The Stat Lab

One of our biggest clients is the local psychiatric hospital...

Sun, 05 May 2013 18:49:30 -0600

One of our biggest clients is the local psychiatric hospital because a good chunk of the facility is rehabilitation and addiction management. Lately, there’s been a population of patients who were coming up positive on the amphetamine drug screen but we have never been able to find anything that could explain it in the confirmations. This is not the most bizarre thing because amphetamines are very volatile so if you have a tiny concentration in the urine, you might lose it in the extraction (which contains dry down steps).

However! One day we got a box full of homemade cigarettes from the hospital which were taken from an “entrepreneur” who was selling them to patients and we were asked to do extractions on them to see if maybe we could find this mystery amphetamine or cross-reactant. (Unrelatedly, I thought the surgeon general’s warning sticker is a really charming touch)

We tried a number of extraction methods but never did find the amphet. In fact what surprised me was the fact that, compared to commercial cigarettes, these were actually really clean!

So I have an interesting case of environmental toxicology. One...

Mon, 25 Feb 2013 18:12:00 -0700

So I have an interesting case of environmental toxicology.

One of the local hospital’s neonatal ICUs has been suffering from an outbreak of bloody diarrhea. Obviously the first thing they suspected was some sort of infection, so they recruited an epidemiologist to puzzle it out, but they quickly ruled out both bacterial and viral infections.

We got a bunch of water samples from them for trace elements analysis and it came back negative. But we also got some baby bottles from them and they had really high zinc levels, so they suspected something is leaching from the bottles.

We then got a bunch of urine samples from the babies and indeed the zinc levels are through the roof.

We asked the clinical toxicologist if this could be related and indeed, high zinc levels can be a cause of bloody diarrhea. Imagine that.

When samples come into our lab and there is any possibility that...

Tue, 29 Jan 2013 20:52:03 -0700

When samples come into our lab and there is any possibility that they can turn into medical-legal issues (eg, impaired at work, related to a crime, but usually drug facilitated assault), we will not run them. In the case of assault, our toxicologist will phone the ordering doctor to tell them the sample has been sequestered and the patient must lodge a complaint with the police so that they can seize the sample and test it in a lab that allows the result to stand up as evidence in court. That is a matter of protecting the victim.

Once upon a time, we were naive and even though the requisition requested rohypnol (flunitrazepam) and the appropriate red flags went up, the GP lied to us and told us that it was clinical, not medical legal, and he was concerned it was contributing to her tremors so we should definitely do the test.

It is a benzodiazepine and our mass spec method is not really good at detecting benzos. Flunitrazepam is also a very low dose drug so our chances of finding it were spotty at best. So we ran it on the gas chromatograph which is no where near as specific as a GSMS but had a method developed for other benzodiazepines. To make things even more sketchy, we don’t and never really had a fully developed method for date rape drugs and the test was tailor made for this one time use by our lab scientists. Our big mistake was performing the test and sending out the report with “Flunitrazepam suspected.”

Several days later, the lab was getting calls from the woman’s lawyers. As it turns out, her husband was drugging her and taking advantage of her, but our results cannot be used outside of a clinical setting, especially not a result like that one. The police ended up seizing the sample anyways. The consequence was that we had used up a good portion of the sample and it took the forensics lab months and months to work out a method that could run the small quantity.

Good news is he was tried and convicted in the end. And also that we learned our lesson.

Hi! I'm taking medical science and was wondering if you know if there's a book out there with practice CSMLS questions? Thanks :)

Tue, 15 Jan 2013 21:33:30 -0700

Hello!

I don’t think there is a book (that I know of), but our instructors kept old copies of the exams for us to practice from, so you can try asking them? I guess my only tip is that when you register for the exam, you also get an MLT competencies list. That is the list of competencies that they have chosen to build the exam out of and you should definitely focus on those.

Also, don’t get too nervous! It is very, very entry level. So entry level that even basic mycology is considered too advanced to be on it. I literally started studying the night before* and did just fine. It is more of a test of endurance than knowledge for sure.

