Addressing antibiotic resistance

Humans face the very real risk of a future without antibiotics. The implications of this are that life expectancy could fall due to people dying from diseases that are readily treatable today. One concern for the future is the re- emergence of diseases that are ‘officially’ extinct, such as tuberculosis (a disease caused by Mycobacterium tuberculosis). The other concern is that without effective antibiotics, human society will no longer be able to conduct the types of medical procedures that can lead to immunosuppression. Such therapies include those for cancer treatments or to address autoimmune disorders.

With regard to this serious issue, Tim Sandle has written a review article for the journal Microbiology & Infectious Diseases. The article can be accessed on-line here: SOJ Microbiology and Infectious Diseases or, alternatively, contact Tim Sandle.

Sandle, T. (2014) Novel Methods to Address Antimicrobial Resistance, SOJ Microbiology & Infectious Diseases, 2 (1): 2-3

Posted by Tim Sandle

Microbes and climate change

Scientists are trying to understand how populations of microorganisms regulate emissions of nitrous oxide from streams and rivers. Nitrous oxide is a potent greenhouse gas and contributor to climate change. The source of the gas is nitrate, a compound made up of nitrogen and oxygen, which is commonly used in fertilizers and finds its way into waterways from agricultural runoff.

Normally, denitrification results in harmless nitrogen gas. In some cases, however, one of the intermediate compounds, nitrous oxide, is emitted instead of nitrogen gas before the denitrification process completes.

Many researchers argue that rates of nitrous oxide production in natural systems may be influenced by the distribution of microorganisms and whether they have the ability to reduce nitrous oxide to nitrogen gas.

For more details, see the Boise State University

Posted by Tim Sandle

The microbial economy

Microbial behavior matches that of economic markets, according to a new paper. Here microbes are said to ‘trade’ with each other. Sounds a little farfetched? Possibly not, although the idea is certainly radical.

In a paper, scientists have posed the question of whether pure economic market behavior (in the full classical liberal concept of markets developed by Adam Smith), can be translated for the interpretation of the behavior of microorganisms. For example, they consider whether such theories can be used to describe the exchange of commodities between organisms without any cognitive ability, such as microbes.

According to the research brief, the authors state:

“Could think of instances where single-celled organisms had been shown to avoid bad trading partners, build local business ties, diversify or specialize in a particular commodity, save for a rainy day, eliminate the competition and otherwise behave in ways that seem to follow market-based principles.

They concluded not only that microbes are economic actors, but also that microbial markets can be useful systems for testing questions about biological markets in general, such as the evolution of partner choice, responses to price fluctuations and the identification of market conditions that drive diversification or specialization.”

According to the authors, their radical idea was inspired by a workshop they attended on biological markets (transactions in which partners, typically animals, exchange commodities for their mutual benefit). From this event, they drew up the basis of their paper. They are of the view that studying microbial exchange systems as miniature markets will give them insight into the many collaborative behaviors of microbes, helping to generate new hypotheses and approaches in the field of social microbiology.

Biological market theory has been around for about twenty years. The basis of this approach is that whenever organisms interact in a way that allows scientists to recognize different classes of ‘traders’ that exchange commodities, such as goods (for example, food, shelter, gametes) or services (such as warning calls, pollination, protection, cleaning) then scientists can formalize such an interaction system as a “biological market”. The basic tenet of the biological market concept is that like in human trading systems shifts in supply and demand cause changes in the exchange value of the commodities traded. Characteristics of biological markets can be found in mating markets, mutualisms between members of different species and cooperation among individuals.

It should be noted that this represents a narrow stream of biology and the ideas do not have majority support among biologists.

The paper has been published in the Proceedings of the National Academy of Sciences (PNAS), in an article titled “Evolution of microbial markets”.

