This summary of the latest Microbiology Twitter Journal Club is going to be different in two ways. Firstly, it's late. Secondly, it's a video. I noticed a while ago that my explanations of papers tended to end up longer than the papers themselves, and I decided to experiment. Here are the results
Field of Science
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Change of address1 year ago in Variety of Life
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Change of address1 year ago in Catalogue of Organisms
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Earth Day: Pogo and our responsibility1 year ago in Doc Madhattan
Showing posts with label Rant. Show all posts
Showing posts with label Rant. Show all posts
The Post Antibiotic Era will take your job away.
In 1934, The Los Angeles Milk Commission gave its employees devastating ultimatum- lose their tonsils or lose their jobs. When our antibiotics stop working, your employer may force you to make a similar choice; and they'd be right.
Infectious bacteria are developing resistances to our medicines at alarming rates, and we are entering a Post-Antibiotic Era. If you want to know how people will cope in this new era, the best place to look is in the past. In the era before antibiotics.
In the early 1930's, scarlet fever and strep throat were much more common than they are today, and much more hazardous. In the worst case scenario, a sore throat could develop into full blown sepsis.
So when a report was published in 1931 describing 71 outbreaks of this disease that could be traced to one common factor, people paid attention. That common factor was milk contaminated with bacteria named Streptococcus epidemicus. These bacteria tended to infect the udders of cows, causing mastitis. Since the udders also happen to be where the milk was produced, bacteria inevitably spread to the milk.
Needless to say, these outbreaks needed to be brought under control.
That responsibility fell to the Los Angeles Milk Commission, implemented a number of rules to prevent any more outbreaks occurring.
The first step was to find any dairy cows infected with the disease. Fortunately, there were already rules in place for this. Cows needed to be certified to be free of S. epidemicus, and any infected cows needed to be isolated from the rest of the herd.
Here is the problem. Both humans and cows could carry S.epidemicus. To control any outbreaks, the same restrictions that applied to cows had to apply to the humans who worked with them. Humans could carry S. epidemicus without any symptoms, and appearing perfectly healthy.
Out of a thousand employees tested, fifty were carriers. This was devastating. They could no longer be allowed to work, for the risk of them causing an outbreak was unacceptable.
There were no available antibiotic treatments to allow these carriers to rid themselves of S.epidemicus, but that didn't mean there were no options. It was known at the time that S. epidemicus survived in human tonsils. If the tonsils were removed, then the bacteria would have nowhere to go, and die off.
In a quote from the Director of the milk commission:
"care is taken in each case to impress upon them that the procedure is not compulsory except that otherwise they must retire from employment at certified dairies"
Basically, the procedure was only compulsory if the workers wanted to keep their jobs.
Unsurprisingly, most of the workers chose to go through the operation.
But sixteen of the infected employees either refused to go through with it, or were refused on the basis of underlying health issues that could render such an operation life threatening. These people were forced out of their jobs, and any dairy in the area was given their details should they attempt to apply for another job in the milk industry. Essentially, they were blacklisted from the industry.
You can say it was cruel that employees were forced into this situation, and you're not wrong. But it was an awful dilemma, and one that is destined to repeat. In a world without antibiotics, people who become carriers of diseases may remain carriers for the rest of their lives. Through no fault of their own, these people will pose a threat to the rest of the population, and it will hurt their chances of working in certain jobs. Would you send your kid to a school where a teacher constantly infects their students with life threatening illness ? Or buy groceries from a man with chronic diarrhoea? Allow yourself to get treated by Typhoid Mary?
None of those sixteen workers ever suffered any symptoms. They may spent their life working in the dairy industry, only to be cast aside. They at least had the option of getting surgery to prevent them from being carriers. Not all bacteria are polite enough to live solely within an easily removed organ.
The Post-Antibiotic Era is coming, and it won't just affect "sick" people, it will have wider effects throughout society. If there is one lesson we can learn from this eighty year old paper, it is that you don't even have to be "sick" for bacteria to ruin your life.
*Streptococcus epidemicus is a defunct classification that tends to be refer to what would be called S. zooepidemicus these days, and S. pyogenes.
Bonynge C.W. (1934). Solution of the Streptococcus Carrier Problem *†, American Journal of Public Health and the Nations Health, 24 (10) 1031-1034. DOI: 10.2105/AJPH.24.10.1031
What reading a scientific paper reveals about you
What do you believe science is ? How do you think that belief affects your life ?
