Thursday, 30 November 2017

Hand surgeons provide update on wild animal bites

The article was prompted by the authors' experience in treating an elderly man who developed a progressive infection of the hand after being bitten on the finger by an opossum. The patient recovered after hospitalization including treatment with intravenous antibiotics.

Dr. Rao and colleagues performed a research review to identify studies of rare animal bites and stings. While many reports have discussed treatment of dog, cat, and snake bites, there has been no recent, comprehensive review focusing on the recommended treatment and potential adverse effects of less-common types of animal bites and injuries.

The review identified 71 articles, including a total of 214 patients, describing less frequently seen bite and sting injuries of the upper limb (hand and arm). Most of the studies were case reports and patient series

Aquatic animals were by far the most commonly reported type of injury, accounting for two-thirds of studies. Stings from jellyfish, lionfish and sea anemones, as well as other venomous aquatic animals, can not only cause severe pain and swelling but may sometimes lead to severe or even life-threatening complications.

Ten percent of studies reported bites by reptiles. Bites by some of these animals, such as beaded lizards, can cause envenomation leading to systemic shock.

Other reports described serious complications resulting from bites caused by small mammals and rodents such as ferrets, skunks, and squirrels. Other categories, including just a few cases each, included serious injuries caused by large mammals, scorpions and centipedes and birds.

The studies suggested that most infections resulting from animal bites are "polymicrobial," caused by several different bacteria or other germs. Infections with multiple, often unfamiliar microbes have the potential to cause tissue destruction and systemic (body-wide) reactions.

Based on the available evidence, Dr. Rao and colleagues outline quick reference principles for the treatment of wild animal bites and stings. These include specific recommendations for preventive antibiotics, providing coverage for unusual bacteria that may be present in infected wounds.


Jacqueline S. Israel, James E. McCarthy, Katherine R. Rose, Venkat K. Rao. Watch Out for Wild AnimalsPlastic and Reconstructive Surgery, 2017; 140 (5): 1008 DOI: 10.1097/PRS.0000000000003754

Posted by Dr. Tim Sandle

Wednesday, 29 November 2017

Bacteria Have a Sense of Touch

Bacteria may not have a central or sensory nervous system as we know it, but they can still physically "feel" the world around them, according to a new study.


It turns out the tiny microorganisms don't just respond to chemical signals - they also have a sense of touch, and can recognise surfaces and respond to them. Our sense of touch is a very important tool for living in the world. It helps avoid hazards and dangerous surfaces, and keeps you from crushing delicate objects.

For bacteria, it helps them determine which type of surface they're in contact with - such as a mucous membrane or intestinal wall - and therefore colonise and attack host cells.

It's what happens in the first few seconds after coming into contact with a surface that's crucial for successful infection, the researchers say.

To explore the mechanism by which bacteria sense surfaces, they studied a harmless species called Caulobacter crescentus.

"We have little knowledge of how bacteria read out mechanical stimuli and how they change their behaviour in response to these cues," says senior researcher Urs Jenal of the University of Basel's Biozentrum.

"Using the non-pathogenic Caulobacter as a model, our group was able to show for the first time that bacteria have a 'sense of touch'. This mechanism helps them to recognise surfaces and to induce the production of the cell's own instant adhesive."

Some bacteria have an appendage called the flagellum - whip-like structures that propel them around. Some have just one flagellum, others have many. The juvenile C. crescentus has a single flagellum that it sheds after a set period, or after it finds a suitable surface to adhere to.

By rotating this flagellum, the bacteria can travel through liquids. But these microorganisms don't have muscles - movement is enabled by energy generated by the transfer of protons down the cell membrane.

And it's this mechanism that allows the bacteria to "feel", the researchers have found. When cells come into contact with surfaces, the motor that drives the flagellum is interrupted. This in turn interrupts the proton flow.

Within seconds of this occurring, the bacteria responds, producing the adhesinthat will anchor it in place.

This knowledge could help us understand dangerous bacteria too, says Jenal.

"Even though Caulobacter is a harmless environmental bacterium, our findings are highly relevant for the understanding of infectious diseases," he explains. "What we discovered in Caulobacter also applies to important human pathogens."

The research has been published in the journal Science.

Microbiological Culture Media: A Complete Guide for Pharmaceutical and Healthcare Manufacturers

Did you realize that 90 percent of quality control microbiology remains reliant upon culture-based methods? Taking this fact into account, Microbiological Culture Media: A Complete Guide for Pharmaceutical and Healthcare Manufacturers serves as an excellent reference because it focuses on microbiological culture media as applied to pharmaceutical microbiology.

In 23 informative chapters, this book covers how media is used in the modern pharmaceutical microbiology setting and recaps the past, signals the future, and helps interpret the present. The book has been written by Tim Sandle.

Pre-order this book through Dec. 15 and save 15%. Enter campaign code MBCM to apply discount during checkout.

