Wednesday, 30 November 2016

LAL roundtable

Tim Sandle has participated in an endotoxin / LAL discussion, published in American Pharmaceutical Review. The discussion addresses key issues like low endotoxin recovery, together with future developments in LAL testing.

Here is an extract: “Dr. Tim Sandle: I think the difference between purified LPS and natural endotoxin complexes is established, and they will behave differently under conditions of the test.

The issue of low endotoxin one is important, although the subject is causing some confusion for LAL users. It would be good to get a consensus between the providers of LAL regents together with a clear signal from the regulators.”

The roundtable discussion appears in:

LAL Roundtable, American Pharmaceutical Review, 19(6): 47-51

The feature can be accessed here: APR

Posted by Dr. Tim Sandle

Tuesday, 29 November 2016

Design and Construction Standards to Build a Cleanroom

To maintain and assure quality, there are specific standards that apply to these spaces and guide the process of constructing and operating the rooms. While adhering to these requirements makes designing and constructing a cleanroom more complex than conventional construction projects, the standards serve as a blueprint for the successful completion of a cleanroom that will meet the exacting demands of the end-user.

Matt Strong has written an interesting article for Controlled Environments titled “Applying Design and Construction Standards to Successfully Build a Cleanroom.”

Here is an extract: “The first step in the cleanroom design process involves creating the Utility Matrix (UM), which outlines detailed specifications on each piece of equipment used in the cleanroom. This document, which is crucial to the cleanroom design, must be created and approved with the participation of the cleanroom operator/user. The UM can be developed directly by the operator, if the expertise exists in-house, or an outside consultant can be brought in to assist in development of the cleanroom layout and process flow. Once it’s completed, designers will use the UM to design the specific support systems required for the cleanroom. The UM remains an important document even after facility construction and should be continually updated throughout the life of the cleanroom.”

The article can be accessed here.

Posted by Dr. Tim Sandle

Monday, 28 November 2016

In silico molecular typing methods for Staphylococcus aureus

Currently, many different methods have been developed for subspecies typing of Staphylococcus aureus. However, there is no “ideal” one because of its disadvantages and thus there is no commonly accepted guidelines for the selection of the optimal typing method for epidemiological investigations. The aim of the study was an in silico comparison of widely used typing methods, including Multilocus sequence typing (MLST), Staphylococcus aureus Protein A (spa) typing, Pulsed-field gel electrophoresis (PFGE), Multiple Locus Variable-number Tandem Repeat Analysis (MLVA) and whole genome multilocus sequence typing (wgMLST), in terms of discriminatory power and coefficients congruence. Quantitative assessment of discriminatory power and correlation of five typing methods: wgMLST, PFGE, MLST, MLVA and spa typing was performed, by targeting the different sites of the Staphylococcus aureus genome (which had evolved at different rates).

This is the basis of a new article of interest. The reference is:

Babenko, A., Turmuhambetova, A., Sandle, T. and Chesca, A. (2016) In silico comparison of molecular typing methods for characterization of Staphylococcus aureus, Acta Medica Mediterranea, 32: 1021-1027

The article can be accessed here.

