Sunday, 30 June 2019

One-Billion-Year-Old Fungus found in the Canadian Arctic

Microphotograph of Ourasphaira giraldae. Image: Corentin Loron et al
Scientists have discovered fossils of a fungus that lived roughly one billion years ago—yes, billion—making it over twice as old as any other fungi specimens identified to date.

Named Ourasphaira giraldae, the new species of fungus was found in the Grassy Bay Formation in the Canadian Arctic. Researchers led by Corentin Loron, a PhD student at Université de Liège, identified key fungal features in micrometer-scale fossils extracted from unexplored shale at this remote site.

The discovery, announced  in Nature, not only pushes the fossil record of fungi back by about 600 million years, it also suggests that other eukaryotic organisms—a group that includes complex multicellular life-forms like animals—may have originated around the same time as O. giraldae, in the mid-Proterozoic age.

For further details, see: Vice

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Saturday, 29 June 2019

Tackling Candia albicans infection by starvation

Image: Lucy Morales

How do you fight a fungal infection that is becoming increasingly resistant to medicine? By starving it, found a team of University at Buffalo and Temple University researchers.

To treat Candida albicans, a common yeast that can cause illness in those with weakened immune systems, researchers limited the fungus' access to iron, an element crucial to the organism's survival.

They did so by using deferasirox, a medication used to treat blood disorders. Tested in mice, the results were promising: investigators decreased iron levels in saliva by four times, which altered the expression of more than 100 genes by the fungus, diminished its ability to infect oral mucosal tissue and caused a two-fold reduction in the organism's survival rate.

"In the absence of novel drug candidates, drug repurposing aimed at using existing drugs to treat diseases is a promising strategy," says Mira Edgerton, DDS, PhD, co-lead investigator of the study and research professor in the Department of Oral Biology at the UB School of Dental Medicine.

Edgerton, along with Sumant Puri, PhD, co-lead investigator and assistant professor in the Kornberg School of Dentistry at Temple University, published the study in March in Antimicrobial Agents and Chemotherapy.

Currently, only three major classes of clinical antifungal drugs exist. However, fungal drug resistance has steadily increased and no new classes of antifungals have emerged in decades, says Edgerton.

Candida albicans, a fungus among the group building resistance, is the agent behind a number of infections. They include oral thrush, a yeast infection in the mouth identified by a white film that coats the tongue and throat, causing painful swallowing; and denture-related stomatitis, a fungal infection that affects nearly two-thirds of U.S. denture wearers that causes inflammation, redness and swelling in the mouth.

The yeast is also the fourth leading cause of hospital-acquired bloodstream infections, which often have high mortality rates, says Edgerton.

Candida albicans is the most abundant fungus in the oral microbiome and relies heavily on saliva as a source for essential elements. Iron, the second most abundant metal in saliva, is a critical nutrient used by the fungus in several cellular processes, including energy production and DNA repair.

In mice, the group added deferasirox to drinking water to lower iron levels in saliva and reduce the availability of iron needed to sustain an infection.

The investigators found that Candida albicans in the mice who received the treatment were less likely to survive attacks by the immune system, subsisting at a 12 percent survival rate compared to a 25 percent survival rate in mice who did not receive the treatment.

The therapy also altered the expression of 106 genes by the fungus, a quarter of which were involved in the regulation of iron metabolism, directly regulated by iron or had iron-related functions. The study is the first report of iron starvation affecting gene expression of Candida albicans in real time during live infection, says Puri.

Other research has shown that treatment with deferasirox does not result in iron deficiency in adults with normal iron levels, forming the potential for preventative treatment for those who are also vulnerable to mucosal infections, says Puri.

See: Sumant Puri, Rohitashw Kumar, Isolde G. Rojas, Ornella Salvatori, Mira Edgerton. Iron Chelator Deferasirox Reduces Candida albicans Invasion of Oral Epithelial Cells and Infection Levels in Murine Oropharyngeal Candidiasis. Antimicrobial Agents and Chemotherapy, 2019; 63 (4) DOI: 10.1128/AAC.02152-18

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Friday, 28 June 2019

How Enterococcus faecalis bacteria causes antibiotic resistant infection

Antibiotic resistant infection is a leading threat to public health worldwide. It has been estimated that by 2050, more people could die from infections that are no longer treatable with antibiotics, than from cancer. Understanding how some bacteria have been able to overcome our natural immune defenses, and new drugs as they are introduced, is the key to preventing a future where up to 10 million people could die each year from antibiotic resistant infection.