This book also takes into consideration that innovations continue to arise with new media recipes that are formulated for the selection of new strains for the application of media in conjunction with rapid microbiological methods.

If you are a microbiologist working in the pharmaceutical and healthcare sectors, you can’t afford not to own this book!

  1. Application of Culture Media in Pharmaceutical and Healthcare Microbiology
  2. History and Development of Microbiological Culture Media
  3. The Science of Culture Media
  4. Common Types of Microbiological Culture Media for Pharmaceutical Microbiology
  5. The Media Kitchen and the Preparation of Microbiological Culture Media
  6. Sterilization of Microbiological Culture Media
  7. Quality Control of Culture Media
  8. Microbial Cultures
  9. The Use of Environmental Isolates in Pharmaceutical Microbiology
  10. The Colony Forming Unit
  11. Microbial Identification and Visual Assessment of Colonies
  12. Qualification of Culture-Based Environmental Monitoring Methods
  13. Incubation Strategies for Environmental Monitoring
  14. Culture Media for Sterility Testing
  15. Culture Media for Media Simulation Trials
  16. Culture Media for Microbial Controls During Pharmaceutical Manufacture
  17. Assessment of Culture Media for Water Testing
  18. Culture Media for Cell Culture Work
  19. Diluents and Neutralizers Required for the Pharmaceutical Microbiology Laboratory
  20. Data Integrity, Computerized Systems and Microbiological Culture Media
  21. Auditing Culture Media Suppliers
  22. Industry Practices Relating Culture Media Use
  23. Growth and Culture Based Rapid Microbiological Methods
For more details see the PDA Bookstore

Posted by Dr. Tim Sandle

Tuesday, 28 November 2017

Role of gut microbiome in posttraumatic stress disorder

PTSD is a serious psychiatric disorder that can develop after a person experiences a life-threatening trauma. However, not everyone exposed to a traumatic event will develop PTSD, and several factors influence an individual's susceptibility, including living conditions, childhood experiences and genetic makeup. Stellenbosch University researchers are now also adding gut bacteria to this list.
In recent years, scientists have become aware of the important role of microbes existing inside the human gastrointestinal tract, called the gut microbiome. These microbes perform important functions, such as metabolising food and medicine, and fighting infections. It is now believed that the gut microbiome also influences the brain and brain function by producing neurotransmitters/hormones, immune-regulating molecules and bacterial toxins.
In turn, stress and emotions can change the composition of the gut microbiome. Stress hormones can affect bacterial growth and compromise the integrity of the intestinal lining, which can result in bacteria and toxins entering the bloodstream. This can cause inflammation, which has been shown to play a role in several psychiatric disorders.
Individuals with PTSD had significantly lower levels of this trio of bacteria compared to trauma-exposed control groups. Individuals who experienced trauma during their childhood also had lower levels of two of these bacteria (Actinobacteria and Verrucomicrobia).


Sian M.J. Hemmings, Stefanie Malan-Müller, Leigh L. van den Heuvel, Brittany A. Demmitt, Maggie A. Stanislawski, David G. Smith, Adam D. Bohr, Christopher E. Stamper, Embriette R. Hyde, James T. Morton, Clarisse A. Marotz, Philip H. Siebler, Maarten Braspenning, Wim Van Criekinge, Andrew J. Hoisington, Lisa A. Brenner, Teodor T. Postolache, Matthew B. McQueen, Kenneth S. Krauter, Rob Knight, Soraya Seedat, Christopher A. Lowry. The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed ControlsPsychosomatic Medicine, 2017; 79 (8): 936 DOI: 10.1097/PSY.0000000000000512

Posted by Dr. Tim Sandle

Monday, 27 November 2017

Risk Based Approach to Environmental Monitoring (webinar)

Regulators frequently cite concerns with environmental monitoring and the lack of a well-thought out rationale. This shortfall can be overcome through the application of risk assessment and scientific approaches. The application of risk assessment applies to selecting location for monitoring and frequencies of monitoring; and for data assessment. This presentation outlines the primary tools that can be used to achieve this.

Instructor: Tim Sandle
Product ID: 504486

Date: Tuesday, 19 December 2017 | Time: 10:00 AM PST, 01:00 PM EST | Duration: 60 Minutes
  • Understanding what environmental monitoring sets out to show, in relation to environmental control
  • Appreciating the limitations of monitoring
  • Understanding risk assessment tools like FMEA and HACCP and how they can be applied to environmental monitoring
  • Worked examples of how to apply risk based approaches for setting monitoring frequencies
  • Worked examples of how to apply risk based approaches for determining monitoring locations
  • Understanding how risk assessment can assist with out-of-limits investigationsWhy Should you Attend
  • To understand different approaches for environmental monitoring through the adoption of risk based methodologies. These tools can either be applied to the workplace or used to benchmark current practice against. The approaches discussed have been presented to FDA and European medicines inspectors.
Areas Covered
  • An overview of environmental monitoring and a biocontamination control strategy
  • Discussion of environmental monitoring methods
  • Introduction to risk concepts, hazard identification and risk assessment
  • Introduction to FMEA
  • Introduction to HACCP
  • Application of risk tools to elements of the environmental monitoring program, such as assessing contamination risks, setting monitoring frequencies, assessing monitoring locations
  • How to determine if too little or too much monitoring is being undertaken
Who will Benefit
  • Microbiologists (QA and QC)
  • QC managers
  • Production managers
  • Quality Assurance personnel
  • Cleanroom engineer
For details se: Online Compliance