Posted by Tim Sandle

Biohazard Control

Working in biological containment facilities or with infectious agents is serious business. The research performed usually entails indigenous or exotic agents with the potential for severe or lethal disease. Two examples of infectious pathogens that have received a lot of attention recently are yellow fever and West Nile virus. Obviously, if released they have the potential to cause extensive harm or damage to people, the environment, and the community. Needless to say, we do not want these agents to get out into the community nor do we want our employees who are working with these agents to be in harm’s way. The foundation for safe operation of any biological containment facility is an effective exposure control plan. This article discusses the basic elements of a comprehensive exposure control plan, what each element should contain, and tips on successful implementation.

The exposure control plan is basically a biosafety manual written to address the unique conditions of the current research, facility design, and personnel operations necessary to carry out the laboratory’s mission. One excellent free reference is the CDC’s Biosafety in Microbiological andBiomedical Laboratories, which contains comprehensive information on biological risk assessment and summary statements for many common infectious agents.

An effective exposure control plan is comprehensive, clearly written in concise terms, well organized, distributed to all people who must enter or work in the containment lab, and, most important, read and understood by all. A good comprehensive exposure control plan will contain at least seven main sections. These are general laboratory function, specific facility design and operational procedures, special laboratory safety equipment and personal protective equipment (PPE), laboratory research practices and procedures, health and medical monitoring requirements, emergency procedures, and employee training. Let’s take a look at each of these chapters to see what they should include.

General laboratory function

The opening section will provide a clear organization of personnel and assign responsibilities for all who work in and support the containment laboratory. How access is controlled is of primary importance. The laboratory director has ultimate responsibility. Access should be restricted to only certified people who are absolutely necessary. Certified means they understand the potential biohazard, have demonstrated proficiency in the laboratory’s procedures, and have complied with the health and medical entry requirements. Proper entry and exiting procedures for staff, visitors, and maintenance/ custodial workers are clearly established in this section as well. Finally, procedures for identifying, reporting, and correcting problems or violations of protocol are detailed.

Specific facility design and operational procedures

Specific laboratory layout and operations are described in this section. Included are security access mechanisms; self-closing, lockable doors; and other security measures. Proper signage indicating agents present, contact information for the principal investigator and other responsible people, and any special requirements are posted at all access points. The design of directional airflow from clean areas toward contaminated areas is described, and procedures for checking proper operation by laboratory staff are outlined. Measures are included for checking and ensuring that the surfaces of all walls, floors, and ceilings are smooth, impermeable, and easily cleaned and that all penetrations are sealed. Pest management is addressed here as well, with an appropriate insect and rodent control program.

Special laboratory safety equipment and PPE

This is arguably one of the most important parts of the exposure control plan. It should explain the PPE that must be worn. Describe where PPE is stored as well as when and where it is used and how it is removed and discarded. It should cover the proper types of gloves, eyewear, and gowns or lab coats to be used. This section also addresses proper use and maintenance of the lab’s safety equipment such as autoclaves, biosafety cabinets, eyewash stations, safety showers, ventilation alarms, and other specially designed containment equipment. Procedures for decontaminating equipment prior to maintenance work should also be included.

Laboratory research practices and procedures

The heart of the exposure control plan is contained in this section. It addresses safe handling and storing of viable material, including biological safety cabinet use, handling frozen samples, and use of secondary containers. Procedures for using and disposing of sharps, found in most containment laboratories, are paramount. Addressed in this section are waste handling and disposal, decontamination, and housekeeping (e.g., cleaning up at the end of the day or after finishing a research protocol).

Health and medical monitoring requirements

The purpose of this section is to provide another level of protection against laboratory-acquired illness by documenting necessary immunizations. Immune-suppressed individuals or persons at increased risk should be strongly discouraged from entering the facility. Depending on the agents present, vaccinations (hepatitis B), antibody testing (TB skin test), or serum storage may be required. The exposure control plan should clearly define with a welldocumented rationale what is required and who is covered.