One way of answering t comes from the way we treat the foundation upon which modern science is built.
The medium that scientists use to communicate their discoveries is the scientific paper. These documents have evolved over the centuries to adapt to the way that science itself has changed. The first scientific journals came into being in the 17th century, in a time when science was more of a hobby for the aristocracy than a significant career in itself. These early papers lack much of the structure of modern journals, and can be disconcertingly easy to read compared to their modern counterparts. But as science became more professional, readers demanded greater transparency to allow them to replicate the experiments they read in the journals, the modern scientific paper came into being. I'm going to make a fairly big generalisation by saying a scientific paper's structure* consists of five parts
- Introduction- Where the authors explain the background of their research. This will reveal to the reader the questions that they intend to ask during their paper, and why those questions may be important.
- Methods- This is where the authors explain how they are going to use the materials they have to hand to answer the questions they have posed in the introduction. This is the part where they put in a lot of the important details of how they set up their experiments.
- Results- Here, the authors explain what they have observed from their experiments, usually in some detail. A savvy reader should be able to see how these observations contribute to answering the overarching "question" of the paper. But for those who can't, there is always...
- The Discussion. Where the authors explain how their observations fit in with what everyone else has published in the scientific literature. They can also take this opportunity to point out where their experiments fall short, and what other questions have been raised or left unanswered by their work.
- References. In any academic article, it is important to cite the work of others, so that the readers can find their work and verify that the author is actually representing it properly, or not. It also allows the author to make their article shorter, simply by pointing to other works which may have already explained their experimental procedures and the concepts they are working with. These are also incredibly important for recognising others in the field who have contributed important research.
When I first started reading papers, it was for writing up specific essays or dissertations. I learned early on that if you spam your bibliography with enough references, you would get better grades. To insure against disaster, such as someone actually reading the reference section, I would read over the abstract to see whether it backed up whatever point I was trying to make.
Soon, my technique had advance to the point where I would read the abstract and the introduction, and then skip to the discussion. I saved time by ignoring the parts of the paper which I didn't understand, and could still competently comment on its findings. I could "read" a ton of papers using this technique, and still had plenty of time to go out partying. I had hacked my undergraduate degree.
Things changed when I started working in a scientific lab. If I wanted to learn a new scientific technique, I had to delve into the methods and the results sections of academic papers. Before I could easily transcribe what the authors of these papers wanted to say by reading the introduction and discussion. Now, I could put myself in their shoes, and see how they decided to answer the questions posed in the paper. I could see how I could do things differently, and more importantly I could see when someone was doing something better, and then use that for my own work. Soon I realised that I wasn't getting the whole picture the way I read academic papers previously. It was not just about reading the methods and the results, it was also about delving through the references sections, to immerse oneself entirely into the experience. Only then can you see the potential gaps in knowledge left by a paper and fully understand what it is actually saying.
But you didn't start reading this for me to tell you what a scientific paper is, or to learn my life story. You want me to tell you about what reading a scientific paper reveals about you, and what you believe science is.
I still run into scientists who only read the introduction and discussions of papers without ever fully engaging with the content. By doing that, they have implicitly made the decision that science is a collection of facts arbitrarily espoused from on high that need to be memorised.
But if you believe that science is more like conversation based on careful analysis of the evidence, then you need to engage with the evidence presented within the paper. If you do manage to delve into these parts of the paper, if you use every tool available to you to understand a paper, to put yourself in the authors shoes, then you'll see the problems they faced as they did, and how they overcame them.
Without that insight, without that knowledge of what goes into science, we end up losing out, and the discourse on science is the worse for it.
Soon, my technique had advance to the point where I would read the abstract and the introduction, and then skip to the discussion. I saved time by ignoring the parts of the paper which I didn't understand, and could still competently comment on its findings. I could "read" a ton of papers using this technique, and still had plenty of time to go out partying. I had hacked my undergraduate degree.
Things changed when I started working in a scientific lab. If I wanted to learn a new scientific technique, I had to delve into the methods and the results sections of academic papers. Before I could easily transcribe what the authors of these papers wanted to say by reading the introduction and discussion. Now, I could put myself in their shoes, and see how they decided to answer the questions posed in the paper. I could see how I could do things differently, and more importantly I could see when someone was doing something better, and then use that for my own work. Soon I realised that I wasn't getting the whole picture the way I read academic papers previously. It was not just about reading the methods and the results, it was also about delving through the references sections, to immerse oneself entirely into the experience. Only then can you see the potential gaps in knowledge left by a paper and fully understand what it is actually saying.
