Tuesday, 19 September 2017

GLP Inspections metrics reflections

An MHRA blog post by Martin Reed looks at collation of the 2015 inspection metrics data.

According to Reed, these data have "highlighted some common themes which I am going to illustrate by sharing some examples with you. All of the situations below have been observed within the past 12 months and have resulted in deficiencies (some major) being raised. The aim of sharing these examples is for organisations to identify if these issues could occur at their own facilities and allow them to pro-actively improve compliance."

The report can be accessed here: MHRA

Posted by Dr. Tim Sandle

Monday, 18 September 2017

Design and control of pharmaceutical water systems

Water-borne microorganisms are ubiquitous and varied in their ability to survive and grow under different conditions. Therefore, an out-of-control water system can cause harm to the patient or adulterate pharmaceutical products. Purification of water is required to prevent interaction with drug substances or other ingredients in the product formulation. Water must also be microbiologically controlled and monitored.

In relation to this, Tim Sandle has written an article for Pharmaceutical Engineering. The abstract reads:

This article assesses some of the requirements for good design, together with the control measures necessary to maintain effective microbiological control in pharmaceutical facility water systems.

The reference is:

Sandle, T. (2017) Design and control of pharmaceutical water systems to minimize microbial contamination, Pharmaceutical Engineering, 37 (4): 44-48

For further details, contact Tim Sandle

Posted by Dr. Tim Sandle

Sunday, 17 September 2017

Magnetized viruses attack harmful bacteria

Antibacterial phages combined with magnetic nanoparticle clusters effectively kill infectious bacteria found in water treatment systems. A weak magnetic field draws the clusters into biofilms that protect the bacteria and break them up so the phages can reach them.

The nanoclusters developed through Rice's Nanotechnology-Enabled Water Treatment (NEWT) Engineering Research Center carry bacteriophages -- viruses that infect and propagate in bacteria -- and deliver them to targets that generally resist chemical disinfection. Without the pull of a magnetic host, these "phages" disperse in solution, largely fail to penetrate biofilms and allow bacteria to grow in solution and even corrode metal, a costly problem for water distribution systems.

The Rice lab of environmental engineer Pedro Alvarez and colleagues in China developed and tested clusters that immobilize the phages. A weak magnetic field draws them into biofilms to their targets. Biofilms can be beneficial in some wastewater treatment or industrial fermentation reactors owing to their enhanced reaction rates and resistance to exogenous stresses, said Rice graduate student and co-lead author Pingfeng Yu. "However, biofilms can be very harmful in water distribution and storage systems since they can shelter pathogenic microorganisms that pose significant public health concerns and may also contribute to corrosion and associated economic losses," he said.

The lab used phages that are polyvalent -- able to attack more than one type of bacteria -- to target lab-grown films that contained strains of Escherichia coli associated with infectious diseases and Pseudomonas aeruginosa, which is prone to antibiotic resistance.

The phages were combined with nanoclusters of carbon, sulfur and iron oxide that were further modified with amino groups. The amino coating prompted the phages to bond with the clusters head-first, which left their infectious tails exposed and able to infect bacteria.

The researchers used a relatively weak magnetic field to push the nanoclusters into the film and disrupt it. Images showed they effectively killed E. coli and P. aeruginosa over around 90 percent of the film in a test 96-well plate versus less than 40 percent in a plate with phages alone.

The researchers noted bacteria may still develop resistance to phages, but the ability to quickly disrupt biofilms would make that more difficult. Alvarez said the lab is working on phage "cocktails" that would combine multiple types of phages and/or antibiotics with the particles to inhibit resistance.


Ling-Li Li, Pingfeng Yu, Xifan Wang, Sheng-Song Yu, Jacques Mathieu, Han-Qing Yu, Pedro J. J. Alvarez. Enhanced biofilm penetration for microbial control by polyvalent phages conjugated with magnetic colloidal nanoparticle clusters (CNCs)Environ. Sci.: Nano, 2017; DOI: 10.1039/C7EN00414A

Posted by Dr. Tim Sandle

Saturday, 16 September 2017

Plan for the introduction of the safety features on medicinal packaging

The European Medicines Agency (EMA) has issued a new guidance document titled “Implementation plan for the introduction of the safety features on the packaging of centrally authorized medicinal products for human use.”

