed by the detection of standard faecal indicator bacteria (SFIB) such as E. coli or certain Enterococcus species. In recent years, isothermal amplification methods have become a useful alternative to polymerase chain reaction (PCR), allowing molecular diagnostics with simple or no instrumentation. In this study, a novel screening method for the molecular detection of Enterococcus spp...
May 13, 2017: Water Research
https://www.readbyqxmd.com/read/28591268/diagnosis-of-mycobacteria-in-bovine-milk-an-overview
#13
Carmen Alicia Daza Bolaños, Carolina Lechinski de Paula, Simony Trevizan Guerra, Marília Masello Junqueira Franco, Márcio Garcia Ribeiro
Tuberculosis remains as the world's biggest threat. In 2014, human tuberculosis ranked as a major infectious disease by the first time, overcoming HIV death rates. Bovine tuberculosis is a chronic disease of global distribution that affects animals and can be transmitted to humans by the consumption of raw milk, representing a serious public health concern. Despite the efforts of different countries to control and eradicate bovine tuberculosis, the high negative economic impact on meat and milk production chains remains, given the decreased production efficiency (approximately 25%), the high number of condemned carcasses, and increased animal culling rates...
June 5, 2017: Revista do Instituto de Medicina Tropical de São Paulo
https://www.readbyqxmd.com/read/28591186/increasing-incidence-of-mucormycosis-in-a-large-spanish-hospital-from-2007-to-2015-epidemiology-and-microbiological-characterization-of-the-isolates
#14
Jesús Guinea, Pilar Escribano, Antonio Vena, Patricia Muñoz, María Del Carmen Martínez-Jiménez, Belén Padilla, Emilio Bouza
We studied 19 cases of proven/probable mucormycosis diagnosed from 2007 to 2015 in our hospital and assessed the microbiological characteristics of the isolates. We recorded the incidence of mucormycosis and clinical and microbiological data of infected patients. Isolates were identified to molecular level and tested for their antifungal susceptibility to azoles, amphotericin B, and liposomal amphotericin B according to the CLSI M-38 A2 procedure. The incidence of mucormycosis in cases/100,000 hospital admissions during 2007-2015 increased significantly with respect to that reported in 1988-2006 (3...
2017: PloS One
https://www.readbyqxmd.com/read/28589386/navigating-the-jungles-of-tropical-infectious-gastrointestinal-pathology-a-pattern-based-approach-to-the-endoscopic-biopsy
#15
Tomas Slavik, Gregory Y Lauwers
International travels and global human migration have had the unforeseen consequence of increasing the exposure of histopathologists in developed countries to the pathology of tropical infectious disease. The gastrointestinal tract (GIT) is often the primary site of infection due to the faecal-oral route of transmission and the high risk of exposure to contaminated water, food or soil when travelling to these regions. Whilst current microbiologic techniques are far more sensitive than histology in detecting infectious pathogens, the histopathologist nonetheless retains a pivotal role in diagnosing tropical GIT disease...
June 6, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28588283/additional-molecular-testing-of-saliva-specimens-improves-the-detection-of-respiratory-viruses
#16
Kelvin Kw To, Lu Lu, Cyril Cy Yip, Rosana Ws Poon, Ami My Fung, Andrew Cheng, Daniel Hk Lui, Deborah Ty Ho, Ivan Fn Hung, Kwok-Hung Chan, Kwok-Yung Yuen
Emerging infectious diseases in humans are often caused by respiratory viruses such as pandemic or avian influenza viruses and novel coronaviruses. Microbiological testing for respiratory viruses is important for patient management, infection control and epidemiological studies. Nasopharyngeal specimens are frequently tested, but their sensitivity is suboptimal. This study evaluated the incremental benefit of testing respiratory viruses in expectorated saliva using molecular assays. A total of 258 hospitalized adult patients with suspected respiratory infections were included...
June 7, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28581505/a-decade-of-discovery-crispr-functions-and-applications
#17
REVIEW
Rodolphe Barrangou, Philippe Horvath
This year marks the tenth anniversary of the identification of the biological function of CRISPR-Cas as adaptive immune systems in bacteria. In just a decade, the characterization of CRISPR-Cas systems has established a novel means of adaptive immunity in bacteria and archaea and deepened our understanding of the interplay between prokaryotes and their environment, and CRISPR-based molecular machines have been repurposed to enable a genome editing revolution. Here, we look back on the historical milestones that have paved the way for the discovery of CRISPR and its function, and discuss the related technological applications that have emerged, with a focus on microbiology...
June 5, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28580195/physical-enrichment-of-transposon-mutants-from-saturation-mutant-libraries-using-the-tradisort-approach
#18
COMMENT
Ian T Paulsen, Amy K Cain, Karl A Hassan
Transposon-insertion sequencing methods are finding their way into the molecular toolbox of many fields of microbiology. These methods can identify the genomic locations and density of transposon insertions in saturated transposon mutant libraries and can be used to make inferences on gene function. For example, where no insertions or very few insertions are identified within a gene in a mutant library grown under permissive conditions, the gene may be essential. Furthermore, where mutations are enriched or lost in a gene after passaging the library through a selective process, the gene is likely to be involved in phenotypes linked to the process...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/28578421/aetiology-and-outcomes-of-suspected-infections-of-the-central-nervous-system-in-children-in-mbarara-uganda
#19
Anne-Laure Page, Yap Boum Ii, Elizabeth Kemigisha, Nicolas Salez, Deborah Nanjebe, Céline Langendorf, Said Aberrane, Dan Nyehangane, Fabienne Nackers, Emmanuel Baron, Rémi Charrel, Juliet Mwanga-Amumpaire
Infections of the central nervous system (CNS) are severe conditions, leading to neurological sequelae or death. Knowledge of the causative agents is essential to develop guidelines for case management in resource-limited settings. Between August 2009 and October 2012, we conducted a prospective descriptive study of the aetiology of suspected CNS infections in children two months to 12 years old, with fever and at least one sign of CNS involvement in Mbarara Hospital, Uganda. Children were clinically evaluated on admission and discharge, and followed-up for 6 months for neurological sequelae...
June 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28575047/utility-of-normalized-genome-quantification-of-helicobacter-pylori-in-gastric-mucosa-using-an-in-house-real-time-polymerase-chain-reaction
#20
Ana Morilla, Santiago Melón, Marta E Álvarez-Argüelles, Edisa Armesto, Henar Villar, María de Oña
Traditional diagnostic assays for Helicobacter pylori detection have their limitations. Molecular methods can improve both diagnosis and understanding of gastric diseases. Here we describe an in-house quantitative real-time polymerase chain reaction (q-rt-PCR) for the detection of H. pylori in gastric biopsies which has been developed and has a detection limit of 10 copies, the specificity of which was tested against other gastric colonizer bacteria. In this study, 199 gastric biopsies from adults with different clinical gastric symptoms were examined...
2017: PloS One
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