Emergency procedures

This segment describes procedures for an accident, spill, release, or exposure that contaminates or injures laboratory staff or the environment. A good reference for putting this section together would be the OSHA bloodborne pathogen standard, 29CFR1910.1030.2 Everyone working in the facility should be thoroughly versed in the emergency procedures. Spill kits should be maintained and biohazard spills decontaminated and cleaned up as soon as possible by properly trained and equipped staff. Any incident should be completely documented with a written report.

Employee training

We wrap up our exposure control plan with the chapter covering employee training. The first step is to make sure everyone who will be working in the containment facility has read and understands this exposure control plan. They should be informed about each infectious agent present, the risks associated with these, and the signs and symptoms of infection or disease. This training, along with bloodborne pathogen training, should be renewed annually and written documentation kept on record.

There you have our quick outline for putting together an effective exposure control plan. We have just touched on each topic briefly in this article. Future articles will probe deeper into select sections, providing additional details as well as tips for success and traps to avoid. Watch this column for more helpful information. As always, the Safety Guys welcome your comments and questions, so we hope to hear from you. Until then, stay safe.

Source: Laboratory Manager

Cleanroom inventor to enter Hall of Fame

The inventor of the modern cleanroom, Willis Whitfield, will be honored posthumously by the National Inventors Hall of Fame for a technology that revolutionized manufacturing in electronics and pharmaceuticals, made hospital operating rooms safer and advanced space exploration.

The inventor of the modern cleanroom, Willis Whitfield, will be honored posthumously by the National Inventors Hall of Fame for a technology that revolutionized manufacturing in electronics and pharmaceuticals, made hospital operating rooms safer and advanced space exploration.

Whitfield, the son of Texas cotton farmers who became a physicist, retired from Albuquerque’s Sandia National Laboratories in 1984 and died Nov. 12, 2012, shortly after the laminar-flow cleanroom invention’s 50th anniversary. With slight modifications, his invention is still the standard.

Whitfield’s solution was to constantly flush out or “sweep” a room with highly filtered air. In an initial model, Whitfield designed a workbench along one wall. Clean air entered the room from a bank of filters that were 99.97 percent efficient in removing particles larger than 0.3 microns. For example, cigarette smoke blown in one side comes out the other as clean air.

The air was circulated in the room at a rate of 4,000 cubic feet or about 10 changes of air per minute. The resulting linear speed of the air is slightly more than 1 mph, which is about the same as that felt walking through a still room.

In a later modification, the air was passed down over the work area instead of across, letting gravity help carry troublesome particles into the floor, which was covered with grating. Filters underneath clean the air and it is circulated back around to re-enter the room.

When Whitfield announced the invention in 1962, researchers and industrialists did not immediately take to it, but within a few short years, $50 billion worth of laminar-flow cleanrooms were built worldwide and Whitfield had been dubbed “Mr. Clean” by TIME Magazine.

Based on a report from PhysOrg

Updates to European Pharmacopeia 8th edition (8.1)

Supplement 8.1 to the Ph. Eur. has been issued.

Implementation date 1st Apr 2014.

The main changes are:

Citric Acid Monohydrate (0456)                                            

This monograph has been revised to indicate its status within the context of international Harmonisation, a collaboration between the Japanese Pharmacopoeia, the United States

Pharmacopeia and the European Pharmacopoeia. A footnote has been included in the text to refer to chapter 5.8. Pharmacopoeial harmonisation

Ethanol (96%) (1317)                                                            

This monograph has been revised to indicate its status within the context of international Harmonisation, a collaboration between the Japanese Pharmacopoeia, the united States Pharmacopeia and the European Pharmacopoeia. A footnote has been included in the text to refer to chapter 5.8. Pharmacopoeial harmonisation.

Absorbance: more-detailed spectrum description given.

