Predicting MRSA Toxicity

A comparative genomic study shows that researchers can use genetic signatures to predict the toxicity of methicillin-resistant Staphylococcus aureus isolates.

An international team led by Ruth Massey at the University of Bath in the U.K. reported a comparative genomic study of 90 methicillin-resistant Staphylococcus aureus (MRSA) strains in Genome Research. Analyzing genome-wide data, Massey and her colleagues were able to predict the toxicity of any given isolate based on genetic signatures. The researchers proposed that their approach could inform similar strategies to better understand other drug-resistant pathogens.







Posted by Tim Sandle

Flow Cytometry handbook (free)

Flow cytometry is a laser-based, biophysical technology employed in cell counting, cell sorting, biomarker detection and protein engineering, by suspending cells in a stream of fluid and passing them by an electronic detection apparatus. It allows simultaneous multiparametric analysis of the physical and chemical characteristics of up to thousands of particles per second.

Flow cytometry is routinely used in the diagnosis of health disorders, especially blood cancers, but has many other applications in basic research, clinical practice and clinical trials.

AbD Serotec are offering a free e-book. The book contains an overview of the principles of light and flow cytometry, basic data analysis and common protocols. It is perfect for students or inexperienced users of this powerful application.

For details see Flow Cytometry

Posted by Tim Sandle

Environmental monitoring webinar

A recorded webinar on environmental monitoring and an innovative new design of agar plate is available to view on the Cleanroom Technology website. The webinar is free to view.

The description of the webinar is:

“With the help of Thermo Scientific™ Triple Wrapped Irradiated Plates, industry leaders John Cobb and Colin Booth will walk viewers through qualification test protocols, guidelines and technical tips needed to successfully reduce the risk of contamination in cleanrooms and isolators. It’s all about giving you the cleanroom confidence you need to succeed.”

To view the webinar, visit CleanroomTechnology.

Posted by Tim Sandle

A Role for Endotoxin in Clinical Depression

Chronic activation of the inflammatory response plays a role in clinical depression.  This inflammation is associated with increases in endotoxin-specific IgA, indicating that bacterial translocation is significant.  An international group of scientists led by the Polish Academy of Science used this observation to develop an animal model for depression using endotoxin injections.  With this model they were able to demonstrate a reversal of endotoxin-induced effects with an antidepressant.  This work, published in the journal Brain, Behavior, and Immunity, underscores the importance of endotoxin in neurobehavioral conditions.

Refer to the following paper:

"A new animal model of (chronic) depression induced by repeated and intermittent lipopolysaccharide administration for 4 months."

Scientists at BioDtech, Inc. have measured previously undetectable levels of endotoxin which could cause activation of the immune system.  BioDtech products are designed to more accurately detect endotoxin and remove it from proteins and DNA.

Posted by Tim Sandle

Review of cleanliness services in hospitals

A draft standard of interest has been published for public comment. It is coded PAS 5748:2014 and titled “Specification for the planning, application, measurement and review of cleanliness services in hospitals”.

It specifies requirements for:

a) governing cleanliness services;

b) assessing risk and categorizing elements and functional areas;

c) providing cleaning tasks, including:

1) identifying cleaning tasks;

2) risk assessment of cleaning tasks;

3) providing method statements;

4) setting cleaning frequencies;

5) setting work schedules;

6) establishing competence;

7) contingency planning;

d) measuring cleanliness on the basis of visual assessment;

e) implementing corrective action;

f) conducting performance analysis and implementing improvement actions;

g) providing a continuous service improvement plan; and

h) reporting cleanliness.

In the draft standard, two types of risk are specifically identified:

infection risk – The risk of infection for patients; and

confidence risk – The risk of a poor public image and the loss of confidence in patients and staff of the organization’s ability to provide a clean, safe environment for care.

To review the standard, please contact your national standards office.

Posted by Tim Sandle

Food-Poisoning Microorganisms

Identification methods can be divided into two groups: phenotypic and genotypic. The genotype–phenotype distinction is drawn in genetics. ‘Genotype’ is an organism’s full hereditary information, even if not expressed. ‘Phenotype’ is an organism’s actual observed properties, such as morphology, development, or behaviour.

This is the introduction to a chapter by Tim Sandle for the new edition of the Encyclopedia of Food Microbiology. The reference is:

Sandle, T., 2014. Biochemical and Modern Identification Techniques: Food-Poisoning Microorganisms. In: Batt, C.A., Tortorello, M.L. (Eds.), Encyclopedia of Food Microbiology, 2^nd edition, vol 1. Elsevier Ltd, Academic Press, pp. 238–243

Written by the world's leading scientists and spanning over 400 articles in three volumes, the Encyclopedia of Food Microbiology, Second Edition is a complete, highly structured guide to current knowledge in the field. Fully revised and updated, this encyclopedia reflects the key advances in the field since the first edition was published in 1999

The articles in this key work, heavily illustrated and fully revised since the first edition in 1999, highlight advances in areas such as genomics and food safety to bring users up-to-date on microorganisms in foods. Topics such as DNA sequencing and E. coli are particularly well covered.

