Thursday, 31 December 2015

Best microbiology news stories of 2015

To complete an interesting year in microbiology, here are some of the most interesting microbiology news stories of the year.

#1 Processed foods alter gut bacteria, trigger inflammatory disease

The composition of bacteria in the human gut shapes whether a person is more prone towards obesity. In turn, this gut composition can be affected by diet with processed foods presenting some modern day challenges.

This was the argument of Professor Andrew Gewirtz, from the Centre for Inflammation, Immunity and Infection, based at Georgia State University. Professor Gewirtz put forth this argument during a lecture delivered to the Parenteral Drug Association (PDA)'s 10th Global Pharmaceutical Microbiology Conference in Bethesda, U.S., on October 20.

Read more:

#2 Fund launched to fight global resistant infections

A new global campaign has been launched called the Fleming Fund, with the aim of harnessing resources to tackle the growing problem of antibiotic resistant pathogenic bacteria.

The U.K. Government is to work alongside the medical charity the Wellcome Trust, the Bill and Melinda Gates Foundation, the Institut Pasteur International Network, and other global organisations to tackle drug-resistant infections. The new body is to be called the "Fleming Fund."

3# Rapid tuberculosis test in development

In a new study, scientists have described the accuracy of three new rapid tests designed to detect drug-resistant forms of tuberculosis.

With the recent series of experiments, scientists based at the University of California, San Diego School of Medicine, collected sputum samples from 1,128 study participants. Each of the samples was examined using the three different tests. Two of the tests used advanced molecular techniques. These methods looked for genetic mutations in the bacterium’s DNA that confer resistance to antibiotics.

Read more:

#4 New type of bacteria-powered energy source

As part of the hunt for new types of energy, especially those that are renewable, microbiologists have been examining the properties of marine bacteria. One species, called Cyanothece 51142, is of particular interest.

Blue-green algae (which are not "true" algae but are cyanobacteria) are ubiquitous. They are found in most parts of the world, widespread especially in freshwater, marine, and terrestrial ecosystems. The bacteria have a number of interesting properties — one is to use the energy from that captured light, through the process of photosynthesis, to produce hydrogen.

Read more:

#5 New class of bacteria busting antimicrobials

A new type of spiral polypeptides, produced at the University of Illinois, may signal a new type of antimicrobial. The polypeptides target the outer membrane of the bacterial cell wall.

Polypeptides are short protein chains and the attack bacteria by perforating the bacterial membrane. This process of "hole punching" happens multiple times, until the bacterial cell breaks up. The technical term is "membrane disruption." The activity can be confirmed using such techniques as neutron and X-ray diffraction, and fluorescent dyes.

Read more:

Posted by Dr. Tim Sandle

Wednesday, 30 December 2015

Gut bacteria signal to the brain when someone is "full"

Lots of food
Big meal and full-up
Twenty minutes after a meal, gut microbes produce proteins that can suppress food intake in animals. New research has shown how these proteins, when injected into mice and rats, act on the brain, reducing appetite, suggesting that gut bacteria may help people control when and how much they eat.

The new evidence coexists with current models of appetite control, which involve hormones from the gut signalling to brain circuits when we're hungry or done eating. The bacterial proteins--produced by mutualistic E. coli after they've been satiated--were found for the first time to influence the release of gut-brain signals (e.g., GLP-1 and PYY) as well as activate appetite-regulated neurons in the brain.

Mealtime brings an influx of nutrients to the bacteria in your gut. In response, they divide and replace any members lost in the development of stool. The study raises an interesting theory: since gut microbes depend on us for a place to live, it is to their advantage for populations to remain stable. It would make sense, then, if they had a way to communicate to the host when they're not full, promoting host to ingest nutrients again.

