Gut Flora and Chron’s Disease

I’m fascinated by the connection between gut flora and overall health. I just stumbled onto this article that discusses the connection between gut flora and Chron’s Disease. It’s based on this paper published in Cell. Recent articles about antibiotic’s role in obesity and papers on gut flora’s influence on the immune system  keep raising the issue: how much do common organisms like E. coli, Clostridium perfringes, and Bacteroides fragilis affect us? How can we use them to diagnose, prevent, or cure disease? I’ll be keeping my eye on future research.



Kelly Swails, MT(ASCP), is a laboratory professional, recovering microbiologist, and web editor for Lab Medicine.


Antibiotic Stewardship

The draft of the federal budget released Tuesday allocates $30 million dollars in CDC funding in order to combat antibiotic resistance. Obviously the 2015 budget isn’t finalized, but even so, it’s encouraging that the Department of Health and Human Services recognizes the need for antibiotic stewardship.

What is antibiotic stewardship, you ask? Basically, it’s a program within a healthcare community that dictates the best practices for prescribing antibiotics. Such programs would be tailored for each setting based on population demographics and antibiograms. Perhaps a program would prohibit prescribing, say, ciprofloxacin for urinary tract infections because a rise in the percentage of strains of E. coli resistant to fluoroquinolones has been noted. Maybe the program would discourage prescribing more than two antibiotics at once to a patient, or suggest antibiotics other than vancomycin (such as levoquin) when treating MRSA.

Creating a stewardship program requires input from several departments (Infectious Disease, Pharmacy, Epidemiology, and the Microbiology Laboratory) as well as acceptance by the clinician population at large. In my experience, this has been the limiting factor. Physicians don’t like being told what they can and can’t do for their patients or the insinuation that they might lack the proper knowledge about antimicrobials and microbiology to provide good patient care. This is a hurdle that hospitals will have to overcome in order to make stewardship programs a success. (Mentioning that such programs can save money and shorten hospital stays could help tip the scales.)

If you’d like to institute a stewardship program at your institution, here are a few links to get you started:

CDC’s Vital Signs about prescribing practices
Antibiotic management guidelines at John Hopkins
Professional practice resources from the Association for Professionals in Infection Control and Epidemiology
The ever-insightful Maryn McKenna over at Superbug discusses the topic at length

Does your institution have an antibiotic stewardship program? If so, what steps did you have to take in order to implement it?


Kelly Swails, MT(ASCP), is a laboratory professional, recovering microbiologist, and web editor for Lab Medicine.

Vinegar to the Rescue

Can a common pantry staple kill bacteria? Possibly, according a paper recently published in mBio. Researchers mixed acetic acid–the main ingredient in white vinegar–with suspensions of bacterial cultures and found that a exposure times as little as 20 minutes reduced the viable bacterial population by 710. The researchers then performed the same experiment, this time swapping out hydrochloric acid for the vinegar; they noted no bactericidal effect. Mycobacterium tuberculosis required a longer kill time (30 minutes vs. 20 minutes) to reach a 810 reduction in population.

These results suggest that vinegar could be used as a cheap-yet-effective disinfectant in resource-poor laboratory settings.




Balance Between Service Obligations and Education

These past couple of days I attended the CAP Residents Forum and USCAP in San Diego. It was both an inspiring and daunting experience. Inspiring because of the breadth and depth of research and amount of scholarly expertise in the room every time I attended a lecture; daunting because of this same fact and also because of the reminder that someday soon I will need to be as expert and competent as these speakers.

With these thoughts in mind, I attended the first half of the morning of the CAP Residents Forum for their “Dating Game” panel where new-in-practice and veteran pathologists spoke about to getting and keeping your first job. It was actually an engaging panel and I learned practical information that was new to me and that will help me not only to obtain my first job but also when I apply for fellowship in a couple of months.

I attended mostly molecular pathology talks and the cytology short course that for someone who hasn’t had cytology yet, was informative. I got to hang out with friends from other programs that I met through the CAP Residents Forum and to hear how they are taught the practice of pathology. These conversations got me to thinking about whether service obligations can compromise our education.