A new study led by a research team from Massachusetts Eye and Ear and Harvard Medical School describes how bacteria adapted to the modern hospital environment and repeatedly cause antibiotic-resistant bloodstream infections. Infections acquired by hospitalized patients are more often antibiotic-resistant than those that occur elsewhere, and hospitals invest considerable effort to prevent them. Despite best efforts, some bacteria are able to persist and circulate among patients, causing repeated infections.

This study examined one of the first sustained hospital outbreaks of a multidrug-resistant bacterium, Enterococcus faecalis, which occurred from the early through the mid-1980s, causing over 60 outbreak strains.

See: Daria Van Tyne, Abigail L. Manson, Mark M. Huycke, John Karanicolas, Ashlee M. Earl, Michael S. Gilmore. Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream. Science Translational Medicine, 2019; 11 (487): eaat8418 DOI: 10.1126/scitranslmed.aat8418

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Thursday, 27 June 2019

National HIV Testing Day

The national HIV Testing Day event organized by the Canadian AIDS Society (CAS) and community-based organizations and local health authorities across Canada is on June 27th with testing events happening at various times at local testing sites in 70 communities across the country.

‘’Building on the success of last year, this event is truly about normalizing HIV testing, increasing Canadians’ capacity to make informed decisions regarding their own sexual health, and decreasing stigma’’ says Gary Lacasse, Executive Director of CAS. HIV Testing Day was created in response to the rising HIV rates being seen in Canada. According to the Public Health Agency of Canada’s 2017 HIV Surveillance Report, there has been a 17.1% increase in the number of new HIV infections in Canada between 2014 and 2017. Stigma and barriers to testing continue to exist, discouraging Canadians from getting tested. The inaugural event in 2018 received national media coverage, raising awareness about the importance of regular testing for HIV and other sexually transmitted and blood-borne infections (STBBI). 

Similarly, a major priority for this year’s event will be to reach the undiagnosed – Canadians who are disproportionately affected by HIV and other STBBI and/or Canadians who have never been tested for HIV and other STBBI. The theme for this year’s Testing Day is “Know Your Status”. 1 in 5 Canadians living with HIV are unaware that they have HIV. The only way to know for certain if you’re HIV-positive is to get tested. 

The sooner you know your status the sooner you can be linked to care. Where available, testing sites will be able to provide immediate HIV test results using point-of-care testing kits. In just a minute, a simple finger-prick test is all you need to know your status. “This national HIV Testing Day provides an opportunity for Canadians to take charge of their health to learn their HIV status, particularly in rural and remote areas with one-minute testing at the point-of-care in both conventional and unconventional settings,” said Livleen Veslemes, of bioLytical Laboratories, the maker of INSTI.

A new component of this project will be the presence of U=U spokespeople at various testing sites. U=U (Undetectable=Untransmissible) is an initiative based on the scientific consensus that when you achieve viral suppression from taking HIV medicine and continue to stay at undetectable levels of HIV, you can stay healthy and have no risk of transmitting the virus to others. 

Where possible, a person living with HIV who is undetectable will be available at participating testing sites to explain the campaign and how someone who is living with HIV can have a healthy sex life and not pass the virus along to others.

This initiative is being organized by CAS and a national steering committee made up of community-based organizations from across the country: the Pacific AIDS Network, the Alberta Community Council on HIV, AIDS Saskatoon, Nine Circles Community Health Centre, the Ontario AIDS Network, COCQ-Sida, ENSEMBLE Greater Moncton (formerly AIDS/Sida Moncton), AIDS Coalition of Nova Scotia, AIDS Committee of Newfoundland and Labrador, the Canadian Aboriginal AIDS Network, and CATIE. In addition to HIV Testing Day on June 27th, this project will also involve the ongoing initiative of providing sexual health resources to these priority populations through a variety of mediums. 

Information on the testing site locations is available at

Identify a national HIV Testing Day site near you, get tested and #KnowYourStatus.

