A 54 year old male with a past medical history of Type II diabetes mellitus and obesity was admitted for a few days history of severe pain over right upper quadrant accompanied by fevers, chills, nausea, vomiting and diarrhea. Physical exam revealed a palpable gallbladder. Ultrasound imaging showed a distended gallbladder with a thickened, edematous and hyperemic wall that was interpreted as acalculus cholecystitis. The patient underwent percutaneous drainage of the gallbladder with plans to undergo a cholecystectomy once the acute phase of his illness stopped. The gallbladder fluid was sent to microbiology for analysis.
Anaerobic plates obtained from organisms growing in thioglycollate broth grew low, convex opaque white colonies. The organisms did not produce the classic double zone of beta hemolysis (Image 1). Gram stain of the culture showed gram positive bacilli that were “boxcar” shaped (Image 2). Aerobic plates had no growth. The organisms were catalase negative and non-motile. MALDI-TOF identified the organism as Clostridium perfringens.
The patient was also placed on piperacillin-tazobactam while in the hospital. His condition improved and he was discharged home with a seven day course of cefpodoxime and metronidazole with a general surgery follow up appointment.
perfringensis a gram
positive bacilli with blunt ends (boxcar shaped). These obligate anaerobes are
spore formers, however these are rarely seen. When seen, they produce
subterminal spores. These organisms cause of crepitant myonecrosis (gas
gangrene), gangrenous cholecystitis, septicemia, and food poisoning. They are present in large numbers as normal
microbiota in the gastro-intestinal tract of humans and animals, the female
genital tract and oral mucosa. Typically, infections are caused by endogenous
strains gaining access to normal sterile sites due to a predisposing factor
that compromise normal anatomy: surgery, trauma, or altered host defense
mechanisms (diabetes, burns, immunosuppression, and aspiration).
Penicillin is recommended in most infections,
however resistance has been reported. Optimal management of intra-abdominal
infection is to achieve appropriate source control and drainage is important.
Outside the city of New Bern, in Craven County, North
Carolina, there is a particular system for residents to dispose of their
garbage. Locals must go to the nearest participating gas station and purchase
stickers which cost about $2.00 each. These stickers must be placed on each bag
of garbage generated in the household, otherwise they will not be picked up
during the weekly trash collection. In order to save money, a group of widows
has formed a club in which members scout out the open dumpsters in town
(usually behind stores or gas stations). Then they call and let group members
know where they can covertly dump their trash for free that week.
This story may seem funny, but for the most part, it is
true. I have no doubt this also occurs in other parts of the country where the
system for trash collection is similar. Why do people behave this way? Are they
purposely trying to circumvent the trash collection system in place or is the
system just not easy for locals to utilize? If you’re having difficulty getting
people to change safety behaviors (like PPE compliance) in your laboratory, you
might need to determine that for the systems you have in place and ask similar
In one laboratory the manager struggles with staff who work
part of the day in a clean office and another part in the lab itself. When the
employees go into the lab for brief periods, they often fail to don their PPE.
Upon further investigation, you would learn that staff are not allowed to keep
their lab coats on their chairs and that all PPE is kept in one lab store room
located on the opposite side away from the offices. The system is set up to reinforce
In another lab the manager placed a permanently-mounted
counter face shield in the chemistry department so that staff would be forced
to use it when popping specimen caps. Staff loaded instrument racks behind the
shield, but when they carried the racks over to the analyzers, their faces were
not protected from splashing. Exposures continued to occur. Here the system is
at play again. A face shield was put in place to change behaviors, but it was
only a partial solution. In order to protect staff fully here, they would need
goggles or a face shield that can be worn. Offer light-weight reusable or
disposable face protection that staff can use easily. Be sure to give them a
say in whatever option is chosen.
Sometimes the system issues are not apparent until there is
a safety event, and unfortunately, that can result in bigger problems. If your
training program does not include regular fire safety training, a small fire
situation may get out of hand quickly. Does your staff have experience handling
a fire extinguisher? Would they easily be able to put out a fire? Do they know
their evacuation routes and meeting places, and could they get there with ease?