Certain aspects of the implementation of the Falsified Medicines Directive (Directive 2011/62/EU) and the new delegated act on the safety features (Commission Delegated Regulation (EU) 2016/161 - "the Delegated Regulation") may impact on the product information and the marketing authorization dossier; in particular the placing of safety features, a unique identifier (UI) carried by a 2-D barcode and an anti-tampering device (ATD), on the packaging of prescription medicines and certain nonprescription medicines for the purposes of authentication and identification.

The European Medicines Agency and the European Commission have prepared this implementation plan to guide applicants and Marketing Authorisation Holders (MAHs) through the regulatory changes necessary to accommodate the new legislative requirements.

The document can be accessed here.

Posted by Dr. Tim Sandle

Friday, 15 September 2017

Good clinical practice inspection metrics

The MHRA has published the 1st April 2015 to 31st March 2016 GCP Inspection metrics report. During the metrics period a total of 102 GCP Inspections were undertaken by the MHRA GCP Inspectorate.

The full report can be accessed here: MHRA

Posted by Dr. Tim Sandle

Thursday, 14 September 2017

British Pharmacopoeia 2018 now available

The BP 2018 comprises of more than 250 new or amended monographs, including those from the European Pharmacopeia. The British Pharmacopoeia (BP) 2018 supersedes the BP 2017 and becomes legally effective on 1 January 2018. This edition incorporates new BP and European Pharmacopoeia monographs and a significant number of revised monographs.

  • 35 new BP monographs, 39 new Ph. Eur. monographs
  • 185 amended BP monographs
  • Four new monographs for unlicensed formulations
  • Four new monographs for herbal medicines
  • All European Pharmacopoeia monographs integrated (9th Edition as amended by Supplements 9.1 to 9.2)
  • Three in-year website and offline download updates to harmonise with the European Pharmacopoeia Supplements 9.3, 9.4 and 9.5

Posted by Dr. Tim Sandle

Wednesday, 13 September 2017

World Sepsis Day

Today is World Sepsis Day.

Here are some key points from World Sepsis Day 2017

What is sepsis?
Sepsis is a life-threatening condition that occurs when the body's response to an infection damages its own tissues and organs. Instead of local inflammation resulting from a local infection, which would be the appropriate response, the body’s entire system goes into inflammation. That’s sepsis. It is the leading cause of death from infection around the world, despite advances in modern medicine like vaccines, antibiotics, and acute care. Millions of people around the world die of sepsis every year.

How can this “inflammation” result in death?
This inflammatory response can lead to dehydration and changes in circulation, for instance a drop in blood pressure. This can compromise the ability of the circulatory system to provide adequately oxygen etc. to the tissues. That leads to dysfunction in various organs, such as the lung, heart, kidney, and brain. It can also lead to shock, multiple organ failure, and death, especially if it is not recognized early and treated promptly. Sepsis is an emergency.

How do I know it is sepsis?
Usually the first symptoms are those associated with the source of infection, such as a cough due to pneumonia or abdominal pain from appendicitis. Fever, a high pulse rate, and accelerated breathing are also signs. Everyone should be aware of the main clinical symptoms that indicate the worsening of an infection. Shortness of breath, reduction in urine output, dizziness, or altered mental status with confusion, agitation, or drowsiness can be signs of organ dysfunctions. In laboratory tests, sepsis often coincides with high white blood cell counts. But in the highly acute phase, and especially in immunocompromised patients, there may also be a decrease in white blood cell counts. In most cases, indicators of inflammation are increased.

Can sepsis be treated successfully?
Yes. The first hours of treatment are the most important. Patients must receive appropriate antibiotic therapy as soon as possible. Blood cultures and cultures from the site of infection under suspicion should be taken to detect the cause. Patients should also have their blood lactate levels measured, as this is a sign of dysfunction in the circulatory system. Patients with severe signs, such as hypotension and elevated lactate levels, should also receive fluids. Depending on the severity of organ dysfunction, they may require treatment in an intensive care unit.
If the sepsis has been caused by an infected foreign object in the body, a stone in the renal pelvis, or a ruptured intestine, then antibiotics alone are not enough. In these cases the focus of the sepsis or the foreign object needs to be removed surgically.