Posted by Tim Sandle

Microbiology World - new edition (free magazine)

A new edition of Microbiology World has been published (issue 3). The current edition features a number of articles that will be of interest to the microbiology community. This includes:

• Cockroach brain can fight infections against infectious diseases by Aleena Shahid and Sikandar K. Sherwani
• The rise of antimicrobial resistant microorganisms by Tim Sandle
• Adulteration in Food by Sachin Aryal
• The methods to detect point mutations using real-time PCR by Sao Bang

There are also other features of interest and a book review.



 The reference for Tim Sandle's article is:

Sandle, T. (2014) The rise of antimicrobial resistant microorganisms, Microbiology World, Issue 2, pp10-16

The current edition can be downloaded here.

Posted by Tim Sandle

MRSA dominates with the help of skin bacteria

There could be an explanation for how the most common strain of methicillin-resistant Staphylococcus aureus (MRSA) rapidly rose to prominence. Research published in mBio®, suggests that the strain recently acquired a number of genes from common skin bacteria that allow it to grow and thrive on the skin where other strains of MRSA cannot.

Since it was first identified in the late 1990s the USA300 strain of MRSA has undergone an extremely rapid expansion across the United States. It is now the predominant cause of community-acquired MRSA skin and soft tissue infections and has been implicated in MRSA outbreaks among professional football teams. The strain is genetically distinguished from other strains by a cluster of genes known as the arginine catabolic mobile element (ACME.)

Using phylogenetic analysis researchers have shown that the modular segments of ACME were assembled into a single genetic locus in Staphylococcus epidermidis (a relatively harmless bacterium typically found on human skin) and then horizontally transferred to the common ancestor of USA300 strains in an extremely recent event that coincided with the emergence and spread of this strain.

The researchers identified one ACME gene in particular, called speG, that conferred on USA300 strains the ability to withstand high levels of polyamines, compounds produced by the skin that are toxic to other strains of MRSA. Polyamine tolerance also gave MRSA multiple advantages including enhanced biofilm formation, adherence to host tissues and resistance to certain antibiotics, according to the study.

The findings suggest that these properties gave USA 300 a major selective advantage during skin infection and colonization, contributing to the evolutionary success of this clone.

For further details see:

P. J. Planet, S. J. LaRussa, A. Dana, H. Smith, A. Xu, C. Ryan, A.-C. Uhlemann, S. Boundy, J. Goldberg, A. Narechania, R. Kulkarni, A. J. Ratner, J. A. Geoghegan, S.-O. Kolokotronis, A. Prince. Emergence of the Epidemic Methicillin-Resistant Staphylococcus aureus Strain USA300 Coincides with Horizontal Transfer of the Arginine Catabolic Mobile Element and speG-mediated Adaptations for Survival on Skin. mBio, 2013; 4 (6): e00889-13 DOI: 10.1128/mBio.00889-13

Posted by Tim Sandle

Discuss the role human gut microbes play in digestive and overall health

World-renowned experts to discuss the role human gut microbes play in digestive and overall health

Friday, March 7, 2014, 9 ― 10:30 a.m. (ET)

                                                                                                                                                                                                       

You are invited to take part in a special online press conference with gut microbiota experts this Friday, March 7, 2014, at 9 a.m. ET. Moderated by UK media medic Dr. Mark Porter, best known for his television and radio work for the BBC, the press conference will inform about factors that can lead to an unbalanced microbiota and will address the consequences of a disturbed microbiota, as well as the way in which diet and nutrition can help (including the use of probiotics and prebiotics). A prospective look at non-bacterial microbes in the gut will also be offered. Topics and speakers include:

 

·         The latest gut microbiota research: key topics at the Gut Microbiota for Health World Summit 2014
Speaker: Prof. Gail Hecht, USA

·         Gas and irritable bowel syndrome: what role does the gut microbiota play?
Speaker: Prof. Giovanni Barbara, Italy

·         How diet and nutrition can help (probiotics and prebiotics at all stages of life)
Speaker: Prof. Francisco Guarner, Spain

·         Non-bacterial microbes in the gut: what are they, how do we characterize them and what do they do?
Speaker: Prof. Gary Wu, USA

·         “Gut Microbes — Importance in Health and Disease”: the theme of the World Gastroenterology Organisation’s upcoming World Digestive Health Day 2014 Speaker: Prof. Francisco Guarner, Spain

 

If you would like to attend the online press conference, register at https://www1.gotomeeting.com/register/365388496.

