Thursday, October 30, 2014

Lab Acquired Salmonella

An interesting bit of lab saftey news came out awhile back that I think hasn't gotten quite enough attention.
Since November 2013, 41 people in 13 states have been sickened by a Salmonella typhimurium outbreak (enterica serotype).

Salmonella typhimurium (pink)
The Salmonella was linked to clinical and university teaching laboratories according to the CDC investigation.
Cases have been reported in Illinois, Indiana, Kentucky, Maine, Massachusetts, Missouri, New Hampshire, New Jersey, Ohio, Pennsylvania, Virginia, Washington, and Wisconsin. The CDC investigation (probably performed mostly by the PulseNet group) revealed via laboratory testing (pulsed-field gel electrophoresis) sequence from commercially available S. typhimurium strains used in laboratory settings for teaching or quality control purposes. Basically, the S. typhimurium strain infecting people and making them ill was identified by PFGE (seperating DNA in a gel matrix based on a changing electric field), and it was similar to the S. typhimurium that could be acquired commercially.

The S. typhimurium strains are known to be present in several teaching laboratories that were associated with ill people. Epidemiological information gathered showed that 18 of the 21 people infected (86%) were enrolled in either a human biology or microbiology course. 15 of those 18 ill persons were students, and three (22%) were employees.
This is not the first outbreak linked to a college laboratory class, in 2011 a total of 109 illnesses were linked to clinical and microbiology teaching laboratories.
These outbreaks of Salmonella and other lab-associated organisms bring up important points about lab safety in teaching labs.
  • Some of the bacteria you work with can make you and others near you sick. Most of the time, lab-bacterial strains are weak and non pathogenic. However, it is possible that they can still cause illness.
  • It is possible to spread bacteria via contaminated lab coats, pens, keys, phones, mp3 players, notebooks, and other items that go in and out of the laboratory. Avoid taking things in and out of the lab.
  • People who work with infectious agents should be careful to handle samples properly and to wash hands appropriately, especially before you prepare any food, baby bottles, before eating, or contacting young children.
  • Non-pathogenic or attenuated bacterial strains should be used when possible in teaching laboratories.
This is what a microbiology teaching lab looks like.
I am guilty of breaking on some occasion most of these rules. I wear an ipod most days (albeit inside my lab coat). I have definitely eaten and drank in the lab, etc. The main thing to consider is handwashing, and proper handling of organisms. And if you are unsure, it is always better to be safe than sorry. 

Sunday, October 19, 2014

Post #7 Ebola, Career Ambition, and Coming Up Short - My PhD Process: How I Survived a PhD in the Biological Sciences and Succeeded Afterward

With all the discussion about the Ebola outbreak that is going on in Africa, I can't help but think about my brushes with Ebola research. Ideally, I would have had more than "brushes" with Ebola by now, however I haven't been able to get a position (postdoc, fellowship, or other) where BSL-4 work is required.

When I was in college, Joseph McCormick and Susan Fisher-Hoch came to my undergraduate school (North Dakota State University) to give a talk and to promote their book "Level 4: Virus Hunters of the CDC". It was a wonderful opportunity to talk with them about their careers. I was always enthralled with the idea of working in BSL-4 conditions, ideally in the field. So I took advantage of a willing group of faculty who let me sit with them for when they talked with the guests (I was the only student). I don't remember specifics, but it had an effect. Plus, I got a signed copy of their book out of the deal!

If you have questions, please use the comments section below!

The options at my undergrad didn't exist for BSL-4 research, nor did it happen during my MS. I applied to UTMB-Galveston for my PhD, but didn't get accepted. I applied and interviewed for a post doc at Texas Biomedical Research Institute (TBRI) in an Ebola lab. Didn't get it (the lab hired someone with previous BSL-4 experience). I applied and interviewed for a fellowship at USAMRIID in an Ebola lab. Didn't get it (got really good, better than expected reviews on my grant application, but DTRA didn't fund it, no go.) I applied for the CDC EIS program three years in a row. Never got an interview. I am certainly not done applying.

