Friday, 24 February 2017

An Analysis Of FDA FY2016 Drug GMP Warning Letters

Pharmaceutical on-line has published a useful overview of FDA warning letters issued in 2016. This comes from Barbara Unger, Unger Consulting Inc.

Here are the headline trends:
  • The number of drug GMP warning letters issued more than doubled over the previous year, from 42 in FY2015 to 102 in FY2016.
  • The compounding pharmacy/outsourcing facility segment continues to attract disproportionate enforcement attention from FDA, receiving more than 50% of the warning letters for the third fiscal year in a row. This suggests that firms are not learning from the enforcement actions taken against others.
  • The number of warning letters issued to API manufacturers and dosage manufacturers is approximately equal in FY2016, with a dramatic increase in the number of warning letters issued to API manufacturers over those issued in FY2015.
  • Excluding the compounding pharmacies and outsourcing facilities, FDA continues to focus enforcement actions outside the U.S. (OUS), where most generic drugs are produced. Over three times as many warning letters were issued to OUS firms compared to domestic firms. Firms in India and China received 71% of the warning letters issued to firms outside the U.S. Warning letters issued to sites in China increased from two in FY2015 to 15 in FY2016.
  • The percent of warning letters that cite deficiencies in data integrity remains consistent at approximately 80% for OUS firms and reaches the same percentage for warning letters issued to sites in the U.S. in FY2016. This year saw a significant increase for U.S. warning letters citing data integrity deficiencies.
  • Import alerts were associated with 17 of the 35 warning letters issued to OUS sites in FY2016. Firms in China and India that received warning letters were the subject of 15 of the 17 import alerts associated with warning letters.
  • The interval between inspection and issuance of warning letters has increased over the past four fiscal years. When import alerts were put in place, they generally occurred in half the time required to issue the associated warning letter.

The article can be accessed here.

Posted by Dr. Tim Sandle

Thursday, 23 February 2017

Advanced Cooling Systems for Blood Product Storage Applications

Century Refrigeration announces that it designs custom, advanced cooling systems for blood product storage applications, including blood banks and laboratories. The customized nature of the solutions ensures that they are capable of the low temperatures and safe and reliable operation required by blood product storage applications.

Large-scale blood product storage is among the most difficult laboratory and medical refrigeration challenges. To comply with regulatory requirements and avoid contaminating this very high-value product, cooling equipment systems must achieve extremely low temperatures and maintain these temperatures steadily. They must also use the safest refrigerants, be designed for maximum reliability and redundancy, and be easy to maintain.

Customized refrigeration solutions engineered specifically for blood storage applications are needed to achieve these goals, as the demands of blood product storage are too great, and ultimately too application-specific, to support the use of off-the-shelf refrigeration technology. To guarantee success, blood product storage refrigeration systems should be custom-designed, with individual components custom-selected and sized to sustain the necessary low temperatures, avoid contamination and product loss, and simplify maintenance.

The experts at Century Refrigeration utilize the company’s cutting-edge cooling technology to design industry-leading blood product storage cooling systems. These systems feature extremely low temperature coils, safe refrigerants, appropriate redundancy, and more. These features ensure total uptime and protect highly valuable blood products in blood bank and laboratory settings.

Century Refrigeration is a division of RAE Corporation.

This is a guest post.

Wednesday, 22 February 2017

Update on Ebola Outbreak and Aftermath in West Africa

WHAT: Live-streamed panel discussion and Q&A with expert MSF medical and operations staff

WHEN: Thursday, February 23, 8 p.m. Eastern Time (recording will be archived online here)

WHERE: Register online here

DETAILS: The Ebola outbreak that swept across West Africa in 2014 and 2015 infected more than 28,600 men, women, and children—and killed more than 11,300 people—before it was contained. Across Liberia, Guinea, and Sierra Leone, schools closed, economies ground to a halt, and health systems collapsed under the strain of the epidemic.