With lists of further reading to help users explore topics in depth, this resource will enrich scientists at every level in academia and industry, providing fundamental information as well as explaining state-of-the-art scientific discoveries.

For details see: Encyclopedia of FoodMicrobiology

To review a copy, please contact Tim Sandle.

Posted by Tim Sandle

Free e-book: How to accelerate early clinical development

Terrapinn have issued a free e-book about clinical development. According to the company:  “In this ebook, we share the thoughts of early clinical development leaders on the challenges, approaches and changes affecting early clinical development.”

The book features:

• Sif Ormarsdottir, MD, PhD, Specialist Gastroenterology and Hepatology, Chair, Hepatotoxicity Safety Knowledge Group, AstraZeneca Ab
• Mikko Kuoppamaki, MD, PhD, Head of Medical Affairs Team, Research & Development, Orion Pharma
• Marek Honczarenko, MD, PhD, Group Medical Director Immunoscience, Exploratory Clinical & Translational Research, Bristol-Myers Squibb

These leaders in clinical research and development will be speaking at Exploratory Clinical Development World Europe this 3-5 June in London. 

For details about the book, see: Health Network

Posted by Tim Sandle

The influence of the gut microbiota on neurology

Can gut microbes manipulate even the mind? New research seems to suggest that the answer is yes.

A mouse study of autism spectrum disorders showed an association between changes in the gut microbiota and ASD symptoms. These findings could indicate that the microbiota have a significant impact on the perturbations associated with neurodevelopmental disorders.

(2013, Cell 155, 1451).

Posted by Tim Sandle

Method offers potential for understanding anti-bacterial resistance

By basing methods on mathematical models and Bayesian analysis, the researchers have succeeded in producing tools for biologists who are interested in jumping genes and the traits they carry with them. This could provide a deeper understanding about how species have evolved, and even find ways to address antibiotic resistance.

The method and model could be used in order to see the kinship between species more clearly than before. The method describes an algorithm and associated software, which will be an important tool for researchers working with bacteria and the genes they transmit laterally, such as for antibiotic resistance.

For further details, see:

J. Sjostrand, A. Tofigh, V. Daubin, L. Arvestad, B. Sennblad, J. Lagergren. A Bayesian Method for Analyzing Lateral Gene Transfer. Systematic Biology, 2014; DOI: 10.1093/sysbio/syu007

Posted by Tim Sandle

Sharpening microscope images

Biological samples bend light in unpredictable ways, returning difficult-to-interpret information to the microscope and distorting the resulting image. To overcome this, new imaging technology developed at the Howard Hughes Medical Institute's Janelia Farm Research Campus rapidly corrects for these distortions and sharpens high-resolution images over large volumes of tissue.

To improve the method, researchers focused on devising an adaptive optics strategy for new microscopy methods that image dynamic processes non-invasively and at high resolution. Such technologies -- such as the Bessel beam plane illumination microscope that Betzig's team developed in 2011 and the simultaneous multiview light sheet microscope developed by Janelia lab head Philipp Keller in 2012 -- perform well on cells or small embryos, but image quality degrades in larger samples.

Those microscopes are used exclusively to image transparent samples, narrowing the scope of the problem.

For further information, refer to:

Kai Wang, Daniel E Milkie, Ankur Saxena, Peter Engerer, Thomas Misgeld, Marianne E Bronner, Jeff Mumm, Eric Betzig. Rapid adaptive optical recovery of optimal resolution over large volumes. Nature Methods, 2014; DOI: 10.1038/nmeth.2925

Posted by Tim Sandle

Variations in the Resistance of Biological Indicators Used to Assess Sterilization

Sometimes, unexplained results occur when using biological indicators. This could be attributable to a failure of the sterilization process or, perhaps, due to a mishandling of the biological indicator. Other reasons could be traced to issues of resistance and variations with the biological indicator itself.

In relation to this, Tim Sandle has written a paper which discusses the “phenomenon of resistance” for the Journal of Validation Technology.

The paper can be found here.

The reference is:

Sandle, T. (2014) Variations in the Resistance of Biological Indicators Used to Assess Sterilization, Journal of Validation Compliance, Vol. 20, Issue 1, Mar 2014

Posted by Tim Sandle

Good Distribution Practice: Questions and Answers

According to A3P, a new set of guidance has been issued about European Union Good Distribution Practice (EU GDP).

