Microbiology Case Study: A 57 Year Old Man with an Infected Drain Site

Clinical History

The patient is a 57 year old male with a history of traumatic brain injury in 2005 resulting in quadriplegia and subsequent neurogenic bladder with chronic spasms. In 2016 the patient underwent cystoprostatectomy, proctectomy, and ureteroenteric anastomosis to colon. The post-operative period was complicated by the formation of a presacral abscess consisting of MSSA and E. coli. Drain placement failed to resolve the abscess and drain studies showed the formation of a fistula to the patient’s rectal stump. The subsequent 3-year period consisted of repeat drain placements and laparotomy to drain and wash out multiple small collections of fluid seen on imaging. Bacterial cultures during this interval grew mixed gram positive and gram negative enteric bacteria, treated primarily with ertapenem. In January of 2020, the patient underwent exploratory laparotomy with debridement and drainage of pelvic abscess. Tissue cultures from the procedure grew MRSA and vancomycin was prescribed for treatment. Vancomycin was switched to daptomycin for more favorable dosing and ertapenem was added to his treatment plan. Four weeks after his operation, the patient reported pain at his drain site and the fluid in his Jackson-Pratt (JP) drain had turned green. Fluid from the JP drain was submitted for microbiological work-up.

Laboratory Findings

Gram stain of the fluid from the JP drain showed neutrophils, many gram negative bacilli, and beaded gram-positive bacilli. Modified Kinyuon testing was positive for acid-fast bacilli (AFB) and cultures were ordered for mycobacteria as well as Nocardia. The gram negative bacilli was isolated and identified as Pseudomonas aeruginosa by MALDI-ToF. The beaded gram-positive bacilli were isolated on CNA agar and identified by MALDI as Mycobacterium chelonae. Concordant morphology was observed on mycobacterial culture. Nocardia culture was overgrown by P. aeruginosa.

Image 1. Gram stain of specimen taken from the patient’s JP drain.
Image 2. CNA agar plate growing gram positive bacilli.
Image 3. 7H11 plate growing acid fast bacilli.

Discussion

Rapidly growing mycobacteria (RGM) include the three most common clinically relevant species: Mycobacterium abscessus, Mycobacterium fortuitum, and Mycobacterium chelonae.

The RGM are environmental organisms found worldwide that usually grow in subculture within one week (eg, rapidly, as compared with other mycobacteria). M. abscessus is the most commonly encountered species of this group isolated from clinical respiratory specimens, M. fortuitum is the most common from non-respiratory specimens, and M. chelonae primarily impacts immunosuppressed patients and may also cause surgical wound infections.

Postoperative infections with RGM have occurred following various procedures including cosmetic surgery procedures, augmentation mammoplasty, laser in situ keratomileusis (LASIK), and heart surgery.1-8 Infection is characterized by multiple recurrent abscesses around the surgical wound.

Diagnosis for non-pulmonary disease is made by culture of the specific pathogen from drainage material or biopsy of the affected site. The isolation of organisms from sterile, closed sites, such as bone marrow or blood or from a skin biopsy (in the setting of multiple lesions), is diagnostic of the disease. Once an isolate has been identified as a nontuberculous mycobacteria (NTM), the species should be identified. However, identification of RGM in most laboratories is either incomplete or imprecise. M. abscessus isolates are frequently identified simply as “M. chelonae/abscessus complex,” or if they are specifically identified as “M. abscessus,” they are not accurately sub-speciated.

Susceptibility testing should be performed against a number of antibacterial agents, however, there is no established minimum inhibitory concentration (MIC) cutoff for susceptibility or resistance. M. chelonae is typically treated with Macrolide antibiotics, particularly azithromycin and clarithromycin. M. fortuitumM. abscessus, and M. chelonae are resistant to the antituberculosis agents rifampinethambutol, and isoniazid, so susceptibility testing of RGM should not be performed with these.