Today, MSF is releasing The Politics of Fear: Médecins Sans Frontières and the West African Ebola Epidemic (Oxford University Press), which examines the motivations behind the decisions made in the international response to the epidemic, the medical advances that emerged, and the lessons learned from the largest mobilization in MSF's history.

A panel of MSF staff members will discuss what this reflection means for the organization’s emergency medical activities going forward and will share information on the post-Ebola medical needs in Liberia, Sierra Leone and Guinea.

PANELISTS: Armand Sprecher, MD, MPH, is an emergency physician and epidemiologist who has worked with MSF since 1997. He has worked in responses to Ebola and other filovirus outbreaks in Uganda in 2000, Angola in 2005, Democratic Republic of Congo in 2007, and West Africa in 2014-2015.

Patricia Carrick is a family nurse practitioner who has worked on and off with MSF since 2001. She has been on five MSF assignments in South Sudan, Malawi, and most recently Sierra Leone during the Ebola outbreak in 2014-2015.

Michiel Hofman is a senior humanitarian specialist for MSF, focusing on research, training, and operational support, as well as publications in the humanitarian field. He is a co-editor of The Politics of Fear.

Mike White is the deputy operational manager for MSF programs in Haiti, Ethiopia, Sudan, South Sudan and Liberia. His MSF field work includes assignments in eastern Ethiopia, South Sudan, northern Nigeria, and Sierra Leone. In 2014 and 15 he worked on MSF’s emergency desk as an operations adviser on South Sudan and Ebola.

MODERATOR: Tim Shenk is a senior press officer with MSF-USA and has completed five field communications assignments with MSF, including in Liberia during the Ebola outbreak.
Posted by Dr. Tim Sandle

Each animal species hosts a unique microbial community

Each animal species hosts its own, unique community of microbes that can significantly improve its health and fitness. This is the implication of a laboratory study that investigated four different animal groups and their associated microbiota. The research found that each species within the group has a distinctive microbial community.

Experiments with two of the groups -- one mammal and one insect -- demonstrated that individuals possessing their natural microbiota digested food more efficiently and had greater survival than those that were implanted with the microbial communities of closely related species.

For details see:

Andrew W. Brooks, Kevin D. Kohl, Robert M. Brucker, Edward J. van Opstal, Seth R. Bordenstein. Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History. PLOS Biology, 2016; 14 (11): e2000225 DOI:10.1371/journal.pbio.2000225

Posted by Dr. Tim Sandle

Tuesday, 21 February 2017

Advances in Aseptic Blow-Fill-Seal Processing

Aseptic blow-fill-seal (B/F/S) systems for the processing of pharmaceutical liquids have experienced rapid and growing acceptance by the pharmaceutical industry over the past 20 years. This has been accelerated by enhancements made to aseptic B/F/S processes based on pharmaceutical industry input and to accommodate the requirements of regulatory agencies. These enhancements were designed to improve product integrity and help ensure patient safety. As a result, the United States Food and Drug Administration and the United States Pharmacopoeia now characterize modern B/F/S technology as an "advanced aseptic process", indicating its use as a preferred technology over other aseptic systems and a better solution for the sterile, aseptic processing of pharmaceutical liquids. Aseptic B/F/S systems offer a unique combination of flexibility in packaging design, low operating cost and a high degree of sterility assurance. Due to its design and functionality, B/F/S processing inherently produces very low levels of particulate matter, and much of the potential for microbial contamination in its critical areas is mitigated by the absence of human intervention in these areas.

This is the basis of a new article by Chuck Reed. The article can be found here.

Posted by Dr. Tim Sandle

Monday, 20 February 2017

The European approach to disinfectant qualification

Tim Sandle has written an overview of the European approach to disinfectant testing for the A3P publication La Vague.

Here is the introduction:

Contamination control is of great importance to healthcare facilities and to pharmaceutical cleanrooms. One way of ensuring the hygiene is maintained is through a cleaning and disinfection regime. After a disinfectant has been chosen based on its chemical properties and expected performance/effectiveness, each disinfectant should be validated to ensure its efficacy. Efficacy is demonstrated through performance testing to show that the disinfectant is capable of reducing the microbial bioburden in either suspension (planktonic state) or from cleanroom surfaces to an acceptable level.