The people factor: investigating the gown

An effective environmental monitoring programme is designed to estimate the microbial content of the room air and surfaces (by incident rate, against alert and action levels, and by assessment of different species) for operations performed within a cleanroom or controlled environment. While individual results are rarely of significance, a well-designed environmental monitoring programme signals conditions contributing to rises in microbial levels. Shifts in microbial trends can be due to ineffective cleaning, disinfection, faulty air handling systems, material and equipment transfer, and the result of personnel related issues. With this latter point the majority of contaminants dispersed into cleanrooms derived from personnel.

Based on this, Tim Sandle has undertaken a review of cleanroom gowns, gown use and gown locations, in relation to microbial contamination. The detection of contamination on the gown either indicates a concern with the practices of an individual operator or a problem with the gown itself. The paper looks at several aspects of gown wearing through a review of data collated over a one year period. The data was studied for four considerations:

Locations most likely to indicate contamination.
Differences between re-laundered and single-use gowns.
Variations of gowns when re-laundered.
Variations in efficiency of gowns when worn over time.

The reference of the paper is:

Sandle, T. (2017) The people factor: investigating the gown, European Pharmaceutical Review, 22 (4): 23-26

For further details, please contact TimSandle

Posted by Dr. Tim Sandle

Sunday, 26 November 2017

Side-effect after antibiotics

Some bacteria are sensitive to penicillin, others are not. While patients swallow antibiotics to destroy harmful microorganisms, their own intestinal microbiota suffers changes. If the introduced unbalance leads to an overgrowth of bacteria producing toxins themselves, intestinal and metabolic disorders can follow. In an interdisciplinary collaboration, Ellen Zechner of the University of Graz, Austria, and her colleagues have researched the role of penicillin-resistant Klebsiella oxytoca enterobacterium in antibiotic-associated hemorrhagic colitis (AAHC).

They first identified a metabolite tilivalline as a critical enterotoxin, which in higher doses damages the intestinal epithelium and can induce colitis. Surprisingly, tilivalline shares its chemical structure with a class of soil bacteria metabolites called pyrrolobenzodiazepines, which are already investigated and applied in clinical trials for their antitumor properties. After having identified the gene cluster for tilivalline synthesis, the scientists performed comprehensive biomolecular and molecular genetic experiments to track down the complete biosynthetic pathway of tilivalline.

Tilivalline itself lacks the DNA-damaging activity of its antitumor antibiotic relatives because the chemical site crucial for DNA interference is blocked. However, Zechner and colleagues found that the source of the blocking, an indole, only enters the biosynthetic pathway at its end. The tilivalline precursor without the indole, which was then named tilimycin, was shown to be a more potent cytotoxin than tilivalline. Surprisingly, the final addition of the indole to tilimycin occurs spontaneously, without the help of any enzyme. This means that "Klebsiella oxytoca is able to produce two pyrrolobenzodiazepines with distinct functionalities depending on the availability of indole," the scientists stated. Indole occurs naturally in the human gut.
Both outcomes, the elucidation of the biosynthetic pathway and the discovery of tilimycin as a stable intermediate metabolite, which is even more toxic to human cells, have important physiological and pharmacological implications. First, the better understanding of the AAHC pathogenesis may lead to new treatment schemes and strategies to avoid or just alleviate antibiotic side reactions. And second, the unusual Klebsiella pathway to the anticancerogenic structures can inspire scientists to develop new approaches for producing anticancer drugs.


Elisabeth Dornisch, Jakob Pletz, Ronald A. Glabonjat, Florian Martin, Christian Lembacher-Fadum, Margit Neger, Christoph Högenauer, Kevin Francesconi, Wolfgang Kroutil, Klaus Zangger, Rolf Breinbauer, Ellen L. Zechner. Biosynthesis of the Enterotoxic Pyrrolobenzodiazepine Natural Product TilivallineAngewandte Chemie International Edition, 2017; DOI: 10.1002/anie.201707737

Posted by Dr. Tim Sandle

Saturday, 25 November 2017

Hacking the bacterial social network

Scientists have determined the molecular structures of a highly specialized set of proteins that are used by a strain of E. coli bacteria to communicate and defend their turf.