Is it normal to feel continually exhausted after having sepsis? Will I recover the energy I had before?
Fatigue after any serious illness, including sepsis, is very common. Your body has gone through a tremendous ordeal; it not only battled an infection, but it also dealt with sepsis, which could have resulted in death. Now that your body has successfully recovered from the immediate danger of sepsis, you need to rest, begin to regain your strength, and rebuild your body’s reserves.
If you continue to be exhausted, there may be other issues going on. You may want to consider a check-up with your doctor or nurse to be sure that other parts of your body, such as your thyroid, are functioning properly. You can also help rebuild your energy and strength by eating a healthy, balanced diet and getting enough physical exercise. Exercising when you are already tired may not seem easy, but if you start slowly, such as with regular walks around the neighborhood, you should be able to build up your energy. Also, check if there are any health rehabilitation programs available to you. In these programs, qualified personnel help you with simple exercise programs and monitor your progress over time.
Many people have cognitive problems like memory loss, inability to concentrate, and difficulty performing mental tasks that used to be easy before sepsis. It seems that the older you are when you get sepsis, the higher the risk of memory problems afterwards.

Can I prevent sepsis?
Preventing infections is the best way to prevent sepsis. Although there are no specific vaccines to prevent sepsis, vaccines are available for certain sepsis pathogens, such as pneumococci. Especially small children, people over 65, and patients who have no spleen should get vaccinated – they are particularly susceptible to pneumococci. This includes people who were born without a spleen as well as people who lost theirs due to an injury, surgery, or aggressive chemotherapy. You can also help prevent infection by maintain a healthy lifestyle with nutritious food, exercise, and rest. Wash your hands frequently. Seek medical help if an illness does not seem to be improving or is getting worse. Do what you can to prevent hospital-acquired infections. If you do get an infection, you can prevent sepsis by treating it seriously.
This means:
• Taking antibiotics as prescribed
• Finishing the entire course of antibiotics
• Don’t take antibiotics needlessly; this helps reduce the chances of developing antibiotic-resistant infections
• Don’t take someone else’s antibiotics
As healthcare professional you can help to reduce hospital acquired infections by following the patient safety program of the WHO.

Are there any specific risk factors that increase a person's likelihood of developing sepsis?
Anyone can get sepsis, even someone who was previously healthy. However, people with diabetes, cancer, HIV infection, previous chemotherapy, as well as corticosteroids users or those with any form of immunosuppression are more susceptible to severe forms of infection. Especially premature infants, small children, people 65 and older, and people with no spleen are more at risk. That risk can be reduced with a vaccination against pneumococci.

Can small wounds lead to sepsis?
If they develop from a local infection to a systematic inflammation, they are a source of sepsis.
We have seen sepsis cases triggered by small cracks at the corner of the mouth, which enable bacteria from the skin to spread into the circulatory system in children and adults.

Why have I never heard of sepsis before?
Sepsis isn’t talked about very often. We hear of people dying of infections. Often it was sepsis. Even today, if someone dies of sepsis due to pneumonia, (infection of the lungs) the cause of death is listed as pneumonia. If someone dies of sepsis after being severely burned, the cause of death is complications due to burns. Because sepsis is seldom listed as the cause of death, many people think it isn’t a problem. That is one of our biggest concerns. Increasing awareness of sepsis is one of our major goals.

Posted by Dr. Tim Sandle

Tuesday, 12 September 2017

Regulators raise concern with rapid method validation

In July 2017 Sage Products Inc. received a warning letter from the U.S. Food and Drug Administration (FDA). Within the warning letter was a concern about the implementation of rapid microbiological method, where the method had been used to replace a compendial method.

In the warning letter, the FDA state “Your firm failed to establish and document the accuracy, sensitivity, specificity, and reproducibility of its test methods.” This relates to the use of a rapid method.

Specifically: “You use the (b)(4) method to screen for microbiological contamination in drugs produced entirely at your facility and those manufactured under contract. This (b)(4) screening method (b)(4) for microbiological examination of your liquid drug products is not adequate for its intended use. You attempted to validate your (b)(4) microbial detection method, but were not able to demonstrate that it could reliably and repeatedly determine whether objectionable microorganisms were present in your drugs.”