Sorry for the roundabout answer. Goodluck on your CSMLS exam!

*This will be tough if you have a lot of notes. I happen to have kept very condensed notes and my entire program basically fit onto 20 sheets of printer paper.

I feel as though I have reached a new level of gross in the...

Sun, 30 Dec 2012 17:48:23 -0700

I feel as though I have reached a new level of gross in the specimens we receive. Nothing quite as horrifying as kidney worms though. The other day as I was walking past the extraction bench for the GC mass spec, I noticed a very distinct alcohol odor. When I looked over, there was a sample cup full of greenish chunky vomit.

Someone had requested an alcohol level on puke.

Alcohol levels are actually done on the GC headspace, not the GCMS. Instead of sampling the extract, the instrument makes use of the volatility of alcohol and samples the space above the sample. The result is a much cleaner and easy to interpret chromatogram. That being said, they don’t have a method in place for extracting vomit (That is more the Medical Examiner’s Office’s domain) and we had to reject the request.

Our GCMS doesn’t do levels and is a qualitative method. Reason being is that 99.9% of our samples are urine (sometimes serum/plasma and syringe contents) and knowing how much of a drug is in the urine literally tells you nothing. It won’t tell you how much the person took, nor when they took it, not if they are a regular user or not, not even if it has any relevance to their clinical presentation (if overdose is suspected).

Something all toxicology labs have but don’t advertise is...

Thu, 15 Nov 2012 21:07:21 -0700

Something all toxicology labs have but don’t advertise is their stock of drug standards that they use for building drug libraries on our instrument, reagent preparation, and controls. Getting even a single ampoule (1mg/mL) involves lots of hoops since the bigwigs need to feel comfortable with people having a freezer full of ultra pure, ultra concentrated (street)drugs.

So, after 8 months of hard lobbying and everyone signing their life away, we finally got approved by the federal government and got our hands on drug standards for desomorphine, better known on the internet for its hype in Russia under the name Krokodil.

You may also be interested to know that its ion profile on the mass spec is shockingly similar to dextromethorphan, the cough syrup.

When we send results, the laboratory information system...

Sat, 18 Aug 2012 23:41:23 -0600

When we send results, the laboratory information system sometimes automatically appends reporting comments to help physicians interpret the results.

Recently, a new comment has attached itself onto Benzodiazepine results on the drug screen saying that Oxaprozin (AKA DayPro) can produce false positive results for up to 10 days. This is strange because the benzo screen was supposed to be pristine but apparently this new fangled drug will cross react in the assay.

How that comment came to be was interesting.

Our esteemed toxicologist (who often donates his body to such pursuits), took four days worth of this prescription medication at maximum dose and collected his own urine to throw on the cobas analyzer and, lo and behold, was positive for benzodiazepines for 10 days.

And thus a reporting comment was born.

Lately I have been working on transitioning to a new position in...

Fri, 03 Aug 2012 18:59:58 -0600

Lately I have been working on transitioning to a new position in Toxicology, which is less of a toxicology department now that it has basically adopted all the labour intensive expensive tests for the lab, almost all of which are some form of chromatography with long, painful manual extraction processes.

On my first day I was greeted with a request for a cannabinoid confirmation on a newborn (literally newborn).

It came back strongly positive and we reckon mom decided to smoke some marijuana to help with her pregnancy. I hope it was worth it to her knowing that her baby is quite possibly going to have neurodevelopmental problems.

Unfortunately, this kind of experience will be par for the course in the new position, as we will get a lot of addicts (to harder drugs) who give birth to poisoned babies.

Now that I work in a private lab and not a hospital lab, poor...

Wed, 13 Jun 2012 17:49:00 -0600

Now that I work in a private lab and not a hospital lab, poor collections are less of an issue for a number of factors. While non-lab-staff (who sometimes do collections in certain departments/hospitals) think we are just being huge jerks when we tell them they did it wrong, there are actually very real consequences for a poor collection.

