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Monday Micro – frozen poop pills! Siouxsie Wiles Oct 13

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It’s still Monday so time for a very quick post about a paper just out in the Journal of the American Medical Association. I’ve blogged before about faecal transplants – giving a patient a dose of faeces from a healthy donor to resolve infection with the diarrhoea-causing bacteria Clostridium difficile.

One of the problems with faecal transplants is the way they are delivered – either by a tube through the nose and into the colon, or the more direct route of up the bum. Researchers at Massachusetts General Hospital in Boston have tried something a little more palatable. They took faecal material, blended it to make a suspension, removed all the particulate matter, added glycerol as a cryoprotectant and then froze it in small amounts inside of capsules that could withstand transit through the acidic environment of the stomach. If you are interested, apparently 48 grams of faecal matter makes 30 capsules.

Next the researchers gave the frozen poop capsules to 20 people with C. difficile infection. This involved patients fasting for 4 hours and then taking 15 capsules each day for 2 days. Nobody suffered any serious side effects and that 2 day course of frozen poop pills cured the diarrhoea of 14 of the 20 patients. Of the 6 people who didn’t respond, 4 of them got better after another course of the poop pills, giving an overall success rate of 90%. This is quite promising data, although the study was small and there was no placebo control group.

It will certainly make things easier if the poop needed for faecal transplants doesn’t need to be fresh, and people are definitely more likely to prefer popping pills to tubes up their noses!

Reference:
Youngster et al. Oral, Capsulized, Frozen Fecal Microbiota Transplantation for Relapsing Clostridium difficile Infection. JAMA Preliminary Communication, October 11, 2014.

The threats of antibiotic resistant superbugs to New Zealand Siouxsie Wiles Sep 26

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In this week’s New Zealand Medical Journal is a paper by Deborah Williamson and Helen Heffernan on antimicrobial resistance in New Zealand (1). This comes hot on the heels of the WHO report which gave a global picture of antibiotic resistance (2), and highlights what the big challenges are for New Zealand.

So what are the antibiotic resistant superbugs that pose a risk to the health of New Zealanders?

According to the authors, there are four main superbugs we need to be watching:
1. Methicillin Resistant Staphylococcus aureus also known as MRSA
2. Extended-spectrum B lactamase (ESBL) producing Enterobacteriaceae, especially E. coli and Klebsiella pneumonia
3. Mycobacterium tuberculosis which causes the lung diseases tuberculosis (TB)
4. Neisseria gonorrhoeae which causes gonorrhoea

What are the key factors driving antibiotic resistance in New Zealand?

The authors highlight three main drivers which they believe are contributing to the problem:
1. The use and overuse of antibiotics in people and animals
2. Transmission of antibiotic resistant microbes in both the community and within healthcare facilities, including rest homes
3. Increasing globalisation – we are importing many of our antibiotic resistant superbugs from abroad

MRSA – a problem of our own making

Over the last few years there has been a huge increase in the number of skin and soft tissue infections caused by S. aureus in New Zealand. Alongside this, there has been a huge increase in prescriptions for a topical antibiotic called fusidic acid. As a consequence, one of the major clones of S. aureus now causing disease in New Zealand is an MRSA clone called AK3 which is resistant to fusidic acid (3).

Importation of resistant superbugs

Some of the superbugs of worry, notably extremely resistant strains of E. coli, K. pneumonia and M. tuberculosis are mainly being imported into New Zealand from countries like India, China and those in south-east Asia. This is going to be an area to watch, especially given the importance of countries like China for trade and tourism in New Zealand.

Gonorrhoea – the tip of the iceburg for sexually transmitted diseases

In New Zealand, sexually transmitted infections (with the exception of HIV) are not notifiable. This means that the data we have on these diseases is based on the voluntary provision of the numbers of diagnosed cases from laboratories and sexual health and family planning clinics. What’s crucial to this is that many people can have no symptoms, hiding the true burden of disease. Gonorrhoea is one of these. While most men will have symptoms when they have the disease, half of women can be asymptomatic. Importantly, untreated infection can lead to infertility in women.