Whenever we use our smartphones to check social media, we face loads of bacteria on the devices -- even more than on toilet seats, according to a University of Arizona study. Those bacteria may have their own form of social network that, like Facebook, allows the single-cell creatures to attract and repel one another.

This insight stems from new research by U.S. Department of Energy (DOE) scientists who have determined the molecular structures of a highly specialized set of proteins. These proteins are used by a strain of E. coli bacteria to communicate and defend their turf.

The work could lead to new biomedical strategies for overcoming pathogenic bacteria that cause infectious diseases such as pneumonia and food-borne illnesses. It is the latest advance from a group of scientists at the DOE's Argonne National Laboratory; the University of California, Santa Barbara (UCSB); and the University of California, Irvine.

The work builds upon the 2005 discovery by UCSB researchers that the bacteria produce toxic proteins, which they can transfer to their neighbors through direct contact to either kill or control them, possibly to gain better access to nutrients. It plays out only in densely populated microbial communities through a process called contact-dependent growth inhibition (CDI).


Karolina Michalska, Grant C. Gucinski, Fernando Garza-Sánchez, Parker M. Johnson, Lucy M. Stols, William H. Eschenfeldt, Gyorgy Babnigg, David A. Low, Celia W. Goulding, Andrzej Joachimiak, Christopher S. Hayes. Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAsNucleic Acids Research, 2017; 45 (17): 10306 DOI: 10.1093/nar/gkx700

Posted by Dr. Tim Sandle

Friday, 24 November 2017

Technical Guide for Design, Control and Monitoring of Single-Use Systems

The Bio-Process Systems Alliance (BPSA) announced today that its new technical guide to Design, Control and Monitoring of Single-Use Systems for Integrity Assurance is now available for download at

The uptake of single-use technologies (SUT) in more critical good manufacturing practices (cGMP) processes and applications has made assurance of integrity a critical quality attribute for both suppliers and end-users.

"I expect this to be one of the most significant documents written in the last five years to support our mission of driving the adoption of single-use technologies worldwide," said Kevin Ott, BPSA Executive Director.

The document provides recommendations to both suppliers and end-users in the single-use technology industry regarding strategies, tools and procedures that can assist in providing enhanced assurance of integrity of single-use systems. It can help end-users convey their specific requirements to the supplier. In turn, suppliers can use the document to demonstrate what they can provide to the end-user.

The technical guide divides best practices into two separate but complementary sections – a risk-based approach and practical tests for SUTs.

The document was written by a working group of end-users and suppliers who recognized the need to provide guidance in the absence of industry standards.

Thursday, 23 November 2017


In an effort to better understand neurological diseases like Alzheimer’s, Parkinson’s and ALS – and develop new ways to treat them – researchers at The Ohio State University Wexner Medical Center have performed the first meta-analysis of all induced pluripotent stem cell models for neurological and neurodegenerative diseases, and created an atlas of how cell characteristics are linked to their genotype.

Findings of the study published online today in the journal EMBO Molecular Medicine.
“Synthesizing this information to understand the phenotypic role of disease-promoting genes and identifying the limitations of our current practices will be crucial steps toward achieving the great translational potential of induced pluripotent stem cell models of neurological diseases,” said Dr. Jaime Imitola, director of the Progressive Multiple Sclerosis Multidisciplinary Clinic and Translational Research Program at Ohio State’s Wexner Medical Center.

Imitola led the study with colleagues in Ohio State’s Neuroscience Research Institute and collaborators at the Nationwide Children’s Hospital, University of South Carolina and University of California Santa Barbara.

Induced pluripotent stem cells (iPSC) are derived from skin or blood cells that have been reprogrammed into an embryonic-like pluripotent state that can be prodded into becoming other cells, such as neurons to treat neurological disorders. The genotype is the set of genes in our DNA which is responsible for a particular trait, while the phenotype is the physical expression, or characteristics, of that trait.

Human disease modeling with iPSCs has enabled researchers to study the disease phenotypes of patient-derived cells directly in the lab. Now, a decade after the discovery of iPSCs, hundreds of patient cell lines and neurological disease phenotypes have been generated. Yet this abundance of phenotypic information has become difficult to follow and interpret, and research practices for iPSC neurological disease modeling varies among different laboratories, Imitola said.

For this study, researchers included 93 out of more than 110 studies initially screened, from which they collected data on phenotypes and genotypes, encompassing 31 neurological diseases that span the pediatric to adult population with a total of 71 gene mutations. As they analyzed the correlation of 663 neuronal phenotypes with genotypic data from 243 patients and 214 controls – and examined research practices and reporting bias in neurological disease models – they found that there is no established standard for the reporting of methods nor a defined minimal number of cell lines.
From the retrospective analysis of the published literature, researchers developed a taxonomy of central nervous system cellular phenotypes in vitro, and revealed that there are previously unrelated genes that show similar disease phenotypes. This work also showed that alterations in patient-derived cells at the level of gene expression correlate with the reported cellular phenotypes, and these dysregulated genes are highly expressed in specific regions of disease in the human brain.