The FDA are concerned about the comparative findings from the USP method and the replacement rapid method: “After receiving three consumer complaints for discoloration of this product, you initiated testing of your retains using both the modified U.S. Pharmacopeia (USP) microbiological limits method and the (b)(4) method. Both analyses found microbial contamination. Notably, the USP modified method (b)(4) found an exceedingly high microbial count of over 57,000 CFU/ml, and also identified Burkholderia cepacia, an objectionable microorganism, in this product lot.”

It seems that the firm elected to run with the results from the alternative method, despite the USP method finding an objectionable microorganism. This led the FDA to state: “Had your firm been utilizing a screening method capable of consistently detecting B. cepacia, these products may not have been released in the first instance.” Part of the reason was “because [the company] failed to include B. cepacia on the list of objectionable organisms.”

The use of the alternative method had also gone against FDA advice: “FDA informed you that your (b)(4) method (b)(4) has not been adequately validated for detecting the presence of microorganisms, including the presence of B. cepacia. In a subsequent meeting on November 30, 2016, FDA advised you to use a verified compendial method for all bulk drug solutions and finished product microbiological testing until you could further assess the suitability of the (b)(4) method.”

The concerns the FDA had with the rapid method were:

“It specifies a (b)(4) dilution factor. USP <62> requires a 1:10 dilution factor. Your dilution factor is (b)(4) times greater than the USP method and provides insufficient detectability to rule out the presence of objectionable microorganisms and unacceptable total counts.”

Furthermore the rapid method it not account for the enrichment step called for in USP <62>. Also “it does not include the scraping step during sample preparation, which your submitted laboratory data indicates is required to validate organism recovery.”

There was also a comment about the use of stressed organism as part of method validation (a controversial point within pharmaceutical microbiology): “it lacks evidence that small numbers of various microorganisms, including those that are injured and stressed, can be reliably recovered. Specifically, sample effect (defined by your firm as the inhibitory effect of a sample on the growth of various microorganisms) data for B. cepacia was collected using a fresh-grown culture, not a stressed organism.”

The final charge was that the method validation did not “establish potential sample interference factors (e.g., enhancing or quenching) for each product formulation.”

There was also criticism about the sampling and sample plan used to ensure the tested sample was representative of the lot. There was also concern that the replacement method, unlike the USP method, did “not provide for potential speciation of the detected microbial contamination in the (b)(4) initial screening test.”

The implications from the FDA letter, as well as signaling a pertinent lesson when implementing a rapid method that needs to be equivalence to or better than the rapid method, are:
  • Does the validation of methods require the use “stressed” organisms?
  • Does validation always need to be against each product formulation (not just the strongest concentration of the most inhibitory ingredient)?
  • How are representative samples built into the validation process?
  • Does a list of objectionable organisms need to be prepared ahead of the method validation? Or is this just a B cepacia issue?

If you have views on this, please add a comment.

Thanks to Nigel Halls for the heads-up about this warning letter and its considerable implications.

Posted by Dr. Tim Sandle

Monday, 11 September 2017

The path towards international harmonization of cleanrooms

Cleanrooms are an established and expected feature of healthcare and pharmaceutical operations; however, their development has been gradual and the origins, in terms of the idea of a ‘clean space’ date back several hundred years.

In the second part of his history of cleanrooms, Tim Sandle looks at the developments from the 1970s and the issuing of the first international standard for cleanrooms and clean air devices – ISO 14644.