 

To learn more about the meeting or if you are interested in attending, please email Aimee Frank, afrank@gastro.org.

 

The microbial communities that reside in the human gut and their impact on human health and disease are one of the most exciting new areas of research today. To address the most recent advances in this rapidly developing field, scientists and health-care professionals from all over the world will come together at the Gut Microbiota for Health World Summit in Miami, Florida, USA, on March 8 and9, 2014. The meeting is hosted by the Gut Microbiota & Health Section of the European Society of Neurogastroenterology and Motility (ESNM) and the American Gastroenterological Association (AGA) Institute, with the support of Danone.

 

For further information on the summit program, please refer to the following website: http://summit-registration.gutmicrobiotaforhealth.com/.

Posted by Tim Sandle

New antifungal treatments

Many antifungal drugs work by binding with sterols in the cell membrane to damage the integrity of the barrier causing cell death. In recent years with changes in medical practice, there is an increase in resistance to antifungal therapies. A thorough understanding of how pathogenic yeasts respond to hypoxic conditions is essential to the discovery and development of new, more effective anti-fungal treatments.

All but a few eukaryotes die without oxygen, and they respond dynamically to changes in the level of oxygen available to them. UCD scientists used genetic analysis to pinpoint an evolutionary switch in regulating response to low oxygen levels in fungi.

One example of ancient oxygen-requiring biochemical pathway in eukaryotes is the biosynthesis of sterols, producing cholesterol in animals and ergosterol in fungi.

The mechanism regulating the sterol pathway is widely conserved between animals and fungi and centres on a protein family of transcription activators named the sterol regulatory element binding proteins (SREBPs), which form part of a sterol-sensing complex.

However, in one group of fungi; the Saccharomycotina, which includes the model yeast Saccharomyces cerevisiae and the major pathogen Candida albicans, control of the sterol pathway has been taken over by an unrelated regulatory protein, Upc2.

New research published in PLoS Genetics by UCD researchers, in collaboration with colleagues from AgroParisTech, France and the University of Kansas, USA, used comparative genomic analysis to investigate the timing of the evolutionary switch from one regulatory mechanism to another; from SREBPs to Upc2.

Using a mixture of genetic and biochemical analysis, the group showed that Upc2 is the main regulator of the hypoxic response in Y. lipolytica, and regulates the levels of sterols in the membrane, while SREBP appears to be a "molecular fossil" that has lost its role as a sterol regulator.

The SREBP gene retains some role in the hypoxic response of Y. lipolytica however, and is required for maximal growth when oxygen levels are low. Derivatives of SREBPs are also required for the growth of several yeast species as filamentous forms, which is important for virulence.

The findings are reveal more about the development of eukaryotes over time but also have tremendous potential for clinical use if they can be applied to the development of more effective anti-fungal therapies.

For further details, refer to:

Sarah L. Maguire, Can Wang, Linda M. Holland, François Brunel, Cécile Neuvéglise, Jean-Marc Nicaud, Martin Zavrel, Theodore C. White, Kenneth H. Wolfe, Geraldine Butler. Zinc Finger Transcription Factors Displaced SREBP Proteins as the Major Sterol Regulators during Saccharomycotina Evolution. PLoS Genetics, 2014; 10 (1): e1004076 DOI: 10.1371/journal.pgen.1004076

The influence of the gut microbiota on obesity and insulin resistance

We live with millions of microorganisms and these bacteria have a profound impact on host physiology. Microbial-responsive signaling by host cells affects metabolic, neurological, inflammatory, immunologic, and host defense functions.