This documents sets out frequently-asked 'questions and answers' regarding the new guidelines on Good Distribution Practice of medicinal products for humans. The GDP guidance was applicable as of 8 September 2013, followed by a revision of November 2013.

Some aspects of the guidance has been confusing or open to misinterpretation, hence the additional 'questions and answers'.

For details see A3P

Posted by Tim Sandle

Triclosan Promotes Staphylococcus aureus Nasal Colonization

An interesting paper in the journal mBio features research that indicates that triclosan is commonly found in the nasal secretions of healthy adults and that the presence of triclosan trends positively with nasal colonization by S. aureus. The researchers demonstrate that triclosan can promote the binding of S. aureus to host proteins such as collagen, fibronectin, and keratin, as well as inanimate surfaces such as plastic and glass. In addition, the research shows that triclosan-exposed rats are more susceptible to nasal colonization with S. aureus. The biocide triclosan is used in many personal care products, including toothpastes, soaps, clothing, and medical equipment. The paper raises questions over the continued application of the product.

For further details see: mBio

Posted by Tim Sandle

Mechanisms for Inflammation Due to Super-Low Dose Endotoxin

Individuals with certain health conditions or with poor lifestyles often suffer with inflammation due to low-level endotoxemia. This can lead to chronic conditions such as obesity, diabetes and atherosclerosis. Recent work from scientists at Virginia Tech and published in The Journal of Biological Chemistry have elucidated the mechanisms that differentiate super-low dose endotoxemia from medium- to high-dose endotoxemia, where the pro-inflammatory response is tempered by an anti-inflammatory response. These results highlight the importance of low-level endotoxin, give insight into the role of endotoxin tolerance and provide a potential therapeutic target for chronic inflammation.

Molecular and Cellular Mechanisms Responsible for Cellular Stress and Low-Grade Inflammation Induced by Super-Low Dose Endotoxin


Scientists at BioDtech, Inc. have measured previously undetectable levels of endotoxin which could cause activation of the immune system. BioDtech products are designed to more accurately detect endotoxin and remove it from proteins and DNA.

Posted by Tim Sandle

EU GMP Chapter 6: Quality Control

According to A3P, a draft version of EU GMP Chapter 6 has been issued.

Principle:

This chapter should be read in conjunction with all relevant sections of the GMP guide Quality Control is concerned with sampling, specifications and testing as well as the organisation, documentation and release procedures which ensure that the necessary and relevant tests are carried out, and that materials are not released for use, nor products released for sale or supply, until their quality has been judged satisfactory. Quality Control is not confined to laboratory operations, but must be involved in all decisions which may concern the quality of the product. The independence of Quality Control from Production is considered fundamental to the satisfactory operation of Quality Control.

Reasons for changes:

Inclusion of a new section on technical transfer of testing methods and other items such as Out Of Specification results.

For details see A3P

Posted by Tim Sandle

Diagnostics for Hospital-Based Antibacterial-Resistant Infections

NIAID recently announced a research funding opportunity to develop and/or produce diagnostics to quickly detect the key bacteria responsible for antibacterial-resistant infections in hospital settings. The request for applications (RFA) will support diagnostics research related to one or more of the following types of bacteria: Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species, and extra-intestinal pathogenic Eschericihia coli. NIAID expects to fund 10-15 awards for a total of up to $12 million in 2015, and the maximum length of each award is 5 years.

NIAID will accept applications through June 19, 2014. View the complete RFA (RFA-AI-14-019).

Posted by Tim Sandle

Hot topics in microbiology

A risk-based approach to microbial control in pharmaceutical production was a recurrent theme at the 21st Pharmig microbiology conference. Susan Birks reports on recent changes to standards for Cleanroom Technology.

To access the article, visit CleanroomTechnology

Posted by Tim Sandle

EU GMP Annex 15 Revisions: Improving Qualification and Validation

Validation and qualification form an important part of the quality system in the pharmaceutical sector and can be defined in different ways. Tim Sandle, Head of Microbiology, BPL, UK discusses some standard definitions from a Good Manufacturing Practice (GMP) perspective.

The article can be viewed on the CleanroomTechnology website here.