What about the lab emergency management plan? Have staff participated in a
table-top drill so they have a basic understanding of how to respond during a
chaotic disaster? These are examples of some safety systems that need to be in
place to keep staff ready and safe at all times.
When people take shortcuts or find ways to circumvent the system, there is usually a pretty good reason, Often, it is the design of the system. In New Bern, elderly women can’t lift large heavy trash bags, so they use smaller bags. They don’t want to pay the same price for a garbage bag sticker that others are paying for big bags. There’s a problem with the system- and those ladies found a way around it. What problems do you see in your lab safety system? If you don’t know what they are, ask around. Staff will talk. It’s better to find out what the workarounds are now and to fix them before an injury or exposure occurs.
–Dan Scungio, MT(ASCP), SLS, CQA (ASQ) has over 25 years
experience as a certified medical technologist. Today he is the
Laboratory Safety Officer for Sentara Healthcare, a system of seven
hospitals and over 20 laboratories and draw sites in the Tidewater area
of Virginia. He is also known as Dan the Lab Safety Man, a lab safety consultant, educator, and trainer.
Jennison Hartong, MLS(ASCP)CM,
PA(ASCP)CM, is a Pathologists’ Assistant who recently went to
Ethiopia to teach grossing techniques. The editors of Lablogatory asked her a
few questions about her experiences.
Lablogatory: How’d you get involved with ASCP’s Center for Global Health?
Jennison: Dr. Milner, Chief Medical Officer of ASCP, initially reached out to one of the pathologists at M.D. Anderson to inquire if any Pathologists’ Assistants (PAs) would be interested in attending a workshop in Nigeria. I reached out and expressed my interest in teaching grossing techniques rather than public speaking (not one of my strengths). Dr. Milner then told me about this opportunity in Ethiopia where pathologists were requesting advanced, gross training in lymph node dissections on breast and colon specimens. I immediately jumped at the opportunity to help in this way.
L: What were your motivations for going?
J: Whether with basic health needs or more complex areas like cancer treatments, I’ve always wanted to use my education and experience to help others and impact lives in areas around the world where certain aspects of healthcare may not be accessible. Before becoming a PA, I was a medical technologist and was always interested in working with Doctors Without Borders, however, I did not have the years of experience to apply. I decided to go to PA school and was disappointed to learn that Doctors Without Borders does not utilize PAs. I figured that dream would have to be accomplished another way, which was why I was so eager to work with the ASCP and their global health initiatives.
Another motivation for going on this trip was
experiencing the work and organizational skills required for making a trip like
this successful. I am currently finishing my second master’s degree in public
health with a focus in health policy and management. I was very interested in
learning everything I could about planning programs to help developing
countries as well as being able to network with like-minded health
L: What did you hope to accomplish while you were there?
J: My main goal of this trip was to help advance Ethiopian residents and pathologists in certain grossing techniques. More specifically, I aimed to assist with lymph node dissections and, as it turned out, how to locate and sample the radial margin in colon cancer cases. I also wanted to experience a different culture than my own, step out of my comfort zone and challenge myself as a PA by teaching others. At the end of this experience, I can say that this trip was definitely a life changing experience and one I am extremely grateful for.
L: What did you learn about lab medicine in Ethiopia?
J: During my week in Addis Ababa, I quickly realized that it was up to me to make this trip as successful as possible. Never before in my professional career were all the decisions up to me, and at first, it was slightly uncomfortable. I was worried I would come across as too bossy or even condescending. However, after meeting Eshetu Lemma, the ASCP local representative, along with the other participants and experiencing their kindness and eagerness to learn, I was newly determined to make this trip an absolutely positive experience for everyone. I made some changes to the training sessions and after the first day, the rest of the week ran smoothly. I learned a lot about how lab medicine is practiced in Ethiopia. I learned that, in the case of a power outage, you carefully set your blade down and wait it out. I learned that resources like aprons and sleeves are not thrown away unless completely used up. I learned that due to cassette shortages, tissue submission is done quite thoughtfully- more so than in the United States. I learned that the overwhelming majority of cancer cases are presented at stage 4 due to issues surrounding resources, fear, myths, and lack of cancer education. But most importantly, I learned that the labs in Addis Ababa, Ethiopia, are doing an amazing job with the resources they are given and are eager for opportunities to positively impact patient care.