For details on the study, see:

Jonathan Breton, Naouel Tennoune, Nicolas Lucas, Marie Francois, Romain Legrand, Justine Jacquemot, Alexis Goichon, Charlène Guérin, Johann Peltier, Martine Pestel-Caron, Philippe Chan, David Vaudry, Jean-Claude do Rego, Fabienne Liénard, Luc Pénicaud, Xavier Fioramonti, Ivor S. Ebenezer, Tomas Hökfelt, Pierre Déchelotte, Sergueï O. Fetissov.Gut Commensal E. coli Proteins Activate Host Satiety Pathways following Nutrient-Induced Bacterial Growth. Cell Metabolism, 2015; DOI: 10.1016/j.cmet.2015.10.017

 Posted by Dr. Tim Sandle

Tuesday, 29 December 2015

Algae and biofuels

algae lake
Algae and anchor
The complete genetic makeup of a species of ecologically important algae, which may aid in biofuel production, has been sequenced by scientists. This is only the second time that researchers have sequenced the genome of one of these ecologically important algae, known as haptophytes.

University of Washington scientists have sequenced the complete genetic makeup of one of these algae. The haptophytestudied is Chrysochromulina tobin. The organism thrives in oceans across the globe. The researchers spent years on a series of experiments to sequence all of Chrysochromulina's genes and understand how this creature turns different genes on and off throughout the day. In the process, they discovered that Chrysochromulina would make an ideal subject for investigating how algae make fat, a process important for nutrition, ecology and biofuel production.

For further details see:

Blake T. Hovde, Chloe R. Deodato, Heather M. Hunsperger, Scott A. Ryken, Will Yost, Ramesh K. Jha, Johnathan Patterson, Raymond J. Monnat, Steven B. Barlow, Shawn R. Starkenburg, Rose Ann Cattolico.Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae).PLOS Genetics, 2015; 11 (9): e1005469 DOI:10.1371/journal.pgen.1005469

 Posted by Dr. Tim Sandle

Monday, 28 December 2015

Shape-shifting Candida albicans

Candida albicans on a Petri dish
A fungus found in the mucus of patients with cystic fibrosis - Candida albicans - has been examined by researchers. It has been discovered that the fungal species has evolved to defend itself against neighboring bacteria.

Candida albicans is a remarkable fungus. Its signature maneuver is shapeshifting -- it can morph from a round, single-celled yeast into a long stringy structure, allowing it to adapt to different environments and making it exceptionally harmful. In a recent study, researchers analyzed 89 mucus samples from 28 cystic fibrosis patients, using both high-throughput genetic sequencing as well as culture-based analysis. Candida albicans was predictably prevalent.

What was surprising is that that some of the fungi began shifting into its stringy shape without any environmental cue -- usually this transformation (filamentation) does not happen spontaneously, but is triggered by the presence of certain substances, such as blood. To see if there could be a genetic explanation, the researchers sequenced the genomes of these samples and found a common denominator. All but one had genetic mutations in a gene known to repress the change shape -- called NRG1.

To find out why certain strains of this fungus would have developed this genetic variation, researchers looked to neighbouring bacteria. As part of an ongoing battle between microbes, certain bacteria, which are also found in cystic fibrosis patients, secrete molecules preventing the fungus from changing into its stringy shape. The researchers tried exposing the mutated fungus to these bacterial rivals. Instead of responding to the bacterial signals, the fungus kept to its stringy form. The researchers believe these fungi have evolved to counter the tactics of their bacterial rivals.

For further details see:

Sang Hu Kim, Shawn T. Clark, Anuradha Surendra, Julia K. Copeland, Pauline W. Wang, Ron Ammar, Cathy Collins, D. Elizabeth Tullis, Corey Nislow, David M. Hwang, David S. Guttman, Leah E. Cowen. Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation. PLOS Pathogens, 2015; 11 (11): e1005308 DOI: 10.1371/journal.ppat.1005308

Posted by Dr. Tim Sandle

Sunday, 27 December 2015

Antimicrobial resistance in bacteria from horses

Funny horse face
Bacterial resistance to antimicrobial agents is a significant problem for both human and veterinary medicine, but little research has been done on the prevalence or mechanisms of resistance in horses and other companion animals, and how such resistance might impact human health.

A new review in the Equine Veterinary Journal reveals that antimicrobial resistance is prevalent in bacteria from horses, particularly E. coli. Also, while methicillin-resistant S. aureus (MRSA) can be common in hospitalized horses, it is less frequently present in the general equine population. The emergence of multidrug resistance in many other bacterial species, however, represents a huge challenge for society.