An example is a nice elderly lady who had gone into emergency and the physician suspected she was going into renal failure. Her initial bloodwork gave the following results (reference ranges in brackets):

Creatinine: 40umol/L (50-105umol/L)
Sodium: 148mmol/L (133-146mmol/L
Chloride: 122mmol/L (96-106mmol/L)
Hemoglobin: 97 g/L (120-160g/L)
White blood cells: 4.0x10^9/L (4.0-11.0 x10^9/L)

Based on these results, the creatinine is way too low to fit renal failure. In fact, it is suspect for other metabolic conditions like liver disease. But her sodium and chloride are quite high. Chloride that high can suggest a number of things, including metabolic acidosis. Hemoglobin is low, and it’s around the point where some physicians would want to give a transfusion, depending on the patient status. The patient was admitted and had followup bloodwork 6 hours later:

Crea: 87umol/L
Na: 140mmol/L
Cl: 111mmol/L
Hgb: 122 g/L
WBC: 9.6x10^9/L

That’s… Quite different! The patient never got transfused or anything (and didn’t even really get much treatment, actually) and that is a huge climb in hemoglobin (a full unit of packed cells would only increase her hemoglobin by about 10g/L as it were). The fact that many things have practically doubled would have made the analyzer flag the results as suspect (AKA failed delta). Notice that the sodium and chloride, previously high, have gone down. Overall, her results are actually quite nice.

But we would have to look into the delta flag either way because that is what we do. After retrieving the first sample from the fridge and comparing it to her current sample, you could see right away there was A Problem. No pictures, unfortunately, but the serum was much more dilute, almost clear, on the chemistry tube from her first draw. Not to mention the hematocrit (ratio of blood cells to plasma) was much, much lower on the first collection.

Knowing that isotonic saline has a sodium of 150mmol/L, the individual who did the first collection had probably skipped phlebotomy 101 and decided it was ok to collect right above an IV site, causing her specimen to be diluted down.

Data entry is a huge bottleneck in our facility when it comes to...

Wed, 06 Jun 2012 22:22:30 -0600

Data entry is a huge bottleneck in our facility when it comes to testing. Entering the patient information, reporting location, and testing requested into the laboratory system probably takes the most amount of hands on time in the entire process.

Of course, patient care should come first, not seeing how many requisitions you can enter, and we have always harped on stopping and double checking your entry before moving on. Missing a test or sending results to the wrong location affects quality of care in many ways (there was once a report from anatomical pathology indicating that a patient had cancer that we could not find the correct physician to send the report to for about a week. The result was a delay in their treatment, leaving the patient knee deep in suspense over their results, and breaching their health privacy since the report went to the wrong location the first time.)

Missing tests, however, is a larger concern than reporting, and you’ll understand if you’ve ever seen some of the requisitions physicians make for us. This one time, microbiology missed a request for an extra plate for a gonococcal culture from a patient’s throat swab. It was noticed too late for the swab to be replanted and she needed a recollect. The unfortunate part is she was a sexual assault patient and it was a terrible thing to put her through more.

A mixed blessing was that the physician had the sense to start her on antibiotics after the first swab was taken, but that meant that on the recollect, the bug would not grow either way and in the end, we never knew the result on that patient.

I just got back from LabCon 2012! What a blast that was. Lots of...

Tue, 05 Jun 2012 19:32:00 -0600

I just got back from LabCon 2012! What a blast that was. Lots of stories and presentations from laboratory professionals across the country and many insights. Not just bench technologists of course; many pathologists, lab managers, internationally trained technologists, quality specialists, lab vendors, lab assistants, you name it! If you ever get a chance to go, I highly recommend it. I got to play with some incredible new technology that toes the line of frighteningly high tech (I’m looking at you, Beckman-Coulter). They also feed you (a lot; at one point there was an ice cream float bar!!), and as a former university student, how can I deny free food?

