Saturday, 19 January 2019

Flows that help bacteria feed and organize biofilms

Under threat of being scrubbed away with disinfectant, individual bacteria can improve their odds of survival by joining together to form colonies, called biofilms. What Arnold Mathijssen, postdoctoral fellow in bioengineering at Stanford University, wanted to understand was how stationary biofilms find food once they've devoured nearby nutrients.

Leading an international team of researchers in creating simulations of how fluids move, Mathijssen found that individual bacteria and biofilms can generate currents strong enough to draw distant nutrients.

When bacteria move, they disturb the liquids that surround them in the microscopic world. The researchers explored the strength of that disturbance in a single bacterium that moves in a way that is similar to many pathogenic species, including those that cause gastritis and cholera. They found that as this bacterium swims forward, it creates a tiny but stable current in the surrounding liquid with fluid moving toward its center and away from the head and tail.

Then, they calculated the flows produced by a colony of randomly arranged bacteria and were surprised to see that it created a strong, consistent tide capable of pulling in nutrients. This occurred regardless of the orientation of each bacterium so long as the colony was thicker in some areas than others, which causes fluid to move from high points to low points. Simulations of more orderly bacteria resulted in even stronger circulation.

Within organized biofilms, the researchers found two common patterns of movement: vortexes and asters. In a vortex pattern, the bacteria move in concentric circles and produce a flow that brings nutrients down to the biofilm's center and then pushes the fluid out the sides. In an aster pattern, the bacteria move toward a central point, creating a flow that moves from the edge of the biofilm until it rises back up, over the center.

"The powerful thing about this is you can add these patterns up," Mathijssen said. "Rather than having to know the position and orientation of every single bacterium, you only need to know the basic patterns that make up the colony and then it's very easy to derive the overall transport flow."

The researchers were able to combine vortex and aster patterns within a single biofilm to determine how the bacteria would push, pull and whirl the fluids around them. As a final test, the researchers took calculations representing the complex, realistic motion of bacteria swarming -- as they might on the surface of a table -- and predicted the strength of that swarm's transport flow. The result were large vortices that spanned distances beyond the boundaries of the biofilm, suitable for keeping the colony fed.


Arnold J. T. M. Mathijssen, Francisca Guzmán-Lastra, Andreas Kaiser, Hartmut Löwen. Nutrient Transport Driven by Microbial Active Carpets. Physical Review Letters, 2018; 121 (24) DOI: 10.1103/PhysRevLett.121.248101

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Friday, 18 January 2019

Consultation on two major texts for the testing of parenteral drugs

The European Pharmacopoeia (Ph. Eur.) Commission is consulting its stakeholders on Ph. Eur. dosage form monograph on Parenteral preparations (0520) and new informative chapter on testing for visible particles (5.17.2)

The pivotal dosage form monograph Parenteral preparations (0520) prescribes the mandatory requirements and tests for preparations intended for injection, infusion or implantation.

The monograph has been modernised to meet current testing requirements e.g. for (sub) visible particles, bacterial endotoxins, uniformity and release, particularly as applied to liquid parenteral preparations.

The monograph also refers to the newly elaborated informative non-mandatory chapter 5.17.2. Recommendations on testing of particulate contamination: visible particles. The requirements for the test method are laid down in chapter 2.9.20, which is also under revision, and a revised text is planned for publication in 2019 (a draft was published in Pharmeuropa 30.2).

The new text highlights the many sources of particulate contamination and states that every effort should be made to avoid their presence.

The two texts have been published for public consultation in Pharmeuropa 30.4 (October issue) and the commenting period ends on 31 December 2018.

See EDQM -

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Thursday, 17 January 2019

Clearest view ever of cell membrane

Cell membranes are formed largely of a bimolecular sheet, a fraction of the thickness of a soap bubble, in which two layers of lipid molecules are packed with their hydrophobic tails pointing inward and their hydrophilic heads outward, exposed to water.

The internal shape and structure of this lipid bilayer have remained largely mysterious after almost a century of research. This is in large part because most methods to examine membranes use detergents, which strip away the lipids that make up much of the membranes' structures.

In a newly published paper in Proceedings of the National Academy of Sciences, the team -- led by Youzhong Guo, Ph.D., of VCU's School of Pharmacy -- used a new detergent-free method that allowed them to examine the membrane of an E. coli cell, with lipids still in place.

Where earlier models had shown a fluid, almost structureless lipid layer -- one often-cited research paper compared it to different weights of olive oil poured together -- the VCU-led team was startled to find a distinct hexagonal structure inside the membrane. This led the researchers to propose that the lipid layer might act as both sensor and energy transducer within a membrane-protein transporter.


