Sunday, 31 December 2017

Raindrops splash pathogens onto crops

Two mechanisms of pathogen dispersal have been discovered. The first is a vortex ring mechanism, where one ring of pathogenic particles propagates and radially disperses after a drop impacts a plant surface. In the other, the pathogens are dispersed by an elastic collision mechanism. Jung describes this in terms of billiard balls: "You have billiard balls forming a triangle shape so if you hit the one ball in the front the other balls will be kicked out."

The identification of these mechanisms was not without its challenges. Pathogens are microscopic, around 10 micrometers, and extremely fast moving with speeds of 1 meter per second, so deducing mechanisms based on their liberation patterns was no simple task. The research team employed strong laser lights and high-speed cameras to capture and track the pathogens.

At the root of this problem is its oppositional nature: Rain is a natural process supplying thousands of gallons of fresh water to crops every year, but at the same time dispersing pathogens and damaging agricultural yields. This research provides insights into possible agricultural solutions for this issue.

Source: American Physical Society's Division of Fluid Dynamics

Posted by Dr. Tim Sandle

Saturday, 30 December 2017

Disposable optical test substrate for detecting harmful microbes

Harmful microbes and toxic micromolecules in food and drinking water can cause serious health problems around the world. For her PhD thesis, VTT researcher Sanna Uusitalo has developed a disposable optical test substrate for use in microbial detection. The aim is to enable cost-effective detection of harmful microbes and toxins.

Uusitalo developed the optical detection of microbial cells using Raman spectroscopy to increase measurement sensitivity via SERS (surface-enhanced Raman scattering) amplification. SERS measurement is based on Raman scattering, whose intensity is increased by the oscillation of free electrons in metal. In some cases, the method can identify a sample to a precision-level of one molecule. The disposable SERS measuring substrate is patterned using a roll-to-roll production method and coating the substrate with thin gold plating.

"The more sensitive the SERS process becomes in the case of challenging cell measurements, the more applications it will have in the future. It would provide a fast and simple method of microbial identification compared to traditional cell cultures and enable the fast identification of microbes in cases, say, of food poisoning, or rapid purity analysis in food industry production facilities," says Uusitalo.

She believes that the first general application of the method will be in explosives detection or the analysis of environmental toxins. Portable Raman measuring devices are already on the market for the analysis of larger sample volumes. Future R&D will also lead to portable SERS measuring devices for measuring very low sample volumes.

Source: VTT Technical Research Centre of Finland

Posted by Dr. Tim Sandle

Friday, 29 December 2017

How bacteria survive in oxygen-poor environments

Biologists have revealed a mechanism by which bacterial cells in crowded, oxygen-deprived environments access oxygen for energy production, ensuring survival of the cell. The finding could explain how some bacteria, such as Pseudomonas aeruginosa, are able to thrive in oxygen-poor environments like biofilms and resist antibiotics. P. aeruginosa biofilm infections are a leading cause of death for people suffering from cystic fibrosis, a genetic condition that affects the lungs and the digestive system.

Bacteria rarely live by themselves as single-celled organisms. Most instead grow in communities, leveraging the strength of numbers to form a biofilm with tissue-like properties similar to a scaffold that serves to fortify the community, making it up to 1,000 times more resistant to most antibiotics.

Each individual cell must on its own extract electrons from food that are then transported along the cell's membrane until they reach an oxygen molecule. The energy released during this metabolic process is used to sustain life. As communities of bacteria continue to grow and form into a biofilm, however, they can become overcrowded, creating an environment where each cell has to compete for limited nutrients and oxygen to survive.

Research has shown that some bacteria, including P. aeruginosa, have evolved different strategies to respond to and cope with the low-oxygen conditions in biofilms. Communities of bacteria can, for example, change the overall structure of the biofilm so that its surface area-to-volume ratio is higher and a larger proportion of the cells inside are able to access the oxygen on the outside. P. aeruginosa can also make molecules called phenazines, which help to shuttle electrons from the inside to the outside of the cell and ultimately to oxygen available at a distance.