The article can be read here.

Posted by Dr. Tim Sandle

Sunday, 19 February 2017

Does studying yellow fever offer Zika clues?

As cases of Zika virus increase there is considerable investigation and research into the virus. One area being looked at for clues is yellow fever virus. A second area involves the use of mouse models.

By Dr. Tim Sandle

Zika virus is a member of the Flaviviridae virus family. In one in four people the disease causes a mild illness known as Zika fever, for up to seven days. The symptoms include fever, rashes, joint pain and conjunctivitis. The biggest risks are infected women and babies born with abnormally small heads and brain defects, a condition called microcephaly.
Yellow fever and Zika viruses have a common characteristic in how they can circumvent an insect’s immune response. This is due to the viruses manufacturing proteins that can suppress the immune response in the host. A similar response occurs in people, when we become infected.
For this reason, researchers have been studying mosquitoes and viral infections. This is based on using gene drive, a method targeting specific genes. The idea is to tip the battle at the genetic level in favor of the mosquito. This tranche of research could eventually lead to a human vaccine.
A second wave of research, also from Texas A&M University, College Station, is finding a means to make an infective mosquito undergo altered behavior so that it will not seek out humans to infect.
The research has been published in the journal Proceedings of the National Academy of Sciences. The paper is titled “Yellow fever virus capsid protein is a potent suppressor of RNA silencing that binds double-stranded RNA.”
In a second wave of research, a different group of researchers are seeing whether mice with healthy immune systems could provide new insights into Zika virus pathology and treatment. This is not straightforward due to the changes that animals undergo when they are infected. Mice, however, can, under certain conditions, be used as ideal models for Zika virus research.
The reason for focusing on mice is because studies have indicated that young mice with specific immune system defects are susceptible to Zika infection. By rearing mice (coded C57BL/6) with functioning immune systems that can be successfully infected with Zika, more detailed studies can be made and to provide the basis for testing treatments.
The second research study has been published in the journal PLOS Pathogens. The paper is headed “Zika (PRVABC59) Infection Is Associated with T cell Infiltration and Neurodegeneration in CNS of Immunocompetent Neonatal C57Bl/6 Mice.”

Saturday, 18 February 2017

Quick Laboratory Safety Tips

There is never a better time than now (excuse the cliche) to evaluate your laboratory safety procedures. For larger facilities, this can be a daunting task but necessary nonetheless. Regardless of lab size, the team at M2 Scientifics has put together this list of 10 quick laboratory safety tips. After you’ve reviewed each of them, you can begin implementation by completing a simple audit. Create a checklist of all 10 and check compliance. Are you in compliance for all of them? Great job! But if not, no worries. Put into practice these quick tips and you’ll be a safety pro in no time!

No Food or Drink in the Lab

This is one of the most common bad habits found among personnel and easily one of that hardest to kick. Everyone enjoys a good coffee or ice water while at work. But removing food and drink from the laboratory has multiple benefits. First, it reduces distraction. When performing critical tasks, any distraction is bad. Remove any and all distractions to help prevent injury or loss. Second, food waste can be messy. Messes reduce efficiency and promote risk of contamination. And last but definitely not least, it is a safety best-practice. A worse case example is one coming out of Tacoma, Washington. A young woman died four days after accidentally ingesting a saline solution containing sodium azide during an AP class.

Work With a Lab Partner

It isn’t always possible to perform experiments or duties with a partner. But if and when it is possible, it should be encouraged to work in teams. Two sets of eyes and hands double the chances of successfully catching a mistake or slip up. Human error is expected. Everyone makes mistakes. Working in teams helps keep each other in check. It also allows quick response if someone is injured.