For details, please contact Tim Sandle

Posted by Dr. Tim Sandle

Sunday, 27 November 2016

New pathogen causes anthrax like disease

A new report has detected a species of Bacillus, genetically distinct to the bacterium that causes anthrax, which causes a similar disease in chimpanzees, gorillas and other animals in Africa.
The newly described bacterium is of significance in terms of environment, ecology and animal health. There is also the possibility that the organism could cause harm to people. The scientists behind the discovery are calling for increased surveillance.
Anthrax is a disease caused by the bacterium Bacillus anthracis, specifically by the spores of the organism. The areas most commonly affected are Africa and southern Asia. The disease is can occur via one of four ways: skin, inhalation, intestinal and injection. The effect of the disease can appear as quickly as one day or up to two months following infection. Many scientists regard anthrax as among the world's major neglected zoonotic diseases.
The main symptoms are blisters forming on the skin that ulcerate and form black centers. This is accompanied by fever, chest pain, and shortness of breath, together with nausea, vomiting and abdominal pain. The disease is confirmed through antibody testing. Treatment is by antibiotics and sometimes antitoxin.
Detection of the bacterium is difficult because of its similarity with two other species of Bacillus: Bacillus thuringiensis and Bacillus cereus (they each are members of the B. cereus group). These are also spore-formers (a means for some bacteria to remain dormant under extreme or unfavorable environmental conditions), found in soil.
The ability of Bacillus species to cause disease relates to virulence factors. Some of these factors are encoded on fragments of genetic material that are exchanged between bacteria called plasmids. With the anthrax causing bacterium - B. anthracis – this organism has two plasmids that are responsible for virulence. These are called pXO1 and pXO2.
The newly characterized organism in Africa that causes ‘anthrax-like’ symptoms is a type of B. cereus. This has been examined at the Robert Koch Institute in Berlin. The organism was isolated from a diseased chimpanzee in Ivory Coast. Typically most B. cereus isolates are non pathogenic. However, some strains can cause food poisoning, due to production of toxins.
Interestingly, the B. cereus bacterium was found to contain the pXO1 and pXO2 'anthrax' plasmids. However it was genetically close to other types of B. cereus and not to B. anthracis. The researchers, led by Dr. Fabian Leendertz,, think the bacterium ‘acquired’ its particular disease causing properties. Moreover, due to its genetic difference the scientists have described the organism as a new species: 'B. cereus biovar (bv) anthracis'.
Further research has tracked down four other isolates of the bacterium, taken from a goat, gorillas, a chimpanzee and an elephant in Cameroon, the Central African Republic, and the Democratic Republic of Congo respectively. Each animal was diseased and died from the disease.
These additional isolates also shared the virulence plasmids pXO1 and pXO2. The evidence points to these organisms sharing a common ancestor, and one different to B. anthracis. The organisms each possessed a mutation in a specific gene; however, the four bacteria possessed different physiological properties.
The implications are potentially significant and could cause significant harm for wildlife. The researchers are calling for increased surveillance and testing. A risk to humans cannot be ruled out. With this, the U.S. Centers for Disease Control and Prevention (CDC) is proposing the addition of Bacillus cereus Biovar anthracis to the list of select agents and toxins as a Tier 1 select agent. This means it would be regarded as a potential bio-terrorism threat. According to Outbreak News Today, the CDC has said: "We are taking this action to regulate this agent that is similar to B. anthracis to prevent its misuse, which could cause a biological threat to public health and/or national security."
The new organism is described in the journal PLOS Neglected Tropical Diseases. The research paper is headed “Bacillus cereus Biovar Anthracis Causing Anthrax in Sub-Saharan Africa—Chromosomal Monophyly and Broad Geographic Distribution.”

Posted by Dr. Tim Sandle

Saturday, 26 November 2016

New bacteria groups discovered underground

One of the most detailed genomic studies of any ecosystem has revealed an underground world of microbial diversity. The research has added dozens of new branches to the tree of life. The bacterial find comes from scientists who reconstructed the genomes of more than 2,500 microbes from sediment and groundwater samples collected at an aquifer in Colorado.

The scientists netted genomes from 80 percent of all known bacterial phyla, a remarkable degree of biological diversity at one location. They also discovered 47 new phylum-level bacterial groups, naming many of them after influential microbiologists and other scientists. And they learned new insights about how microbial communities work together to drive processes that are critical to the planet's climate and life everywhere, such as the carbon and nitrogen cycles.

Between the 47 new bacterial groups reported in this work, and 35 new groups published last year has led to a doubling of the number of known bacterial groups.

For further details see:

Karthik Anantharaman, Christopher T. Brown, Laura A. Hug, Itai Sharon, Cindy J. Castelle, Alexander J. Probst, Brian C. Thomas, Andrea Singh, Michael J. Wilkins, Ulas Karaoz, Eoin L. Brodie, Kenneth H. Williams, Susan S. Hubbard, Jillian F. Banfield. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nature Communications, 2016; 7: 13219 DOI:10.1038/ncomms13219

Posted by Dr. Tim Sandle

Friday, 25 November 2016

Reshaping our ideas of bacterial evolution

The shape of bacteria does not influence how well they can move -- this is the surprising finding of new research which could have major implications for the future of the scientific and medical industries.

Published in Nature's new Ecology & Evolution journal, the results refute long-held theories that there should be a strong link between the evolution of shape in bacteria and their ability to move.

Setting them apart from larger living organisms such as fish, seals and whales -- for which shape is very important to their ability to swim efficiently -- this new discovery highlights the unusual nature of the environment in which bacteria live.

The extensive study was conducted by Dr Fouad El Baidouri and Professor Stuart Humphries from the School of Life Sciences at the University of Lincoln, UK, together with Dr Chris Venditti from the University of Reading and was funded by a Leverhulme Trust Research Leadership Award. The team drew together information on 325 different species of Firmicutes bacteria to help address a gap in global scientific knowledge about how the shape of single-cell organisms like bacteria affects their mobility, lifestyle and pathogenicity (ability to cause disease).