But as for the blog, for the next little bit, I am going to do a series on preanalytics (one from each discipline) and why they are so important in patient care. After all, you may be the best bench tech in the world, but if the specimen you got was no good, your results will be no good. And a very large majority of laboratory errors are the result of a preanalytic error, sadly.

So anyways, this is just a post saying that I am… Finally returning to tumblr (for real this time). Thank you, followers, for sticking around!

Today, I gained a new horror story to add to my belt of weird...

Sat, 14 Apr 2012 22:37:56 -0600

Today, I gained a new horror story to add to my belt of weird clinical oddities. I received a tube full of kidney stones, probably post lithotripsy since it was pretty ground up. This is not weird at all since we get about 3-4 stones a day for composition analysis.

However, when I looked at the requisition, it said on there, “?worms in kidney”. I had no idea what that meant since I didn’t know worms could be in kidneys, but when I shook the tube and examined more closely, I saw a bunch of tiny bugs that looked like half a centimeter long millipedes crawling around. Perfectly alive.

I think felt some sympathy kidney pains.

Long time no see, Tumblr! I have been busy with personal things...

Mon, 09 Apr 2012 10:56:51 -0600

Long time no see, Tumblr! I have been busy with personal things and I apologize.

The first of our month of Instrument Shenanigans, the Tigris, our gen-probe analyzer, is a qualitative nucleic acid test based on transcription-mediated amplification which we use for gonorrhea and chlamydia testing in chemistry. At some point in our run, the instrument got contaminated and about 40 patients all tested positive for chlamydia in a batch run. Chlamydia is pictured above in the vacuoles of a cell off a pap smear (we were actually running urines).

Luckily, the tech on the bench was astute enough to notice this before results were filed, so it was all resolved in the end.

Lab test: CBC histograms

Sun, 04 Mar 2012 19:55:57 -0700

Anonymous asked: hematology histograms (how to read them/compare with a peripheral blood smear), por favor?

Sure thing! A lot of people just glance at them since the numbers are what really drive the testing process (when to do a manual differential, when to look at the history, etc), but the histograms are pretty helpful in anticipating what to expect in a smear.

Background:

Complete blood counts are ordered on nearly every routine blood draw, so there is basically no escaping hematology. I won’t go into the technology of the coulter analyzer, since that is a whole post in itself for another day.

Three histograms generated in a CBC: the RBC, WBC, and platelets. Not only the histograms supply us with information about RBC’s, WBC’s, and platelets frequency, their distribution, and average sizes, but also depict the presence of cell subpopulations. They are important for helping the operator visualize numeric results, verify abnormal patterns, and help pick out interferent particles.

First, the cell size is determined (this actually happens at the same time as the count through impedence), and a graph is made to show the frequency of cells of each size. The X-axis is the fL size thresholds, and the Y axis is the relative number of cells in each size range. A mean raw data curve is drawn on top of this to smooth it out a bit. The mean cell volume is derived from this histogram as well.

Red Blood Cells

That’s our nice normal red cell histogram, which counts everything from 36fL to 360fL in size. The coincidence demarcated in that graphic is when more than one cell passes through the aperture at a time but is counted as one. But since there is a direct relationship between cell concentration and effective aperture volume, this is easily corrected by instrument in its report. A normal RBC histogram has the following features:

One main population
The curve begins at the baseline 36fL, goes up, and comes all the way down to baseline at around 200-250fL
The peak is fairly narrow
A small population typically occurs to the right of the main population.

It’s actually really hard to find pictures of these things on the net, so you’ll have to forgive me for not having good visuals….

But the histogram is probably the most handy when you have a dimorphic population such as this:

Where the mean cell volume will look deceptively normal (your normal-large and very small cells will average out), but your histogram will become bimodal (two peaks). Bimodal curves may be seen in cold agglutinin disease (many red cells will agglutinate and the instrument will think it is one really big rbc), in iron deficiency anemia (microcytic) with recent blood transfusion, in sideroblastic anemia especially in the acquired forms, and in megaloblastic anemia (macrocytic anemia) with recent blood transfusion.