Another strategy is to make alternative versions of terminal oxidases, enzymes in the membrane that transfer electrons to oxygen, which use oxygen more efficiently or are better at scavenging oxygen when its concentration is low. While there have been numerous studies done to examine the importance of these enzymes and strategies for P. aeruginosa growth, they've largely been conducted in well-oxygenated liquid cultures in the lab. When P. aeruginosa infects an actual host, such as a human, it often grows as a biofilm and encounters vastly different conditions.


Jeanyoung Jo, Krista L Cortez, William Cole Cornell, Alexa Price-Whelan, Lars EP Dietrich. An orphan cbb3-type cytochrome oxidase subunit supports Pseudomonas aeruginosa biofilm growth and virulenceeLife, 2017; 6 DOI: 10.7554/eLife.30205

Posted by Dr. Tim Sandle

Thursday, 28 December 2017

Transforming Bioburden Risk with Digital Asset Intelligence

In the context of aseptic pharmaceutical manufacturing, the smart asset approach serves a dual role for risk management: 1) it allows for automated, touchless environmental monitoring to support sterilization surety during production; and 2) it provides traceability and pedigree data from sterile processing through manufacturing to support FDA regulated facilities so that products can be released to inventory at a higher frequency, and with minimized risk due to contamination.

This is the subject of an article published by Pharmaceutical Manufacturing. Here is an extract:

“By enabling sterilization-proof electronic data to be written directly onto environmental monitoring equipment, and collected digitally at multiple prescribed points throughout the production process, cGMP manufacturers can see dramatic improvement in their productivity, while yielding more accurate and thorough data collection for compliance reporting and recall containment.”

The article can be accessed here: Pharma Manufacturing

Posted by Dr. Tim Sandle

Wednesday, 27 December 2017

Ending TB means investing in R&D

There were 10.4 million new cases of active TB in 2016—of which only 6 million were diagnosed and notified. Drug-resistant infections are on the rise. There remains a dire need for better, faster-acting drugs, a new vaccine, and technologies that quickly diagnose TB and determine the degree of drug-resistance.

Science is not holding us back, funding and political will to implement is.

The WHO estimates that R&D budgets need more than US$1 billion annually to turn around the odds of patients potentially losing years of their lives to a toxic treatment course, missing the opportunity for treatment due to poor diagnostics, or contracting TB in the first place because of an ineffective vaccine.

The WHO also reports that despite accounting for about 2 percent of deaths globally, TB receives only 0.25 percent of the estimated US$265 billion spent worldwide on medical research each year.

Simply put, TB science is woefully underfunded. Governments must work together to dramatically reshape the investment landscape.

Today, the time needed to treat drug-resistant TB ranges from nine months to two years or more—and yet in common practice the success rate is only about 50 percent. The majority of drugs that these patients are given are probably not helping at all—but they are producing side effects, everything from nausea and dizziness to deafness and kidney failure. For some, the treatment can be worse than the disease itself.

A true point of care test is needed to find the 4 million missing patients every year, where and when they first seek care. New diagnostic technology is critical to ensure that the right treatment regimens are used—right from the start—to prevent the lengthy and arduous road to diagnosis and cure faced by many patients.

Making matters worse, there is no vaccine that can effectively play a major role in eliminating this disease. Today, the Bacillus Calmette–GuĂ©rin vaccine is the only TB vaccine available. It is nearly a century old, only moderately effective in preventing severe TB in infants and young children, and it doesn’t adequately protect teens and adults, who are most at risk for developing and spreading TB.

Progress has been made but we need a greater commitment. There are 12 different TB vaccine candidates in clinical trials today, a significant increase from 2000—when there were zero. Data from multiple mid- and late-stage efficacy trials will become available over the next 3 years, providing data that will help optimize and accelerate TB vaccine development. But it will take a significant increase in resources to achieve critical breakthroughs—and to reach success quickly

Similarly, only a handful of drug candidates were being tested in clinical trials. Today there are more than 30. Two new experimental treatments show promise—one that might be able to cure all forms of TB except for the most drug-resistant strains (known as extensively drug-resistant TB or XDR-TB), and another that might be able to cure XDR-TB. Both could take substantially less time and money than current treatments.