Use Warning Signs

Anything that poses a particular threat should be labeled and HIGHLY visible! I can’t stress this enough. Bright colors, bold lettering and placement in prominent locations is a must. Consider using warning signs outside of the standard places. Chemicals and solutions are required to be marked by OSHA guidelines. But what about high-decibel noise areas? Trip hazards? And don’t forget circuit breakers. Electricity is used in abundance in any laboratory where equipment and instruments are being used. Make sure breakers are clearly marked. Appropriate warning labels and markings are essential to laboratory safety success.

Budget For Lab Safety Equipment

Maintaining a strict budget is key to any laboratory safety plan. When drafting a new budget or revising current spend, make sure funds are set aside to buy safety equipment. These items include eye wash stations and solution, protective gloves, goggles and safety glasses, ear plugs, splash guards, lab coats, fire extinguishers, and plenty more. It can get costly to purchase and maintain adequate measures. But nothing is more valuable than the well-being and safety of personnel. Budgeting for it will remove future funding concerns and the situation of having to decide what is more important in a pinch.

Costs associated with training should also be considered. There may be some production downtime to facilitate training courses. Props, paper handouts, and hourly wages all ring up a bill. Remembering to add these costs to your safety fund will prevent surprises.

Store Flammable Chemicals in Fireproof Cabinets

Fire is dangerous. Duh, right?! Make sure all flammable chemicals, solvents and aerosols are secured in fireproof cabinets. Leaving them out in the open is asking for disaster. Remember those warning signs? Post reminders throughout the lab wherever flammable items are being used. Something as simple as “Don’t Forget – Put Back in Fireproof Cabinet” (I’m sure you could word that much better but you get the point) can go a long way. You may consider making this an item on your daily inventory management inspection. 

Create a Laboratory Safety Manual

When bringing on new staff members, most organizations will provide an employee handbook or some sort of policy guideline. Why not also provide a laboratory safety manual? Drafting a clear and concise policy regarding all requirements and best-practices not only acts as a handy reference, but also reduces liability in the event termination must occur. After the team members read the manual, ask that they sign it and make it clear that their signature signifies they understand and will abide by the rules. If you notice foul play or feel that an employee is consistently disregarding safety rules, you may decide it necessary to terminate them. Their signature will provide proof that they read and understood the lab safety manual in the event of legal proceedings.

Conduct Unannounced Inspections

What good is a bunch of policies and procedures if they are going unchecked? Put together a safety audit checklist and perform random, yet routine inspections. Making them random and unannounced will alleviate the possibility of personnel “tidying up” for the inspection. Nobody likes a pop-quiz. But when safety is a priority, they must be done. Over time, well developed laboratory safety training and inspections will create good habits. These habits are invaluable.

Practice Routine Safety Drills

Remember the good ol’ days back in elementary school when safety drills were an exciting surprise? As kids, we didn’t understand just how valuable those drills were. They prepared us for worst-case scenarios and emergency disasters. If the time ever came where these practices were necessary, we were armed with the training and knowledge we had. Guess what? Nothing has changed as we get older. As previously mentioned, good habits are essential to ongoing safety practices. Conducting routine drills will prepare students and staff members for emergencies. Identify emergency exits, meeting areas, and individuals that can assist as guides in the event evacuation is necessary. Make sure everyone is completely aware of the plans. Providing handouts or literature with maps is a bonus. Lab managers dread ever having to experience an emergency. But being well prepared is more than half the battle.

Delegate Tasks

You’ve got a lot to do as a lab manager or supervisor. Another great way to make sure everything is running efficiently is to delegate tasks. Assign various team members duties that will help keep lab safety protocols in place. For example, one member could make sure all warning signs are present while another keeps inventory of chemicals. Spread out the responsibility to allow yourself the time necessary to focus on the bigger picture. Training, delegation and inspection should be all that you have to do once it all comes together like clockwork.

Encourage and Promote Personal Safety

There is nothing more effective than positive motivation and excitement. Laboratory safety isn’t exactly a party favorite. However, with a little added personality, carefully planned pep-talks and sharing of personal experiences can really make all the difference. Adding a little humility by sharing examples of mistakes you’ve made makes it all more real and relatable. And who doesn’t enjoy having some fun? I sure do. Incorporate some humor while speaking about laboratory safety policies and you’ll get more than just laughs. The things you teach will be more memorable.