But you didn't start reading this for me to tell you what a scientific paper is, or to learn my life story. You want me to tell you about what reading a scientific paper reveals about you, and what you believe science is.
I still run into scientists who only read the introduction and discussions of papers without ever fully engaging with the content. By doing that, they have implicitly made the decision that science is a collection of facts arbitrarily espoused from on high that need to be memorised.
But if you believe that science is more like conversation based on careful analysis of the evidence, then you need to engage with the evidence presented within the paper. If you do manage to delve into these parts of the paper, if you use every tool available to you to understand a paper, to put yourself in the authors shoes, then you'll see the problems they faced as they did, and how they overcame them.
Without that insight, without that knowledge of what goes into science, we end up losing out, and the discourse on science is the worse for it.
*I should note that your mileage may vary for this structure. There are some shorter papers which dispense entirely with the methods, and include them all with the results. If you are reading the medical literature, you may come across case reports, which have a slightly different structure because often the Doctor doesn't seek out the question, the question finds them in the form of a patient with an odd manifestation of a disease.
If you are reading a paper with no results or methods, then the document you are holding is most likely a review of the literature, and completely different to the kinds of articles we are discussing here.
Antibiotics & Agriculture part 5: Stokstad's Genie
When Robert Stokstad discovered antibiotic growth promoters, he was operating in industrial farming's nascent era. In the 1920's, farmers realised that with the right levels of vitamin supplements, they could raise chickens indoors safely cocooned from the outside environment. But this innovation came with some costs, as chicks born in this environment had poor survival, and didn't grow as fast as they did in the wild.
Stokstad's discovery of growth promoters was like a wish come true. Just by adding a low dose antibiotics, we could help more chicks survive into adulthood, and allow them to grow to full size whilst saving money feeding them. But, just like in any morality tale, wishes can come with consequences.
It turns out that the wholesale saturation of the industrial farming environment with antibiotics provided the perfect incubator for antibiotic resistance.
There have been a number of dangerous outbreaks of antibiotic resistant pathogens which can be traced directly to their usage in the agricultural industry. Salmonella, E.coli and even some strains of Staphylococcus aureus have acquired resistance to antibiotics from farms.
Even more disturbing is that agricultural antibiotic usage has increased the numbers of resistance genes in the overall environment. These genes have been proven to transfer between different bacterial species. Even if the bacteria they reside in are themselves not a threat to human health, these genes can be transferred to pathogens that are threats.
The mounting evidence of this threat prompted some countries to act.
In 1984, after hearing reports that consumer confidence in meat safety was dropping, due to the antibiotic resistance threat, Swedish farmers requested a ban on all growth promoters. They were the first country to implement a ban, but they were not the last.
If you wanted to show the pitfalls of banning agricultural growth promoters, you can find no better example than that of the Netherlands. In these cases, the ban came into force before the farmers could improve infection control practices. As a result, they were beset by outbreaks of bacterial disease that required the use of more therapeutic antibiotics. In the Netherlands, this meant that there was no net change in the amount of antibiotics sold to the agricultural industry.
Sweden was not immune to this effect. Whilst the initial results of the ban showed promising reductions in antibiotic use, it was also characterised by increases in disease outbreaks on farms. The appetite for therapeutic antibiotics increased in direct response to these outbreaks, until it eventually rose to pre-ban levels.
When Denmark embarked on a similar plan to ban antibiotic growth promoters, they did so with an eye on the experiences of previous nations. With this system, they managed to reduce antibiotic use by around 90%. Somehow their ban managed to reduce infections without changing the welfare of their animals, and still managed to keep the Danish pig industry competitively priced.
So why did the Danish experience differ so much from the experiences of other nations ?
When they implemented the ban, they also ensured there was a comprehensive monitoring system in place to send out the alarm if new antibiotic resistant bacteria were produced, and a way of regulating the doses of therapeutic antibiotics given by veterinarians. They didn't ban all of their growth promoters at once. They first rolled back the use of avoparcin in 1995, then followed it with a ban on virginiamycin in 1998, and then finally a ban on all growth promoters in 2000. This gave the farmers the time to change the way they did farming to compensate for the loss of these growth promoters.