The clinicians in our case suspected that the M. chelonae culture from the patient’s JP drain was most likely a contaminant as the same organism was never isolated from previous tissue or fluid cultures. He was continued on daptomycin, ertapenem, and ciprofloxacin was added to cover P. aeruginosa. The patient responded well with resolution of his localized symptoms at the site of the JP drain. Unfortunately, he continues to suffer from multiple, recurring presacral abscesses.

References

  1. Rimmer J, Hamilton S, Gault D. Recurrent mycobacterial breast abscesses complicating reconstruction. Br J Plast Surg 2004; 57:676.
  2. John T, Velotta E. Nontuberculous (atypical) mycobacterial keratitis after LASIK: current status and clinical implications. Cornea 2005; 24:245.
  3. Freitas D, Alvarenga L, Sampaio J, et al. An outbreak of Mycobacterium chelonae infection after LASIK. Ophthalmology 2003; 110:276.
  4. Sampaio JL, Junior DN, de Freitas D, et al. An outbreak of keratitis caused by Mycobacterium immunogenum. J Clin Microbiol 2006; 44:3201.
  5. Edens C, Liebich L, Halpin AL, et al. Mycobacterium chelonae Eye Infections Associated with Humidifier Use in an Outpatient LASIK Clinic–Ohio, 2015. MMWR Morb Mortal Wkly Rep 2015; 64:1177.
  6. Toy BR, Frank PJ. Outbreak of Mycobacterium abscessus infection after soft tissue augmentation. Dermatol Surg 2003; 29:971.
  7. Centers for Disease Control and Prevention (CDC). Mycobacterium chelonae infections associated with face lifts–New Jersey, 2002-2003. MMWR Morb Mortal Wkly Rep 2004; 53:192.
  8. Wallace RJ Jr, Brown BA, Onyi GO. Skin, soft tissue, and bone infections due to Mycobacterium chelonae chelonae: importance of prior corticosteroid therapy, frequency of disseminated infections, and resistance to oral antimicrobials other than clarithromycin. J Infect Dis 1992; 166:405.
  9. Wallace RJ Jr, Brown BA, Onyi GO. Susceptibilities of Mycobacterium fortuitum biovar. fortuitum and the two subgroups of Mycobacterium chelonae to imipenem, cefmetazole, cefoxitin, and amoxicillin-clavulanic acid. Antimicrob Agents Chemother 1991; 35:773.

-Will Humphery, MD is a 1st 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.

What Does Patient Advocacy Mean for Pathologists?

As pathologists, patient advocacy and safety have quite unique meanings as compared to our colleagues on the wards and in the clinics. It is such a unique opportunity to affect further care and treatments, depending on how testing is used. I find the combination of patient advocacy within the clinics an opportunity for pathologists to possibly meet patients and learn from our clinical colleagues about how much the lab truly affects patient care. 

At my institution, we have what is designated as “Diagnostic Management Teams” (DMT). At each DMT, our clinical pathology teams perform actions such as writing interpretations for difficult test panels or review the charts to make sure teams have changed their patients to the proper antibiotics. . In our coagulation DMT, we write the interpretations for complex esoteric coagulation studies to ensure: 1. the right tests were ordered, and if they weren’t, we recommend which are appropriate, 2. these complex tests are explained in a way that is understandable to our clinical colleagues and 3. proper patient care and safety for tests which are very critical to patients. To add a layer to this complex testing system, we also have the opportunity to attend benign hematology clinic with one of our attendings. I found this experience to be rather eye opening. Pediatrics hematology clinic is an interesting place whose patients are diagnosed with a wide variety of diseases. A vast majority of these pediatric patients have a parent who has been deemed a “bleeder” or a “clotter” at some point in their lives, or the patients themselves have exhibited such conditions. Often, the parents do not have a definitive diagnosis, and so the investigation begins. The hematologist, who also is one of the coagulation DMT attendings, will order panels which fit with clinical history not only on the patient but more often than not on their parents as well. This allows the DMT to analyze the nuances of the complex coagulation system, even down to multimer gels to figure out which type of von Willebrand disease a patient may have. Although these clinic visits may seem superficial, they give families such a comfort to know a classification of their disease, how it can be treated and if it has been passed down to the actual patient, their child.  One such instance, we actually produced a family pedigree with the type of von Willebrand disease within them and then did confirmation testing. Seeing the delivery of information and subsequent relief on the patients’ faces is always a gentle reminder of how much we affect and advocate for our patients in the lab, which starts with the order or a “simple test.”