Posted by Dr. Tim Sandle

Friday, 17 February 2017

Insight into the functioning of human gut bacteria

The human large bowel ("gut") is colonised by an extremely dense population of bacteria, collectively termed the microbiota or "gut flora."

Recent research indicates that the microbiota is important for human health and nutrition and has been linked with auto-immune diseases, cancer and obesity. The function and composition of the microbiota is dependent on the ability of individual micro-organisms to acquire nutrients such as starch and other dietary polysaccharides in the highly competitive environment of the human large bowel.

This process of nutrient acquisition is carried out by protein machines embedded in the bacterial cell envelope. In many microbiota members, this machine is a two-component complex consisting of a substrate binding protein (termed SusD) and a channel-forming transport protein (termed SusC).

The team at Newcastle University today report that they have purified and determined the first three-dimensional atomic structures of SusCD complexes by X-ray crystallography and have established how the nutrients are transported into the bacterial cell.

The SusCD complexes function like a pedal bin, with SusD forming the lid on the SusC bin. In the absence of substrate, the lid can open. After substrate capture, the lid closes and the substrate moves into the bin for transport into the cell.

The study provides fundamental insights into the functioning of the microbiota and understanding the human-gut flora symbiosis. Results such as these are a timely and necessary complement to most current microbiota research, which is largely focused on answering systems biology questions such as "who is there and when?."

By linking mechanistic and systems biology, the study could also provide insights to manipulate the composition of the microbiota via interference with critical nutrient uptake processes.

For further details, see:

Amy J. Glenwright, Karunakar R. Pothula, Satya P. Bhamidimarri, Dror S. Chorev, Arnaud Baslé, Susan J. Firbank, Hongjun Zheng, Carol V. Robinson, Mathias Winterhalter, Ulrich Kleinekathöfer, David N. Bolam, Bert van den Berg. Structural basis for nutrient acquisition by dominant members of the human gut microbiota. Nature, 2017; DOI: 10.1038/nature20828

Posted by Dr. Tim Sandle

Thursday, 16 February 2017

New target for taming Ebola

A team of scientists led by Ronald Harty, a professor of pathobiology and microbiology at the University of Pennsylvania's School of Veterinary Medicine, has identified a mechanism that appears to represent one way that host cells have evolved to outsmart infection by Ebola and other viruses. In a new paper, he and colleagues reveal that host cells sequester viral proteins away from the plasma membrane within the cell, thus preventing viruses from spreading.

Harty says that finding a way to amplify this molecular interaction could lead to a novel antiviral strategy against Ebola that could temper the pathogen's damage.

The scientists knew that, in infections with Ebola as well as many other viruses, including Marburg, rabies and HIV, viral matrix proteins, such as Ebola VP40, interacted with host proteins through short protein motifs: the PY motif on the viral protein and the WW motif on the host cell protein. Prior to this current study, all of the known interactions enabled the virus to bud efficiently from the cell.

In the current work, the researchers screened for new WW motifs from mammalian cell proteins that bound tightly to the PY motif of Ebola virus' VP40 protein. Not every PY motif binds to every WW domain; the interaction is specific, like a lock and key.

The screen turned up some proteins that the Penn team had explored before but also a new one, a protein called BAG3, known as a chaperone protein, which under normal physiological conditions acts to promote cell survival.

After confirming that Ebola VP40 interacted with full-length BAG3 in mammalian cells specifically via the WW domain, the researchers went on to test its functionality in influencing budding. They used a test that avoids manipulating the actual Ebola virus, which is too dangerous for the Penn Vet laboratory. Instead, they examined virus-like particles, which are produced by the virus's matrix protein, VP40, and are not infectious but accurately mimic the budding step of infection.

When the researchers examined cells expressing either Ebola or Marburg VP40 and then added in BAG3, they found that VLP budding went down in a dose-dependent manner. When they mutated the WW domain of BAG3 so it couldn't interact with VP40's PY domain, budding levels remained unchanged.