In preparation for the ban, Danish farms implemented basic infection controls. The routine disinfection of workers clothes, the workers themselves and their vehicles is now standard in many countries, to prevent the transfer of diseases between farms. Veterinary vigilance became watch words, with herds regularly inspected to ensure that outbreaks were caught and dealt with as early as possible.
The authorities also madee sure that every part of their system was committed to the reduction of antibiotic use. Veterinarians were prevented from directly selling antibiotics to farmers, they could only issue prescriptions, removing a potential conflict of interest. The numbers of antibiotic prescriptions given to specific herds was carefully monitored. Farms that were consuming high levels antibiotics could be spotted more easily under this system, and given the appropriate support.
Denmark also brought in new laws which changed the way that their pigs were raised and weaned. They recognised that a lot of their infection problems could be traced to their piglets being weaned too early and forced into an infection riddled world without the protective antibodies in their mother's milk, and immune systems not fully able to deal with the infection riddled world into which they were being exposed.
When Denmark put its ban in place, it did so with the knowledge that a massive full spectrum ban on antibiotic growth promoters could potentially harm its precious pork industry. When they drew up plans to ban antibiotic growth promoters, they paid attention to the science. They thought carefully about the consequences of the ban, and how they could best compensate for these effects using the best science available. Then they brought in the ban slowly, allowing farmers and veterinarians time to adapt to the new system, and ensured that the incentives presented by this new system were geared to limiting further usage of antibiotics.
In 2006, a broad ban on all antibiotic growth promoters was implemented across the European Union in response to mounting public pressure. Countries across the EU are now for better or for worse have to adapt their farming strategies to compensate for the loss of antibiotic growth promoters.
There are signs that the ban is working. The numbers of antibiotic resistance genes in the environment are decreasing.
But let's not pop the champagne corks just yet. There are a few problems with these bans that require further inspection.
In the initial stages of all the bans, outbreaks of bacterial disease often occur more frequently. In some scenarios, Veterinarians can be reticent in prescribing more antibiotics to treat these diseases, leaving the animals to suffer longer, and exposing them to greater risk of death. Improvements to infection control and animal husbandry only go so far in preventing outbreaks of disease. The situation in some countries is so bad that banning agricultural antibiotics actually increases the numbers of therapeutic antibiotics being used. The levels of antibiotics in some cases reaches the levels seen before the ban.
Every time an antibiotic is used, be it in animals, or in humans, has a chance of increase the numbers of resistant strains in the population. Taking this viewpoint, you may say that some of these bans have no effect at all. But you would be ignoring a crucial detail.
In his Nobel prize speech, Fleming himself gave a warning about how mass underdosing could trigger the creation of antibiotic resistant strains, yet within ten years underdosing became standard practice within the agricultural industry.
It is crucial that we make sure that antibiotics are always used responsibly. The key reason why banning antibiotic growth promoters was that it was one demonstrable case in which antibiotics were used irresponsibly.
The other key problem with these bans is that no one knows the extent to which it will affect human health. It should prevent new strains of antibiotic resistant bacteria evolving on farms, such as livestock associated MRSA, or antibiotic resistant Enterococci.
However, expecting these bans to eliminate all antibiotic resistance is to unfairly place all of the blame on farming and agriculture for our current situation. The primary environment in which antibiotic resistant bacteria most commonly evolve, and where they are at their most dangerous, is found in hospitals. Any antibiotic resistance genes which have already made the jump into this environment are here to stay. Regulating antibiotic use in hospitals is difficult, because that is where we, as humans, need them the most. As much as we may worry about how the price of meat may be affected, if we cannot accept that relatively minor sacrifice, we will not be able to accept the changes and the costs needed to eradicate antibiotic resistance from our healthcare systems.
The genie of antibiotic resistance is out of the bottle, but it wasn't just Robert Stokstad who had a hand in releasing it. We may sneer at growth promoters because they are the worst example of how we have squandered antibiotics. We may lament at how some faceless evil within the agri-business made the calculation that our future is worth trading for cheaper meat today. But we all had a hand in shaking the genie out of its bottle. We still have a hand in determining our own future. Even those of us who currently live in Europe may soon be inundated with american meat raised antibiotic growth promoters if certain trade agreements are successful. They will once again be faced with the same choice facing everyone else in the world, the choice between a full stomach today or better health tomorrow.