Shifts in the histogram will be observed in microcytic anemia (left shift) or macrocytic anemias (right shift). Depending on the cause, the width of the peak (red cell distribution width) will likely also increase. This means there are lots of cells in a whole host of different sizes.

When the curve does not start at baseline, suspect extremely small cells and cell fragments, giant platelets, white cell fragments, etc. When it does not come back down to baseline, suspect either agglutination. In some cases when the patient has leukemia and a very high white cell count, some of these will be counted as RBCs and you will also see an extended right peak.

White Blood Cell histograms:

A typical WBC histogram has the following points:

the counting threshold begins at 35 fL
the curve should be at or very close to baseline at this threshold
There should be nothing below the 35fL cut off point

This histogram has something called a high takeoff. Note that it doesn’t start at baseline and it looks like there are interfering particles at that size range. These can be nucleated red blood cells, clumped/aggregated platelets, red cells inclusion bodies, unlysed mature red blood cells (premature infants and in patients with higher osmotic resistance), intracellular parasite, or other less common interferents, so a blood film is made and a manual smear review is done.

As the normal histogram has valleys between the regions, the instrument will flag results where the valleys do not dip as low as they should. A peal in the region between the lymphocytes and mononuclear cells are typically blast cells, plasma cells, or increased eosinophils and basophils.

A peak between mononuclear cells and the granulocytes includes immature granulocytes, blasts, and eosinophils. A large peak or failure to come back down to baseline on the far right side of the curve usually indicates a high absolute granulocytic count and/or presence of toxic granulation, both of which can be observed in infection or burns.

Don’t forget that multple flags can exist on the same patient.

Platelet histograms:

A normal histogram (in black) has the following features:

The curve exists between 2-20fL.
A best fit line drawn overtop the data curve fits between 0-70fL
Both curves are parallel and start and stop at baseline.

The lower region between 0 to 2 fl can be expanded by air bubbles, dust, electrical and electronic noises, whereas the upper region (over 20 fl) can be made larger by microcytic red cells, red blood cell fragments (schistocytes), WBC fragments, giant platelets, clumped platelets, and platelets satellitism.

Because the histogram area is so small, the most the instrument tends to do with it is set an R flag and ask you to review it. It is pretty good at picking out giant platelets and will put a comment on the print out though. A lot of the smears we do are for platelet review only.

Mean platelet volume/platelet distribution width is actually a little more helpful than the histograms themselves. Large platelets(>10fL) suggests immature platelets, which can be normal, but can also be associated with sickle cell, following splenectomy, and Idiopathic thrombocytopenic purpura. Small (<7fL) platelets can be caused by several anemias (aplastic, megaloblastic, hemoglobinopathies). These conditions are also associated with an increase in distribution width.

Happy National Med Lab Week! I have some material lined up for...

Thu, 01 Mar 2012 21:40:29 -0700

Happy National Med Lab Week!

I have some material lined up for the week, but drop me a message with what you would like to see and I will see what I can do for you.

The video is of phagocytosis of Shigella sp bacteria. I had a...

Sun, 19 Feb 2012 13:17:21 -0700

The video is of phagocytosis of Shigella sp bacteria.

I had a coworker who was serotyping someone’s positive stool. They ended up getting it on their hand and didn’t wash well enough. Shigella has a very low infectious dose (about 10-200 bacteria) and serotyping uses incredibly concentrated suspensions. So… she got shigellosis and basically spent the week on the toilet with diarrhea while holding a bucket for her vomit.

Cysts of Pneumocystis jiroveci (formerly carinii) in...

Sun, 29 Jan 2012 15:18:53 -0700

Cysts of Pneumocystis jiroveci (formerly carinii) in bronchoalveolar lavage, Grocott’s methenamine silver stain.

In this induced argentaffin reaction, chromic acid oxidation forms aldehydes from fungal cell wall polysaccharide components. The reaction is similar to the Periodic acid Schiff reaction, but since the chromic acid is a much stronger oxidizer, background staining by collagen and basement membrane is suppressed (they are oxidized past the aldehyde stage). The aldehyde groups then react with the silver nitrate, reducing it to a metallic silver, thus blackening the site.