Knocking down levels of naturally occurring BAG3 with synthetic strands of RNA did just the opposite, increasing budding.

"With all of these assays, there was a consistent effect on budding levels, either up or down," Harty said.

Enhancing such an interaction, perhaps in combination with other therapies that attack the virus at other stages of its life cycle, could give the immune system the opening it needs to overcome an infection.

Using confocal microscopy and fluorescently labeled proteins, the scientists discovered that BAG3 appeared to be sequestering VP40 in the cell's cytoplasm away from the plasma membrane where the viral particles would need to go in order to bud off and spread to infect other cells. Their work identified BAG3 as the first WW containing host protein to negatively affect virus budding.

Although the group has not yet tested the VP40-BAG3 interaction with live Ebola or Marburg virus -- those experiments are planned -- they did find that BAG3 limits budding of a recombinant vesicular stomatitis virus that contains the Ebola PY motif.

"We used that to show that this works in a live virus infection," Harty said. "Taken together, we're hoping and assuming that it works the same way with the authentic Ebola virus."

In addition to testing BAG3 interactions with the Ebola and Marburg virus, Harty's lab also plans to further investigate what BAG3 is doing to VP40, whether it's simply sequestering it or whether it's modifying or degrading it.


Jingjing Liang, Cari A. Sagum, Mark T. Bedford, Sachdev S. Sidhu, Marius Sudol, Ziying Han, Ronald N. Harty.Chaperone-Mediated Autophagy Protein BAG3 Negatively Regulates Ebola and Marburg VP40-Mediated Egress. PLOS Pathogens, 2017; 13 (1): e1006132 DOI:10.1371/journal.ppat.1006132

Posted by Dr. Tim Sandle

Wednesday, 15 February 2017

Good Practice Guidelines for Blood Establishments

EU directive integrates Council of Europe Good Practice Guidelines for blood establishments

Good Practice Guidelines have been prepared through co-operation between the European Directorate for the Quality of Medicines & HealthCare of the Council of Europe (EDQM) and the Commission of the European Union (EU). The elaboration of the Good Practice Guidelines included substantial public consultations giving stakeholders an opportunity to comment on the draft version.

The Good Practice Guidelines were adopted by the European Committee (Partial Agreement) on Blood Transfusion (CD-P-TS) of the Council of Europe during its plenary session in November 2016. The document is an integral part of the 19th Edition of the Council of Europe Guide to the Preparation, Use and Quality Assurance of Blood Components, Appendix to Recommendation No. R (95) 15 of the Committee of Ministers, referred to below as the “Guide”.

Following adoption of the Good Practice Guidelines by the European Commission, European Union and European Economic Area Member States shall ensure that Blood Establishments take fully into account the standards and specifications set out in those Guidelines when implementing their quality system, in line with the new Commission Directive (EU) 2016/1214. In order to bring into force the laws, regulations and administrative provisions necessary to comply with this Directive by 15 February 2018, some member states need to translate the text of the Good Practice Guidelines into their national language. To expedite this process, a verbatim copy of the text of the Good Practice Guidelines that will be published in the Guide is downloadable as a document here.

Posted by Dr. Tim Sandle

Tuesday, 14 February 2017

Trial vaccine for leprosy

Leprosy, also known as Hansen’s disease, is caused by the bacterium Mycobacterium leprae. These Gram-positive, rod-shaped bacteria depend greatly on their host for survival - they have lost many important metabolic genes through the process of “reductive evolution”. Because of this, they are only able to grow inside host cells. Interestingly, humans and armadillos are the only known, definitive hosts for M. leprae.

Leprosy can be treated with a combination of antibiotics and corticosteroids. Drug-resistant strains of bacteria are popping up, so many researchers are working to develop a vaccine. The BCG vaccine for tuberculosis (caused by Mycobacterium tuberculosis, a close relative of M. leprae) has been used with some success to prevent leprosy in both India and Brazil. However, the American Leprosy Missions and the Infectious Disease Research Institute (IDRI) have teamed up to develop a vaccine that consists of four key proteins, and it is currently in clinical trials. The IDRI has also developed a flash-drive-sized diagnostic test for leprosy. If the vaccine is successful, the researchers hope to use the diagnostic test to pinpoint populations most in need of vaccination.