For someone who is CP-oriented, I am at a program that is heavy on the surgical pathology (we do 17 months; previous classes did many more). And most of us are trained at academic institutions but my program also has rotations at a VAhospital and two community private practice hospitals. Life is different at the community hospitals but I hear that most residents will go on to practice in this type of setting. The volume can be high, there may be many tumor boards/conferences to present at or attend, and the turnover time is so strictly adhered to that you might not always be able to get protected preview time – even if eventually you do get to sign-out with the attendings after they’ve verified a case.

But does it matter about protected preview time if you don’t look at the verified diagnosis before you sign out with your attending? Does your program have CP residents covering autopsy call? Do your residents gross on Saturdays? Just what constitutes service obligations interfering with resident education in your perspective? Working in a clinical setting, patient safety and service obligations can take on a predominant role, but the quality of our work cannot suffer. So what makes for the right balance between service obligations and resident education and what can we do to ensure that resident education is made a priority?



Betty Chung, DO, MPH, MA is a second year resident physician at the University of Illinois Hospital and Health Sciences System in Chicago, IL.

Service Snippets

I’ve gotten some great responses regarding my recent blogs on Customer Service, and want to share some of these with you. Good ideas always generate more good ideas, and I think you will find these fun ideas very interesting. As we know, patients can usually only judge our quality and testing performance by what they see and what they experience at the drawing station…so, with permission to share, here are two excellent ones:

Children are often the most difficult to draw, and take more time and technique than adults. One laboratory draw station, part of a large metropolitan children’s hospital, has a system that works to help keep children occupied and parent’s angst levels lower during the busiest times. When patients show up for a phlebotomy and the wait is greater than 15 minutes, they are given a “restaurant beeper” and a coupon for the coffee/juice cart outside on the patio, and then are paged when the phlebotomist is ready for them.

A 25 bed rural hospital in West Virginia surprises a lot of people when they go out to the parking lot, and do a “vehicle draw” for patients that have difficulty making it into the hospital, for older patients who struggle with wheelchairs etc., or if someone is just too ill to come into the building. The staff is truly committed to serving their patients and proud that something so small can make such a difference. 

Perhaps these two fine examples (as well as the one from our colleagues in Africa) will generate some ideas about how your operations might make little changes that accommodate patients, and provide the best service you can offer—which we know directly translates to showing patients the quality we are proud of as laboratory professionals. Explore it with your teams, get some ideas going, and make it work for you.

I will be leaving soon for another global experience with colleagues from another part of our world and we will be working on the pre-analytical processes (including the importance of customer service) for our external AND internal customers. I’ll be writing my next blog “live from Kyrgyzstan!”

In the meantime, I’d be interested to know what you’d like me to ask our colleagues while I’m there. You can email me at  and perhaps we’ll get a little international dialogue on the topic…and as always, I look forward to hearing your comments and ideas for building better laboratories and processes around the world, and at home in our own communities!


Beverly Sumwalt, MA, DLM, CLS, MT(ASCP) is an ASCP Global Outreach Volunteer Consultant.

Newborn Screening – a History

Inborn Errors of Metabolism (IEM) are genetic disorders that often occur as enzyme deficiencies which interfere with the normal biochemical processes of the human body. Very often these disorders are not apparent at birth because the mother’s biochemical processes work for the baby in the womb. Shortly after birth, the infant begins to get into significant trouble when his own enzymes are deficient or insufficient to carry the biochemical load. Many of these disorders are eminently treatable, allowing the treated individual to lead a normal life or a life whose quality is vastly improved over untreated individuals. Thus detecting IEM and treating them before the baby becomes ill is the primary purpose of newborn screening (NBS) programs worldwide. The seeds of newborn screening (NBS) in the US began back in the early 1960s when Dr. Robert Guthrie developed a bacterial inhibition assay for phenylalanine and demonstrated that it could be used to screen entire populations for the presence of a devastating yet treatable disease called phenylketonuria (PKU). In 1960 Maine became the first State to offer newborn screening for PKU to all infants born in Maine.

In the years that followed this advent, the prevalence of NBS grew slowly and sporadically. Along the way there was debate over which disorders to include; at one time a disorder had to meet a long list of criteria to be included. In addition, the NBS performed in any given state is dependent on that state’s ability and willingness to fund the program. Even today, NBS is not nationally mandated but is in the purview of the individual states. Each state decides which disorders to screen for.