References
The WHO's internal evaluation on the termination of antimicrobial growth promoters in Denmark
http://www.who.int/gfn/en/Expertsreportgrowthpromoterdenmark.pdf
Danish Pig production in a European Context
http://www.lf.dk/~/media/lf/Aktuelt/Publikationer/Svinekod/LFEUBenchUK110318.ashx
Cogliani C., Goossens H. & Greko C. (2011). Restricting Antimicrobial Use in Food Animals: Lessons from Europe, Microbe, 6 (6) 274-279. DOI:
Stokstad's discovery of growth promoters was like a wish come true. Just by adding a low dose antibiotics, we could help more chicks survive into adulthood, and allow them to grow to full size whilst saving money feeding them. But, just like in any morality tale, wishes can come with consequences.
It turns out that the wholesale saturation of the industrial farming environment with antibiotics provided the perfect incubator for antibiotic resistance.
There have been a number of dangerous outbreaks of antibiotic resistant pathogens which can be traced directly to their usage in the agricultural industry. Salmonella, E.coli and even some strains of Staphylococcus aureus have acquired resistance to antibiotics from farms.
Even more disturbing is that agricultural antibiotic usage has increased the numbers of resistance genes in the overall environment. These genes have been proven to transfer between different bacterial species. Even if the bacteria they reside in are themselves not a threat to human health, these genes can be transferred to pathogens that are threats.
The mounting evidence of this threat prompted some countries to act.
In 1984, after hearing reports that consumer confidence in meat safety was dropping, due to the antibiotic resistance threat, Swedish farmers requested a ban on all growth promoters. They were the first country to implement a ban, but they were not the last.
If you wanted to show the pitfalls of banning agricultural growth promoters, you can find no better example than that of the Netherlands. In these cases, the ban came into force before the farmers could improve infection control practices. As a result, they were beset by outbreaks of bacterial disease that required the use of more therapeutic antibiotics. In the Netherlands, this meant that there was no net change in the amount of antibiotics sold to the agricultural industry.
Sweden was not immune to this effect. Whilst the initial results of the ban showed promising reductions in antibiotic use, it was also characterised by increases in disease outbreaks on farms. The appetite for therapeutic antibiotics increased in direct response to these outbreaks, until it eventually rose to pre-ban levels.
When Denmark embarked on a similar plan to ban antibiotic growth promoters, they did so with an eye on the experiences of previous nations. With this system, they managed to reduce antibiotic use by around 90%. Somehow their ban managed to reduce infections without changing the welfare of their animals, and still managed to keep the Danish pig industry competitively priced.
So why did the Danish experience differ so much from the experiences of other nations ?
When they implemented the ban, they also ensured there was a comprehensive monitoring system in place to send out the alarm if new antibiotic resistant bacteria were produced, and a way of regulating the doses of therapeutic antibiotics given by veterinarians. They didn't ban all of their growth promoters at once. They first rolled back the use of avoparcin in 1995, then followed it with a ban on virginiamycin in 1998, and then finally a ban on all growth promoters in 2000. This gave the farmers the time to change the way they did farming to compensate for the loss of these growth promoters.
In preparation for the ban, Danish farms implemented basic infection controls. The routine disinfection of workers clothes, the workers themselves and their vehicles is now standard in many countries, to prevent the transfer of diseases between farms. Veterinary vigilance became watch words, with herds regularly inspected to ensure that outbreaks were caught and dealt with as early as possible.
The authorities also madee sure that every part of their system was committed to the reduction of antibiotic use. Veterinarians were prevented from directly selling antibiotics to farmers, they could only issue prescriptions, removing a potential conflict of interest. The numbers of antibiotic prescriptions given to specific herds was carefully monitored. Farms that were consuming high levels antibiotics could be spotted more easily under this system, and given the appropriate support.
Denmark also brought in new laws which changed the way that their pigs were raised and weaned. They recognised that a lot of their infection problems could be traced to their piglets being weaned too early and forced into an infection riddled world without the protective antibodies in their mother's milk, and immune systems not fully able to deal with the infection riddled world into which they were being exposed.