The reference is:

Sandle, T. (2017) The development of cleanrooms: an historical review – Part 2– The path towards international harmonisation, IST The Journal, Summer 2017, pp1-5

To view a copy contact Tim Sandle

Posted by Dr. Tim Sandle

Sunday, 10 September 2017

Battle-plan blueprints for attacking disease-causing bacteria

The scientists, led by Fellow Emeritus in Trinity's School of Biochemistry and Immunology, Professor Martin Caffrey, used next-gen X-ray crystallography techniques to 'look under the bacterial bonnet' and produce a molecular blueprint that may be used to design drugs that minimise off-target effects and attack any structural weaknesses.
The research, which shows that one key enzyme used in the common bacteria Pseudomonas aeruginosa and Escherichia coli is remarkably similar in structure in both species, has recently been published in leading international journal Nature Communications. These two bacteria opportunistically infect people, and can cause fatalities.
Professor Caffrey said: "The structural blueprints of the two bacteria -- while very similar -- differ in their fine detail. These subtle differences might be exploited to design species-specific therapies with a reduced likelihood for the development of antibiotic resistance."
Both Pseudomonas aeruginosa and Escherichia coli are medically important, causing problems in tens of thousands of patients every year. Both are known to have developed resistance to a plethora of first-choice drugs used to treat them. And with antimicrobial resistance on the rise in general, the World Health Organization has advised that a post-antibiotic era, in which minor injuries and common infections could prove fatal, is looming.
New drugs are badly needed. However, while the new blueprint of the bacterial enzyme 'Lnt' offers hope for drug development, the process of creating effective candidates is not an easy one. Firstly, similar enzymes are present in humans and other animals, so any drug would need to be sufficiently specific to only affect the bacterial enzyme. Secondly, the biological structure of any drugs that would bind to the bacterial enzymes and inhibit them is likely to be similar to the structure of molecules that inhibit the innate immune response. In other words, stopping the bacteria in its tracks may also slow the body's natural response to infection.

Speaking about the difficulty in designing 'silver-bullet' drugs that could turn the tide, and about the next steps in his team's work, Professor Caffrey added: "The structural blueprints generated as part of this study provide a basis whereby the differences between the bacterial enzyme and the immune response proteins might be exploited with the goal of producing a drug that only hits the bacterial target."

Posted by Dr. Tim Sandle

Saturday, 9 September 2017

New mechanism for bacterial division discovered in some bacteria

Scientists show how some pathogenic bacteria -- such as the mycobacteria that cause tuberculosis -- use a previously unknown mechanism to coordinate their division. The discovery could help develop new ways to fight them.

Most rod-shaped bacteria divide by splitting into two around the middle after their DNA has replicated safely and segregated to opposite ends of the cell. This seemingly simple process actually demands tight and precise coordination, which is achieved through two biological systems: nucleoid occlusion, which protects the cell's genetic material from dividing until it replicates and segregates, and the "minicell" system, which localizes the site of division around the middle of the cell, where a dividing wall will form to split it in two.

But some pathogenic bacteria, e.g. Mycobacterium tuberculosis, don't use these mechanisms. EPFL scientists have now combined optical and atomic force microscopy to track division in such bacteria for the first time and have discovered that they use instead an undulating "wave-pattern" along their length to mark future sites of division.


Haig A. Eskandarian, Pascal D. Odermatt, Joëlle X. Y. Ven, Mélanie T. M. Hannebelle, Adrian P. Nievergelt, Neeraj Dhar, John D. McKinney, Georg E. Fantner. Division site selection linked to inherited cell surface wave troughs in mycobacteriaNature Microbiology, 2017; 2: 17094 DOI: 10.1038/nmicrobiol.2017.94

Posted by Dr. Tim Sandle

Friday, 8 September 2017

How big bacteria can grow depends on how much fat they can make

Bacterial cells in carbon-rich media grow twice as big as those in carbon-poor media. New research shows they can grow big, however, only if they can make fats with the carbon. The membrane that defines the boundary between the inside and outside of the cell is made almost entirely of fat. So it's not really surprising that fat synthesis would limit cell size.

Scientists grew the bacteria Salmonella typhimurium in more than 20 different media with varying nutrient compositions. In the nutrient-poor media, the cells grew slowly and were small; in the nutrient-rich media, they grew faster and were larger.