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Wednesday, 26 June 2019

Antimicrobial photodynamic therapy

An article of interest:

Antibiotic resistance is an increasing healthcare problem worldwide. In the present study, the effects of antimicrobial photodynamic therapy (APDT) of ZnPc and ZnPc-integrated TiO2 nanoparticles (ZnPc-TiO2)2) were investigated against Staphylococcus aureus. A light emitting diode (LED) (630–700 nm, 17.4 mW/cm2)2) was used on S. aureus at different light doses (8 J/cm2 for 11 min, 16 J/cm2 for 22 min, 24 J/cm2 for 33 min) in the presence of the compounds under the minimum inhibitory concentration values. Both compounds showed similar phototoxicity toward S. aureus when high light doses (16 and 24 J/cm2) were applied. In addition, the success of APDT increased with an increasing light dose.

See: Journal of Porphyrins and Phthalocyanines "Antimicrobial photodynamic therapy against Staphylococcus aureus using zinc phthalocyanine and zinc phthalocyanine-integrated TiO2 nanoparticles".

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Tuesday, 25 June 2019

Global Opportunity to Tackle Antibiotic Production Waste

Global policy makers gathered at The Hague in the Netherlands for the International Ministerial Conference on antimicrobial resistance (AMR).

Experts are calling for a greater focus on antibiotic production in order to tackle AMR and ensure the effectiveness of antibiotics in the future. Sustainable production is notably not a focus in the WHO’s AMR Global Action Plan, despite the fact that:
  • There are 700,000 AMR related deaths each year predicted to rocket to 10 million deaths in 2050, more than all cancers combined
  • Only 8 large R&D based and generic pharmaceutical companies set limits on antibiotics in their wastewater
  • The amount of pharmaceutical effluent leaking into Europe’s waterways is estimated to increase by 2/3rds by 2050
  • Antibiotics have been found in 65%of the world’s rivers, including the Thames where 5 antibiotics were found at up to 3 times the safe levels
  • In Bangladesh waterways have been found to harbour 300 times the safe levels of antibiotics

Readers can download the media kit of three infographics (on AMR and health, AMR and the environment and an AMR timeline) here. Also included are case studies of sustainable manufacturing, the AMR industry alliance, and sustainable procurement practices in Sweden and Norway

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Monday, 24 June 2019

Use of Hazard Analysis and Critical Control Points (HACCP) for EM locations

In the first part of a review of HACCP methodology (“Use of Hazard Analysis and Critical Control Points (HACCP) - Part 1: Assessing microbiological risks”) the application of HACCP as a tool for conducting microbiological risks assessments was discussed. This piece considered the approach taken to HACCP and the primary areas of microbiological concern to which the qualitative risk tool can be applied to.

This second example offers a case study of how HACCP can be applied to a practical setting: the identification of environmental monitoring locations, by considering, in the HACCP lexicon, monitoring locations as ‘critical control points’.

The selection of appropriate locations for environmental monitoring is a key aspect of any robust environmental monitoring program. If the locations are not in meaningful locations, the strength of the program is undermined. By ‘meaningful locations’ this means locations that reveal, through the data collected, an indication of potential product contamination. Contamination can arise through airborne deposition or by direct transfer, which signals the need for selecting locations that indicate this likelihood and the use of appropriate sampling methods to detect both airborne risks and surface risks (either fixed surfaces, on equipment, or on people). The HACCP approach provides a useful framework for such an assessment.

Tim Sandle’s follow up paper to his first HACCP article has been published. The reference is:

Sandle, T. (2019) Use of Hazard Analysis and Critical Control Points (HACCP) – Part 2: Determining Environmental Monitoring Locations, Journal of GxP Compliance, 23 92): 1-10

For further details, please contact Tim Sandle

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Sunday, 23 June 2019

Revision of the Drinking Water Directive

On 1 February 2018, the European Commission published a proposal for a recast of the Directive on the quality of water intended for human consumption (the Drinking Water Directive). The proposal responds to the European Citizens’ Initiative, Right2Water, and builds on a fitness check which concluded that the 20-year old directive is fit for purpose, but needs updating. The main elements of the proposal consist of updating the water quality standards, introducing a risk-based approach to the monitoring of water, improving and streamlining the information provided to consumers, harmonising the standards for products in contact with drinking water, and imposing obligations to improve access to water.

In the European Parliament, the Committee on Environment, Public Health and Food Safety (ENVI) adopted its report on 10 September 2018. A plenary vote on the amendments, and on opening interinstitutional negotiations, took place on 23 October 2018. Although the Council reached a general approach on 5 March 2019, the Parliament concluded its first reading in plenary on 28 March 2019. Trilogue negotiations in view of reaching an early-second reading agreement could thus begin in the new parliamentary term.