Weihua Qiu, Ziao Fu, Guoyan G. Xu, Robert A. Grassucci, Yan Zhang, Joachim Frank, Wayne A. Hendrickson, Youzhong Guo. Structure and activity of lipid bilayer within a membrane-protein transporterProceedings of the National Academy of Sciences, 2018; 201812526 DOI: 10.1073/pnas.1812526115

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Wednesday, 16 January 2019

Real-time Mycoplasma Contamination Detection for Biomanufacturing

Aseptic and Sterile Processing: Control, Compliance and Future Trends

Here is the most important text discussing aseptic and sterile manufacturing to be published in the last decade that looks at both today and tomorrow in regard to these two vital processing procedures.

The Editors realized that there was an urgent imperative for the relevant subjects to be reassessed and represented. To achieve this objective, along with many subject matter experts, they produced a book that is foremost practical. It has been designed for those involved with aseptic and sterile processing to take away many learning points and apply these principles to aseptic and sterile processing within the pharmaceutical and healthcare sectors.

Drawing on experience, they made every effort to incorporate sound science into the practices described, not least to emphasize why new paradigms are required but to provide wide-ranging guidance and offer depth and scope. This is why chapters on human error, risk assessment, depyrogenation, bioburden testing and so on, are extensively covered. It is the aim of the Editors to help readers reassess legacy definitions and historical understandings and move them toward concepts that will help them think in new ways about equipment and processes that will reach the highest standards and evaluate them through science-based risk assessments.

Available from the PDA Bookstore:

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Tuesday, 15 January 2019

Ph. Eur. Section 3. Materials and containers

The European Pharmacopoeia (Ph. Eur.) Commission decided to restructure Section 3. of the Ph. Eur. on materials and containers. A new Subsection 3.3. has been added to Section 3. in order to cover specific medical devices: containers for human blood and blood components, and materials used in their manufacture; transfusion sets and materials used in their manufacture; syringes.

The new structure of Section 3. will be published in the 10th Edition of the Ph. Eur. which will enter into force on 1 January 2020.

See EDQM -

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Monday, 14 January 2019

Human microbiome and contamination control

The human body is an intricate system that hosts trillions of microbial cells across the epithelial surface, and within the mouth and gut. These microorganisms play a role in human physiology and organ function, including digestion and immunity. The microorganisms also impact on the outside environment as they are shed from the skin or deposited through different orifices. This latter issue has important implications for cleanrooms in pharmaceuticals and healthcare. In recent years, far greater detail about the numbers and complexity of these microorganisms has been gained through the Human Microbiome Project and related research.

In relation to this subject, Tim Sandle has written a review paper.

This paper summarizes some of important findings that have emerged from the Human Mirobiome Project and considers how the findings can inform our understanding of cleanroom microbiology, and presents some thoughts as to whether our enhanced understanding of the human microbiota of the skin should influence the types of controls, supported by testing, that needs to be in place within cleanrooms.

The questions posed by this paper in relation to cleanroom microbiology are:
  • Do environmental monitoring methods remain sufficient in light of Human Microbiome Project findings?
  • Is sterility test media suitable for recovering cleanroom contaminants?
  • Should cleanroom microbiologists be as concerned with anaerobic bacteria as they are with aerobic bacteria?
  • Does the test panel used for disinfectant efficacy tests need to change?
  • Similarly, does the culture media growth promotion panel need to alter?
  • Can the Human Microbiome Project findings aid with the assessment of microbial data deviations?
  • Are cleanroom gowning practices adequate?
The reference is:

Sandle, T. (2018) The Human Microbiome and the implications for cleanroom control, European Journal of Parenteral and Pharmaceutical Science, 23 (3): 89-98

For a copy, please contact Tim Sandle.

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Sunday, 13 January 2019

How to Choose and Validate Your Ready-to-Use (RTU) Media

Media that is bought into labs in a ready to go or Ready to Use (RTU) format goes by many different descriptions such as Ready Prepared Media, Pre-Plated Media/Pre-Poured Media (PPM), Ready-to-Rehydrate;  there's no shortage of terms just as there is an almost limitless choice of presentations from broths in bags, ready to rehydrate media in bags and film plates, solid agar in bottles for melting and prepoured plates. But how to choose a supplier that will be best for your lab?

Rapid Microbiology are carrying an exclusive interview with Barbara Gerten, Senior Scientist Traditional Microbiology with Merck KGaA we find out what makes a good media supplier and how to introduce a new RTU media into your lab's schedule.

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Saturday, 12 January 2019

Microbiological Standards for Medicines

Australia - Therapeutic Goods Order No.77 Microbiological standards for medicines (TGO 77) has been in force since 2010. It was automatically repealed (sunset) on 1 October 2018 in accordance with the Legislative Instruments Act 2003. A new instrument, Microbiological Standards for Medicines 2018 TGO 98 succeeded TGO 77 on this date to provide continuing clarity on the requirements for microbiological quality of medicines.