At first glance, the TB diagnostics pipeline looks healthy. However, emerging game-changers are at risk due to underfunding at the clinical trial stage. In addition, very few diagnostic candidates would address the most critical need—a point of care test for primary care facilities. Diversification of the point of care pipeline, and identification of new biomarkers are urgently needed.

While the meeting in Moscow will inform future discourse on TB, it must also serve as a springboard toward decisive action against the disease. TB is the world’s deadliest infectious disease and efforts to curb it remain underfunded. We are calling on governments to make major commitments to fund the R&D that will end TB once and for all.

Tuesday, 26 December 2017

Fungal spore 'death clouds' key in gypsy moth fight

A fungus known to decimate populations of gypsy moths creates 'death clouds' of spores that can travel more than 40 miles to potentially infect populations of invasive moths, according to a new study.

The study describes a new method for tracking the geographic range of this airborne insect pathogenic fungus from areas of a disease outbreak.

Better understanding of the distances these killer spores travel could help researchers correlate the fungus' range with weather patterns to better predict how bad gypsy moth damage will be in a given year.

The fungal pathogen (Entomophaga maimaiga) first appeared in New England in 1989 and only infects gypsy moths. The pollen-sized spores stick to caterpillars when they walk over them. Once attached, a spore uses enzymes to create a hole and enter the caterpillar's body, where a cloaking mechanism allows the fungus to remain undetected by the moth's defenses. Over four to six days, the fungus multiplies and then kills the host, after which new spores are literally shot from the cadaver into the air, where they become windborne.

From May through June, when gypsy moth caterpillars are feeding and before they pupate, the fungal pathogen can run through up to nine infection cycles, while the numbers of infections increase dramatically. During the study, the researchers found the peak caterpillar death rate due to E. maimaiga reached 86 percent, meaning that if you found 100 caterpillars munching leaves that day, 86 of them would die within the week.


Tonya D. Bittner, Ann E. Hajek, Andrew M. Liebhold, Harold Thistle. Modification of a Pollen Trap Design To Capture Airborne Conidia of Entomophaga maimaiga and Detection of Conidia by Quantitative PCR. Applied and Environmental Microbiology, 2017; 83 (17): e00724-17 DOI: 10.1128/AEM.00724-17

Posted by Dr. Tim Sandle

Monday, 25 December 2017

Efforts to Combat Antibiotic-Resistant Bacteria Through Science

Bacterial infections that resist antibiotics are a major problem in the United States. According to the U.S. Centers for Disease Control and Prevention (CDC), antibiotic-resistant infections are responsible for at least 2 million illnesses and 23,000 deaths each year. In 2015, the U.S. government launched the National Action Plan for Combating Antibiotic-Resistant Bacteria (CARB) (link is external)pdf. Guided by the plan, NIAID and other NIH components work with government, academic, and industry partners on a wide range of projects aimed at understanding and controlling antibiotic resistance. To mark this year’s Antibiotic Awareness Week, November 13-19, we highlight a few of these efforts.

Appropriate antibiotic use starts with accurate diagnosis. Among the research projects working toward developing reliable, rapid diagnostics is an innovative test being developed by the NIAID-supported Antibacterial Resistance Leadership Group. 

This tool analyzes patterns of gene expression in a patient’s blood sample to determine if respiratory symptoms stem from a bacterial infection—which may be susceptible to antibiotics—or are caused by a virus, which are not affected by antibiotics. When doctors can quickly differentiate between bacterial and viral respiratory infections, they can prescribe antibiotics only when appropriate.

Clinical trials are an important way to gather information about experimental antibiotic compounds, reformulations of older drugs, and licensed antibiotics. For example, the NIAID-supported Sexually Transmitted Infections Clinical Trials Group recently completed a Phase 2 trial that found the investigational oral antibiotic Zoliflodacin to be well-tolerated and effective against uncomplicated gonorrhea. Plans are underway to continue testing Zoliflodacin in a Phase 3 clinical trial.