For details, see:

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Saturday, 22 June 2019

Electricity-conducting bacteria yield secret to tiny batteries

Credit: Edward H. Egelman

A new discovery about how strange bacteria that live in soil and sediment can conduct electricity. The bacteria do so, the researchers determined, through a seamless biological structure never before seen in nature -- a structure scientists can co-opt to miniaturize electronics, create powerful-yet-tiny  batteries, build pacemakers without wires and develop a host of other medical advances.

Microbiologists had thought that Geobacter sulfurreducens conducted electricity through common, hair-like appendages called pili. Instead, a researcher at the University of Virginia School of Medicine and his collaborators have determined that the bacteria transmit electricity through immaculately ordered fibers made of an entirely different protein. These proteins surround a core of metal-containing molecules, much like an electric cord contains metal wires. This "nanowire," however, is 100,000 times smaller than the width of a human hair.

This tiny-but-tidy structure, the researchers believe, could be tremendously useful for everything from harnessing the power of bioenergy to cleaning up pollution to creating biological sensors. It could actually serve as the bridge between electronics and living cells.

Geobacter bacteria play important roles in the soil, including facilitating mineral turnover and even cleaning up radioactive waste. They survive in environments without oxygen, and they use nanowires to rid themselves of excess electrons in what can be considered their equivalent to breathing. These nanowires have fascinated scientists, but it is only now that researchers at UVA, Yale and the University of California, Irvine, have been able to determine how G. sulfurreducens uses these organic wires to transmit electricity.

Journal Reference

Fengbin Wang, Yangqi Gu, J. Patrick O’Brien, Sophia M. Yi, Sibel Ebru Yalcin, Vishok Srikanth, Cong Shen, Dennis Vu, Nicole L. Ing, Allon I. Hochbaum, Edward H. Egelman, Nikhil S. Malvankar. Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers. Cell, 2019; 177 (2): 361 DOI: 10.1016/j.cell.2019.03.029

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Friday, 21 June 2019

Paper stickers to monitor pathogens are more effective than swabs

Using paper stickers to collect pathogens on surfaces where antisepsis is required, such as in food processing plants, is easier, and less expensive than swabbing, yet similarly sensitive.

"The porous structure of paper seems able to collect and accumulate [bacterial] contamination," said first author Martin Bobal, technical assistant, Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Department for Farm Animal and Public Health in Veterinary Medicine, The University of Veterinary Medicine, Vienna, Austria. "This requires mechanical contact, for example by hand, or by splashed liquids."

In the study, the investigators, who specialize in monitoring cheese production, chose to target the organism Listeria monocytogenes, a pathogen that commonly contaminates raw milk and other raw dairy products, including soft cheeses such as Brie, Camembert, and Feta. They used qPCR, a method of quantifying DNA samples to determine the numbers of these bacteria, as well as of Escherichia coli.

Surfaces in food processing plants must be cleaned regularly. Unlike swabs, artificially contaminated stickers provided a record of contamination that took place over at least two weeks, despite washing, flushing with water, or wiping with Mikrozid, an alcohol-based disinfectant, to simulate cleansing practices. "Recovery [of DNA] from the stickers was rather variable, at around 30%, but did not distinctly decrease after 14 days of storage," the report stated. "This suggests the possibility of sampling over two weeks as well."

In a proof of concept experiment, the researchers placed stickers at multiple locations that frequently undergo hand contact -- such as on light switches and door handles -- for one to seven days. Both bacterial species were detected repeatedly from these stickers.
Unlike stickers, swabbing is impractical on complex surfaces, such as door handles, light switches, and other fomites (objects likely to be contaminated with, and spread infectious organisms) and does a poor job of taking up bacteria from dry surfaces, according to the report.

"In the food production facility, conventional swabbing as a standard method can only expose a momentary snapshot," the investigators wrote. "For example, it is not possible to reconstruct information about yesterday's status after cleansing has been performed. In addition, when moistened swabs or contact-plate sampling methods are used, they bring with them growth medium into a supposedly clean environment, making subsequent disinfection necessary."

The investigators showed that plain paper stickers could trap not only bacterial pathogens and related DNA, but dead, and viable but non-culturable pathogens, which also can pose a threat to public health.

"A major advantage of stickers is in handling: they are easy to distribute and to collect," the authors concluded. "We put the stickers directly into the DNA-extraction kit's first protocol step. We did not encounter any inhibition or loss of information during DNA-extraction, nor during qPCR," said Mr. Bobal.