TGO 98 reflects the current requirements of TGO 77 without regulatory change. It specifies the minimum microbiological requirements with which a medicine must comply throughout its shelf life, i.e. which medicines must comply with a Test for Sterility and Bacterial Endotoxin testing; which medicines must comply with a preservative efficacy test; and the acceptance criteria for microbiological quality that apply to nonsterile medicines.

TGO 98 and its Explanatory Statement are registered on the Federal Register of Legislation.


Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Friday, 11 January 2019

Draft PIC/s guidance on good practices for data management and integrity in regulated environments

A revised Draft PIC/S Guidance on Good Practices for Data Management and Integrity in Regulated GMP/GDP Environments (PI 041-1 (Draft 3) has been prepared by the PIC/S Working Group on Data Integrity, co-led by Australia TGA and UK MHRA.

The document is subject to a focused stakeholder consultation seeking substantive comments from trade and professional associations on specific questions relating to the proportionality, clarity and implementation of the guidance requirements. In parallel to this stakeholder consultation, the new draft will be applied by PIC/S Participating

Authorities on a trial basis for a new implementation trial period. The consultation period will last 3 months and run from 30 November 2018 to 28 February 2019.


Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Thursday, 10 January 2019

FDA aims to harmonize the global scientific and technical standards for generic drugs

FDA has submitted a proposal to ICH recommending the development of internationally harmonized guidelines on scientific and technical standards for generic drugs.

ICH is the global venue for harmonization of standards for pharmaceutical products, including both new drugs and generic drugs. Although many existing ICH guidelines are
applicable to generic drugs, historically ICH has focused on standards for new drugs. As a result, there are areas specific to generic drugs where harmonized guidance is lacking.

FDA envisages that harmonization of scientific and technical standards can potentially bring important benefits. These include allowing developers to use data they develop in support of a generic drug in one region to support approval in other regions.

Plus increasing consistency in the quality of generic medicines globally by implementing common standards that simultaneously meet the requirements of multiple regulatory authorities; and, increasing the effectiveness of regulatory oversight (and reducing costs) by providing regulators more opportunities for information sharing with counterparts in sister agencies.


Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Wednesday, 9 January 2019

162nd Session of the European Pharmacopoeia Commission

At its 162nd Session in Strasbourg on 20-21 November 2018, the European Pharmacopoeia (Ph. Eur.) Commission adopted 16 new texts:

Four general chapters: Quantification and characterisation of residual host-cell DNA (2.6.35);
Powder flow properties by shear cell methods (2.9.49); Scanning electron microscopy (2.9.52) and Process analytical technology (5.25).

Three monographs elaborated under the P4 procedure for products still under patent
protection: Dronedarone hydrochloride (3039); Prasugrel hydrochloride (3040) and Tapentadolhydrochloride(3035).

Plus monographs on:
  • Benzydaminehydrochloride(2759)
  • Tetracaine(2909)
  • Topiramate(2616)
  • Vincamine(1800)
  • Serratulacoronata (2754)
  • Cocoabutter(2607)
  • Squalene(2805)
  • Infectious pancreatic necrosis vaccine(inactivated )for Salmonids(3063)
  • Abelmoschicorolla (2827)

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Tuesday, 8 January 2019

A microbe's membrane helps it survive extreme environments

Within harsh environments like hot springs, volcanic craters and deep-sea hydrothermal vents -- uninhabitable by most life forms -- microscopic organisms are thriving. How? It's all in how they wrap themselves.

Stanford University researchers have identified a protein that helps these organisms form a protective, lipid-linked cellular membrane -- a key to withstanding extremely highly acidic habitats.

Scientists had known that this group of microbes -- called archaea -- were surrounded by a membrane made of different chemical components than those of bacteria, plants or animals. They had long hypothesized that it could be what provides protection in extreme habitats. The team directly proved this idea by identifying the protein that creates the unusual membrane structure in the species Sulfolobus acidocaldarius.

The structures of some organisms' membranes are retained in the fossil record and can serve as molecular fossils or biomarkers, leaving hints of what lived in the environment long ago. Finding preserved membrane lipids, for example, could suggest when an organism evolved and how that may have been the circumstance of its environment. Being able to show how this protective membrane is created could help researchers understand other molecular fossils in the future, offering new evidence about the evolution of life on Earth.

Archaea are sometimes called the "third domain of life," with one domain being bacteria and the other being a group that includes plants and animals -- collectively known as eukaryotes. Archaea includes some of the oldest, most abundant lifeforms on the planet, without which the ecosystem would collapse. Archaea are particularly anomalous microbes, confused with bacteria one day and likened to plants or animals the next because of their unique molecular structures.