L: Is what you learned there applicable to your work in the States?
J: I’ll take what I learned there and incorporate it into my work here in the States. I’ve gained confidence in my ability as a health professional and reignited my passion to help others.
To put it simply, this trip has been life
changing. It has allowed me to experience and accomplish a lifelong dream for
which I am forever grateful. I’m hopeful that my future holds more
opportunities to serve other communities and help strengthen cancer programs in
-Jennison Hartong,MLS(ASCP)CM, PA(ASCP)CM is a board certified Pathologists’ Assistant, specializing in surgical and gross pathology working mainly in oncology cases. Before attending graduate school, she worked as a Medical Laboratory Scientist (MLS) at Lurie Children’s Hospital of Chicago, Illinois. Upon graduating, Jennison started working at Memorial Sloan Kettering Cancer Center. In 2018, she relocated to Houston and currently works at M. D. Anderson Cancer Center in Houston, Texas. In May of 2019, Jennison will graduate with a second Master’s in public health with a focus in health policy and management from New York Medical College. She plans to use her extensive lab experience and newfound knowledge of public health to help bring basic healthcare to communities that would otherwise not have access to these necessities.
As a part of my
Molecular Genetic Pathology fellowship, we experience a clinical component to
training in addition to all of the laboratory training we receive. This last
month, I rotated through Cancer Genetics, where genetic counselors discuss
genetic testing with patients with a personal or family history of cancer. The
counselors describe the process of genetic testing and help chose genetic tests
to look at the patient’s risk for an inherited cancer syndrome.
looking forward to the certainty that will come from a genetic test, because it
is the wave of the future and they think you can learn so many things from your
genetics. The truth, however, can be much less clear. Up to 30% of people receive
a Variant of Uncertain Significance (VUS) as their genetic test result. This
rate increases as larger panels are test more genes.
represents a variation in a person’s gene that doesn’t have enough information
to say that it is benign or pathogenic. This gray zone is very uncomfortable
and confusing for patients and providers alike. There are several cases where
someone acted on a VUS as if it were a pathogenic variant and ended up having
radical interventions like a bilateral mastectomy.
We know that as
scientific and medical knowledge increases, our ability to reclassify these
variants improves. For laboratories, this means periodic reanalysis of previously
reported variants. If this process is not properly set up, it can be very
laborious and extensive. Furthermore, not only was a timeline for variant
reanalysis unknown, but also the likelihood of variants becoming upgraded or
downgraded had not been described.
studies helped provide some answers to these questions. The first, published in
JAMA, comes from the cancer genetic group I was working with, led by Dr. Theo
Ross M.D. Ph.D., worked in conjunction with Myraid (Lab that first started
testing the BRCA genes, and now tests many more) to determine how often
variants were reclassified. Looking at 1.1 million individuals tested at
Myriad, the average time to reclassification for a VUS was 1.2-1.9 years (Mersch
J et al Jama 2018). Additionally, 90% of VUS were downgraded to benign/ likely
benign representing 97% of patients with a VUS. This figure from the paper
shows how the time to issuing a reclassification (amended report) has decreased
I worked on the
second study, which looked at variant reclassification in childhood epilepsy
genetic testing (SoRelle et al JAMA Peds 2019). The results, published in JAMA
Pediatrics, also found most patients had a VUS reclassified to benign/likely
benign. However, several clinically significant changes (reclassified to or
from pathogenic/ likely pathogenic) occurred as well (Figure 3).
there was a linear relationship between the time the test was reported and the
rate of variant reclassification (Figure 4). We found that 25% of patients with
a VUS would experience a reclassification within 2 years.
conclusions of the two studies are somewhat similar:
patients with a VUS experience a downgrade reclassification to likely benign or
reclassification should be performed at least every 2 years
of reclassification may differ by disease type. Investigation by a similar
study design should be performed in other genetic diseases.
JA, Thodeson DM, Arnold S, Gotway G, Park JY. Clinical Utility of
Reinterpreting Previously Reported Genomic Epilepsy Test Results for Pediatric
Patients. JAMA Pediatr. 2018 Nov 5:e182302.