As a valuable resource for the research community, researchers developed the iPhemap – an online database of phenotypic information of iPSC neurological diseases that can be referenced, updated and continually refined by researchers worldwide – to share knowledge and develop new, more effective therapies.

“Our phenogenetic map can be used to build new hypotheses in the field of neurological disease modeling, and to identify potential new opportunities to design novel drug strategies,” said first author Ethan W. Hollingsworth, a neural stem cell research assistant at Ohio State’s Wexner Medical Center and a hematology/oncology clinical research intern at Nationwide Children’s Hospital.

“The ultimate goal of this research is to be able to determine the phenotypes and genotypes relationship in neurological diseases where there is no mutation, or there are small genetic changes in neurons and oligodendrocytes from patients with progressive multiple sclerosis or sporadic Alzheimer’s disease to find new medications to stop neurodegeneration,” Imitola said.

Wednesday, 22 November 2017

Justification of starting materials for the manufacture of chemical active substances

Reflection paper on the requirements for selection and justification of starting materials for the manufacture of chemical active substances

The EMA has revised and re-issued its reflection paper on API starting materials in order to further clarify what information firms should supply. The paper centers on the following problem statement:

Disagreements between applicants and quality assessors on the suitability of proposed starting materials have become more frequent in recent times. This suggests that the current guidelines, intentionally high level to allow application to the wide range of chemical syntheses submitted to regulatory authorities, are open to interpretation. Furthermore, it is increasingly common for applicants to propose very short synthetic routes with complex custom-synthesized starting materials. Another trend is for some, or all, of the active substance manufacture to be outsourced to third parties. The use of external sources for any steps in a manufacturing process may lead to a higher degree of risk to quality of the active substance than would be expected were the full manufacturing process to be carried out by the applicant or a single active substance manufacturer alone. This document strives to expand on some of the points in ICH Q11 in order to harmonise opinions between assessors and clarify the requirements for applicants.

Additionally, the information submitted by applicants or Active Substance Master File (ASMF) holders to justify the selection of starting materials and their proposed specifications is often insufficient to allow adequate assessment of suitability.4 A detailed description of the manufacturing process of the active substance is required, along with a flow chart of transformations employed to synthesize starting materials including all solvents, reagents, catalysts and processing aids used, in order to facilitate a proper assessment. Since steps deemed critical should be carried out under Good Manufacturing Practice (GMP), an appraisal of the criticality of all transformations in the full synthetic route on the quality of the active substance is needed. The description of the manufacturing process should be sufficiently detailed to demonstrate that the process and its associated control strategy will consistently provide active substance of satisfactory quality. Starting materials can only be justified once the criticality of all steps has been discussed. Often, starting materials are selected and then only subsequent steps are discussed. This is not sufficient. A scheme of synthetic steps carried out to synthesize the proposed non-commodity starting materials should be provided as part of the justification of starting material selection.

For details see: EMA

Posted by Dr. Tim Sandle

Tuesday, 21 November 2017

Q&A production of water for injections by non-distillation methods

Q&A production of water for injections by non-distillation methods – reverse osmosis and biofilms and control strategies – a new document of interest from the European Medicines Agency.

The document states: “Production of water for injection by other methods than distillation has been allowed in the EU since April 1st 2017. A draft additional guidance was published in 2016 and a Final Version of this document provides a set of questions and answers (Q&A) which are intended to provide preliminary guidance until such time the on-going revision of Annex I of the GMP guide is complete.”

For further details see: EMA

Posted by Dr. Tim Sandle

Monday, 20 November 2017

Cleanroom Management in Pharmaceuticals and Healthcare - special offer

Dear Reader,

Euromed Communications have recently brought out a new 2017 edition of the Cleanroom Management in Pharmaceuticals and Healthcare. Since the first edition of this book in 2013 there have been many changes to the approach and methods for cleaning and certifying cleanrooms, most notably the revisions to Parts 1 and 2 of the ISO 14644 series of global cleanroom standards. In addition to setting out the principal changes in these revised standards, many of the other chapters in the book have been updated to reflect their requirements, bringing current practices and Good Manufacturing Practice regulations up-to-date. The book is edited by Tim Sandle and Madhu Raju Saghee.

This book was reviewed in the May issue of Pharmig News and full details of the book can be found on the Euromed Communications website.

The publishers are offering a special discount to readers of this site and of the Pharmig, Sterility Assurance & Pharmaceutical Microbiology LinkedIn Groups at 20% off the cover price.

Thus the special offer costs for the new manual are as follows:

Hard back: £196 (~$260)
Paperback: £152 (~$200)

If you wish to take up this offer simply send an email to mentioning the code ‘Pharmig20’ and you or your company will be invoiced accordingly.

