The effect of antibiotics on swine gut microbiomes

As promised, here is more information about the research of mine (+ lovely coauthors) that was published today.  The below article was posted on the mBiosphere blog and was written by Merry Buckley (please use this original source when reposting).  I am reposting it because it 1) has a cute picture, 2) gives a nice framework and summary of the paper, and 3) I am feeling too lazy to write my own synopsis for you.  Enjoy!   

Antibiotics stimulate gene exchange in swine gut microbes

Antibiotics: they’re not just for curing the sick. Livestock farms in the U.S. regularly use antibiotic drugs as feed additives to boost animal growth, but a study in mBio this week reveals new evidence that adding antibiotics to pig feed stimulates gene exchange in the guts of these animals, a development that could move antibiotic resistance genes where they’re not wanted.

Using antibiotics in animal feed saves farms money, but opponents argue the practice encourages antimicrobial resistance among bacteria that could well be consumed by humans. Today, livestock producers in the U.S. use an estimated 24.6 million pounds of antimicrobials for nontherapeutic purposes every year.

The study by Allen et al. adds to what we know about what happens to the microorganisms that populate animal digestive tracts when they are exposed to these low, persistent levels of anitbiotics. Researchers at USDA’s National Animal Disease Center (NADC) in Ames, Iowa studied how two in-feed antibiotic formulations affect prophages, segments of DNA found in bacteria that can encode antibiotic resistance genes and other genes that impact bacterial fitness. Prophages can cut themselves out of the larger chromosome of DNA in a process called induction, then replicate and package themselves as viruses. These viruses explode the cell from the inside, then move on to infect other organisms and deliver their genes.

Lead author Heather K. Allen says when pigs were fed antibiotics, the actual numbers of antibiotic resistance genes carried by the phages remained steady, but the microorganisms still reacted to the presence of antibiotics. Prophages underwent a significant increase in induction when exposed to antibiotics, indicating that medicating the animals led to increased movement of prophage genes among gut bacteria.

“Induction of the prophages is showing us that antibiotics are stimulating gene transfer,” says Allen. “This is significant because phages have previously been shown to carry bacterial fitness genes such as antibiotic resistance genes.”

Studies that explore the impacts of in-feed antibiotics most often focus on the bacterial residents of the gut, according to Allen, but phages and other viruses move a significant amount of genetic information around the community. This makes changes in prophage induction an important collateral effect of antibiotic treatment, she says. Resistance genes are the unit of currency among microbes experiencing the duress of an antibiotic, so following the movement of genes is arguably more important than following certain changes in bacterial communities. And if bacteria in humans acquire resistance genes from animals, there can be serious health consequences.

“What’s important is the transfer of a gene that could get into the wrong place at the wrong time,” says Allen. “Increased gene transfer is a critical event in the evolution of gut bacteria.”

A breath and...breathe

photo by Sam

For me, the best parts of the holiday season are spending time with loved ones and taking a break from the usual routines.  I took a break from this blog (thank you for tolerating that) and from work, both of which were refreshing and much needed.

November got so crazy!  It started off with two scientific presentations, one here and one in The Netherlands, and ended with a holiday.  In between I had to review proofs of a manuscript that has my name on it and is being published tomorrow, go to Iowa City for a surgical follow-up, and be interviewed for a press release regarding the aforementioned manuscript.  I almost forgot to re-up for yoga, that's how discombobulated I was with all of these unusual tasks.

But I most certainly did sign up for another five weeks of yoga.  I must stay centered and stretched.

The surgical follow-up involved many mammograms of the right breast.  Suspicious shadows were noted, due to the scar tissue from the needle-localized biopsy last April.  Suspicious shadows were further visualized by ultrasound and palpated by radiologists and surgeons.  Importantly, Dr. Surgical Oncologist is not at all concerned and is certain that the suspicious shadows are scar tissue.  I, too, am certain.  Unfortunately this scar tissue will probably always be there, so I will probably always have extra -grams and -sounds and -scans.  An irony that a procedure to remove suspicious breast tissue left perpetually suspicious breast tissue in its wake.

After the appointment but before returning home, I had lunch at Masala.  All vegetarian Indian food buffet, all delicious.  I will say that it was odd to eat at a buffet by myself.  I enjoy (dare I say "savor"?) time alone, and I don't mind dining alone, but adding the buffet variable made things less enjoyable.  I found that I ate altogether too quickly and had trouble timing the second trip.  It's hard to slow the pace of consumption when there is no one to visit with between bites.