In 2013 there were 3,334 cases of gonorrhoea in New Zealand (4). What is shocking is that 1,145 of these cases were in young people under the age of 19. In fact, there has been a 43% increase in the rate of gonorrhoea in 15–19 year old women between 2009 and 2013. Less than half of sexually active young people report using condoms (5) which goes some way to explaining why our rates are rising. If we end up with a completely untreatable strain of N. gonorrhoeae taking hold in New Zealand this could have a huge impact on our future fertility.

References:
1. Williamson DA & Heffernan H (2014). The changing landscape of antibiotic resistance in New Zealand. New Zealand Medical Journal.
2. World Health Organisation (2014). Antimicrobial resistance: global report on surveillance 2014. ISBN: 978 92 4 156474 8.
3. Williamson DA et al (2014). High Usage of Topical Fusidic Acid and Rapid Clonal Expansion of Fusidic Acid-Resistant Staphylococcus aureus: A Cautionary Tale. Clin Infect Dis. pii: ciu658.
4. Sexually transmitted infections in New Zealand 2013. Institute of Environmental Science and Research Limited.
5. Clark TC et al (2013). Youth’12 Overview: The health and wellbeing of New Zealand secondary school students in 2012. Auckland, New Zealand: The University of Auckland.

Fighting antibiotic resistance: from Obama to TV3! Siouxsie Wiles Sep 25

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Ascomycetes
Ascomycetes“. Licensed under CC BY-SA 2.5 via Wikimedia Commons.

Last week President Obama signed an Executive Order aimed at combating antibiotic resistant superbugs. The order establishes a task force and a Presidential Advisory Committee which will look at how the US can implement a national strategy to deal with antibiotic resistance. The order covers areas such as surveillance, antibiotic use (now being called antibiotic stewardship) as well as promoting new and next generation antibiotics and diagnostics.

Speaking of which, Massey University’s Dr Heather Hendrickson and myself featured in a recent TV3 3rd Degree episode on antibiotic resistance in New Zealand, showcasing the work that we are doing in our labs. You can watch our clip from the episode here.

In my lab we are starting to collaborate with researchers at Landcare Research to screen the thousands of species of New Zealand and Pacific fungi that have never been mined for new antibiotics. We are currently writing lots of grants to try to get some money to support this work but if you’d like to help get started and are a New Zealand-based user of Facebook then please consider voting for our project for the People’s Choice Award for an AMP scholarship. And tell all your friends!

Monday Micro II – lockdowns, manslaughter and murder Siouxsie Wiles Sep 22

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The Ebola outbreak in west Africa continues. According to the CDC’s website, as of the 14th September the number of reported cases was up to 5,347 including 2,630 deaths. The virus is now in five countries. Here’s the latest:

Guinea (942 cases/601 deaths)

A team of health care workers, journalists and local officials have been reported to have been killed by villagers while on a drive to raise awareness of the symptoms of Ebola and how to seek help. Clearly suspicion that health care workers are spreading the disease is still widespread.

Sierra Leone (1673 cases/562 deaths)

Sierra Leone has been in lockdown since Friday with a three day curfew in place so that officials could try to get to grips with the numbers of people infected. There are reports of burial teams being attacked.

Liberia (2710 cases/1459 deaths)

There are reports that Liberia has run out of beds for all but the sickest Ebola patients and the healthcare system is collapsing.

Senegal (1 case/0 deaths)

So far there has been just one case of disease in Senegal, a Guinean man who was under surveillance for having had contact with an Ebola patient but who escaped by road to Dakar to stay with relatives. He arrived on the 20th of August and sought medical treatment on the 23rd when he started to have fever, diarrhoea, and vomiting. He was treated for malaria and went back to stay with his relatives. He was hospitalised on the 26th August and finally diagnosed with Ebola. Question is, how many family members and healthcare workers did he infect? The incubation period is almost up so we should know soon.

Nigeria (21 cases/8 deaths)

Ebola spread to Nigeria via American-Liberian Patrick Sawyer, who contracted Ebola from his sister and then travelled by air to Nigeria. He collapsed at the airport and died 5 days later. For a little while it looked like Nigeria might have managed to put a lid on Ebola, but human nature appears to have thwarted that. Nigeria’s Daily Post reports that a diplomat who contracted Ebola from Mr Sawyer, and survived, may be facing manslaughter charges. He evaded quarantine and travelled from Lagos to the city of Port Harcourt where he was secretly treated in his hotel room. The doctor who treated him contracted Ebola and has now died, but not before having contact with a lot of people while symptomatic.