Posted by Tim Sandle

EU and US progress in the fight against antimicrobial resistance

The European Commission (EC) and the US Department of Health and Human Services (HHS) have published a progress report on the Transatlantic Taskforce on Antimicrobial Resistance (TATFAR). The report outlines the advances made during the first TATFAR implementation period of 2011 to 2013, and renews the commitment of US and EU health authorities to pursue specific goals in their joint battle against antimicrobial resistance (AMR). Notable outcomes of TATFAR activities for the reporting period include:

Adoption of procedures for timely international communication of critical events that might indicate new resistance trends with global public health implications

Publication of a report on the 2011 workshop, “Challenges and solutions in the development of new diagnostic tests to combat antimicrobial resistance” on the TATFAR website

Joint presentations to the scientific community to increase awareness on the available funding opportunities on both sides of the Atlantic

Why a Transatlantic Taskforce?

Antimicrobial resistance is increasingly recognised as serious cross-border health threat of global dimension which requires a multi-sectorial and global response. Studies estimate that antimicrobial-resistant infections result in at least 25 000 deaths in 29 countries in Europe and 23 000 deaths in the US every year. In addition, antimicrobial resistance costs the EU and the US billions every year in avoidable healthcare costs and productivity losses.

With these factors in mind, TATFAR was created following the 2009 US–EU Presidential Summit. The taskforce aims to improve collaboration between the EU and US in three key areas:

1) appropriate therapeutic use of antimicrobial drugs in medical and veterinary communities,

2) prevention of healthcare and community-associated drug-resistant infections,

3) strategies for improving the pipeline of new antimicrobial drugs.

Although significant progress in reducing specific types of infections has been made in the EU and the US, the global problem of AMR continues to grow. Therefore, the original mandate of the taskforce that ran through 2013 has recently been extended for at least two additional years.

What’s next?

TATFAR originally identified and adopted 17 recommendations for collaboration between the EU and the US, where common actions can deliver the best results in the prevention and control of AMR. Of these, 15 will continue, along with one new recommendation, for the EU and US partner agencies to focus on moving forward.

Forthcoming publications from the taskforce during 2014 that will provide a foundation for further specific joint collaborative actions include:

• A report summarising the strategies hospitals in the EU and US should include as part of their programs to improve antimicrobial prescribing practices.
• A joint publication summarising the existing methods for measuring antimicrobial use in hospital settings.
• A joint publication describing the need for new vaccines for healthcare-associated infections (HAIs).
• A joint publication comparing the results of the EU and US point prevalence surveys, which are used to estimate the burden of HAIs in each population.

Thanks to Brian Matthews for the information.

Posted by Tim Sandle

Resistant Enterobacteriaceae and non - fermenters

John Otter presented at the HIS / IPS Spring Meeting recently. His presentation was titled "Dissecting the epidemiology of resistant Enterobacteriaceae and non-fermenters". The meeting was entitled: “What’s that coming over the hill? Rising to the challenge of multi-resistant Gram-negative rods”.

According to Dr. Otter:

"My exploration of the differences in the epidemiology of resistant Enterobacteriaceae and non-fermenters (mainly A. baumannii) was designed to prompt anybody tempted to conflate these two related problems to think twice. Resistant Enterobacteriaceae and non-fermenters do share the same response to the Gram-stain and can be resistant to key antibiotics occasionally through shared mechanisms (principally the carbapenemases). But that’s about it. Otherwise they’re like chalk and cheese. (A. baumannii = chalk, which turns to dust; Enterobacteriaeae = a good cheese, which ultimately ends up in the gut.)"

The slides for the presentation are available for view via the HIS/IPS, here.

Posted by Tim Sandle

Modern Approaches to Pharma Cleanroom Design

Tim Sandle has written an article for Controlled Environments Magazine on the design of cleanrooms, considering the physical and the microbiological aspects.

Here is an extract:

“The performance of a cleanroom is defined by a set of complex interactions between the airflow, sources of contamination and heat, position of vents, exhausts, and any objects occupying the space. Consequently, changes to any of these elements will potentially affect the operation of the cleanroom and could invalidate aspects of the room design.”

To read the article, go to Controlled Environments

Posted by Tim Sandle

New technique moves closer to HIV & Hepatitis C vaccines

Plans for a new type of DNA vaccine to protect against the deadly HIV and Hepatitis C viruses have taken an important step forward, with researchers applying for a patent based on new research. The work has focused on utilizing the so-called "accessory" or "messenger" cells in the immune system, called dendritic cells, to activate an immune response. These are a type of white blood cell that play a key role during infection and vaccination. These are a type of white blood cell that play a key role during infection and vaccination.

The research is still in the pre-clinical phase, with a patient study due next year.

