The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Urinary tract infections (UTIs) are a severe public health problem and are caused by a range of pathogens, but most commonly by Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Enterococcus faecalis and Staphylococcus saprophyticus. High recurrence rates and increasing antimicrobial resistance among uropathogens threaten to greatly increase the economic burden of these infections. In this Review, we discuss how basic science studies are elucidating the molecular details of the crosstalk that occurs at the host-pathogen interface, as well as the consequences of these interactions for the pathophysiology of UTIs. We also describe current efforts to translate this knowledge into new clinical treatments for UTIs.

/pdf/urinary-tract-infections-epidemiology-mechanisms-of-3j8ivu97xb.pdf

Urinary tract infections: epidemiology, mechanisms of infection and treatment options

A panel of experts was convened by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA) to update the 2010 clinical practice guideline on Clostridium difficile infection (CDI) in adults. The update, which has incorporated recommendations for children (following the adult recommendations for epidemiology, diagnosis, and treatment), includes significant changes in the management of this infection and reflects the evolving controversy over best methods for diagnosis. Clostridium difficile remains the most important cause of healthcare-associated diarrhea and has become the most commonly identified cause of healthcare-associated infection in adults in the United States. Moreover, C. difficile has established itself as an important community pathogen. Although the prevalence of the epidemic and virulent ribotype 027 strain has declined markedly along with overall CDI rates in parts of Europe, it remains one of the most commonly identified strains in the United States where it causes a sizable minority of CDIs, especially healthcare-associated CDIs. This guideline updates recommendations regarding epidemiology, diagnosis, treatment, infection prevention, and environmental management.

/pdf/clinical-practice-guidelines-for-clostridium-difficile-4hs0j01jnf.pdf

Clinical Practice Guidelines for Clostridium difficile Infection in Adults and Children: 2017 Update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA)

Structure and nanostructure in ionic liquids.

Dangerous, antibiotic resistant bacteria have been observed with increasing frequency over the past several decades. In this review the factors that have been linked to this phenomenon are addressed. Profiles of bacterial species that are deemed to be particularly concerning at the present time are illustrated. Factors including economic impact, intrinsic and acquired drug resistance, morbidity and mortality rates, and means of infection are taken into account. Synchronously with the waxing of bacterial resistance there has been waning antibiotic development. The approaches that scientists are employing in the pursuit of new antibacterial agents are briefly described. The standings of established antibiotic classes as well as potentially emerging classes are assessed with an emphasis on molecules that have been clinically approved or are in advanced stages of development. Historical perspectives, mechanisms of action and resistance, spectrum of activity, and preeminent members of each class are discussed.

Antibiotics and Bacterial Resistance in the 21st Century

Copyright: © 2012 Gilmore BF, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Proteases as Selective Activators of Triggered Drug Release: A Potential Answer to the Problem of Biomaterial-Associated Infections?

Proteases as Selective Activators of Triggered Drug Release: A Potential Answer to the Problem of Biomaterial-Associated Infections?

In traditional medicine marine extracts are extensively used as therapies for diabetes. With the increasing rate of incidence of type 2 diabetes mellitus and rising cost of treatments, we investiga...

https://www.tandfonline.com/doi/pdf/10.1080/26388081.2020.1852519

Profiling the activity of edible European macroalgae towards pharmacological targets for type 2 diabetes mellitus

A Bioadhesive Patch Containing 5-Aminolevulinic acid for Photodynamic Therapy of Vulval Pathologies

Medical devices of the urinary tract are in commonplace usage in modern urology and are likely to remain the cornerstone of many surgical interventions in the field. This is despite the fact that their effective use is still drastically hindered by the formation of biofilm and encrustation which can cause obstruction and blockage of the device, as well as significant morbidity in the patient. This chapter examines the in vitro encrustation models available for evaluation and preliminary assessment of new biomaterials, coatings and drug-eluting devices for use in the urinary tract, aimed at resisting surface encrustation and microbial biofilm formation.

Brendan Gilmore

Papers

Proteases as Selective Activators of Triggered Drug Release: A Potential Answer to the Problem of Biomaterial-Associated Infections?

Profiling the activity of edible European macroalgae towards pharmacological targets for type 2 diabetes mellitus

A Bioadhesive Patch Containing 5-Aminolevulinic acid for Photodynamic Therapy of Vulval Pathologies

Models for the assessment of biofilm and encrustation formation on urological materials

The inactivation of bovine cathepsin B by novel N-chloro-acetyl-dipeptides: Application of the Houghten ‘tea bag’ methodology to inhibitor synthesis