For further details, see:

T. W. Maddox, P. D. Clegg, N. J. Williams, G. L. Pinchbeck. Antimicrobial resistance in bacteria from horses: Epidemiology of antimicrobial resistance. Equine Veterinary Journal, 2015; 47 (6): 756 DOI:10.1111/evj.12471

Posted by Dr. Tim Sandle

Structural issues of the tegument regions adjacent to the melanocytic nevi

This  study  aims  at  structurally  observing  the  tegument  regions adjacent  to  the  areas  where  melanocytic  nevi  are  found.  The  study  aimed  at      analyzing the structural      tumors  accompanying  the  melanocytic  nevi  located  on  the  scalp.  Such  structural  analysis  of  the  melanocytic  nevi  is  required  because  of  the increased  frequency  of  occurrence  of  these tumors’ from early age; in turn this requires competent medical control for the elimination of   the   nevi   in   sufficient   time   due   to   the potential   for   malignant   degeneration.   The malignant  transformation  of  the  melanocytic nevi   is   triggered   by   external   factors,   in addition   to   the   genetic   factors   which   are responsible  for  the  potential  of  the  nevus  to form.     Moreover,     we     must     take     into consideration  the  influence  of  traumatizing the  melanocytic  nevi  and  their  potential  for malignant degeneration.


Chesca, A., Sandle, T., Babenko, D. and Azizov, A. (2015) Structural  issues of the tegument regions adjacent  to the melanocytic nevi, Annals of the Romanian Society for Cell Biology, 20 (1): 7-10

The paper is available to view here.

Posted by Dr. Tim Sandle

Saturday, 26 December 2015

Classic microbiology: Louis Pasteur

Few people have saved more lives than Louis Pasteur. The vaccines he developed have protected millions. His insight that germs cause disease revolutionised healthcare. He found new ways to make our food safe to eat.

Pasteur was the chemist who fundamentally changed our understanding of biology. By looking closely at the building blocks of life, he was at the forefront of a new branch of science: microbiology.

Louis Pasteur was probably the greatest biologist of the nineteenth century. He developed the germ theory of disease, which was a significant breakthrough in medicine that ultimately improved the health of everyone on the planet. He was also able to prove that life itself did not "spontaneously come into being" through a series of experiments using a sterilized flask. He successfully showed that life can only be generated from existing life, thus closing debate - so he thought - that had obsessed science and theology for a long time (though current ideas and successes in the field of "creating life" has re-opened the issue).

Pasteur also showed that fermentation - a process used in baking and brewing - was caused by microorganisms. As a result of this work he went on to develop the process for sterilizing milk and this was named after him - pasteurization.

He is also credited with the development of vaccines, most notably for rabies and anthrax. Pasteur was keen to develop vaccines for other diseases. He turned his attention to anthrax. Anthrax was fatal to humans, and could wipe out entire populations of farm animals. Anyone who could prevent the disease would not only save lives, but also stood to make money. German doctor Robert Koch had already found the bacteria that caused the disease. Now Pasteur announced he'd discovered a vaccine, and successfully immunised 31 animals – although recent studies of his notebooks have revealed he exaggerated how much original work he did; he'd actually drawn on other people's findings.

 In addition, he identified and eliminated disease in silkworms. He was also interested in the idea of panspermia that was promoted by Lord Kelvin in 1871, and went on to examine the Orgeuil meteorite for signs of life.

Posted by Dr. Tim Sandle

Friday, 25 December 2015

Microbiology cartoons

As this is a rest day for pharmaceutical microbiology, enjoys these cartoons!

Posted by Dr. Tim Sandle

Thursday, 24 December 2015

Season's Greetings

Season's Greetings to all readers of Pharmaceutical Microbiology.

Many thanks for your support over the year.