Reading the WHO report, it sounds like he either didn’t know the diplomat he was treating had Ebola, or was in complete denial. Read this and weep:

After onset of symptoms, on 11 August, and until 13 August, the physician continued to treat patients at his private clinic, and operated on at least two. On 13 August, his symptoms worsened; he stayed at home and was hospitalized on 16 August. Prior to hospitalization, the physician had numerous contacts with the community, as relatives and friends visited his home to celebrate the birth of a baby. Once hospitalized, he again had numerous contacts with the community, as members of his church visited to perform a healing ritual said to involve the laying on of hands. During his 6 day period of hospitalization, he was attended by the majority of the hospital’s health care staff. On 21 August, he was taken to an ultrasound clinic, where 2 physicians performed an abdominal scan. He died the next day.The additional 2 confirmed cases are his wife, also a doctor, and a patient at the same hospital where he was treated. Additional staff at the hospital are undergoing tests. Given these multiple high-risk exposure opportunities, the outbreak of Ebola virus disease in Port Harcourt has the potential to grow larger and spread faster than the one in Lagos.

Several hundred people are now under surveillance so it’s a case of ‘watch this space’. Judging by the number of close contacts the doctor had with people while symptomatic, it’ll be amazing if there aren’t many more cases.

Skeptical Thoughts – gendered marketing Siouxsie Wiles Sep 22

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I’ve started a new radio slot called ‘Skeptical Thoughts’ on Sunday evenings on Graeme Hill’s Weekend Variety Show on Radio Live. A couple of weeks ago we talked about what a scam gendered marketing is – when companies repackage the same product and market it specifically for men or women, often charging different amounts. Australian show The Check Out did a great piece on the topic:

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Speaking of gendered marketing, Nanogirl and fellow Sciblogger Dr Michelle Dickinson tweeted this monstrosity (“for working men”) a few days ago:

mans hand sanitisor

WTF?! Perhaps unsurprisingly, Michelle’s tweet thanking Mitre 10 for removing the sexist product from their shelves was met with a cry of “PC gone mad” by some.

sexism

Which is sad, as it misses the point that products like that in places like a DIY store perpetuate the myth that women can’t do DIY and make women feel excluded. Also sad is the fact that tweet was from the CEO of a tech company.

*sigh*

Lighting up Wellington’s waterfront Siouxsie Wiles Aug 31

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For the last week, Wellington has been positively glowing thanks to the lux festival. This year I collaborated with artist Brittany Byrne to bring a touch of bioluminescence to the proceedings – rather appropriate given the genes that encode bacterial bioluminescence are known as the lux operon.

Previously Brittany created Nimbus – a work involving hundreds, if not thousands, of wooden pegs, suspended in the air and which made a very satisfying sound when touched.

Our piece was called Vibrio Nimbus, and from the outside looked like a boring old shipping containing.

IMG_2642

But on the inside, Nimbus’ wooden pegs had been replaced with hundreds of plastic conical tubes and the sonic nature of Brittany’s previous work exchanged for light, provided by trillions of glowing bacteria. When the tubes were gently jostled, they glowed a little brighter for a brief time, thanks to the little extra oxygen being supplied. Here’s a picture I took – Vibrio Nimbus was a bit like bringing one of Waitomo’s glow worm caves to the Wellington waterfront.

vibrio nimbus

A huge thanks has to go to the Bioluminescent Superbugs Lab and Una Ren for preparing all the media needed to keep Vibrio Nimbus glowing – the bacteria needed replacing with a fresh batch every other day. Brittany and her team became quite adept at growing microbes this week! And if you need reminding about the glowing Vibrio and where it is normally found, check out the Astrosquid animation below.

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Bacterial art in Melbourne – Market of the Mind Siouxsie Wiles Aug 25

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Let's make some bacterial art!

Let’s make some bacterial art!

This week I’ve had the pleasure of taking part in Australia’s National Science Week. My week started in Hobart, Tasmania, where I got to hang out with science communication superstars Carin Bondar, Derek Muller (AKA Veritasium) and Destin Sandlin (AKA Smarter Every Day), performing on stage with them at an event made possible by Science Alert.