Professor Humphries explained: "Many evolutionary biologists have asked why animals are shaped the way they are, but until now the scientific community has relied on mathematical models to predict the relationship between shape and movement in bacteria. We expected swimming bacteria to be rod-shaped in order to reduce their energy costs, but experimental tests are rare and, surprisingly, analyses of this relationship in an evolutionary context are lacking entirely.

"Our research has produced evidence that these theoretical predictions don't match reality, at least in this group of bacteria, and it therefore makes a major contribution to our understanding of the evolution of bacteria."

The researchers employed new ways of exploring the evolution of bacteria to more accurately assess the form and function of the cells.

Dr El Baidouri said: "The main focus of our research is to understand why bacteria come in so many different forms, but in order to understand this we needed to find out which bacteria have which shape. With no datasets available, we saw a clear need to collect morphological and ecological data on bacteria -- a task which took several months, and is still ongoing.

"We fully expected to confirm a widely-held belief, backed by strong theoretical predictions, that rod-shaped cells would move more effectively than coccoid (spherical) cells, and that shape and motility had co-evolved. We used a number of approaches to confirm our findings, and to our great surprise we didn't find any association between the two traits."

Contrary to recent evidence, the study also found that neither the ability to cause disease nor the lifestyle of these bacteria (whether it is free-living or host-associated) are affected by shape. These results suggest that, for this group of bacteria at least, they have an even greater evolutionary flexibility than previously thought.

Mass starvation looming for Siberian reindeer

One of the world’s largest concentration of reindeer is to be found in the Yamal Peninsula in northwestern Siberia. A new report presents worrying evidence that the reindeer are threatened with starvation.

In the region of Russia, hundreds of thousands of reindeer are to be found. Many are herded by the indigenous Nenets people. For 2016-2017 a new report suggests that many of the reindeer are threatened due to a scarcity of food.

The report comes from the International Union for Conservation of Nature, and it has declared the reindeer to be vulnerable. Since 1990 there has been a steady decline in the population, with a 20 percent decline (around 80,000 animals) over the past twenty-five years.  This is due to scarcity of food and the root cause is climate change.

The largest decline occurred in 2013, when 61,000 reindeer starved to death on the peninsula. This occurred due to atypically thickly layers of snow and ice blocking and obscuring access to food - lichen and other vegetation.

The cause of the unusual ice and snow was attributed to retreating sea ice in the adjoining Barents and Kara Seas, which adjoin the peninsula. The researchers put the sequence of events into a flow diagram, which has been summarized by Laboratory Roots as:

Warming → Sea ice decline → Increased precipitation and winter temperatures → [Rain-on-snow] events → Reindeer mortality.

Essentially, warming temperature causes the melting of ice, which leads to high levels of evaporation and humidity. These temperature effects cause increased rainfall. The rain soaks the snowy ground, and when this is followed by a fall in temperature, the snow freezes leading to a thick layer of ice forming. The layer can prove too thick for the reindeer to smash through.

According to the lead researcher, Dr. Bruce Forbes: “Reindeer are used to sporadic ice cover, and adult males can normally smash through ice around 2 centimeters thick. But in 2006 and 2013, the ice was several tens of centimeters thick”

The concern is that a similar event will occur this coming winter, based on climate predictions. This is based on reducing ice in both the Arctic Sea and the Kara Sea, as collated by the National Snow and Ice Data Center, which is linked to the University of Lapland in Finland.

The findings are published in journal Biology Letters. The paper is titled “Sea ice, rain-on-snow and tundra reindeer nomadism in Arctic Russia.”

Posted by Dr. Tim Sandle

European Antibiotic Awareness Day: Update

On European Antibiotic Awareness Day (18th November), the European Association of Hospital Pharmacists (EAHP) has issued a call for all citizens to become students in prudent use. An update from Hospital Pharmacy Europe:

Speaking in Brussels, at an event organised by the European Centre for Disease Prevention and Control, Tajda Miharija Gala, EAHP Vice-President and policy lead on antimicrobial resistance (AMR), said"Working together at the European level to tackle the cross-border health threat of antimicrobial resistance, a relentless focus must be placed on achieving prudent use of antibiotics.

Succeeding in this endeavour has many components, including continuing to educate the public about the importance of appropriate use of antibiotics. Hospital pharmacists, alongside other healthcare professionals, need to assist patients in becoming students of prudent use, via direct counselling. In addition to this, all health systems can still achieve more in respect to antimicrobial stewardship in hospitals. Within multi-disciplinary teams the hospital pharmacist can lead on matters such as reviewing antibiotic serum levels and duration of therapy, advising on the cessation or amendment of inappropriate antibiotic treatments, educating other healthcare professionals on the restricted use of certain antibiotics, and counselling patients on their antibiotic therapy.