For further details, see the following paper in Immunology & Cell Biology:

Tessa Gargett, Branka Grubor-Bauk, Tamsin J Garrod, Wenbo Yu, Darren Miller, Lee Major, Steve Wesselingh, Andreas Suhrbier, Eric J Gowans. Induction of antigen-positive cell death by the expression of Perforin, but not DTa, from a DNA vaccine enhances the immune response. Immunology and Cell Biology, 2013; DOI: 10.1038/icb.2013.93

Posted by Tim Sandle

The Importance of Quality Control in the Production of Parenteral Drugs

Cara N. Wilder and Elizabeth Kerrigan have written an interesting article for the American Pharmaceutical Review on QC testing during pharmaceutical manufacturing. Here is an extract:

“Microbial contamination of parenteral products is one of the most serious issues currently facing the pharmaceutical industry. Injectable drugs, which are administered directly into the circulatory system, bypass a number of innate human immune defenses associated with the gastrointestinal system. Therefore, to ensure the sterility of each of these products prior to patient administration, pharmaceutical companies must adhere to strict government regulations regarding quality control. Maintaining and following a robust quality control program is integral to quality standards and meeting regulatory requirements.

Adding to these pressing concerns are compounding pharmacies that function inappropriately as drug manufacturing companies, but are not legally required to adhere to federal drug manufacturing regulations. Rather, they function under more lenient state policies that govern their operation, but do not enforce quality control analysis. This lack of regulation and oversight has led to several significant microbial outbreaks, which have resulted in multiple deaths from use of contaminated parenteral steroids, cardioplegia solutions, and intravenous drugs. These events highlight the importance of effective pharmaceutical sterility procedures as well as the need for updated regulatory control policies governing the operation of compounding pharmacies. In this article, we will discuss current practices and issues associated with pharmaceutical quality control analysis, how these can affect patient health and safety, and what could be done to remedy the issue.”

To read the article, go to APR.

Posted by Tim Sandle

Effects of antibiotics on gut flora

Researchers have revealed that antibiotics produce changes in the microbial and metabolic patterns of the gut. The researchers have analyzed the bacteria, genes, enzymes and molecules that form the gut microbiota of patients treated with antibiotics.

The key finding is that antibiotics affect the gut flora. The biodiversity of the bacteria that form the gut microbiota, according to the results, decreases during treatment.

The open access research paper is:

A. E. Perez-Cobas, M. J. Gosalbes, A. Friedrichs, H. Knecht, A. Artacho, K. Eismann, W. Otto, D. Rojo, R. Bargiela, M. von Bergen, S. C. Neulinger, C. Daumer, F.-A. Heinsen, A. Latorre, C. Barbas, J. Seifert, V. M. dos Santos, S. J. Ott, M. Ferrer, A. Moya. Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut, 2012

Posted by Tim Sandle

HEPA Filtration

“There are four mechanisms at work: capture by straining, impaction, interception, and diffusion. Straining/sieving is defined as when a particle is too large and becomes trapped between two filter fibers. Impaction is when a particle of relatively greater mass is unable to follow the curved streamline around the fiber and, as a result of momentum, travels in a straight line into the filter fiber and sticks. Interception occurs when a section of a particle “runs into” a filter fiber. Diffusion capture occurs when particles leave the streamline due to random collisions with the surrounding fluid molecules and strike the fibers, where they again stick.”

The above text is from an on-line article introducing HEPA filters by Jason Kelly for Controlled Environments.

To read the article and to learn about HEPA filtration go to CE.

Posted by Tim Sandle

Contamination Control Under Foot

Tim Sandle has written an article for Controlled Environments Magazine on the control of contamination in cleanrooms, with a focus on microorganisms transferred in on feet or via cart wheels.

Here is an extract:

“One area of concern is the entry of personnel and the movement of equipment into and out of cleanrooms. Traditional ways to control these activities have centered on gowning techniques and the cleaning of equipment. To accomplish this, cleanroom mats are frequently used to remove particles from footwear and from trolley wheels. Research undertaken at an independent laboratory—and described in this article—evaluates the performance of temporary adhesive mats and semi-permanent polymeric flooring in retaining contamination from footwear, and particle generation from removing layers of the adhesive mats.”

To read the article, go to Controlled Environments

Posted by Tim Sandle

Understanding Cleanroom Classifications

Jeanne Moldenhauer has written an informative article on cleanroom classifications for Controlled Environments Magazine.

Here is an extract:

“Many global companies choose to use this classification system. All of these systems are acceptable for use. However, we have also tended to link the systems together, e.g., ISO 5/Class 100/Grade A. This type of linkage is seen in the FDA’s Guidance for Aseptic Processing (2004). If you are manufacturing an aseptic product and use this linked classification system it is not likely to be an issue. However, if you are not manufacturing an aseptically processed product, choosing to link the classification systems together may lead to other consequences.”