Additionally, NIAID-supported investigators are conducting trials to determine the best ways to use licensed antibiotics, studying, for example, how long, how much and whether antibiotic treatment is needed at all. One trial found that shorter treatment for middle ear infections in young children is less effective than the current 10-day treatment recommendation. Other studies found that two off-patent antibiotic treatments (clindamycin and trimethoprim–sulfamethoxazole) work very well against skin infections caused by community-associated methicillin-resistant Staphylococcus aureus (MRSA).

Fostering innovation in antibiotic development requires participation from both the private and public sectors. To meet this goal, NIAID, the Biomedical Advanced Research Development Authority, a component of the U.S. Department of Health and Human Services, and the Wellcome Trust, are collaborating on a global public-private initiative called CARB-X. This program is investing in early discovery and development of novel antibiotics, vaccines, and rapid diagnostics.

NIAID is providing technical support and drug development services to CARB-X awardees, including preclinical testing and manufacturing. NIAID is also exploring non-traditional approaches to address antibiotic resistance, such as harnessing good bacteria in the human microbiome to prevent and treat bacterial infections and advancing bacteriophage therapy, which is a virus that can attack and destroy harmful bacteria. In addition, NIAID-supported researchers are using genomic sequencing and other advanced technologies to better understand how bacteria develop antibiotic resistance.  Scientists can leverage this information to help inform the development of improved diagnostics, therapeutics, vaccines, and antimicrobial strategies.

To learn more about accomplishments during the first two years of implementation of the National Action Plan for Combating Antibiotic-Resistant Bacteria, check out the Progress Report for Years 1 and 2.

Source: NIAID

Sunday, 24 December 2017

Season's Greetings!

Season's Greetings!

Thank you for supporting Pharmaceutical Microbiology over this past year. The website and the various groups continues to grow and feature a range of microbiology, pharmaceutical and healthcare related news stories.

All the best for the holiday season.

Dr. Tim Sandle

Saturday, 23 December 2017

Kill switches for engineered microbes gone rogue

Stable autonomous kill switches ensure biocontainment of living microbes designed as devices for medicine or the environment. New research outlines two new types of kill switches that address these challenges. The new kill switches are self-sufficient and highly stable in bacterial populations that evolve, and they last over many generations.

They can ensure that only bacteria with intact synthetic gene circuits survive, or confine bacteria to a target environment at 37°C (body temperature) while inducing them to die at lower temperatures, as demonstrated during bacterial exit from a mouse intestinal tract.

For the kill switch, the "Essentializer," researcher’s leveraged previously engineered "memory element" that allows E. coli bacteria to remember an encounter with a specific stimulus in their environment.

The memory element, derived from a bacteria-infecting virus called bacteriophage lambda, either remains silent or reports the occurrence of a signal by permanently turning on a visible reporter transgene that the scientists can trace. The signal can be any molecule, for example, an inflammatory cytokine in the gut or a toxin in the environment.

In their recent study, the team devised a way that ensures the memory element is not lost from the genome during the evolution of the bacterial population over more than a hundred generations. During that time, the genomes of individual bacteria acquire random mutations, which also could potentially occur in the memory element, destroying it in their wake.

The researchers introduced the Essentializer as a separate element at another location in the bacterium's genome. As long as the memory element remains intact, either of the two bacteriophage factors that control its function also inhibits the expression of a toxin gene encoded by the Essentializer.

However, the toxin gene remains somewhat "leaky," still producing residual amounts of toxin that can kill the cell. To keep those residual toxin levels at bay, the researchers included a second gene in their kill switch, which produces low levels of an anti-toxin that can neutralize small amounts of the toxin.


Pamela A. Silver et al. Rational Design of Evolutionarily Stable Microbial Kill SwitchesMolecular Cell, November 2017 DOI: 10.1016/j.molcel.2017.10.033

Posted by Dr. Tim Sandle

Friday, 22 December 2017

Will Amazon’s Next Big Move Be Pharmacy Delivery?