Combatting antimicrobial resistance involves everyone, including those in other sectors such as farming and veterinary care. We therefore encourage the European Commission to be bold in defining the roles of different professions within the next EU Action Plan on AMR. A team works best when there is total clarity on individual responsibilities."

Posted by Dr. Tim Sandle

Thursday, 24 November 2016

Measuring the forces of biology

Many key cellular processes rely on the physical interplay between biological components to perform functions. The "parts list" in these processes is similar: Microtubules, semi-rigid tubes of protein, can serve within the cell as scaffolding, roadways, and a building material for machinery; some proteins serve as fasteners, binding and releasing other materials; and motor proteins use chemical energy to push and pull materials along microtubules, or move the microtubules themselves.

To form the mitotic spindle, two organelles called centrosomes move into position on opposite sides of two identical sets of chromosomes massed near the center of the cell. From each of the centrosomes, a dense network of microtubules is assembled, reaching toward and around the mass of chromosomes. Some of the microtubules connect to the chromosomes, while others connect the two centrosomes, forming a cage around the chromosomes. Ideally, microtubules from each centrosome connect exclusively with one of each of the chromosomes in the set. Then the microtubules -- aided by proteins and motor proteins -- begin to shorten and move, pulling the chromosomes toward the centrosomes, until the two sets have been separated.
To read about research associated with this, see the Rensselaer Polytechnic Institute (RPI).

Posted by Dr. Tim Sandle

Wednesday, 23 November 2016

Showing how bacteria make biofilms cell-by-cell

Princeton researchers have shown the mechanics of how bacteria build up slimy masses (biofilms), cell by cell. When encased in biofilms in the human body, bacteria are a thousand times less susceptible to antibiotics, making certain infections, such as pneumonia, difficult to treat.

The researchers chose Vibrio cholerae for their model biofilm organism because of its long history of study and threat to human health, causing the diarrheal disease cholera. A curved, rod-shaped bacterium, V. cholerae lives as a free-swimming cell in brackish water or saltwater. When V. cholerae makes contact with a food particle, perhaps on the shell of a crab or a shrimp, or a human intestinal cell during disease, the bacterium attaches itself and begins to reproduce. The expanding colony's members secrete a glue-like substance to keep from getting washed away and to protect themselves from competing bacteria.

At first, the bacterial colony expanded horizontally on the given surface in the experiment. As each cell split, the resulting daughter cells firmly attached to the surface alongside their parent cells. Squeezed by increasing numbers of offspring bacteria, however, the cells at the heart of expanding colony were forced to detach from the surface and point vertically. The bacterial colony thus went from a flat, two-dimensional mass to an expanding, three-dimensional blob, all held together by gunk in the developing biofilm.
The Princeton team looked deeper into the genetics behind this cellular behavior. A single gene, dubbed RbmA, is key to behavior in which new cells connect in such a way to develop a three-dimensional biofilm. When the researchers deactivated the gene, a big, diffuse and floppy biofilm formed. When RbmA performed as normal, though, a denser, stronger biofilm resulted as the cells stayed linked to each other. Thus, RbmA provides the biofilm its resilience, providing insight into a potential Achilles heel that could be targeted for therapeutic intervention.
Ongoing work is now measuring the physical forces experienced by cells uplifting at the biofilm's center so the overall mechanics can be precisely worked out.
For further details, see:
Jing Yan, Andrew G. Sharo, Howard A. Stone, Ned S. Wingreen, Bonnie L. Bassler. Vibrio choleraebiofilm growth program and architecture revealed by single-cell live imaging. Proceedings of the National Academy of Sciences, 2016; 113 (36): E5337 DOI: 10.1073/pnas.1611494113

Posted by Dr. Tim Sandle

Tuesday, 22 November 2016

Antimicrobial Resistance in the Environment

The class of chemicals characterized as biocides are used in all parts of society from home to hospital, to farms and industry. The presence of biocides selects for genes in microorganisms that can protect against their lethal effects. These biocide resistance genes are often the same genes as antibiotic resistance genes (i.e. cross-resistance), or they can be co-located on plasmids, for example, which means when biocides are present the microorganism will also co-select for antibiotic resistance genes (i.e. co-resistance).