To read the article, go to Controlled Environments

Posted by Tim Sandle

50th Anniversary of LAL Reagent Development

The American Pharmaceutical Review is running a special feature marking the “50th Anniversary of LAL Reagent Development”. The feature takes the form of a roundtable discussion about the importance of LAL and its future development.

The participants are:

• John Dubczak, General Manager, Charles River, Endotoxin and Microbial Detection
• Tim Sandle, Ph.D., Head of Microbiology, Bio Products Laboratory Ltd.
• Lakiya Wimbish, Product Manager, QC Testing Solutions Lonza Pharma&Biotech–Bioscience Solutions. 

The article appears in the March 2014 edition (volume 17, issue 2).

Posted by Tim Sandle

Pharmaceutical Regulatory Inspections

‘Pharmaceutical Regulatory Inspections’ is a new book edited by Madhu Raju Saghee. The book contains practical advice and insight to help different types of pharmaceutical organisation prepare for GMP inspections. The book also provides an overview of current regulatory issues.

In over 600 pages and twelve chapters this unique book provides a focussed account of regulatory issues from pre-approval inspections and the inspection itself to postinspection and maintaining compliance. This is a book that every pharmaceutical company will wish to study before and during any inspection process to ensure a successful outcome.

The chapters are:

• Basic concepts of global GMP requirements by Tim Sandle and Madhu Raju Saghee
• FDA Drug Regulation and Enforcement by Seth Mailhot
• System based approach to GMP inspections by David Barr and Tim Sandle
• Preparing for preapproval inspections by Ron Johnson
• Effectively managing and surviving FDA inspections by John Avellanet
• Guide to successful EU inspection management by Siegfired Schmitt and Nabila Nazir
• Regulatory requirements for Japanese GMP inspections by Yoshikazu Hayashi
• Preparing and management of international inspections by Andreas Brutsche and Tim Sandle
• Handling and responding to post inspectional observations by Tim Sandle, Madhu Raju Saghee and David Barr
• Preparing for regulatory inspections of sterile facilities: the focal points by Tim Sandle
• Preparing for regulatory inspections of API facilities: the focal points by Siegfried Schmitt and Richard Einig
• Optimising tour regulatory compliance by Mark Tucker

For further details about this impressive and comprehensive book, see Euromed.

Posted by Tim Sandle

Salmonella data now at your fingertips

Forty years of data on a major cause of food poisoning now is available to the public, the food industry, and researchers in a new report from the Centers for Disease Control and Prevention (CDC). The data, collected by state and federal health officials, provides a wealth of information on Salmonella, the top foodborne cause of hospitalizations and deaths in the United States.

Available for hands-on web access for the first time, the Atlas of Salmonella in the United States, 1968-2011 summarizes surveillance data on 32 types of Salmonella isolates from people, animals, and other sources. The information is organized by demographic, geographic and other categories.

To access the Atlas, please visit Salmonella

Posted by Tim Sandle

Sequencing yeasts

A problem in evolutionary biology has been turned into a new tool to better understand phylogeny in closely related species. Re-sequencing ribosomal DNA in closely related yeast species has given them new information about the origins of modern yeast strains and a useful tool for evolutionary biologists.

Over the past few years, through studies carried out on yeast DNA, biologists have begun to learn that something that looks like a simple cog in all living things is actually performing an intricately choreographed dance. In the same way that the Charleston differs from the Waltz, the dance displayed by this cog is faster and uses different steps from other parts of the yeast machinery. What's more, the dancers leave footprints behind in their DNA.

The team at National Collection of Yeast Cultures at the Institute of Food Research have made a computer app to spot these footprints, and to decode the footprints in order to learn more about the rhythm of the dance and how the dance partners have come together and moved apart. The 'dancers' in question are the ribosomal RNA genes which give shape to the ribosome, a tiny protein-making machine found in all living cells.

If the ribosome goes wrong the cell dies, so its blueprint is highly protected. Not so protected though that small changes in the DNA, our footprints, don't occur. Biologists often use these changes to map various bits of the tree of life, so it is important to be able to track even the smallest alterations.

With funding from the Biotechnology and Biological Sciences Research Council, the NCYC team have now achieved this, using huge DNA datasets to uncover the footprints left behind in yeasts.

For further details, see: Norwich BioScience Institutes

Posted by Tim Sandle

Cleanroom Cleaning and Disinfection: Eight Steps for Success

Cleanrooms in healthcare and pharmaceutical facilities must be kept in a state of microbiological control. This article outlines eight key steps for keeping a cleanroom clean.

Tim Sandle has written an article for Controlled Environments, outlining the main points to consider for cleaning and disinfecting cleanrooms in order to achieve contamination control.