As late as 1997, only 2 disorders (PKU and congenital hypothyroidism) were screened for by all 50 states. However in the mid- to late 1990’s a technological development revolutionized NBS. The ability to screen for up to 50 different IEM from a single dried blood spot punch using tandem mass spectrometry changed the face of NBS. The American College of Medical Genetics (ACMG) fielded a task force called the Newborn Screening Expert Group which published a recommendation in 2006 entitled “Newborn Screening: Toward a Uniform Screening Panel and System”(1). This Group recommended a set of 29 “core conditions” that every state should screen for, as well as a set of “secondary conditions” that will be picked up during the differential diagnosis of the core conditions. They also revised the inclusion criteria into a set of three basic criteria for disease inclusion in NBS programs: the disorder must be detectable within 24-48 hours of birth, before it’s clinically detectable, a screening test with appropriate sensitivity and specificity must be available, and the disorder must be treatable with benefits to treatment. Currently all 50 states screen their newborns for the 29 Core Conditions recommended by the ACMG and the US Department of Health and Human Services. Thanks to a laboratory technology, NBS is now much closer to being standardized than ever before and covers the majority of the most common IEM.




-Patti Jones PhD, DABCC, FACB, is the Clinical Director of the Chemistry and Metabolic Disease Laboratories at Children’s Medical Center in Dallas, TX and a Professor of Pathology at University of Texas Southwestern Medical Center in Dallas.

All I Really Need to Know I Learned in Residency

If you are old as I am (I was a non-traditional medical student), then you might remember a book called All I Really Need to Know I Learned in Kindergarten that remained on the NYT Bestseller List for an impressive two years back in the 80s. It was full of aphorisms of how a simpler perspective might prove to be a better and/or happier way to live. So, I’ve been wondering all week while frantically trying to get my USCAP poster done before the rush fee deadline goes into effect (I guess I never learn)…do we really learn everything we need to know to be good pathologists during residency?

Training programs are variable – some make you work for it while others, not so much. But in the end, the day after graduation, we are all expected to be full-fledged competent pathologists…as if, in those magical 24 hours, we have all become smarter, have mastered our inefficiencies and time management issues, and are suddenly better than we were a short time before.  But honestly, since you probably spent that last day not in pathology mode, the only thing that we can be sure of is that you are 24 hours older. Despite the differences in our training, the majority of us will go on to pass our boards, and scary thought, practice the day after we graduate (although that might mean postponement until after fellowship).

Residents are also variable in terms of how and what they learn. I admit that I never expect to be the best at surgpath, especially grossing. But I do keep trying and hope that I don’t hurt patients in the process. I hope to at least survive until I’m done with surgpath for good. And I know regardless, it will still help me whether I decide to go into molecular pathology or hematopathology or a combination of both. I do know that I excel on my most of my CP rotations. But what do we need to do to learn and improve on our deficiencies and move past our comfort zones? For me, I’m comfortable in the lab since I went to graduate school, originally was a dual degree medical student, and had a decade of research experience prior to medical school but I’d love to hear advice and stories of how residents improved their grossing skills and surgpath differentials or finally triumphed over that weakness or deficiency that kept showing up on your evaluations.

Despite where we train (even at the best programs), I’ll bet that most of us in our initial years will need to know the following, but not in any particular order:

  1. When in doubt or you don’t know, ask for help from someone you trust and respect
  2. The printed word…whether journals, textbooks, or Google…is your friend, so use it, and use it often
  3. Sticky notes or checklists really do help keep us organized
  4. There is never enough time in the day so plan and use it wisely
  5. Getting angry (at ourselves or others) really won’t help so re-direct that energy towards something positive
  6. You are never too old to learn something new
  7. If at first you don’t succeed, keep trying until you do (hopefully)
  8. Learning doesn’t stop with graduation
  9. Make time for yourself to recharge your batteries
  10. Despite everything we do, we will make mistakes, but try to learn from them so we don’t repeat them.



Betty Chung, DO, MPH, MA is a second year resident physician at the University of Illinois Hospital and Health Sciences System in Chicago, IL.