Martin Bobal, Anna Kristina Witte, Patrick Mester, Susanne Fister, Dagmar Schoder, Peter Rossmanith. A novel method for sampling and long-term monitoring of microbes using stickers of plain paper. Applied and Environmental Microbiology, 2019; DOI: 10.1128/AEM.00766-19

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Kamari and Kinect Partner to Fund HIV Testing Programs in Africa

Kamari, a project building an ecosystem of mobile gaming and lotteries with existing licenses in over seven African countries, has partnered with Kinect, a blockchain-based health technology platform focused on advancing the United Nations Sustainable Development Goals (SDGs), to fund and promote new HIV testing programs in countries across the African continent.

Kinect and Kamari, both focused on development across Africa, have formed an official partnership with the intention of promoting health initiatives and increase the detection of infectious diseases, aimed to support the United Nations SDG #3: Good Health and Well Being. The two projects have proposed the establishment of a special, multi-country lottery to encourage untested males between the ages of 18 to 34 years to undergo an HIV test at participating clinics with the goal of promoting education and treatment for infected individuals.

"HIV infection is a serious issue in many African countries and the ongoing spread of the disease by untested individuals, has been incredibly difficult to address,” said Toby Carroll, Kinect Chairman. “We believe that this partnership with Kamari and the proposed lottery to incentivise those untested individuals to take their first test, will lead to increased education, treatment and hopefully reduce the spread of the disease.”

Kinect is a health focused technology company, which works in close alignment with Ministries of Health and large global charities across Africa, to improve the wellbeing of the African people. Kinect has also been operating in Mumbai, India for the last four months with its blockchain enabled electronic health record and patient incentivisation system working seamlessly to improve patient treatment programs.

Kamari is a new multi-country initiative with existing gaming, online casino, and lottery licenses across multiple African countries with the goal of building a united mobile gaming and lottery ecosystem for over one billion people. By integrating existing infrastructure and licensing with a standardized currency for gaming and payments, Kamari will instantly offer a better experience to hundreds of millions of people across Africa.

"Africa will be a multi-currency universe creating benefit and liquidity to all from the unbanked to the commercially astute,” said Dr. Christopher Cleverly, CEO of Kamari. “Kinect has a model that will thrive on an interoperable platform of shared values created through collaboration. This will be a game changer for medical data and application on the continent. "

Kinect recently formed a partnership with ZEU Crypto networks and its Canadian Stock Exchange listed company, St Georges Eco-Mining to develop its private permissioned blockchain that can integrate with major platforms including Cardano and EOS. ZEU Crypto Networks are investing US$2.45m into Kinect to enable development and expansion in existing operations.

Since 2016, Kinect has raised US$5.75m to bring the platform and business development to its current state and ensure successful expansion across Africa and other emerging economies with the greatest need.

Kinect and Kamari have entered into a US$2.5m coin swap to fund the initiative.

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Thursday, 20 June 2019

New 3D microscope visualises fast biological processes better than ever

IMAGE: Tobias Wüstenfeld

Researchers from the European Molecular Biology Laboratory (EMBL) in Heidelberg have combined their expertise to develop a new type of microscope. The revolutionary new light-field microscopy system makes it possible to study fast biological processes, creating up to 200 3D images per second. Initial tests have already delivered new insights into the movement of blood cells in a heart.

“Many important biological processes occur in three dimensions and on millisecond timescales,” says Lars Hufnagel on the rationale for developing the new microscope. Capturing these fast processes is a big challenge in biology. And showing them not only in 2D but in 3D is – next to the needed high resolution – the second main aspect of modern microscopy.

The new light-field microscopy system developed by EMBL group leaders Lars Hufnagel, Robert Prevedel and their teams overcomes both hurdles at once. “Our new method allows us to study processes both in 3D and on timescales of 200 images per second,” says Robert Prevedel. Lars Hufnagel adds: “On top of that, it delivers up to ten times better, namely truly isotropic, resolution than classic light field microscopy.”

Previously developed microscopes, mostly based on light-sheet approaches, have also attempted to image fast biological processes but have only achieved much slower speeds than the new technique. As such, they were too slow to see dynamic processes within hearts and neuronal cells.