What’s the reason? See:

Stephen Vadia, Jessica L. Tse, Rafael Lucena, Zhizhou Yang, Douglas R. Kellogg, Jue D. Wang, Petra Anne Levin. Fatty Acid Availability Sets Cell Envelope Capacity and Dictates Microbial Cell SizeCurrent Biology, 2017; 27 (12): 1757 DOI: 10.1016/j.cub.2017.05.076

Posted by Dr. Tim Sandle

Thursday, 7 September 2017

Antibiotic resistance linked to household disinfectant triclosan

British scientists have found a connection between a significant mechanism of antibiotic resistance to the disinfectant triclosan. This chemical is found in many common domestic products. A report by Tim Sandle.
The research comes from two research centers: University of Birmingham and Norwich Research Park. For the scientists the results were unexpected and they discovered that certain bacteria which had mutated to develop resistance to quinolone antibiotics had also become more resistant to the common disinfectant triclosan. This is thought to happen because the quinolone-resistance mutation affected the way the bacteria hold DNA inside their cells. These mutants also appear to activate various self-defense mechanisms. The activation of these mechanisms-appears to provide triclosan resistance.
Quinolone antibiotics are a family of synthetic broad-spectrum antibiotic drugs. As medicines they exert an antibacterial effect by preventing bacterial DNA from unwinding and duplicating. Triclosan is an antibacterial and antifungal agent found in many consumer products, such as toothpaste, soaps, and detergents. Its efficacy as an antimicrobial agent is controversial. This relates to how well triclosan actually works as an antimicrobial agent and whether it makes a significant difference in killing or removing bacteria compared with, say, soap and water.
In addition, it may have an adverse environmental impact by accumulating in the environment and exerting influence over the ecosystem. For this reason triclosan has been banned in many regions, especially when used in hand hygiene products which readily run off into public sewers. Scientists are concerned that triclosan is increasingly detected in organisms living in waste-water and also in human blood plasma and in breast milk. The harmful effects, beyond water, are unknown but represented a cause for concern.
Commenting on the research findings, lead scientist Dr Mark Webber stated: "We think that bacteria are tricked into thinking they are always under attack and are then primed to deal with other threats including triclosan.” The effect was seen with Escherichia coli bacteria. The results are significant given the widespread use of triclosan and its tendency to remain in the environment.
What is unknown is whether the reverse can happen; that is if triclosan exposure could lead to the development of antibiotic resistant strains? This is a more controversial point since acquired bacterial resistance to disinfectants has not been definitively proven.
The research findings are published in the Journal of Antimicrobial Chemotherapy. The research is titled “Quinolone-resistant gyrase mutants demonstrate decreased susceptibility to triclosan.”

Posted by Dr. Tim Sandle

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Ebola detected in semen of survivors two years after infection

Ebola virus RNA can persist in the semen of survivors more than two years after the onset of infection researchers at the University of North Carolina at Chapel Hill have found. The research team, which included investigators from Ohio-based Clinical Research Management and the ELWA Hospital in Liberia also observed the detection of Ebola virus RNA in the semen of men who had previously had a negative test of their semen in some cases.

These findings led the study team to suggest revision of the 2016 World Health Organization guidelines relating to the sexual transmission of Ebola, which calls for men who survive Ebola virus disease (EVD) to undertake measures such as abstinence and the use of condoms for at least 12 months after the onset of EVD or until their semen has tested negative for Ebola virus RNA twice.

The study team also reports that the men whose samples tested positive for Ebola virus RNA were more likely to be older than those with a negative result. Those who had Ebola virus RNA detected in their semen also complained of vision problems at a higher rate than male survivors without evidence of Ebola virus RNA in their semen. The researchers recommend future studies investigate the source of viral persistence and whether the detection of viral RNA signifies the presence of infectious virus.


William A Fischer II et al. Ebola Virus RNA Detection in Semen More than Two Years After Resolution of Acute Ebola Virus InfectionOpen Forum Infectious Diseases, 2017 DOI: 10.1093/ofid/ofx155/4004818

Posted by Dr. Tim Sandle

Wednesday, 6 September 2017

MRSA survival chances predicted by DNA sequencing

Sequencing the DNA of the MRSA superbug can accurately identify patients most at risk of death and could help medics develop new treatments as we move towards personalised medicine. MRSA is a Staphylococcus aureus bacterium that has become resistant to most types of antibiotics, and up to 20 per cent of patients with invasive infections die.

Whilst S. aureus is a common bacterium that lives on the skin, if it gets inside the body through a cut it can cause septicaemia (blood poisoning). This potentially life-threatening infection affects thousands of patients every year in the UK.