(Edited extract from Laboratory Roots)

Posted by Dr. Tim Sandle

Monday, 13 February 2017

Control of transmission mechanism mediated of calcium pulses

A new medical article of interest. looking at the effects of calcium ion depletion on the human cell.

The abstract reads:

Given the importance of calcium for good functioning of the body and knowing its involvement in signaling mechanisms and intercellular transport (which involves mechanisms related to the translation of transmembrane signals), the study outlined combines theoretical and practical data relating to the these processes. Theoretical information is supported by data collected from medical practice. Here attention is paid to the body structures involved in pathologies and changes that have occurred due to imbalance of calcium ions within different structures and at the level of cellular ultrastructure. With the presentation of the structural components, these bring into focus various kinds of diseases associated with calcium ion pulses.

The reference is:

Chescha, A., Sandle, T. and Gyurka, G. A. (2016) Considerations on the structures involved in the control of transmission mechanism mediated of calcium pulses, Annals of The Romanian Society for Cell Biology, 21 (1): 1-6

For further details see: RG

Posted by Dr. Tim Sandle

Sunday, 12 February 2017

Antimicrobial resistant bacteria detected in air pollution

Areas subject to air pollution contain a growing concentration of bacteria that are resistant to antimicrobials, according to a new study. Consequently, air movement may provide a new ways for their transmission.
By Tim Sandle

The study, highlighting a growth in airborne or air-carried antimicrobial resistant bacteria, has come from China, with a focus on Beijing. The extent of antimicrobial resistance has been assessed at the genetic level, with the detection of DNA from genes that make bacteria resistant.
The study has been led by Professor Joakim Larsson, of the Sahlgrenska Academy and the University of Gothenburg. Professor Larsson is especially concerned about air as a potential vector for spreading antimicrobial resistant pathogens.
Antimicrobial resistance (including resistance to antibiotics) is the biggest risk faced by human societies. The implications are that life expectancy could fall due to people dying from diseases that are readily treatable today.
With the new research, Professor Larsson’s team tested air samples for genes that make bacteria resistant to antibiotics. From a total of 864 samples, DNA was tested and related back to its source. One area of concern was the detection of a series of genes that provide resistance to carbapenems. These are a group of ‘last resort antibiotics’ and they are administered for infections caused by bacteria that the most resistant to antimicrobials. Carbapenems are members of the beta lactam class of antibiotics, which kill bacteria by binding to penicillin-binding proteins and inhibiting cell wall synthesis.
Importantly, the findings cannot indicate if the bacteria are alive in the air. This narrows the risk somewhat; however, the potential for genetic transfer with viable bacteria, upon contact, remains.
The study is, however, only a starting point. The researchers plan to assess whether antimicrobial resistance can indeed spread through air. Here the focus will move to a study of the air within the vicinity of European sewage treatment plants. Sewage plants are regularly called out as potential sites for the spread of antimicrobial resistance. This is because, with so many different types of bacteria coming together in sewage plants, this provided optimal conditions for organisms to swap genes that confer resistance. This also means antibiotic-resistant bacteria could evolve much faster than they would in isolation.
Data will be cross-checked in relation to the air and to the sewage. Additional samples will be taken from people who live in close proximity to sewage plants.
The research findings are published in the journal Microbiome and the research paper is titled “The structure and diversity of human, animal and environmental resistomes.”

Saturday, 11 February 2017

Model to predict how microbiomes may respond to change

Scientists studying microbiomes have created a framework for predicting how the composition of these complex microbial communities may respond to changing conditions.

The review study, led by Jennifer Martiny, professor of ecology & evolutionary biology at the University of California, Irvine, appears in the Nov. 5 issue of Science. It presents a far-reaching assessment of microbiomes that could affect efforts to improve human health and the health of all Earth's ecosystems.