Please note this offer ends on 10 December 2017.

Tim Sandle, on behalf of Euromed Communications

Microbial Control of Pharmaceutical Water Systems

Tim Sandle has written an article for Pharmaceutical Engineering:

Water needs to be microbiologicallycontrolled. Microorganisms are ubiquitous and varied in their ability to survive and grow under different conditions. An out-of-control water system can cause harm to the patient or adulterate pharmaceutical products. This article assesses some of the requirements for good design together with the control measures necessary to help to maintain effective microbiological control in pharmaceutical facility water systems.

The reference is:

Sandle, T. (2017) Design and Control of Pharmaceutical Water Systems to Minimize Microbiological Contamination, Pharmaceutical Engineering, 37 (4): 44-48

For further details, please contact Tim Sandle

Posted by Dr. Tim Sandle

Sunday, 19 November 2017

Biocidal cleaners may spread multidrug resistance in MRSA

Multidrug resistance to MRSA and reinfection with MRSA, said corresponding author Jonathan Shahbazian, MPH, were the most important in this study. The study also showed that whether used in humans or companion animals, the antibiotic clindamycin was not associated with the risk of multi-drug resistant bacteria in the home.

Treatment with mupirocin, an antibiotic used to treat skin infections and to eradicate MRSA from the nasal passages in order to prevent its spread from sneezes, is weakly associated with mupirocin resistance in the household environment.

In the study, the investigators collected samples from the home environments and companion animals of households enrolled in a large randomized controlled trial, which took place over a 14 month period. They tested whether household-wide efforts to eradicate MRSA -- which included daily use of nasal mupirocin ointment and chlorhexidine body wash -- were successful in reducing recurrence of MRSA among adults and children who had previously been diagnosed with a MRSA skin or soft tissue infection. They repeated sampling in 65 homes three months after the residents had been treated for MRSA, or, as a control, after they had been educated about MRSA.

The investigators concluded that a better understanding of what causes home environmental MRSA to become multidrug resistant, and thus harder to treat, could help in identifying which households are more likely to harbor multidrug resistant MRSA, so that these could be targeted for eradication of the pathogen.


J. H. Shahbazian, P. D. Hahn, S Ludwig, J Ferguson, P Baron, A Christ, K Spicer, P Tolomeo, A. M. Torrie, W. B. Bilker, V. C. Cluzet, B Hu, K Julian, I Nachamkin, S. C. Rankin, D. O. Morris, E Lautenbach, M. F. Davis. Multidrug and mupirocin resistance in environmental methicillin-resistant Staphylococcus aureus (MRSA) collected from the homes of people diagnosed with a community-onset (CO-) MRSA infection. Applied and Environmental Microbiology, 2017; AEM.01369-17 DOI: 10.1128/AEM.01369-17

Posted by Dr. Tim Sandle

Saturday, 18 November 2017

Examining the lifestyles of microbes

Scientists are identifying and characterizing more microbes each year using DNA sequencing technologies. As each new species is sequenced, scientists add it to the microbial "tree of life," creating a virtual census of what's there.

Turns out it's not an easy job. To put things in perspective, scientists aren't sure how many microbes even exist. Estimates vary widely from millions to trillions.

University of Delaware professor Jennifer Biddle and Rosa Leon-Zayas, who completed post-doctoral work at UD earlier this year, recently described new details about microbes known as Parcubacteria in a paper published in Environmental Microbiology.

The Parcubacteria were found in sediment samples collected by James Cameron within the Challenger Deep region of the Mariana Trench during the Deepsea Challenge Expedition. Leon-Zayas' doctoral advisor, Doug Bartlett at Scripps Institution of Oceanography, was a chief scientist on the expedition.

"From a scientific perspective, Challenger Deep was an invaluable opportunity to collect samples from the deepest part of the ocean," said Leon-Zayas, the paper's lead author, now an assistant professor at Willamette University.

Scientists traditionally have learned how microbes work by growing and studying them in petri dishes and beakers. It wasn't until DNA sequencing advanced to include the ability to separate and test microbes present in environmental samples (such as soils or sediments) that scientists realized they had missed a huge portion of bacteria now called the Candidate Phyla Radiation (CPR).

One group of CPR microbes called the Parcubacteria had been seen in the groundwater and shallow sediments of a few places on land, but it had only been intensively studied in sediment samples from an aquifer near Rifle, Col.

When Cameron collected sediment samples at the bottom of the trench, the scientists discovered that many different species of Parcubacteria live there, too.

"We were interested in seeing if the microbes living at the bottom of the ocean had the same lifestyle as the microbes living in soils in Rifle, Colorado," said Biddle, a marine microbiologist and associate professor in the College of Earth, Ocean, and Environment's School of Marine Science and Policy.