Below are two links. The first is for the grant I wrote, "Generation of a Gold Nanorod Vaccine against Ebolavirus and Marburgvirus". The second link is to the reviewer's comments.

1. Generation of a Gold Nanorod Vaccine against Ebolavirus and Marburgvirus
2. Reviewer's comments

I am more than likely not done applying to BSL-4 positions. At this point, I have a pretty diverse resume, and I have found I am happy doing a variety of jobs. Therefore, it may not happen. I am not going to focus only on BSL-4 jobs just because they are too few and geographically sparse. However, if the right opportunity presents itself, I would be all over it.

Good luck to everyone in the field working on the Ebola outbreak. It is a dream of mine.

  • Lance D. Presser has a PhD in microbiology and immunology and is a clinical/public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
  • Follow Lance @ldpsci

  • INSPIRE Excelencia!

    I know sometimes I come off a bit negative about things, especially as it relates to my PhD experience. However, it wasn't all bad and recently I was reminded of one of the better experiences.


    A few weeks back the INfluence Student Potential and Increase Representation in Education (INSPIRE) program at Rosalind Franklin University of Medicine and Science (RFUMS) received national recognition as a pathway for Latino students interested in graduate education and possible careers in the health and biomedical sciences.

    INSPIRE was one of the 14 finalists from a pool of 217 competitors for the 2014 Examples of Excelencia award. The award recognizes programs from across the nation that increase academic opportunities and achievement for Latino students.

    I would never want to oversell, but I would like to think I had a fairly major hand in developing the INSPIRE program. Along with Dr. Rasgado-Flores and Christina Lopez (who were the brains behind the organization, and who recruited me to help) we developed the program, and set about recruiting faculty, and graduate students to participate. We then set about spreading the word to local high schools and began interviewing students. We also did some fundraising, community outreach, etc. It was a great experience and I was proud to be the GSEO (graduate student executive officer - yes i just made that title up).

    INSPIRE was designed as an eight-week mentoring and research program which provides an opportunity for hands-on biomedical research. A mentoring/tutoring aspect is provided as well. Lunch-philosophy sessions with mentors, course-work review, college and career planning, etc. are all part of the INSPIRE program.

    We want to increase the number of qualified students from underrepresented populations who complete advanced-degree health programs and serve their community as practicing health professionals,” said Hector Rasgado-Flores, PhD, faculty advisor and RFUMS associate professor of physiology. “INSPIRE is about removing barriers to higher education.” (Side note: Dr. Rasgado-Flores is an inspiration himself. An incredibly charismatic and gifted speaker, he is always a student favorite lecturer. He is also a gifted pianist and composer)

    According to the U.S. Department of Education, just four percent of Latinos attain a master’s or higher degree. FOUR PERCENT! This video is a presentation that Dr. Rasgado-Flores has given. In it are some amazing statistics higher education and the Latino population.

    And now the victory lap!

    As one of this year’s finalists, Rosalind Franklin University of Medicine and Science is at the forefront of meeting the challenge of improving higher educational achievement for Latino students,” said Sarita Brown, president of Excelencia in Education. “No longer should policymakers and institutional leaders ask how to improve college success for Latinos — we have the largest accumulation of proven examples and tested strategies that show them how. Today’s question is do leaders have the will to put these practices into action?”

    Thank you Excelencia in Education for the recognition. Thank you Dr. Rasgado-Flores and Ms. Lopez for the opportunity to help out. Good luck in the future!

    UPDATE!

    Check out the new YouTube Video!


  • Lance D. Presser has a PhD in microbiology and immunology and is a clinical/public health laboratorian.
  • Hire Lance for any of your microbiology, virology, teaching, editing, grant writing, or public health consulting needs.
  • Follow Lance @ldpsci