The research is particularly interesting because the classification for archaea is still debated by taxonomists. They were only separated from the bacteria and eukaryote domains in the past two decades, following the development of genetic sequencing in the 1970s.


Zhirui Zeng, Xiao-Lei Liu, Jeremy H. Wei, Roger E. Summons, and Paula V. Welander. Calditol-linked membrane lipids are required for acid tolerance in Sulfolobus acidocaldarius. Proceedings of the National Academy of Sciences, 2018; DOI: 10.1073/pnas.1814048115

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Monday, 7 January 2019

Effective training for keeping cleanrooms clean

Controlled environments required for the manufacture of pharmaceutical products are cleanrooms and they are assigned a class through meeting a set standard for airborne particles. Once a grade is assigned, a series of other physical and microbial parameters need be met: HEPA filtration, control of the air through air changes and pressure differentials; staff wearing appropriate garments; adequate cleaning and disinfection. While such measures can be introduced through the Quality by Design approach and good procedures, to achieve ongoing control requires effective training.

In relation to these important issues, Tim Sandle has written an new article. The introduction reads:

“Traditional training has served the industry well, but it does not always deliver expected outcomes. Moreover, classroom-style training can be expensive and where it is not sufficiently engaging; the message does not always sink in. For these reasons, many pharmaceutical companies are turning to e-learning.”

The link to the article is:

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Sunday, 6 January 2019

Modeling the microbiome

The gut microbiome -- the world of microbes that inhabit the human intestinal tract -- has captured the interest of scientists and clinicians for its critical role in health. However, parsing which of those microbes are responsible for effects on our wellbeing remains a mystery.

The human gut microbiome as yet is too diverse to fully analyze. Instead, the research team, led by Carnegie Institution for Science biologist Will Ludington, used the fruit fly as a model organism to tease apart how the presence of particular gut bacteria could lead to physical and behavioral effects in the host organism.
In their paper, "Microbiome interactions shape host fitness," Carlson, Jones, Ludington and colleagues examine the interactions between five core species of bacteria found in the fly gut, and calculate how the presence or absence of individual species influences aspects of the fly's fitness, including lifespan, fertility and development. "The classic way we think about bacterial species is in a black-and-white context as agents of disease -- either you have it or you don't," Ludington said. "Our work shows that isn't the case for the microbiome. The effects of a particular species depend on the context of which other species are also present."

Building on previous research that found the presence versus the absence of bacteria affected the longevity of an organism (sterile hosts lived longer), the researchers' work on this project revealed that the situation is far more nuanced. For example, the presence of certain bacteria might increase the host's fecundity, while others might decrease longevity. "As we examined the total of what we call a fly's fitness -- it's chances of surviving and creating offspring -- we found that there was a tradeoff between having a short lifespan with lots of offspring, versus having a long lifespan with few offspring," Ludington explained. "This tradeoff was mediated by microbiome interactions."

To decipher these interactions, Ludington performed a combinatorial assay, rearing 32 batches of flies each inhabited by a unique combination of the five bacteria. For each bacterial combination, Ludington measured the fly's development, fecundity and longevity. The analysis of the interactions required Carlson and Jones to develop new mathematical approaches.

What the study shows, the researchers said, is that the interactions between the bacterial populations are as significant to the host's overall fitness as their presence -- the microbiome's influence cannot be solely attributed to the presence or absence of individual species. "In a sense," said Jones, "the microbiome's influence on the host is more than the sum of its parts."


Alison L. Gould, Vivian Zhang, Lisa Lamberti, Eric W. Jones, Benjamin Obadia, Nikolaos Korasidis, Alex Gavryushkin, Jean M. Carlson, Niko Beerenwinkel, William B. Ludington. Microbiome interactions shape host fitness. Proceedings of the National Academy of Sciences, 2018; 201809349 DOI: 10.1073/pnas.1809349115

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Saturday, 5 January 2019

Weights and measures

An interesting post from ISO:

“The world’s scientific community is making a fundamental change in how we measure things by redefining the kilogramme, the kelvin, the ampere and the mole, four of the seven base units of the International System of Units (SI). An ISO and IEC series of standards plays a crucial role.

Did you know that the humble kilogramme has, until now, been defined by an object that weighs… one kilogramme? And that the measurement unit of temperature – the kelvin – is based on an intrinsic property of water? While this has worked for centuries, the world’s leading scientists have found that, over time, these definitions have been shown to not be 100 % stable. So, today, they formally agreed that all of the measurement units will now be defined by constants of nature rather than physical objects – the biggest change in international measurement since 1875.”

For the full post see:

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

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