First feasibility study on fish heart

To demonstrate the capabilities of the new technique, the team studied the beating heart and blood flow in medaka – also known as Japanese rice fish – in real time. The medaka was used as it is a well understood model organism. In addition, blood cells move fast – up to one millimetre per second – which was a challenge for any existing microscope.

The images delivered by this test showed for the first time how individual blood cells move through the two heart chambers. “This opens up completely new possibilities,” says co-author Joachim Wittbrodtfrom the Centre for Organismal Studies at Heidelberg University. “In showing how genetic backgrounds or mutations have an effect on the dynamics of heartbeats, the new technology can be used to research heart defects.”

Interdisciplinary research and development

Constructing the new microscope was an interdisciplinary effort. The researchers within the two EMBL groups have backgrounds in various scientific fields: the multidisciplinary team comprised physicists, engineers, computer scientists and, of course, biologists.

“This new microscope demonstrates that EMBL is not only at the forefront of molecular biology research but also an important place to research and develop new technologies needed within the field,” says Hufnagel.

Next step: neurons

The study on the medaka heart was only the first test for the new microscope. Robert Prevedel is looking forward to using the microscope to study the activity and dynamics of neuronal cell populations in these animals. “Future camera developments can further increase the imaging speed. This would make our new microscope technique an attractive tool to study the dynamics within small neuronal networks on millisecond time scales in 3D,” concludes Prevedel.

Source article: Nils Wagner, Nils Norlin, Jakob Gierten, Gustavo de Medeiros, Bálint Balázs, Joachim Wittbrodt, Lars Hufnagel and Robert Prevedel: 'Instantaneous isotropic volumetric imaging of fast biological processes'. Nature Methods, published online on 29 April 2019. DOI: 10.1038/s41592-019-0393-z

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Wednesday, 19 June 2019

New technology to improve tissue imaging

The issue: Even as digital pathology makes rapid advances worldwide -- with more physicians analyzing tissue images on "smart" computers to diagnose patients -- there are no reliable standards for the preparation and digitization of the tissue slides themselves.

That means poor quality slides get mixed in with clear and accurate slides, potentially confusing or misleading a computer program trying to learn what a cancerous cell looks like, for example.

Bioengineering researcher Anant Madabhushi and Andrew Janowczyk, a senior research fellow in Madabhushi's Center for Computational Imaging and Personal Diagnostics, have developed a program that they say will ensure the quality of digital images being used for diagnostic and research purposes.

The new tool incorporates a series of measurements and classifiers to help users flag corrupted images and help retain those that will aid technicians and physicians in their diagnoses.

The application is "open source" -- or free for anyone to use, modify and extend. It can be accessed through an online repository. It was developed by Janowczyk about 18 months ago after discovering what he believed to be a surprising number of poor-quality slides from the well-known Cancer Genome Atlas, home to more than 30,000 tissue slides of cancer samples.

See: Andrew Janowczyk, Ren Zuo, Hannah Gilmore, Michael Feldman, Anant Madabhushi. HistoQC: An Open-Source Quality Control Tool for Digital Pathology Slides. JCO Clinical Cancer Informatics, 2019; (3): 1 DOI: 10.1200/CCI.18.00157

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Tuesday, 18 June 2019

New research shows weakness with antimicrobial paints

Antimicrobial paints offer the promise of extra protection against bacteria. But Northwestern University researchers caution that these paints might be doing more harm than good.
In a new study, the researchers tested bacteria commonly found inside homes on samples of drywall coated with antimicrobial, synthetic latex paints. Within 24 hours, all bacteria died except for Bacillus timonensis, a spore-forming bacterium. Most bacilli are commonly inhabit soil, but many are found in indoor environments.

"If you attack bacteria with antimicrobial chemicals, then they will mount a defense," said Northwestern's Erica Hartmann, who led the study. "Bacillus is typically innocuous, but by attacking it, you might prompt it to develop more antibiotic resistance."

Bacteria thrive in warm, moist environments, so most die on indoor surfaces, which are dry and cold, anyway. This makes Hartmann question the need to use antimicrobial paints, which may only be causing bacteria to become stronger.

Spore-forming bacteria, such as Bacillus, protect themselves by falling dormant for a period of time. While dormant, they are highly resistant to even the harshest conditions. After those conditions improve, they reactivate.

"When it's in spore form, you can hit it with everything you've got, and it's still going to survive," said Hartmann, assistant professor of civil and environmental engineering in Northwestern's McCormick School of Engineering. "We should be judicious in our use of antimicrobial products to make sure that we're not exposing the more harmless bacteria to something that could make them harmful."