Microbiomes are collections of microscopic organisms -- such as bacteria, viruses, archaea, fungi, protozoa, algae and plankton -- that inhabit ecosystems as varied as the human digestive tract, the ocean and soil. For instance, the 100 trillion microbes in the human gut -- which vastly outnumber the "human" cells in our bodies -- are critical to our health and development.

A few grams of soil or sediment may contain tens or even hundreds of thousands of microbial species, each interacting with the others. Together, they are largely responsible for the processing of nutrients and carbon in soil -- regulating the decomposition of waste materials, the regeneration of soil fertility and greenhouse gas emissions.

The study delves into microbial evolutionary processes and explores previous research showing that microbial traits -- particularly with bacteria -- vary predictably in how they have evolved across the "tree of life." For example, some traits, such as photosynthesis, evolved a long time ago and are shared by large groups of genetically related bacteria. Other traits, such as sensitivity to a particular virus, have evolved many times in many small groups.

Patterns of microbiome diversity among samples can reveal more information than previously thought when paired with the evolutionary history of microbial traits. Microbiologists could use this information to narrow down the reasons for differences in microbiome diversity among many samples.

The planet hosts a vast variety of microbial communities, from those in undersea volcanos and plant ecosystems to untold numbers of microbes in the human body that fight disease. These microbiomes share many similar traits, and further research on them could reveal basic information about Earth and its inhabitants.


J. B. H. Martiny, S. E. Jones, J. T. Lennon, A. C. Martiny.Microbiomes in light of traits: A phylogenetic perspective. Science, 2015; 350 (6261): aac9323 DOI:10.1126/science.aac9323

Posted by Dr. Tim Sandle

Friday, 10 February 2017

Unique microbial photosynthesis discovered

Researchers at Washington State University have discovered a new type of cooperative photosynthesis that could be used in engineering microbial communities for waste treatment and bioenergy production.

Prosthecochloris aestaurii, a green-tinged, plant-like microbe, comes from the extreme environment of Hot Lake, a high salinity lake in northern Okanogan County near Oroville, Wash. Discovered and identified a few years ago by researchers at the U.S. Department of Energy's Pacific Northwest National Laboratory and Southern Illinois University, the bacterium is able to photosynthesize, using sunlight along with elemental sulfur or hydrogen sulfide to grow.

The researchers noticed that P. aestuarii tended to gather around a carbon electrode, an electricity conductor that they were operating in Hot Lake. The researchers isolated and grew P. aestuarii and determined that, similar to the way half of a battery works, the bacterium is able to grab electrons from a solid electrode and use them for photosynthesis. The pink-colored Geobacter sulfurreducens meanwhile, is known for its ability to convert waste organic matter to electricity in microbial fuel cells. The bacterium is also used in environmental cleanup.

G. sulfurreducens, like animals and humans, can't photosynthesize. It consumes organic compounds, such as acetate, and "breathes" out carbon dioxide.

The bacterium is known for its ability to donate electrons to a solid electrode. As it consumes acetate, it generates electrons, which can be collected as electricity.

The researchers found that P. aestuarii could accept electrons generated from G. sulfurreducens and use them in a new type of anaerobic photosynthesis never before seen. Similar to how a battery or fuel cell works, the bacteria transfer electrons. They feed off each other to grow under conditions in which neither could grow independently.

From an ecological perspective, this new form of metabolism may play an important role in carbon cycling in oxygen free zones of poorly mixed freshwater lakes. It may also present new possibilities for engineering microbial communities for waste treatment and bioenergy production.

For further details see:

Phuc T. Ha, Stephen R. Lindemann, Liang Shi, Alice C. Dohnalkova, James K. Fredrickson, Michael T. Madigan, Haluk Beyenal. Syntrophic anaerobic photosynthesis via direct interspecies electron transfer. Nature Communications, 2017; 8: 13924 DOI:10.1038/NCOMMS13924

Posted by Dr. Tim Sandle