Whether you’re looking for the latest bestselling novel, a kayak or a coffin, you can buy just about anything on Amazon. If their latest endeavor is successful, the Internet giant may also be where you turn when you need prescription medication. Reports indicate Amazon has obtained wholesale pharmaceutical licensing in 12 states within the past year. What could Amazon be offering in the pharmaceutical industry, and what will this mean for other distribution centers?

Special report by Megan Ray Nichols

Same-Day Delivery

Pharmaceutical delivery isn’t a strange concept — most independently owned pharmacies have offered prescription delivery as a free service for decades. Even if you live in a big city, you can probably find at least one little pharmacy still offering that sort of service.

Amazon has been debating the idea of pharmaceutical deliveries for a quite a few years now — it’s a topic that’s come up at nearly every board meeting for the past several years. They’ve even started offering same-day delivery of non-prescription pharmacy items from Bartell Drugs in Seattle as a test platform.

When you look at this information, along with the fact that Amazon is seeking — or, perhaps, has already hired — a health care program manager, it appears they’re looking to make the move into pharmacy delivery. This move could benefit patients who are unable to make the trip to their local pharmacy, or those who require medication that is not easy to obtain locally. From a logistical perspective, the most important part of pharmaceutical delivery is keeping the medications secure, especially any medication that needs to be temperature-controlled throughout shipment.

Wholesale Licensing

Amazon’s move toward obtaining pharmaceutical licenses is the first step toward creating a pharmacy distribution network where consumers can have their medications, medical devices or other prescription items delivered directly to their home, rather than having to visit a pharmacy in person.

If this is the direction Amazon is heading, they have quite a few more steps to complete. First, they would need to obtain wholesale pharmacy licenses in the remaining 38 states — a task experts predict could take up to two additional years. Amazon would also have to obtain pharmacy licensing to enable them to fill individual prescriptions.

Some sources also suggest the Internet giant is looking to either purchase a pharmacy benefits management company, or partner with one. If you’re not familiar with the term, a pharmacy benefits manager, or PBM, handles the communication between pharmacies and insurance companies — making sure the prices on the medication are correct, and that the insurers are paying or reimbursing pharmacies where appropriate.

Specialty Pharmacy

Amazon may not be moving into traditional pharmacy services — all this planning and license acquisition may be a precursor to the company moving into specialty pharmacy services instead. Specialty pharmacy covers things like complicated drugs and treatments, administered at home, that may not be available at your neighborhood pharmacy. Things like treatment for HIV/AIDS, blood diseases, MS and cancer all fall under the specialty pharmacy umbrella.

By stepping into the ring, Amazon could potentially change the game, making it easier and possibly more affordable for patients to obtain their necessary medications while adding millions of dollars of additional revenue to their bottom line each year.

By way of comparison, CVS reports specialty pharmacy accounts for approximately $50 billion of revenue for them every year. Experts are predicting this form of pharmacy could bring in more than $240 billion a year by 2021. The majority of this type of pharmaceutical distribution takes place by mail — which is where Amazon excels.

It is important to note that this is all speculation — industry experts are looking at the steps Amazon has taken and the licenses it has received because this information is all public record, but the company has yet to make an official statement about its intentions. It is possible they won’t announce anything until after their preparations are complete, or even just before they’re ready to go live.

They’re playing their cards close to the chest with this one, but if they are planning to step into the world of mail-order pharmacy, Amazon could quickly become one of the biggest competitors in the field.

Thursday, 21 December 2017

New technique gauges microbial communities by biomass

A new technique devised by researchers from North Carolina State University and the University of Calgary provides a more in-depth look at the composition of and activity within microbial communities -- the microscopic life within our bodies and all around us.

Rather than relying on a survey of the number of microbes present in a certain sample, the new technique attempts to assess the biomass -- the protein abundance -- of those microbes, which include bacteria, viruses and other tiny forms of life. Microbial communities play an important role in animal and plant health and disease, as well as in important environmental processes such as decomposition of organic matter and nutrient cycling in soils and oceans. Studies on these communities have become increasingly widespread in recent years.

The researchers tested the new method in Rocky Mountain alkaline soda lakes, slimy bodies of water with high salinity and pH values. They found, in one of the lakes, that the new method was able to identify algae that weren't found by the more common "counting" method.