Leon-Zayas used a sorting technique to separate the microbial cells from the sediment particles so that scientists could amplify and sequence the microbe DNA. The researchers then characterized the individual microbial genomes. Based on the genes that are present in the genome -- sections of DNA that define what metabolisms a cell is capable of -- scientists can infer what the bacteria is doing.

This genomic sequencing revealed that Parcubacteria from the deep sea have a fairly simple metabolism; but the genomes were larger than that of their terrestrial cousins and even had a few extra features. In particular, these features indicated the bacteria may be able to perform anaerobic respiration, using things like nitrate to breathe instead of oxygen.

Parcubacteria also seemed to have more proteins and enzymes associated with cold environments, not surprising since the bottom of the Mariana Trench is cold and dark.

"It makes sense that organisms at the bottom of the ocean might have to be more self-sufficient. The environment is extreme and there isn't as much food," Biddle said.


Rosa León-Zayas, Logan Peoples, Jennifer F. Biddle, Sheila Podell, Mark Novotny, James Cameron, Roger S. Lasken, Douglas H. Bartlett. The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1). Environmental Microbiology, 2017; 19 (7): 2769 DOI: 10.1111/1462-2920.13789

Posted by Dr. Tim Sandle

Friday, 17 November 2017

Bacterial signalling in sharper resolution

The complex signalling networks bacteria use to adapt to their environments have become clearer following new research.

John Innes Centre researchers used a study of the plant-growth promoting bacterium Pseudomonas fluorescens to develop an advanced analysis method which, they hope, will increase our capacity to understand plant and human diseases.

Until recently, investigations into bacterial signalling have tended to look at different aspects of gene regulation in isolation. Building on these individual approaches, the John Innes team used a range of lab, computational and mathematical techniques to integrate data obtained from multiple different microbiological experiments.

This approach has enabled them to build a comprehensive 'signalling map' for the key bacterial protein Hfq, which controls virulence and stress responses in many clinically and agriculturally important species.

Dr Jacob Malone, the project leader associated with the work explained: "Our technique allows us to follow every gene and protein in a bacterial cell, and say how it changes and at what level that change occurs, in response to a given signal input.

"We are using the same data sets as previous studies but we have developed a way of integrating the data using mathematics and programming. If you consider the individual elements of a movie: the photography, the soundtrack and the script; by combining them you get a whole movie -- something greater than the sum of the parts. This is the same principle, only with genetics."


Lucia Grenga, Govind Chandra, Gerhard Saalbach, Carla V. Galmozzi, Günter Kramer, Jacob G. Malone. Analyzing the Complex Regulatory Landscape of Hfq – an Integrative, Multi-Omics Approach. Frontiers in Microbiology, 2017; 8 DOI: 10.3389/fmicb.2017.01784

Posted by Dr. Tim Sandle

Thursday, 16 November 2017

ISO/IEC 17025 moves to final stage of revision

Calibration as well as testing and analysing a sample is the daily practice of more than 60 000 laboratories worldwide, but how can they reassure customers about the reliability of their results?

Over the years, ISO/IEC 17025, General requirements for the competence of testing and calibration laboratories, has become the international reference for testing and calibration laboratories wanting to demonstrate their capacity to deliver trusted results. The International Standard, published jointly by ISO and IEC (International Electrotechnical Commission), contains a set of requirements enabling laboratories to improve their ability to produce consistently valid results.

However, the laboratory environment has changed dramatically since the standard was last published, leading to the decision to revise the standard and integrate significant changes. Steve Sidney, one of the Convenors of the working group revising the standard, explains: “The last version of ISO/IEC 17025 was published in 2005. Since then, market conditions have changed and we felt we could bring some improvements to the standard.”
Heribert Schorn, working group Convenor who also participates in IECEE (System of Conformity Assessment Schemes for Electrotechnical Equipment and Components), adds: “The revision was needed to cover all the technical changes, technical developments and developments in IT techniques that the industry has seen since the last version. Additionally, the standard takes into consideration the new version of ISO 9001.”

This standard is of high significance for the IEC Conformity Assessment Community as it outlines the basic requirements for testing within all Conformity Assessment Schemes and Programmes operating within the IECEE, IECEx, IECQ and IECRE Conformity Assessment Systems.

The review was started in February 2015 as a result of a joint proposal by the International Laboratory Accreditation Cooperation (ILAC) and the South African Bureau of Standards (SABS), who is a member of ISO and hosts the IEC National Committee. The standard’s revision process has now reached the Final Draft International Standard (FDIS) stage, the last leg of development before publication.

The main changes:

The revision of ISO/IEC 17025 takes into account the activities and new ways of working of laboratories today. The main changes are as follow:

The process approach now matches that of newer standards such as ISO 9001 (quality management), ISO 15189 (quality of medical laboratories) and ISO/IEC 17021-1 (requirements for audit and certification bodies). The revised standard puts the emphasis on the results of a process instead of the detailed description of its tasks and steps.