-Jeff SoRelle, MD is a Molecular Genetic Pathology fellow at the
University of Texas Southwestern Medical Center in Dallas, TX. His
clinical research interests include understanding how the lab intersects
with transgender healthcare and advancing quality in molecular
Ah, the blue chip – not much fun to see after spending a day
preparing the libraries and running clonal amp overnight. There are a couple possible explanations for
a blue chip, and you can figure them out by looking at the metrics of the
The test fragments serve as a
control for the sequencing run. They are
spiked into the mixture of library ISPs before they are loaded on the
chip. These will allow you to figure out
where the problem occurred if you encounter a blue chip. If the Test Fragments are detected and are of
sufficient quality, then this means the sequencing run worked and the problem
most likely occurred before sequencing, during library prep or clonal
amplification. If the Test Fragments are
not detected, then it could mean one of two things – one – the clonal
amplification did not work for either the library or the Test Fragment ISPs, or
– two – the sequencing run was somehow at fault. Let’s take a look at both examples.
Troubleshooting a Blue Chip
In the event you see a blue chip,
first, check to see what kinds of ISPs showed up after the analysis. For the chip pictured above, there were ISPs
that had product on them, as you can see in the Live category (6,475,553 ISPs
or 95.3% of the ISPs, shown in the screenshot below). This means clonal amp was successful for a
small number of the library ISPs. Next,
there were also Test Fragments detected, at 433,392 ISPs or 6.7% of the total
ISPs. Scroll down to the bottom of the
page, and you will see how the Test Fragments sequenced. We like to see the Percent 50AQ17 and Percent
100AQ17 at least in the 80’s, but even still, you can see that these were
detected and were sequenced. Because of
this, the sequencing run looks to be fine, so most likely the problem occurred
before sequencing. In this case, we
believe the library prep did not yield the expected 100pM concentration, so the
library pool was over-diluted prior to clonal amplification. The library prep was repeated, and clonal
amplification was run on the new pool of libraries, and the sequencing was
In this next example, we have the
other possibility. This chip was blue as
well (this is a 520 chip, instead of a 530, to explain the different sized
First, there are only 2.7% Live
ISPs, so even lower than the chip above.
But the even stranger thing was that there were 0.0% Test Fragments, and
at the end of the analysis, there were absolutely no ISPs left to be analyzed,
library or Test Fragment. This was the
only time we had ever seen a chip like this; generally, if we had blue chips,
they were like the previous example. We
looked at our library pool quant and it was in the expected range, so we did
not believe it was a library prep issue.
The sequencing initialization was successful and did not have any
errors, so we did not believe it was a sequencing problem. We repeated clonal amplification with the
same library pool and had successful sequencing. In speaking with our Field Application
Scientist, it was decided it must have been a failure of one of the reagents of
the clonal amplification – either a Taq was not present or something, so the
clonal amplification never occurred, or something similar.
Hopefully you will not experience
too many of these blue chips, but if you do, I hope you are a little more
prepared to troubleshoot! Happy
-Sharleen Rapp, BS, MB (ASCP)CM is a Molecular Diagnostics Coordinator in the Molecular Diagnostics Laboratory at Nebraska Medicine.
Maryam Zenali1*, Dmitriy Akselrod2, Eric Ganguly3, Eswar Tipirneni4 and Christopher J. Anker5*
Pathology, 2 Department of Radiology, 3 Division of
Gastroenterology, and 5 Division of Radiation Oncology, The
University of Vermont Medical Center (UVMMC), Burlington, VT and 4
Department of Hematology Oncology, Central Vermont Medical Center (CVMC), The
University Of Vermont Health Network, Adult Primary Care, Berlin, VT
A 57 year old woman with a personal and family history of breast cancer presented with early satiety and dysphagia for 5 months. Her abdominal computed tomography (CT) scan (Image 1 A) showed marked thickening of an apparently featureless gastric wall (A, blue arrows indicating the mucosal [rightward pointing] and serosal [leftward pointing] aspects of the gastric wall). Prominent gastrohepatic lymph nodes were noted as well. Her fluoroscopic upper GI study (Image1 B), following administration of barium and effervescent crystals (a double contrast effect to allow for mucosal evaluation), showed thickened rugal folds (B red arrow) and pooling of barium within an antral ulcer (B blue arrow). A subsequent CT scan (Image 1 C) after administration of intravenous and enteric contrast, confirmed marked diffuse gastric wall thickening (C blue arrows again indicating the mucosal [rightward pointing] and serosal [leftward pointing] aspects of the gastric wall) (Image 1, composite radiographs A-C).