Posted by Dr. Tim Sandle

Wednesday, 23 December 2015

Microbiota of a Pharmaceutical Water System-A Metadata Study

Bacterial populations inhabiting pharmaceutical grade water systems were investigated over a fifteen year period. The systems analyzed were mains water, purified and Water-for-Injection (WFI). Samples of water were tested by membrane filtration and the samples cultured using R2A agar. Culture based methods and phenotypic identification methods were used to characterize the isolates. The research was undertaken to produce an in-depth study of the microbiota of pharmaceutical grade water systems. The results presented act as a benchmark for industrial and pharmaceutical microbiologists to review comparable systems against, as well as to present a review of the typical culturable microorganisms recoverable from pharmaceutical water systems

To access the article, see: microbial water study

 Posted by Dr. Tim Sandle

Tuesday, 22 December 2015

Cleaning Endoscopes (hospital infection)

A free paper concerning hospital infection control.

 Cleaning of endoscopes should begin at bedside, immediately after use, and should begin with thoroughly flushing the channels and rinsing/wiping the outside of the endoscope using detergent solution.
Posted by Dr. Tim Sandle

Monday, 21 December 2015

Guide for Determining the Confidence Interval Using Excel

A handy guide for the number crunchers - Guide for Determining the Confidence Interval Using Excel

Posted by Dr. Tim Sandle

Bacteria on the Brain

A brilliant surgeon offered an untested treatment to dying patients. Was it innovation or overreach? An interesting article published in the New Yorker. Free to read, by 


"Muizelaar had devised the procedure in collaboration with a young neurosurgeon in his department, Rudolph Schrot. But as the consent form crafted by the surgeons, and signed by Egan and his wife, made clear, the procedure had never been tried before, even on a laboratory animal. Nor had it been approved by the Food and Drug Administration. The surgeons had no data to suggest what might constitute a therapeutic dose of Enterobacter, or a safe delivery method. The procedure was heretical in principle: deliberately exposing a patient to bacteria in the operating room violated a basic tenet of modern surgery, the concept known as “maintaining a sterile field,” which, along with prophylactic antibiotics, is credited with sharply reducing complications and mortality rates. “The ensuing infection,” the form cautioned, “may be totally ineffective in treatment of the tumor” and could cause “vegetative state, coma or death.”

Posted by Dr. Tim Sandle

Sunday, 20 December 2015

Restoring Africa’s health systems after Ebola

Sierra Leone may have been declared Ebola-free, but the outbreak brought an already weak health system to its knees, writes Jane Feinmann in the British Medical Journal.

The charity Doctors of the World is well versed in bringing care to the most vulnerable people in both developing and developed countries, which is why we’ve chosen it for The BMJ’s Christmas appeal this year. Please give generously

When does an emergency such as an outbreak of Ebola end? That’s the question that the charity Doctors of the World is asking readers of The BMJ to consider this Christmas in the face of evidence that healthcare in Sierra Leone, which was under-resourced and poorly performing before the outbreak, is now close to collapse.

For more: see BMJ.

Posted by Dr. Tim Sandle

Cleanrooms and clean air

Cleanrooms are highly controlled environments where the air quality is monitored to ensure the extreme standards of cleanliness required for surgical units and for hospital pharmacies.

Please find a free paper on this subject below.

Posted by Dr. Tim Sandle

Saturday, 19 December 2015

Ready-to-Use Wipes

Infection Control Today have a free report on ready-to-use disinfection wipes.

The traditional towel-and-bucket method of environmental cleaning is being replaced in many hospitals by ready-to-use disinfectant wipes. These pre-soaked disposable wipes are increasingly used for the disinfection of near-patient surfaces to prevent the spread of microorganisms and the emergence of nosocomial infections. This report explores the benefits of ready-to-use wipes as well as reviews the key factors that impact wipes' efficacy.

To view the report, see: Infection Control.

Posted by Dr. Tim Sandle

Friday, 18 December 2015

ISO 14644 Energy efficiency in cleanrooms - part 16

ISO TC209 WG13 14644 Energy efficiency in cleanrooms - ISO14644 part 16 is now at the draft stage for review.

The draft states: “Although varying greatly in function and size, the energy consumption of cleanrooms can be over 10 times higher than that for offices of similar size. A considerable amount of energy is required to provide large amounts of filtered and conditioned air to achieve specific levels of air cleanliness. Air movement fans can account for 35% to 50% of this, due to the power required to overcome the high pressure differentials needed to operate high efficiency filters and other circulation components in the cleanroom system. Production of this type of high quality air can consume up to 80% of the total energy used in a typical manufacturing facility. Additional energy is also used to achieve temperature and relative humidity control.”