There is tantalizing evidence indicating that the gut microbiota plays a significant role in the development of obesity, obesity-associated inflammation, and insulin resistance. An altered gut microbiota has been associated with obesity and diabetes (Diabetes. 2014 Jan 15). In addition, increased levels of circulating bacteria or bacterial products are associated with insulin resistance.

Posted by Tim Sandle

FDA's New Guidance On Medical Device Development Tools

The FDA has recently issued a guidance document relating to medical development tools. The policy is intended to support the development and timely evaluation of innovative medical devices.

The guidance describes a process for “qualification” of an MDDT, which reflects the FDA’s determination that within a specified context of use (the use parameters for which the MDDT has been validated); the results of an assessment that uses an MDDT can support device development and regulatory decision-making. Definitions of applicable terms, criteria for evaluating an MDDT for a specific context of use, considerations for qualification, and the required contents of a qualification submission are also included.

For details see: FDA

Posted by Tim Sandle

Implementation of Good Distribution Practices

The MHRA have issued some guidance for the implementation of Good Distribution Practices (GDP). This follows a recent update to EU guidance.

According to the Agency:

“Following publication of the revised Guidelines for GDP by the European Commission, the following explanatory note has been prepared in order to clarify the interpretation of the guideline by MHRA. The document is not intended to provide an in depth explanation of the published guideline, and should be read in conjunction with the guide, in order to clarify the expectations of the MHRA Inspectorate for those areas that may be open to individual Member State interpretation.”

The MHRA interpretation can be found here: MHRA

Posted by Tim Sandle

How bacteria evade antibiotics

A step forward has been made in understanding how a subset of bacterial cells escape being killed by many antibiotics. It appears that cells become "persisters" by entering a state in which they stop replicating and are able to tolerate antibiotics. Unlike antibiotic resistance, which arises because of genetic mutations and is passed on to later generations, this tolerant phase is only temporary, but it may contribute to the later development of resistance.

For further details, refer to the following research paper:

S. Helaine, A. M. Cheverton, K. G. Watson, L. M. Faure, S. A. Matthews, D. W. Holden. Internalization of Salmonella by Macrophages Induces Formation of Nonreplicating Persisters. Science, 2014; 343 (6167): 204 DOI: 10.1126/science.1244705

Posted by Tim Sandle

Rare Disease Day

Today, Feb 28, is the seventh Rare Disease Day. Rare Disease Day is an annual, awareness-raising event co-ordinated by EURORDIS at the international level and by National Alliances and Patient Organisations at the national level.

The main objective of Rare Disease Day is to raise awareness amongst the general public and decision-makers about rare diseases and their impact on patients’ lives.

A disease or disorder is defined as rare in Europe when it affects fewer than 1 in 2000. A disease or disorder is defined as rare in the USA when it affects fewer than 200,000 Americans at any given time.

One rare disease may affect only a handful of patients in the EU (European Union), and another touch as many as 245,000. In the EU, as many as 30 million people alone may be affected by one of over 6000 rare diseases existing.

• 80% of rare diseases have identified genetic origins whilst others are the result of infections (bacterial or viral), allergies and environmental causes, or are degenerative and proliferative. 
• 50% of rare diseases touch children. 
• Characteristics of rare diseases

Over 6000 rare diseases are characterized by a broad diversity of disorders and symptoms that vary not only from disease to disease but also from patient to patient suffering from the same disease.

Relatively common symptoms can hide underlying rare diseases leading to misdiagnosis and delaying treatment. Quintessentially disabling, the patients quality of life is affected by the lack or loss of autonomy due to the chronic, progressive, degenerative, and frequently life-threatening aspects of the disease.

For further details see: Rare Disease Day






The fact that there are often no existing effective cures adds to the high level of pain and suffering endured by patients and their families.
Posted by Tim Sandle