To access the article, go to Controlled Environments.
Posted by Tim Sandle

WHO’s first global report on antibiotic resistance

WHO has released its first global report on antimicrobial resistance. The report indicates “resistance is occurring across many different infectious agents” but the primary focus of the report is on “antibiotic resistance in seven different bacteria responsible for common, serious diseases such as bloodstream infections (sepsis), diarrhoea, pneumonia, urinary tract infections and gonorrhea.” What appears to be of greatest concern is the worldwide presence of bacteria resistant to carbapenems, hard-hitting, “last resort” antibiotics.

The new WHO report provides the most comprehensive picture of antibiotic resistance to date, with data from 114 countries.

A new report by WHO–its first to look at antimicrobial resistance, including antibiotic resistance, globally–reveals that this serious threat is no longer a prediction for the future, it is happening right now in every region of the world and has the potential to affect anyone, of any age, in any country. Antibiotic resistance–when bacteria change so antibiotics no longer work in people who need them to treat infections–is now a major threat to public health.

“Without urgent, coordinated action by many stakeholders, the world is headed for a post-antibiotic era, in which common infections and minor injuries which have been treatable for decades can once again kill,” says Dr Keiji Fukuda, WHO’s Assistant Director-General for Health Security. “Effective antibiotics have been one of the pillars allowing us to live longer, live healthier, and benefit from modern medicine. Unless we take significant actions to improve efforts to prevent infections and also change how we produce, prescribe and use antibiotics, the world will lose more and more of these global public health goods and the implications will be devastating.”

Key findings of the report

The report, "Antimicrobial resistance: global report on surveillance", notes that resistance is occurring across many different infectious agents but the report focuses on antibiotic resistance in seven different bacteria responsible for common, serious diseases such as bloodstream infections (sepsis), diarrhoea, pneumonia, urinary tract infections and gonorrhoea. The results are cause for high concern, documenting resistance to antibiotics, especially “last resort” antibiotics, in all regions of the world.

Key findings from the report include:

• Resistance to the treatment of last resort for life-threatening infections caused by a common intestinal bacteria, Klebsiella pneumoniae–carbapenem antibiotics–has spread to all regions of the world. K. pneumoniae is a major cause of hospital-acquired infections such as pneumonia, bloodstream infections, infections in newborns and intensive-care unit patients. In some countries, because of resistance, carbapenem antibiotics would not work in more than half of people treated for K. pneumoniae infections.
• Resistance to one of the most widely used antibacterial medicines for the treatment of urinary tract infections caused by E. coli–fluoroquinolones–is very widespread. In the 1980s, when these drugs were first introduced, resistance was virtually zero. Today, there are countries in many parts of the world where this treatment is now ineffective in more than half of patients.
• Treatment failure to the last resort of treatment for gonorrhoea–third generation cephalosporins–has been confirmed in Austria, Australia, Canada, France, Japan, Norway, Slovenia, South Africa, Sweden and the United Kingdom. More than 1 million people are infected with gonorrhoea around the world every day.
• Antibiotic resistance causes people to be sick for longer and increases the risk of death. For example, people with MRSA (methicillin-resistant Staphylococcus aureus) are estimated to be 64% more likely to die than people with a non-resistant form of the infection. Resistance also increases the cost of health care with lengthier stays in hospital and more intensive care required.

Ways to fight antibiotic resistance

The report reveals that key tools to tackle antibiotic resistance–such as basic systems to track and monitor the problem–show gaps or do not exist in many countries. While some countries have taken important steps in addressing the problem, every country and individual needs to do more.

Other important actions include preventing infections from happening in the first place–through better hygiene, access to clean water, infection control in health-care facilities, and vaccination–to reduce the need for antibiotics. WHO is also calling attention to the need to develop new diagnostics, antibiotics and other tools to allow healthcare professionals to stay ahead of emerging resistance.

This report is kick-starting a global effort led by WHO to address drug resistance. This will involve the development of tools and standards and improved collaboration around the world to track drug resistance, measure its health and economic impacts, and design targeted solutions.

How to tackle resistance

People can help tackle resistance by:

• using antibiotics only when prescribed by a doctor;
• completing the full prescription, even if they feel better;
• never sharing antibiotics with others or using leftover prescriptions.

Health workers and pharmacists can help tackle resistance by:

• enhancing infection prevention and control;
• only prescribing and dispensing antibiotics when they are truly needed;
• prescribing and dispensing the right antibiotic(s) to treat the illness.

Policymakers can help tackle resistance by:

• strengthening resistance tracking and laboratory capacity;
• regulating and promoting appropriate use of medicines.