When Denmark put its ban in place, it did so with the knowledge that a massive full spectrum ban on antibiotic growth promoters could potentially harm its precious pork industry. When they drew up plans to ban antibiotic growth promoters, they paid attention to the science. They thought carefully about the consequences of the ban, and how they could best compensate for these effects using the best science available. Then they brought in the ban slowly, allowing farmers and veterinarians time to adapt to the new system, and ensured that the incentives presented by this new system were geared to limiting further usage of antibiotics.
In 2006, a broad ban on all antibiotic growth promoters was implemented across the European Union in response to mounting public pressure. Countries across the EU are now for better or for worse have to adapt their farming strategies to compensate for the loss of antibiotic growth promoters.
There are signs that the ban is working. The numbers of antibiotic resistance genes in the environment are decreasing.
But let's not pop the champagne corks just yet. There are a few problems with these bans that require further inspection.
In the initial stages of all the bans, outbreaks of bacterial disease often occur more frequently. In some scenarios, Veterinarians can be reticent in prescribing more antibiotics to treat these diseases, leaving the animals to suffer longer, and exposing them to greater risk of death. Improvements to infection control and animal husbandry only go so far in preventing outbreaks of disease. The situation in some countries is so bad that banning agricultural antibiotics actually increases the numbers of therapeutic antibiotics being used. The levels of antibiotics in some cases reaches the levels seen before the ban.
Every time an antibiotic is used, be it in animals, or in humans, has a chance of increase the numbers of resistant strains in the population. Taking this viewpoint, you may say that some of these bans have no effect at all. But you would be ignoring a crucial detail.
In his Nobel prize speech, Fleming himself gave a warning about how mass underdosing could trigger the creation of antibiotic resistant strains, yet within ten years underdosing became standard practice within the agricultural industry.
It is crucial that we make sure that antibiotics are always used responsibly. The key reason why banning antibiotic growth promoters was that it was one demonstrable case in which antibiotics were used irresponsibly.
The other key problem with these bans is that no one knows the extent to which it will affect human health. It should prevent new strains of antibiotic resistant bacteria evolving on farms, such as livestock associated MRSA, or antibiotic resistant Enterococci.
However, expecting these bans to eliminate all antibiotic resistance is to unfairly place all of the blame on farming and agriculture for our current situation. The primary environment in which antibiotic resistant bacteria most commonly evolve, and where they are at their most dangerous, is found in hospitals. Any antibiotic resistance genes which have already made the jump into this environment are here to stay. Regulating antibiotic use in hospitals is difficult, because that is where we, as humans, need them the most. As much as we may worry about how the price of meat may be affected, if we cannot accept that relatively minor sacrifice, we will not be able to accept the changes and the costs needed to eradicate antibiotic resistance from our healthcare systems.
The genie of antibiotic resistance is out of the bottle, but it wasn't just Robert Stokstad who had a hand in releasing it. We may sneer at growth promoters because they are the worst example of how we have squandered antibiotics. We may lament at how some faceless evil within the agri-business made the calculation that our future is worth trading for cheaper meat today. But we all had a hand in shaking the genie out of its bottle. We still have a hand in determining our own future. Even those of us who currently live in Europe may soon be inundated with american meat raised antibiotic growth promoters if certain trade agreements are successful. They will once again be faced with the same choice facing everyone else in the world, the choice between a full stomach today or better health tomorrow.
References
The WHO's internal evaluation on the termination of antimicrobial growth promoters in Denmark
http://www.who.int/gfn/en/Expertsreportgrowthpromoterdenmark.pdf
Danish Pig production in a European Context
http://www.lf.dk/~/media/lf/Aktuelt/Publikationer/Svinekod/LFEUBenchUK110318.ashx
Cogliani C., Goossens H. & Greko C. (2011). Restricting Antimicrobial Use in Food Animals: Lessons from Europe, Microbe, 6 (6) 274-279. DOI:
#MicroTwJC : The Creation of a Superbug
The year was 2004. The patient was a 6 month old baby girl. She was about to enter thoracic surgery, when the doctors found that she was harbouring methicillin resistant Staphylococcus aureus. Now, in most western hospitals, the origin of this bacterium would not be a mystery. But this was a hospital based in the Netherlands. The Dutch have a "search and destroy" mentality when it comes to dealing with superbugs, and have been very successful at keeping their hospitals free of MRSA. They wanted it to stay that way. They had to find the source of this MRSA, and put a stop to it. The hospital equipment was scrutinised for any traces of the bacterium. None could be found.