The gastric body distended poorly with insufflation and demonstrated thickened, erythematous, edematous folds with erosions (Image 2, endoscopy image). On endoscopic ultrasound, the total thickness of the stomach was 12 mm with expanded wall layers in the proximal stomach to the antrum and a thickness of 3.5 mm in spared areas. Biopsies were obtained; the corresponding H&E and keratin stains are provided (Image 3, composite photomicrographs A-B).
Based on the original radiographic imaging that led to the biopsy, what are the differential diagnoses?
A 19 year old woman with no significant past medical history
presented to an outside clinic with psychological distress after passing a worm
per rectum. She had no other complaints or symptoms.
Adult cestodes (tapeworms) have long, ribbon-like bodies
made up of proglottids (egg-producing segments) that develop at the posterior
of a scolex (specialized structure for attachment to the small intestine of a
host). Taenia has 32 species, 2 of
which are medically important for causing taeniasis: Taenia saginata and Taenia
solium (beef and pork tapeworm infection, respectively). These parasites
are distributed worldwide, with T.
saginata being more common than T. solium.
The lifecycle of Taenia
involves adult, egg, and larval stages. Adults release gravid proglottids and
eggs that are passed in feces. The eggs reach pasture land via soil or water
and are ingested by an intermediate host. For T. saginata, the intermediate host is a herbivore (cow), as eggs of
T. saginata do not infect humans, and
for T. solium, the intermediate host
is a pig, human, or other animal. Ingested eggs hatch and release the hexacanth
oncosphere (6-hooked embryo) that can penetrate tissues. Over 2 to 3 months,
infective cysticerci (0.5 to 2.0 mm in diameter larvae) develop in muscles. Of
note, only T. solium can cause
cysticercosis (extra-intestinal larval forms within human tissues, ie. the
human becomes the intermediate host) and this can be life-threatening if
cysticerci invade the brain. When humans consume raw or undercooked beef/pork
meat that is infected, cysticerci will attach to the small intestinal mucosa
and, over 3 to 5 months, mature into the adult form. The adult T. saginata can reach 4 to 12 meters in
length and the adult T. solium can
reach 1.5 to 8 meters in length. Adult tapeworms can live within intestines for
over 25 years while gravid proglottids and eggs are passed in stool.
Infections are usually asymptomatic or cause mild
indigestion, anorexia, and abdominal discomfort. The eggs can be identified by
ova and parasite examination (Figure 1) or a cellulose tape preparation of
perianal skin. The oncosphere must be visualized to avoid misidentifying a
pollen grain. However, eggs of Taenia
species and Echinococcus species are
indistinguishable. Diagnosis is also made by recovering gravid proglottids from
the anal opening or passed in feces (Figures 2 and 3). Distinguishing the two
species can be done by examining gravid proglottids for the number of lateral
uterine branches present on one side of a central uterine stem. T. saginata have 15 to 30 lateral
uterine branches while T. solium have
7 to 13 branches. Both species have a small anterior scolex (measuring 1 to 2
mm in diameter for T. saginata and 1
mm in diameter for T. solium) with 4
suckers. Definitive identification is possible since T. solium’s scolex has a rostellum (crown) with 2 rows of hooks
whereas T. saginata’s scolex bears no
rostellum or hooks. Treatment is a single dose of praziquantel and successful
treatment is defined as passing zero proglottids over 4 consecutive months.
-Adina Bodolan, MD is a 3rd year anatomic and clinical pathology resident at the University of Vermont Medical Center.
-Christi Wojewoda, MD, is the Director of Clinical Microbiology
at the University of Vermont Medical Center and an Associate Professor
at the University of Vermont.