Policymakers and industry can help tackle resistance by:

• fostering innovation and research and development of new tools;
• promoting cooperation and information sharing among all stakeholders.

The report–which also includes information on resistance to medicines for treating other infections such as HIV, malaria, tuberculosis and influenza–provides the most comprehensive picture of drug resistance to date, incorporating data from 114 countries.

Highlights of the report by WHO region

WHO African Region

The report reveals major gaps in tracking of antibiotic resistance in the WHO African Region, with data gathered in a limited number of countries. While it is not possible to assess the true extent of the problem with the data available, that which is available is worrying. Significant resistance is reported for several bacteria that are spread in hospitals and communities. This includes significant E. coli resistance to third generation cephalosporins and fluoroquinolones–two important and commonly used types of antibacterial medicine. In some parts of the region, as many as 80% of of Staphylococcus aureus infections are reported to be resistant to methicillin (MRSA), meaning treatment with standard antibiotics does not work.

WHO Region of the Americas

The Pan American Health Organization, WHO’s Regional Office for the Americas, coordinates the collection of data on antibiotic resistance from hospitals and laboratories in 21 countries in the Region. The results show high levels of E. coliresistance to third generation cephalosporins and fluoroquinolones–two important and commonly used types of antibacterial medicine–in the Americas. Resistance to third generation cephalosporins in K. pneumoniae is also high and widespread. In some settings, as many as 90% of Staphylococcus aureus infections are reported to be methicillin-resistant (MRSA), meaning treatment with standard antibiotics does not work.

WHO Eastern Mediterranean Region

Data in the report show extensive antibiotic resistance across the WHO Eastern Mediterranean Region. In particular, there are high levels of E. coli resistance to third generation cephalosporins and fluoroquinolones–two important and commonly used types of antibacterial medicine. Resistance to third generation cephalosporins in K. pneumoniae is also high and widespread. In some parts of the Region, more than half of Staphylococcus aureus infections are reported to be methicillin-resistant (MRSA), meaning that treatment with standard antibiotics does not work. The report reveals major gaps in tracking of antibiotic resistance in the Region. WHO’s Regional Office for the Eastern Mediterranean has identified strategic actions to contain drug resistance and is supporting countries to develop comprehensive national policies, strategies and plans.

WHO European Region

The report reveals high levels of resistance to third generation cephalosporins in K. pneumoniae throughout the WHO European Region. In some settings, as many as 60% of Staphylococcus aureus infections are reported to be methicillin-resistant (MRSA), meaning that treatment with standard antibiotics does not work. The report finds that although most countries in the EU have well-established national and international systems for tracking antibiotic resistance, countries in other parts of the Region urgently need to strengthen or establish such systems. WHO’s Regional Office for Europe and its partners are supporting these countries through the newly-established Central Asian and Eastern European Surveillance of Antimicrobial Resistance network (CAESAR). The aim of CAESAR is to set up a network of national systems to monitor antibiotic resistance in all countries of the WHO European Region for standardized data collection so that information is comparable.

WHO South-East Asia Region

The available data reveal that antibiotic resistance is a burgeoning problem in WHO’s South-East Asia Region, which is home to a quarter of the world’s population. The report’s results show high levels of E. coli resistance to third generation cephalosporins and fluoroquinolones—two important and commonly used types of antibacterial medicine–in the Region. Resistance to third generation cephalosporins in K. pneumoniae is also high and widespread. In some parts of the Region, more than one quarter of Staphylococcus aureus infections are reported to be methicillin-resistant (MRSA), meaning that treatment with standard antibiotics does not work. In 2011, the health ministers of the Region articulated their commitment to combat drug resistance through the Jaipur Declaration. Since then, there has been growing awareness of the need for appropriate tracking of drug resistance, and all countries have agreed to contribute information to a regional database. Dr Poonam Khetrapal Singh, WHO Regional Director for South-East Asia, has identified drug resistance as a priority area of WHO’s work in the Region.

WHO Western Pacific Region

Collaboration on tracking of antibiotic resistance between countries in the WHO Western Pacific Region was established in the 1980s, but suffered setbacks following a series of emergencies in the early 2000s. However, many countries in the region have long-established national systems for tracking resistance. Recently, WHO’s Regional Office for the Western Pacific has taken steps to revive the regional collaboration. The report reveals high levels of E. coli resistance to fluoroquinolones–an important and commonly used type of antibacterial medicine–in the Region. Resistance to third generation cephalosporins in K. pneumoniae is also widespread. In some parts of the Region, as many as 80% of Staphylococcus aureus infections are reported to be methicillin-resistant (MRSA), meaning that treatment with standard antibiotics does not work.

The report can be accessed in full here.



Posted by Tim Sandle