There are two main strains of MRSA found in UK hospitals, called CC22 and CC30.

For the first time a team of scientists led by the Milner Centre for Evolution at the University of Bath were able to study blood samples from around 300 patients with septicaemia, looking at how the different MRSA strains behaved and assessing their lethality.

They examined the genetic code of the infecting MRSA bacteria, and paired this information with individual risk factors for each patient, including age, presence of any other illnesses, and noted whether the patient was still alive after 30 days of the infection and if deceased whether MRSA contributed to their death.

Paired together this information allowed the team predict with high accuracy the individual's probability of surviving the MRSA infection.


Mario Recker, Maisem Laabei, Michelle S. Toleman, Sandra Reuter, Rebecca B. Saunderson, Beth Blane, M. Estee Török, Khadija Ouadi, Emily Stevens, Maho Yokoyama, Joseph Steventon, Luke Thompson, Gregory Milne, Sion Bayliss, Leann Bacon, Sharon J. Peacock, Ruth C. Massey. Clonal differences in Staphylococcus aureus bacteraemia-associated mortalityNature Microbiology, 2017; DOI: 10.1038/s41564-017-0001-x

Posted by Dr. Tim Sandle

Tuesday, 5 September 2017

Unknown virus discovered in 'throwaway' DNA

Finding new viruses has historically not been an easy process. Cells do not grow on their own, so must be cultured in a laboratory before they can be analysed, which involves months of work. But the Oxford research represents a massive opportunity for the future.

Next-Generation Sequencing has revolutionised genomics research and is currently used to study and understand genetic material. It allows scientists to gather vast amounts of data, from a single piece of DNA, which is then collated into huge, online, genome databases that are publicly accessible.

A chance discovery has opened up a new method of finding unknown viruses. Researchers have revealed that Next-Generation Sequencing and its associated online DNA databases could be used in the field of viral discovery. They have developed algorithms that detect DNA from viruses that happen to be in fish blood or tissue samples, and could be used to identify viruses in a range of different species.


Amr Aswad, Aris Katzourakis. A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence dataVirus Evolution, 2017; 3 (2) DOI: 10.1093/ve/vex016

Posted by Dr. Tim Sandle

Monday, 4 September 2017

Fungi associated with sandstorms

A new research paper of interest:

Background: The impact of sandstorm dust events on local air quality and public health are becoming a greater concern in the Kingdom of Saudi Arabia. Among sandstorm dust particles, airborne fungal spores cause serious respiratory ailments to those who are exposed to the dust. Although the study of dust storm material has attracted research interest, little work has been carried out in Saudi Arabia and no major study has been conducted in the Al-Zulfi, Riyadh province region. Hence, the aim of the study was to investigate airborne fungal allergen concentrations in sandstorm dust in the Al-Zulfi city, Saudi Arabia.

Materials and Methods: During the study period, 12 sandstorm dust samples and 3 control samples were collected from various locations (educational campus, people gathering, and recreational places) by gravitational plate exposure method using Sabouraud dextrose agar. Following incubation, the fungal colonies were identified by microscopic and morphological identification.

Results: A total of 2590 fungal isolates were identified among 36 exposures of sandstorm dust samples. From the samples dematiaceous fungi and hyaline fungi were observed, divided 56.2%, 43.8%, respectively. The incidences of predominant fungal genera were Fusarium (21%), Cladosporium (15.8%), Ulocladium (11.1%), Aspergillus (10.9%), and Alternaria (8.6%).

Conclusion: Our observations infer that some of the most important allergenic fungal spores are predominantly observed in sandstorm dust samples and incidences of dematiaceous fungi are higher than hyaline fungi. This study highlights the need for precautionary safety measures to protect the public against sandstorm dust exposures.

The reference is:

Vijayakumar, R., Al-Aboody, M.S., Alturaiki, W., Suliman A. Alsagaby, S.A., Sandle, T. (2017) A study of airborne fungal allergens in sandstorm dust in Al-Zulfi, central region of Saudi Arabia, Journal of Environmental and Occupational Science, 6 (1): 27-33 (DOI: 10.5455/jeos.20170120094512)

For a copy, please contact Tim Sandle

Posted by Dr. Tim Sandle