It can be a bit tricky to time since different organisms take up stain at different rates. Pneumocystis can be missed if you understain, but other organisms will come out a black blob (thus making it impossible to see the internal structure) if you overstain.

Anon left asks about this in rapid succession, so I guess that...

Sun, 15 Jan 2012 21:20:00 -0700

Hypersegmentation

Hypolobated small megaloblast

Giant band cells

Erythroid precursors

Anon left asks about this in rapid succession, so I guess that is my cue to talk about megaloblastic anemia, haha.

Megaloblastic anemia is a non-hemolytic anemia, usually attributed to either B12 deficiency (impaired absorption because of a gastrectomy, pernicious anemia, inflammation, or transcobalamin deficiency) or Folate deficiency (dietary, drug related impairment of use, loss though kidney). Both are cofactors in DNA synthesis, especially of thymidine. The result is nuclear cytoplasmic asynchrony wherein the nucleus matures slower than the cytoplasm, and you can see all the cells are a little off looking as a result.

In your smear, you won’t see much in the way of retics, but there will be extensive hypersegmentation of neutrophils, large platelets, huge macrocytes/macroovalocytes, tear cells, schistocytes, pancytopenia, and howell-jolly bodies. A few giant bands and metamyelocytes much sneak into the circulation too. Things are generally just. Big.

The bone marrow will have very distinct megaloblastic changees. The myeloid:erythroid ratio will be decreased but the marrow is almost always hypercellular. Very early erythroid precursors predominate over late precursors because of ineffective erythropoiesis. In contrast to the comically large myeloid precursors, megakaryocytes are small and hypolobated because they have so much DNA they are affected the most by impaired synthesis.

Hi, I'm a first year medlabsci student and I'm just curious how you got the job you did? Did you get hired on after clinicals or did you have to apply for lots of jobs? Do you work in Ontario?

Sat, 14 Jan 2012 15:31:05 -0700

Hello!

I did get my job after clinicals (not in ON), but it was kind of a mad scramble because you have to remember there are a ton of other people in your class applying for the same jobs as you. It will, of course, depend on the timing (2 years before me, managers from around the province were practically tripping over themselves trying to give you their business card and begging you to work for them because there was such a huge job vacuum, for instance) and where you want to work. I just applied for about 13 jobs before I got a call back, but it would have been a lot easier if I had also applied for all the temporary positions that were floating around. There’s something in the water or something because there are always pregnant people in the lab and chances are your first job will be covering somebody’s maternity leave.

Just keep in mind that your first job will probably not be the one you stay at, but never scoff at an opportunity because people in the field tend to stay more or less in the field and gathering experience is very important. Also, take the international licensing exams even if you don’t feel like you want to work in the states or wherever because you never know where you will be in five years and it is way easier than studying all over again.

(A hint: The US has a little more leeway in their employment and several positions were made specifically for my classmates who coldcalled them when there were no positions posted)

SEM of fibroblast cells infected by the herpes simplex virus....

Fri, 13 Jan 2012 15:30:00 -0700

SEM of fibroblast cells infected by the herpes simplex virus. Fibroblasts are normally long and star-shaped. The HSV2 infected the cells 24 hours earlier, causing them to shrink and become rounded. HSV2 is a DNA-containing virus that causes genital herpes, an important sexually- transmitted disease.

I have a friend who is a virologist and was doing work with adenovirus at one point. Once, he held up a tube after ultracentrifuging a tube to purify the virus and a drop of it had splashed into his eye (and that is why you wear goggles).

He went down into emergency (after flushing at the eyewash station) and the first thing they asked was, “It’s not Herpes Simplex is it?” because herpes keratitis is the leading cause of adult blindness in North America. He didn’t go blind because it was adeno, but it was a ferocious case of conjunctivitis regardless. Ironically, he now researches HSV.