They eliminated the MRSA from the baby, and then sent her home with her parents. But when they followed up, the baby was once again colonised with MRSA. They went through the same process again and again, until they realised that the baby was continuously being re-infected with the bacterium from an unknown source. The doctors found that the babies parents were also carriers of MRSA. but where did they get the disease from ? If it wasn't coming from the hospital, then where was it coming from ?
It turned out that the family lived on a farm raising pigs. The pigs were tested. They were the source of the MRSA.
Other pigs on different farms in that area also carried this strain of MRSA. A number of other cases of farmers and vets catching MRSA off their pigs. They concluded that farmers were 760x more likely to get an MRSA infection than any other Dutch people. Further research revealed that 39% of pigs entering a slaughterhouse carried MRSA. Hospitals in close proximity to pig farms tended to see more patients with MRSA than hospitals that were far from pig farms. This MRSA appears to be different from the hospital associated MRSA's we are more familiar with. It is primarily carried by pigs, and was a leading cause of MRSA infection in the Netherlands.
So now we know that pigs can carry MRSA, it is time to ask an important question. How did they get MRSA ? How did this particular strain evolve ? These are the questions that this weeks #MicroTwJC paper aims to answer.
They eliminated the MRSA from the baby, and then sent her home with her parents. But when they followed up, the baby was once again colonised with MRSA. They went through the same process again and again, until they realised that the baby was continuously being re-infected with the bacterium from an unknown source. The doctors found that the babies parents were also carriers of MRSA. but where did they get the disease from ? If it wasn't coming from the hospital, then where was it coming from ?
It turned out that the family lived on a farm raising pigs. The pigs were tested. They were the source of the MRSA.
Other pigs on different farms in that area also carried this strain of MRSA. A number of other cases of farmers and vets catching MRSA off their pigs. They concluded that farmers were 760x more likely to get an MRSA infection than any other Dutch people. Further research revealed that 39% of pigs entering a slaughterhouse carried MRSA. Hospitals in close proximity to pig farms tended to see more patients with MRSA than hospitals that were far from pig farms. This MRSA appears to be different from the hospital associated MRSA's we are more familiar with. It is primarily carried by pigs, and was a leading cause of MRSA infection in the Netherlands.
So now we know that pigs can carry MRSA, it is time to ask an important question. How did they get MRSA ? How did this particular strain evolve ? These are the questions that this weeks #MicroTwJC paper aims to answer.
Science, It's a meritocratic thing?
#sciencegirlthing meme confused me, because when I started at university, there was a 60:40 girl boy ratio on my science course. There seem to be plenty of girls going into science courses, but where do they go? This got me thinking about something that I wanted to blog about a while ago, but was too angry to do anything other than mash the keyboard with my own face.
In my early days working in the lab, I had the fortune to work with an amazing post doc. This post doc always knew what they were doing. Some days, they would be the first one in the lab, and last one out. Not because anyone told them to, not because they felt it gave them an air of arrogant superiority, but because the experiments demanded it. Through an extraordinary level of organisation, they managed to do a huge amount of work with very little time. It was an acknowledged fact in our lab that this post doc was some sort of superhero. Seeing that level of dedication, organisation and productivity affected me a lot, and I still am attempting to emulate their example.
So hearing that she wanted to get out of science sent my head spinning.
After which I was directed to look at the academics in higher positions. Most of them were men. It doesn't take a genius to see that something was going on.
There is a phrase that I've heard bandied about a number of places, "Too smart for science". Occasionally a lab will be blessed with an amazing student who, despite being excellent at science decides that they'll be better off doing another career, because the job opportunities are so small. And they do well, because they are smart enough to excel at anything they do. But it is still a loss for science.
So when you present such a person with a game so stacked against them, is it any surprise when they cash their chips and go elsewhere ? Why go through the sacrifice and hard work of a career in science when there is very likely no pay off at the end of it.
So seeing someone who had played such a key inspiration for me, decide that science wasn't the best use for her talents, was devastating. Hence the face/keyboard/laptop chewing implied earlier. Because I had my main preconceptions of science shattered.
I realised that no matter how good I am as a scientist, some arbitrary crap that I have no control over can prevent me from pursuing a career. Actually we don't always have the best people solving our scientific problems because the system is tipped against a lot of them. This is a career where the smartest people don't get to the top, they get out.
Can we really claim science is a meritocracy when we are haemorrhaging some of our best talent ?
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