Regarding the work things, the manuscript should be coming out tomorrow, and someone at the journal thinks it's a cool article.  So she decided to write up a press release for it, and interviewed me over the phone.  I was quite nervous because I've never been interviewed for my science before.  I felt a lot of pressure to say things perfectly, which made me say them horribly imperfectly.  But I survived, and I'll do better next time.  I'll post the manuscript when it's available, and I'll save the summary of the science until then.  Needless to say, the hub-ub surrounding getting this article out has felt intense and distracting.

Thanksgiving, therefore, couldn't have been timed better for me.  I needed to take a deep breath, step away from my month of diverse yet pivotal events, and just breathe for a few days.  I spent excellent time with the usual family...

photo by Sam

photo by Sam

...and with family from afar.  I played games, I made deviled eggs, I went to playgrounds, and I stitched the last stitch of Eleanor's Christmas stocking.  This last item is significant because I worked on it during nearly every Herceptin treatment these past 8 months.  I suppose it's a bummer that I will always think of chemotherapy when I look at that dang stocking, but it was a great task to have during that time.

Which reminds me, the Wednesday before Thanksgiving was my first free third Wednesday in one full year. That is, it was my first Wednesday free from Herceptin treatment when I should have been receiving Herceptin treatment.  That deserves a celebration and a blog post unto itself.

Hopefully I will carry the rejuvenation from the holiday weekend for several days, if not weeks, to come.

Was your holiday pleasant, if not fantastic?  Did you have a moment to breathe?

The Netherlands

I arrived in the Amsterdam area airport with 24 hours to spend before conference time.  My conference was providing free shuttles from the airport to the conference town (Egmond aan Zee), so I opted for an airport-based tour of Amsterdam.  Best 50 euros I've ever spent.  

The tour lasted 2.5 hours and was given by a fabulous guide in a small van.  It was nearly a personal tour, as there were only two patrons.  We made several stops in and around the city, including by the I amsterdam sign (get it?  I [am] AMsterdam?)

 Amsterdam is full of canals, such as the one below.  Indeed, the whole country is full of canals.  Did you know that if it weren't for enormous pumps operating 24/7, nearly half of the country would be under water?  The famous Dutch windmills used to be the primary water-expelling mechanism for the country, but now they have some impressive technologies to do the job.  The Dutch are hydraulic experts; New Orleans should give them a call.

We also drove past Anne Frank's house, the royal palace, the harbor, and the red light district.  I saw three ladies in windows.  But the highlight of the tour was stopping at a small farm to see how they made cheese and wooden shoes.

The Netherlands is a flat and agricultural country, and very picturesque.  I saw many different types of crops and livestock.  The occasional windmill dotted the landscape.  According to Fabulous Tour Guide, only about 100 of the classic Dutch windmills remain, and although they are not operational they are preserved.  The strategy for upkeep is to let people live in them rent-free as long as they take care of them.  I saw a man out tending his windmill's lawn on a Sunday afternoon.  A clever solution to a historical preservation problem, but bizarre nonetheless.    

Immediately upon arrival in Egmond aan zee I headed for the beach.  It was less than a block from my hotel and visible from my room.  The sun was setting and I just couldn't wait to take it all in.

 

The view of the town from the beach.

In the morning, I still had a few hours before the conference was to start.  So I decided to rent a bike and explore the area.  Finding the bike shop pretty much introduced me to the whole town, so I was more interested in a country ride.  I found a few maps, mostly in Dutch, and was nearly dissuaded from the seemingly complicated navigation of a country ride.  Instead I tucked the maps in my backpack and just started riding.  What a marvelous choice!  There are bike lanes or paths along every road, and it turns out that my chosen route was the Prince's Route (or something) and therefore clearly marked.  It was very beautiful, even in the slight fog.

The route paralleled a national forest/sand dune preserve.  I was lucky to see so much nature in a small country of 15 million people.

And then the fog lifted as I rolled into Bergen aan zee, the town just north of Egmond aan zee on the coast.  

So of course I had to park the bicycle and explore this beach as well.

I pedaled back to Egmond aan zee, returned the bike, and was only 20 minutes late to the conference.  Nice!  The rest of the time I worked very, very hard and took virtually no more pictures.  Save one.  Across from my hotel I realized that there was a tall dune with a path leading up it.  So during one of the conference breaks I scurried up to explore.  Below is a panoramic of the town.  Notable landmarks from the left:  my hotel, the lighthouse, the church in the town square, and the church by the bike shop.

A fast trip, but a great trip.  