One problem with antimicrobial products -- such as these paints -- is that they are not tested against more common bacteria. Manufacturers test how well more pathogenic bacteria, such as E. coli or Staphylococcus, survive but largely ignore the bacteria that people (and the products they use) would more plausibly encounter.

"E. coli is like the 'lab rat' of the microbial world," Hartmann said. "It is way less abundant in the environment than people think. We wanted to see how the authentic indoor bacteria would respond to antimicrobial surfaces because they don't behave the same way as E. coli."


Jinglin Hu, Sarah B. Maamar, Adam J. Glawe, Neil Gottel, Jack A. Gilbert, Erica M. Hartmann. Impacts of Indoor Surface Finishes on Bacterial Viability. Indoor Air, 2019; DOI: 10.1111/ina.12558

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Monday, 17 June 2019

Cleanroom Particle Counting: Assessing Data for Trends and Patterns

Given the requirement for particle count trending it is surprising that there is little published on the subject and a paucity of examples for the reader to assess. While there are many different approaches that can be taken, improvements to quality reporting are driven through example. To partly address the shortfall of literature on particle count trending, this paper considers some different ways to assess particle data, in terms of routine assessments and where a statistical comparison of data is required. With the latter, this is less straightforward given that particle count data does not follow normal distribution.

In relation to this, Tim Sandle has written a new paper. The reference is:

Sandle, T. (2019) Cleanroom Particle Counting: Assessing Data for Trends and Patterns, Journal of GxP Compliance, 23 92): 1-10

For further details, please contact Tim Sandle

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Sunday, 16 June 2019

Why certain strains of bacteria are associated with diabetic wounds that do not heal

About 10 percent of U.S. citizens have been diagnosed with diabetes, and one quarter of these patients will develop a wound that does not heal. In the worst case outcome, which occurs in up to 25 percent of these wound-developing patients, the wounds will require an amputation. Many patients who develop these ulcers may not notice the initial signs, since the high blood glucose of diabetes can lead to a lack of feeling and deformation of the feet. As a result, patients with diabetes commonly develop foot ulcers that may go unnoticed over time.

Current treatments are insufficient, meaning patients can live with these wounds for months or even years without healing. The mortality rate associated with diabetic foot ulcers is equivalent to that of breast cancer and prostate cancer combined -- higher than 70 percent when they lead to amputation.

"While wounds don't receive the attention of other diseases, they're incredibly common, and our study increases our understanding of how microbes impair or promote healing," said the study's senior author Elizabeth Grice, PhD, an associate professor of Dermatology. The lead author, Lindsay Kalan, PhD, now an assistant professor of Medical Microbiology and Immunology at the University of Wisconsin School of Medicine and Public Health, began this work as a post-doctoral researcher in Grice's lab.

Previous studies have used lower resolution techniques to catalogue the microbes that reside in chronic wounds. This study built on that research by using higher resolution DNA sequencing to identify specific species and subspecies and how they are related to patient outcomes. Researchers collected samples from 46 patient ulcers every two weeks for six months, or until the wound healed or was amputated.

S. aureus, a common and difficult-to-treat pathogen, was found in the majority of wounds, but researchers note the presence of the bacteria itself did not predict whether or not a wound would heal. However, the high resolution DNA sequencing showed certain strains of S. aureus were only in the wounds that did not heal over the course of the study. Further testing revealed that the "non-healing" strain was better equipped to cause tissue damage and evade antibiotic treatments. Researchers further validated their findings in mice.

They also noted that another common microbe found in diabetic wounds, Alcaligenes faecalis, was associated with quicker healing.

"It is possible there are bacteria that actually benefit the wound, and we can use what we learned in this study to develop new treatment strategies for non-healing wounds," Grice said. "We hope this research will eventually help identify patients at risk for bad outcomes and lead to treatment innovations that these patients desperately need."

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Saturday, 15 June 2019

On-chip drug screening for identifying antibiotic interactions in eight hours

A KAIST research team developed a microfluidic-based drug screening chip that identifies synergistic interactions between two antibiotics in eight hours. This chip can be a cell-based drug screening platform for exploring critical pharmacological patterns of antibiotic interactions, along with potential applications in screening other cell-type agents and guidance for clinical therapies.