With a stronger focus on information technologies, the standard now recognizes and incorporates the use of computer systems, electronic records and the production of electronic results and reports. Modern-day laboratories work increasingly with information and communication technologies and the working group felt it was necessary to develop a chapter on this topic.

The new version of the standard includes a chapter on risk-based thinking and describes the commonalities with the new version of ISO 9001:2015, Quality management systems – Requirements.

The terminology has been updated to be more in step with today’s world and the fact that hard-copy manuals, records and reports are slowly being phased out in favour of electronic versions. Examples include changes to the International Vocabulary of Metrology (VIM)and alignment with ISO/IEC terminology, which has a set of common terms and definitions for all standards dedicated to conformity assessment.

A new structure has been adopted to align the standard with the other existing ISO/IEC conformity assessment standards such as the ISO/IEC 17000 series on conformity assessment.

The scope has been revised to cover all laboratory activities including testing, calibration and the sampling associated with subsequent calibration and testing.

Using ISO/IEC 17025 facilitates cooperation between laboratories and other bodies. It assists in the exchange of information and experience and helps harmonize standards and procedures, as Warren Merkel, another Convenor of the working group, explains. “ISO/IEC 17025 impacts the results delivered by laboratories in a number of ways. The standard requires them to meet criteria for competence of their personnel, the calibration and maintenance of their equipment and the overall processes they use to generate the data. This requires laboratories to think and operate in a way that ensures their processes are under control and their data are reliable.” Results also gain wider acceptance between countries when laboratories conform to the standard.

Developed jointly by ISO and IEC in the Committee on conformity assessment (CASCO), the new version of ISO/IEC 17025 will replace the 2005 version and is scheduled for publication at the end of this year.

Posted by Dr. Tim Sandle

Tuesday, 14 November 2017

FDA approves first ever ‘digital pill’

An innovative medical device, in the form of a pill containing a built-in sensor has been developed and been given approval, based on safety and efficacy data, by U.S. authorities.

by Tim Sandle

What is being heralded as the world’s first ‘digital’ pill has gained approved by the U.S. Food and Drug Administration (FDA). The pill is called Abilify MyCite. The pill contains a medication called aripiprazole, which treats conditions like schizophrenia, bipolar disorder and depression. Also combined with the pill is an ingestible sensor. The pill comes after several years of research and is a venture between the Japanese pharmaceutical company Otsuka and digital medicine service Proteus Digital Health.

It is the sensor that creates the ‘digital’ or ‘smart’ pill. The purpose of the sensor, according to The Verge, is to record when the pill has been taken. This happens by a signal being sent to a wearable patch (fixed to the left rib cage); and then from the patch to a mobile device such as a smartphone via Bluetooth. The patch has additional functionality. It records activity levels, sleeping patterns, steps taken, and heart rate. The patch needs to be replaced every seven days.

The purpose of this is to determine when a pill has been taken. This either acts as a reminder  to patients that they have (or to verify that they have not) taken their required dose of medication; or, for more serious cases where a patient has been sectioned as the result of a mental disorder, to enable medics to record the fact that a medication has been taken.
Failure to take medications has societal and economic consequences, such as putting a strain on the hospital system. According to Dr. William Shrank, chief medical officer of the health plan division at the University of Pittsburgh Medical Center, who spoke with the New York Times on this subject: “When patients don’t adhere to lifestyle or medications that are prescribed for them, there are really substantive consequences that are bad for the patient and very costly.”

The sensor is only the size of a grain of sand. It is manufactured from silicon, copper, and magnesium. In terms of how the sensor works, an electrical signal is activated when the sensor comes into contact with stomach acid.

It is a common problem with medications, either through forgetfulness or as a conscious act, when patients do not taken the medicines prescribed to them. The digital pill aims to redress this.

Commenting on the go-ahead for the digital pill to be marketed, Mitchell Mathis, who is the director of the Division of Psychiatry Products in the FDA, told PharmaPhorum: “Being able to track ingestion of medications prescribed for mental illness may be useful for some patients.”

The regulator added: “The FDA supports the development and use of new technology in prescription drugs and is committed to working with companies to understand how technology might benefit patients and prescribers.”

The agreement relates to both parts of the smart medication: Abilify and Proteus Health’s sensor and patch, for the U.S. market. A label warning will accompany the product. This will state that the combined smart system has not been shown to improve patient compliance and that there are concerns about the effectiveness of the tracker in real-time since detection may be delayed. Nevertheless, the digital pill is likely to become popular with the medical establishment. The price of the pill has yet to be announced.

The Wall Street Journal opines that there could now be a raft of approval requests for other digital pills. The paper also notes that the FDA are preparing to hire more staff with understanding of software development in relation to medical devices.

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