After Hobart I traveled to Melbourne for a week of school talks followed by a weekend of fun getting people to draw in glowing bacteria, first at Market of the Mind and then at Living Science. The idea is that people draw a picture on a sheet of paper and then trace over their design onto a petri dish using a cotton swab and a solution of Vibrio fischeri, the bacterium that lives in symbiosis with the Hawaiian bobtail squid. When the bacteria have grown, I then take a photo of the glowing petri dishes and put the pictures up on flickr. You can see the pictures from Market of the Mind here.

And if you want to learn a little more about Vibrio fisheri and Euprymna scolopes watch the animation below or better yet get the beautiful book by Gregory Crocetti, Ailsa Wild and Aviva Hannah Reed.

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Yet another science metric – the Kardashian Index Siouxsie Wiles Aug 08

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Twitter exploded last week after Neil Hall, a professor at the University of Liverpool who studies the genomes of the parasites that cause malaria and sleeping sickness, published a (supposedly satirical) paper in the journal Genome Biology. Rather than read his paper, I recommend you read the annotated version. But first, here’s the abstract:

In the era of social media there are now many different ways that a scientist can build their public profile; the publication of high-quality scientific papers being just one. While social media is a valuable tool for outreach and the sharing of ideas, there is a danger that this form of communication is gaining too high a value and that we are losing sight of key metrics of scientific value, such as citation indices. To help quantify this, I propose the ‘Kardashian Index’, a measure of discrepancy between a scientist’s social media profile and publication record based on the direct comparison of numbers of citations and Twitter followers.

Ummm, communicating through social media is “gaining too high a value”?? That’s hilarious. In my experience, being active on social media is given no value by the majority of the establishment (ie silverbacks like Prof Hall). And as to citation indices being a “key metric of scientific value”? Of value to other academics maybe. But science is valuable outside of academia too, and citation indices will rarely capture that.

To calculate a scientist’s Kardashian Index (K-index), Prof Hall says we first need to calculate the number of twitter followers a particular scientist should have, using the following equation:

F= 43.3C^0.32 (Eq 1)

Where F is the number of twitter followers and C is the number of citations.

The K-index is then calculated using a second equation

K−index = F(a)/F(c) (Eq 2)

Where F(a) is the actual number of twitter followers the researcher has and F(c) is the number they “should” have given their citations.

As Prof Hall explains:

“…a high K-index is a warning to the community that researcher X may have built their public profile on shaky foundations, while a very low K-index suggests that a scientist is being undervalued. Here, I propose that those people whose K-index is greater than 5 can be considered ‘Science Kardashians’…”

Prof Hall did a “preliminary proof-of-concept study” using a “randomish selection of 40 scientists”. You can see how they scored in Figure 1 of his paper:

s13059-014-0424-0-1

Prof Hall goes on to conclude:

I propose that all scientists calculate their own K-index on an annual basis and include it in their Twitter profile. Not only does this help others decide how much weight they should give to someone’s 140 character wisdom, it can also be an incentive – if your K-index gets above 5, then it’s time to get off Twitter and write those papers.

Dr Michelle Dickinson, our very own Nanogirl worked out her K-Index and scored 35, the same as Prof Brian Cox. Both clearly need to get back to writing their papers.

There are so many things wrong with Prof Hall’s piece it’s hard to know where to begin. As I say, check out the great annotated version of his paper by Red Ink which points out some of them. Dr Kate Clancy has also written a nice post explaining why this bit of fun isn’t actually funny and Dr Keith Bradnam has turned it on its head suggesting the Tesla index as a measure of scientific isolation.

What really makes my blood boil about Prof Hall’s new index is that he named it after Kim Kardashian, who according to Wikipedia, is a reality TV star famous for being the daughter of OJ Simpson’s defense lawyer, a friend of wealthy socialite Paris Hilton and star of a sex tape. She is now a successful business women with several clotheslines and fragrances to her name and an estimated fortune of $45 million.

Ms Kardashian’s most recent venture is a smartphone game in which players have to build a career in Hollywood, accumulating wealth and fans. You have to give it to her. That lady has a sense of humour. Ms Kardashian is famous for being famous and not ashamed in the slightest. But she is hardly alone. In fact, she appears to be just one of a new breed of such celebrities.