Antibiotic susceptibility testing, which determines types and doses of antibiotics that can effectively inhibit bacterial growth, has become more critical in recent years with the emergence of antibiotic-resistant pathogenic bacteria strains.

To overcome the antibiotic-resistant bacteria, combinatory therapy using two or more kinds of antibiotics has been gaining considerable attention. However, the major problem is that this therapy is not always effective; occasionally, unfavorable antibiotic pairs may worsen results, leading to suppressed antimicrobial effects. Therefore, combinatory testing is a crucial preliminary process to find suitable antibiotic pairs and their concentration range against unknown pathogens, but the conventional testing methods are inconvenient for concentration dilution and sample preparation, and they take more than 24 hours to produce the results.

To reduce time and enhance the efficiency of combinatory testing, Professor Jessie Sungyun Jeon from the Department of Mechanical Engineering, in collaboration with Professor Hyun Jung Chung from the Department of Biological Sciences, developed a high-throughput drug screening chip that generates 121 pairwise concentrations between two antibiotics.
The team utilized a microfluidic chip with a sample volume of a few tens of microliters. This chip enabled 121 pairwise concentrations of two antibiotics to be automatically formed in only 35 minutes.

They loaded a mixture of bacterial samples and agarose into the microchannel and injected reagents with or without antibiotics into the surrounding microchannel. The diffusion of antibiotic molecules from the channel with antibiotics to the one without antibiotics resulted in the formation of two orthogonal concentration gradients of the two antibiotics on the bacteria-trapping agarose gel.

The team observed the inhibition of bacterial growth by the antibiotic orthogonal gradients over six hours with a microscope, and confirmed different patterns of antibiotic pairs, classifying the interaction types into either synergy or antagonism.
Professor Jeon said, "The feasibility of microfluidic-based drug screening chips is promising, and we expect our microfluidic chip to be commercialized and utilized in near future."

See: Seunggyu Kim, Fahim Masum, Ju-Kang Kim, Hyun Jung Chung, Jessie S. Jeon. On-chip phenotypic investigation of combinatory antibiotic effects by generating orthogonal concentration gradients. Lab on a Chip, 2019; 19 (6): 959 DOI: 10.1039/c8lc01406j

 Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

Friday, 14 June 2019

How E. coli clones take over human gut

Researchers from University of Birmingham investigated how and why a clone of E. coli called ST131 -- dubbed a 'superbug' because it is resistant to multiple drugs -- has become the major cause of drug resistant E. coli infections, but not so dominant that it has wiped out other clones that do not have multi-drug resistance.

Escherichia coli (E. coli) is a type of bacteria common in human and animal intestines, and forms part of the normal gut flora -- the bacteria that exist in the bowel. There are a number of different types of E. coli and, while the majority are harmless, some can cause serious food poisoning or infections including in the urinary tract or bloodstream.

The number of cases of E. coli have risen by 27% from 32,309 in 2012-13 to 41,060 in 2017-18. The rise has been linked to an increase in antibiotic resistant infections caused by so-called 'superbugs'.

The most globally dominant clone of E. coli that is resistant to multiple drugs is called ST131. Earlier research has shown that while ST131 emerged and rapidly spread in the late 1990s, it caused no more than 20% of clinical cases of E. coli once it had emerged on the scene. This is because of a type of evolutionary selection called negative frequency dependency selection (NFDS).

It is now known that while there are significantly dominant drug resistant clones of E. coli such as ST131 and other new ones are emerging all the time, it seems highly unlikely that any of them are ever going to become a completely dominant clone because this process called NFDS controls the balance across the whole E. coli population.

As part of the research the scientists also analysed almost 1,000 genome sequences of strains within ST131 to see if they could find any genetic patterns that may explain how this process happens. It was found that in the ST131 clone there was a lot of variation in the genes that are involved in allowing the bacteria to colonize in the human gut when compared to those in non-drug resistant bacteria that are very closely related to ST131.

The implications are that if a person is going to get a bloodstream or urinary infection from E. coli it usually comes after it has colonized in the gut, therefore we now know that genetically something has happened to this superbug which allows it to colonise the gut far more competitively than other E. coli.

See: Alan McNally, Teemu Kallonen, Christopher Connor, Khalil Abudahab, David M. Aanensen, Carolyne Horner, Sharon J. Peacock, Julian Parkhill, Nicholas J. Croucher, Jukka Corander. Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection. mBio, 2019; 10 (2) DOI: 10.1128/mBio.00644-19

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

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