To address these issues, the aim of the standard will be to outline ways to reduce energy use while at the same time maintaining standards.

Those interested in reviewing the draft should contact their national standards body.

Posted by Dr. Tim Sandle

Thursday, 17 December 2015

Health 1000 formats modified to adjust the dose antibiotics to treatment duration

Antibiotic awareness news from Spain:

A thousand forms of drugs have changed since 2012 in Spain to adjust the dose to the patient needs treatment. It is one of the actions taken by this government to rationalize the use of antibiotics in the country, as stated by the Minister of Health, Social Services and Equality, Alfonso Alonso, who took part today in the commemoration of the European Day for Use prudent use of antibiotics.

To read the report, see: European day for the prudent use of antibiotics

Posted by Dr. Tim Sandle

Wednesday, 16 December 2015

Antibiotic resistance emerges from diverse evolutionary paths

A major breakthrough in understanding how pathogenic microbes develop resistance to antibiotic drugs has been reported in Nature Communications. By examining combinations of seven mutations in dihydrofolate reductase that microbes can acquire to gain trimetoprim resistance, researchers found that evolution toward proceeds along less direct paths than might be expected, as cells range through a multipeaked adaptive landscape and delay commitment to a single genotypic fate.

Posted by Dr. Tim Sandle

Tuesday, 15 December 2015

Dysbiosis and gynecologic cancers

Dysbiosis is perturbation of the normal microbial flora in our body. It impacts many key cellular metabolic processes resulting in multiple diseases including cancer. Bacterial vaginosis, uterine cancer, ovarian cancer and endometrial cancer are suspected to be promoted by dysbiotic microbiomes. How does dysbiosis ultimately promote carcinogenesis? Read this comprehensive review on the microbiome and cancer.

Related articles

1. Vaginal and gastrointestinal microbiomes in gynecologic cancers: a review,
Chase et al., 2015

2. Metabolic signatures of bacterial vaginosis,
Srinivasan et al., 2015

Posted by Dr. Tim Sandle

Monday, 14 December 2015

Melanized (black) fungal contamination in pharmaceutical products

A review of melanized (black) fungal contamination in pharmaceutical products—incidence, drug recall and control measures – is a new review article by R. Vijayakumar, M. Saleh Al-Aboody and Tim Sandle.

The article summary is:

The aim of this study was to describe the incidence of contamination of pharmaceutical products by melanized fungi and to consider control measures in relation to bioburden and cleanrooms. This study reviews and analyses pharmaceutical product recalls and offers incidence rates of fungal detection from a typical cleanrooms. The recalls include some serious cases which resulted in the loss of life. Of different types of fungal contamination incidences some of the most damaging have been due to melanized fungi (‘black mould’), such as Exserohilum rostratum. The focus of the article is with melanized fungi. The study concludes that, from the review of recent pharmaceutical product recalls, fungal contamination is either increasingly common within cleanroom environments or the accuracy of sampling and the level of reporting has risen. The prevalence of melanized fungi in pharmaceutical facilities rests on specific virulence factors particular to these types of fungi, which are outlined. The article identifies a gap in the way that such fungi are screened for using available cultural methods. The article provides some control strategies, including assessing the suitability of disinfectants and biocides, for reducing the risk of melanized fungal incidences within the pharmaceutical facility. Understanding the fungal risk to pharmaceutical products remains a poorly understood and often overlooked aspect of pharmaceutical microbiology. This article helps to identify this risk and offer some guidance to those involved with pharmaceutical products manufacture in relation to bio-contamination control strategies.

The reference is:

Vijayakumar, R., Saleh Al-Aboody, M. and Sandle, T. (2015) A review of melanized (black) fungal contamination in pharmaceutical products—incidence, drug recall and control measures, Journal of Applied Microbiology, Accepted Article: doi:10.1111/jam.12888

For further details, please contact Tim Sandle


Posted by Tim Sandle