That Prof Hall chose to name his index after a vacuous woman is a wonderful example of everyday sexism. Make no mistake, while Prof Hall’s piece is supposedly satirical, it is a snide swipe at those with a passion for communicating science using a derogatory association with a woman to do so. And he got his paper published in a peer reviewed journal where it will no doubt provide ammunition to those who already belittle the work science communicators do, all with a citation to back their bigotry.

The light at the end of the tunnel though was the #AlternativeScienceMetrics hashtag that was spawned on twitter, storified here by @mcdawg. Gems like these:

From @Protohedgehog: The Sean Bean index, measuring the number of times you write a great paper, only to have it killed by peer review

From @IanMulvany: the george Lucas index, how often a later paper totally invalidates earlier work that you did

From @OSIRISREx: The Viral Factor: how many times your research is misinterpreted into a factoid on a pop social media page

From @quicklyround: The Ulysses Factor – papers cited by everybody but that nobody has actually read to the end

From @LouWoodley: The Lindt Factor – the number of bars of chocolate needed to make the “minor revisions” requested

From @Koalha: Sacrificial efficiency: number of accepted papers / burnt out grad student

Jason McDermott discusses the pros and cons of some of them on his blog. Which would get your vote?!

Ebola outbreak – updates and links Siouxsie Wiles Aug 03

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As the Ebola outbreak worsens, the WHO has announced a US$100 million response plan to help bring the outbreak under control by scaling up control measures and helping neighbouring at-risk countries prepare for any cases.

According to the latest WHO update, between 24 and 27 July, a total of 122 new cases of Ebola and 57 deaths were reported from Guinea, Liberia, Nigeria, and Sierra Leone. This brings the number of cases up to 1323 with 729 deaths. Sadly, it would seem that healthcare workers are still becoming infected, with reports that Sierra Leone’s top Ebola doctor has died.

Ian Mackay is charting all the data from the WHO’s Ebola updates while the UK’s Channel 4 have made a clicable map of the outbreak here.

A scary development has been the death of a man in Nigeria – he arrived in Lagos by air via Lomé, Togo, and Accra, Ghana. The man was symptomatic when he arrived in Nigeria which means he would have been infectious at least on his last flight. Officials are now trying to trace all he may have come into contact with on his travels. According to the report, 59 contacts (15 from among the airport staff and 44 from the hospital) have been identified so far.

The fact the man was American, of Liberian decent, and due to return to his family in Minnesota has now put the Ebola outbreak firmly on the radar of the US press. There are also now reports that two infected US aid workers are going to be evacuated from Liberia for treatment in Atlanta.

There is a good article here looking at how easily infectious diseases spread on planes. The answer from simulations seems to be ‘not very’, suggesting only those in the few rows around the infected person are at risk. As Ebola is spread through bodily secretions, this would also mean the potential for transmission by touching surfaces also touched by someone infectious.

And finally, Daniel Bausch and Lara Schwarz speculate on why Guinea and why now in a paper just published in the open access journal PLOS Neglected Tropical Diseases. In an nutshell, it’s likely to be due to the movement of bats and poverty driving people further into remote areas looking for resources to survive. Add to that porous borders and impoverished and neglected healthcare systems and you get an outbreak of this magnitude.

The academic publishing scam – how much research funding are we losing to journal subscriptions? Siouxsie Wiles Aug 01

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Currently doing the rounds on twitter is this on the massive profits made by academic publishers:

profits

If you are in Australia or New Zealand and want to know how much is spent just on purchasing subscriptions to academic journals then there is a very handy tool on the Council of Australian University Librarians website.

In 2013 New Zealand’s universities spent $51,135,180 on journal subscriptions.

That’s just our universities, so doesn’t include our CRI’s or independent research institutes. $51,135,180 to access work funded by the tax payer published in pay-walled journals that rely on unpaid labour by university academics for peer review and editorial duties.

subs

To put that figure in perspective, the only funder of investigator-led blue-skies research in New Zealand, the Marsden Fund, awarded $59,000,000 in funding in 2013 – enough to fund 109 projects for 3 years.

In other words, we spend almost as much on buying access to research as we spend on blue-skies research.

I vote we scrap the subscriptions and use the money to double the Marsden Fund, giving each project an allocation to publish their results open access. Makes sense to me!

Hat/tip to Alex Holcombe (@ceptional) and Fabiana Kubke (@Kubke).

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