Dr. Andrew C Singer has written an interesting blog post on antimicrobial resistance. Here is an extract:

“The problem with antimicrobial resistance (AMR), globally, is the combination of: 1) increased prevalence of antibiotic resistance; 2) rapid spread of AMR due to global travel; 3) antibiotic misuse; and 4) too few new antimicrobials in development. National, regional and global AMR Action Plans have been drafted to tackle many of these problems. Thorough reviews, such as the O’Neill AMR Reviews, provide a useful overview of these challenges and some mitigation measures. However, symptomatic of the O’Neill Reviews and AMR Action Plans is their under appreciation of the role that the environment plays in the selection, spread and transmission of AMR. Discussions of the environment are typically limited to the pharmaceutical manufacturing plants as a source of antibiotics and the role that sewage and farm run-off can play in dissemination of antibiotics. The discussions on these issues are superficial and narrow in scope.

Current AMR Action Plans and the O’Neill Reviews see antibiotics as the primary driver of AMR; hence, all mitigating measures are focused solely on reducing their use and release into the environment. This vision of the challenge of AMR is not helpful as it omits other AMR drivers that could be, on their own, more important than antibiotics for selecting, maintaining and spreading AMR in the environment, let alone as a collective group of AMR drivers.”

The full post can be accessed here.

Posted by Dr. Tim Sandle

Monday, 21 November 2016

The Science Of Christmas

This book looks at many of the traditions of Christmas and takes an amusing, sideways look st the science behind Christmas. Just how fast will Santa need to travel to deliver gifts to all the children? Where did tinsel come from and is it safe? Why do reindeer have red noses? And more!

Posted by Dr. Tim Sandle

Mold Monitoring and Control in Pharmaceutical Manufacturing Areas

Tony Cundell has written an important article on fungi for American Pharmaceutical Review.

The introduction reads:

“Recent high profile product recalls associated with mold contamination has resulted in more attention from the FDA to fungal isolation in environmental monitoring and product testing in the pharmaceutical industry. Companies need to anticipate these FDA concerns especially with respect to the upcoming regulatory inspections and institute remediation when mold is found in their products and manufacturing facilities to protect patient safety.”

In the article, Cundell reviews fungal isolation media and enumeration methods for cleanrooms, as well as identification strategies.

The article can be accessed here.

Posted by Dr. Tim Sandle

Sunday, 20 November 2016

Rapid test for Salmonella in chicken developed

Microbiologists and technologists have joined forces to come up with a rapid and easy-to-use method to detect Salmonella in food such a chicken. The device contributes to contamination control.
Despite multiple warning about food storage and hygiene, foodborne diseases, like those derived from Salmonella bacteria, show little sign of going away. This means that safety and assurance are as reliant upon regular checks of food preparation establishments and food manufacturers as with good hygiene practices.
Salmonella is a Gram-negative rod shaped bacterium (the Gram-negative refers to the outcome of a cell staining test, relating to the structure of the organism’s cell wall).
To help on the detection front a new device has been developed at the University of Florida Institute of Food and Agricultural Sciences. The new method is a magnetic bead immunoassay. This is a diagnostic immunoassay that uses magnetic beads as labels in lieu of conventional enzymes. The assay involves the specific binding of an antibody to its antigen, where a magnetic label is conjugated to one element of the pair, with detection via a device called a magnetometer.
To test the device, scientists artificially contaminated food with Salmonella. These food samples were next tested using Salmonella-specific antibodies combined with a signal amplification technique. The test results showed Salmonella bacteria present after 15 hours.
The method therefore showed an accurate detection rate and the results were obtained far more quickly than with conventional cultural methods (which can take up to three days). This means an effective rapid microbiological method has been developed.
In a research note, the lead scientist Professor Soohyoun Ahn said: "The test has great potential as a simple monitoring system for foodborne pathogens in food samples, which can improve food safety and public health.”
Longer term it is hoped the method can be used to detect other potential food related pathogens like Escherichia coli.
The new device is described in the Journal of Food Safety. The associated research paper is titled “Magnetic Bead-Based Immunoassay Coupled with Tyramide Signal Amplification for Detection of Salmonella in Foods.”

Posted by Dr. Tim Sandle

Saturday, 19 November 2016

Spatiotemporal microbial evolution on antibiotic landscapes

An interesting research paper, considering a new way to examine the development of antibiotic resistance:

A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)–plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front. While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front, we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behind more sensitive lineages. The MEGA-plate provides a versatile platform for studying microbial adaption and directly visualizing evolutionary dynamics.

For further details, see Science.

Posted by Dr. Tim Sandle