I'm in the Netherlands!

In March my boss was invited to give a seminar at a conference in the Netherlands in November.  He was unavailable, so the conference settled for a replacement speaker:  me.  It was a lengthy process to get all of the ducks in a row, but a mere six weeks ago the dust settled and my flight itinerary appeared in my inbox.  I guess it's official.

I'm giving a presentation on alternatives to agricultural antibiotics.  I won't post my slides, but I will post a link to my accepted manuscript (huzzah!) that I'm heavily summarizing, when it becomes available.

The conference doesn't start for a few more hours, and I've been enjoying myself immensely!  The conference is not in Amsterdam, but I wanted to see Amsterdam, so here is the tour that I wanted to take:  

Do be do be do! Unfortunately this tour was cancelled due to a festival celebrating the original Santa Claus.  But I found a different tour that was FANTASTIC.  It included a few quick stops, including a tour of a cheese factory.  It was a quaint little farm where we spoke with the 8th-generation cheese maker.  Huzzah for keeping the business in the family for so long! 

I'm off to see if I can rent a bicycle for an hour or so.  This country has bike paths flanking nearly every major road, and bike lanes on nearly every non-major road.  Incredible. 

Image

"As I child I had expected my liberation to come from getting a new face to put on, but now I saw it came from shedding something, shedding my image."--Lucy Grealy in Autobiography of a face


I read the most remarkable book, cited above.  Ms. Grealy was diagnosed with Ewing sarcoma in her jaw when she was nine years old.  Her jaw was removed from one side of her face.  She underwent 2.5 years of weekly, debilitating chemotherapy and a year or so of concurrent radiation.  She survived.

The obvious and fascinating point of the book is to present what it is like to go through virtually your entire life, the teenage years in particular, with such a dramatically unique face.  She underwent nearly 30 attempted reconstructive surgeries over 18 years.  She developed numerous psychological tricks to cope with these physical and emotional hardships.  In particular, she coached herself that she was ugly.

She decided that she had to tell herself that she was ugly in order to cope with the teases dished out by boys and men (at some point she states that girls and women never taunted her).  The following is my interpretation, but it seems that rather than undergo an internal counter-argument, it was more effective for her to agree with them.  I think I can understand this logic.  If you tell yourself that you know you are ugly, a tease is no longer a tease but rather a pointless declaration of the truth.  I can see it as a survival mechanism at the expense of one's self-esteem.

The hardest part to read about is her disappointment with the reconstructive surgeries.  They all failed because her tissue was so severely irradiated that the transplanted tissue would not "take".  It would simply be re-absorbed over the course of several months, and she would be left with her lack of a jaw line in spite of the lengthy, painful attempt to restore it.  With each reconstruction, her hopes to no longer be "ugly" would rise, and with each failure she would recede farther from society.

In the end she had accepted an end to the surgeries.  The last attempt seemed to have a slightly better cosmetic outcome than all of the previous attempts.  But she couldn't reconcile that the face she saw in the mirror was actually her face.  This is because she had gone her whole life looking the way one looks without half of a jaw, and now that it was at least partially corrected she didn't look like herself.  But apparently she looked more acceptable to society?  So as she tried to reconcile this paradox, she avoided looking at her reflection for over a year.  Avoiding her face helped her accept that she had a face; she was no longer waiting for her face to be constructed.

It's a beautiful book with a universal message:  you are beautiful.  

"Why couldn't they just stop complaining so much, just let go and see how good they actually had it?  Everyone seemed to be waiting for something to happen that would allow them to move forward, waiting for some shadowy future moment to begin their lives in earnest." --Lucy Grealy, Autobiography of a Face

A prosthesis at last, just in case

I am now the proud owner of a prosthetic left breast.  The breast doesn't actually have handedness, but since I only have a spot for it on my left side I define it as a left breast.  It is triangular in the two dimensions that are flush with my skin, and teardrop-shaped in the third, protruding dimension.  It is pleasantly squishy--a bit more firm than a gel-filled ice pack but more pliable than rubber.

These descriptions will have to suffice for now because I decided not to photograph it yet.  I didn't know how:  do I lay it on the table?  Do I hold it up to my chest?  Do I let my smiling children hold it up for the camera?  I don't yet feel emotional ownership for this left breast and so any of these options seem satisfactory on one level, but on another level I don't want to accidentally disrespect the left breast in a careless photographic portrayal.  And so once again I rely on my words.