The researchers also used the new method to examine an existing data set of saliva from multiple human mouths and found a lot more variation in microbial communities than previous studies showed.


Manuel Kleiner, Erin Thorson, Christine E. Sharp, Xiaoli Dong, Dan Liu, Carmen Li, Marc Strous. Assessing species biomass contributions in microbial communities via metaproteomics. Nature Communications, 2017; 8 (1) DOI: 10.1038/s41467-017-01544-x

Posted by Dr. Tim Sandle

Wednesday, 20 December 2017

Draft EU GMP Annex 1 released

The PIC/S Secretariat has notified that the revised EU-PIC/S GMP Annex 1 on the Manufacture of Sterile Medicinal Products has reached Step 2 of the revision process and on 20 December 2017, the PIC/S and EMA published the draft revision of Annex 1 for public consultation.

The consultation period will last 3 months and run from 20 December 2017 to 20 March 2018.

The revised Annex 1 has been prepared in co-operation with the EMA, World Health Organization (WHO), and PIC/S in order to maintain global alignment of standards, and provide assurance of product quality. The document is subject to parallel public consultation by the European Commission (EC), WHO and PIC/S.

Key changes from the earlier PIC/S Annex are:
  • Introduction of new sections: scope, utilities, environmental and process monitoring sections and glossary.
  • Introduction of the principles of Quality Risk Management (QRM) to allow for the inclusion of new technologies and innovative processes.
  • Restructuring to give more logical flow.
  • Addition of detail to provide further clarity.
The revised Annex 1 is downloadable on the PIC/S website (site link) or via this direct link.

The draft has been formatted with prescribed line and page numbers to support a joint international consultation within TGA, PIC/S, WHO and the EC.

Posted by Dr. Tim Sandle

2017 Author of the Year – Journal of GXP Compliance

Tim Sandle has been awarded '2017 Author of the Year – Journal of GXP Compliance' by the Instiute of Validation Technology. This is for Dr. Sandle's contributions to the Journal of GXP Compliance, includig:

Biodecontamination of Cleanrooms and Laboratories Using Gassing Systems V21 #1

Matrix Approach for the Qualification of a Pharmaceutical Facility Autoclave V21 #4

Pharmaceutical Microbiology: Current and Future Challenges V21 #4

Tuesday, 19 December 2017

How the immune system identifies invading bacteria

The body's homeland security unit is more thorough than any airport checkpoint. For the first time, scientists have witnessed a mouse immune system protein frisking a snippet of an invading bacterium. The inspection is far more extensive than researchers imagined: the immune system protein, similar to those in humans, scans the bacterial protein in six different ways, ensuring correct identification.


Jeannette L. Tenthorey et al. The structural basis of flagellin detection by NAIP5: A strategy to limit pathogen immune evasionScience, 2017; DOI: 10.1126/science.aao1140

Posted by Dr. Tim Sandle

Monday, 18 December 2017

How to gown properly for cleanrooms

As shown below, three videos showing how to gown properly when entering cleanrooms.

Practical workshop on good cleanroom gowning from Simon Fiala – Key Account Manager, COMPREI Reinraum.

Posted by Dr. Tim Sandle

Sunday, 17 December 2017

Purified Water Monograph: New Draft in European Pharmacopoeia 9.4

A draft of the monography to Purified Water was published in the European Pharmacopoeia, which includes a new section on Elemental Impurities:

“Elemental impurities: If purified water in bulk does not meet the requirement for conductivity prescribed for Water for injections (0169) in bulk, a risk assessment according to general chapter 5.20 Elemental impurities is carried out. The risk assessment should consider the role of water in the manufacturing process, in particular when water is used in a process but is no longer present in the final product.”

Another change that will enter into force on 1 April 2018, is that the appearance and the nitrate level of purified water do not have to be tested anymore. The USP and the Japanese Pharmacopoeia, as well, do not include these requirements. The testing for appearance and nitrate level are still requested by the Indian and Chinese Pharmacopoeia.

See: Ph. Eur.

(Source of news: PDA: 

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