Acquisition of my prosthesis was surprisingly tedious.  It took five different fittings to get the correct breast-bra combo.  We first had to special order some prostheses.  The cancer outreach center did not stock any prostheses in my size, although I can proudly say I do not require the smallest prosthesis available (just the second smallest).  Then the shape was an issue, so we had to order the decided size in a different style.  Then the bras were the issue.  With a prosthesis, one typically wears a special bra that has a pocket for the prosthesis.  One can probably wear a prosthesis in a normal bra, but the pocket is nice to keep the prosthesis in place and to protect the skin from rubbing on the somewhat sticky prosthesis.  So I tried many, many different pocket bras.  It was difficult finding a bra that was complementary to (if not equalizing of) the prosthesis and Ms. Right Breast.  At long last we found one bra-breast combo that actually worked well.  Unfortunately, this bra was a rather impractical blue.  It is and will always be my first prosthesis bra, but we also settled on an imperfect fit in order to include a practical champagne-colored bra in my prosthesis-wearing repertoire.  

At first I was excited to have a prosthesis option available!  I slipped the breast in the pocket and put on the bra.  I was a bit self-conscious about choosing to wear a breast to work that day, so I chose a shirt that I presumed would hide the prosthetic breast just as I rely on it to hide the empty space.  And indeed I may have hidden it well.  I received no comments, but why would I?  What would someone say, regardless of if it were positive or negative?  "Did you get a new breast?  It looks great!" or "Did you get a new breast?  Hmm, you should get your money back."  It was false to imagine I would get affirmation for my choice to wear a prosthetic breast one day.  But I kept hoping for it as if I were sporting a new pair of glasses or shoes.  Also disappointing was how much I hated wearing a bra again.  It was the first time I'd worn a bra in months, if not a year.  I had forgotten how many millions of places it pulls and rubs and hikes and heats.  

Needless to say my shiny new prosthetic left breast is tucked away in its special box, in its original bag.  The scratchy new bras are stuffed into my overflowing (um...why?) undergarment drawer.  But they are at my disposal should I ever desire to increase my physical discomfort at the expense of my emotional comfort.  Maybe at a wedding reception with an open bar I can reconcile this dichotomy.                     

Freedom

This is it.  I finally made it to the eve of the end of my cancer treatments.  Tomorrow is my last herceptin therapy.  I will get my energy back, I will get my third Wednesdays back, I will get my freedom back.  Despite the momentousness of the occasion, I am entirely underwhelmed by Tomorrow.  This surprises me because I thought I would be unable to contain my excitement.  On the contrary, my excitement is entirely contained.  Per usual, I think this deserves an analysis.

I have read that cancer patients sometimes have a hard time ceasing therapy because they have grown attached to their caregivers.  Also, patients wonder how they can possibly return to life without cancer.  These feelings can sometimes turn into depression.  I think it remains to be determined if I will be susceptible to this, but I don't expect depression to be a big factor.  I will still see Dr. Oncologist every three months for PET scans.  I will still see my favorite nurse around town with her son.  And I can't WAIT to return to life without cancer.  Cancer made me needy, and I don't like being needy.  Sign me up for self-sufficiency, please!  

Right now my lack of enthusiasm for tomorrow seems to be related to something I've posted about before, which is accomplishing a goal that I never should have had.  Also, I'm feeling a strong urge to get cancer treatment out of the way so that I can get back to Living.  I acknowledge that getting to this point was no small feat, it's just hard to embrace a celebratory mentality given the subject matter.  I guess I would say that I successfully toughed it out.  Yay?

But there is something that I was inspired to celebrate tomorrow:  my oncologist.  She is brilliant and caring and attentive and thoughtful.  Any guesses what I did to show her my appreciation?  That's right.  I made her a blanket.

    
It's my 12-hour afghan pattern and it makes the coziest blanket in the universe.  For Dr. O I chose three oceanic shades of blue because I envisioned the blanket providing a wave of calm and warmth after a long day of helping sick people.  THIS is where my excitement lies:  in giving her this blanket.

In related news, during the making of this blanket I acquired a protege.  It was only a matter of time, really.

Go, Azalea, go!

I'll end this post with a premature poke tally.  It includes both tomorrow's and the previous herceptin poke, plus the PET scan poke.  I suppose that this is where the poke tally ends?  I must say, I am grateful for that port, otherwise the poke tally would be much, much higher.  Possibly even doubled.  Port, I'm not going to make you a blanket, but I appreciate you.    

port  40

right arm 13

tummy  6

left arm  6

right breast 2++

left breast  1+

superior vena cava 1

T9 vertebral body  1