-Melissa Hogan, MD is Chief Resident  in her fourth year in anatomic and clinical pathology at Vanderbilt University Medical Center and will be starting her Cytopathology fellowship at VUMC in 2020. She is currently Chair-Elect of ASCP Resident Council. She is passionate about patient care and medical education.

COVID-19 and the Rural Laboratory

When I was approached about writing an essay about our rural lab, I was initially stymied. There’s a universality about the work we do; tech work is pretty much the same wherever you go. A differential is a differential in the biggest cities and smallest towns. The thing that makes us unique is that we’re 50 miles from a city with a full-service hospital and many of our patients are elderly and don’t drive, so we try to cobble together as much care as we can give them in a clinic setting.

Our clinical laboratory is a small independent lab in Cairo, IL, midway between Memphis and St. Louis. We are attached to a regional system of rural clinics that provides care for the residents of the poorest counties in Illinois. We are the only high-complexity FQHC lab in the country, and we’re extremely proud of the work we do with our limited financial and geographical resources.

Our part in battling the COVID-19 pandemic feels a little odd compared to the work of hospital labs. We see our job as keeping our patients out of the overburdened hospitals for as long as possible. We screen everyone who presents with a fever for flu and strep. That includes the prisoners from the two local prisons, the nursing home patients in all the small towns scattered around rural southern Illinois, the teachers, daycare and home health workers. The criteria for a C-19 test is still very stringent in Illinois and most of our patients don’t yet meet it. We generally send them home with free samples of over-the-counter palliative meds, instructions about avoiding other people, and what new symptoms they should watch for.

Even so, we’re running low on basic supplies: PPE, swabs, disinfectant, etc. Like everyone else, we’re having trouble finding more. Yesterday I took a couple of hours to open every cabinet and paw through every box, hunting for overlooked supplies. There was a stash of sixty N95 masks in a closet and forty painter’s masks left over from when the lab was built. The box claims the masks “have N95 properties”…whatever that means. Hopefully we won’t have to find out. I distributed the N95 masks to the clinics that were running low and traded a box of disposable lab coats to our local clinic for 3 hazmat suits for our lab staff. I sent a few dozen more nasopharyngeal swabs to the prison with instructions to use them sparingly. We’re currently backordered until mid-April for more.

All the techs I know (locally and all around the country) are pretty fatalistic about this. We expect to be infected. We’re hoping it’ll be later rather than sooner and we’re trying to protect our more medically fragile and/or elderly colleagues. As you probably know, the average age of MTs in this country is about my age…56. A new virus brings attention to the medical lab profession, and that causes a brief uptick in new interest in our field, but we’re chronically understaffed and techs are retiring faster than we can train new ones to replace them.

In the meantime, of course, we continue to test and treat our regular patients. Mostly poor, mostly elderly, for the diabetes, hypertension, cardiovascular diseases and cancers that are the meat and potatoes of rural health. The concession they’ve made to social distancing is that less of them hug me, although a fair number say “If it’s my time, it’s my time” and hug me anyway. Many of our patients don’t drive, and they arrive one by one on the transit vans designed to seat 12 that pick them up from home. I wonder if the van driver disinfects between patients. I wonder if the patients know he ought to. I assume they hug him, too, so it probably doesn’t matter. This coronavirus crisis will eventually wind down, but the ongoing needs of medically underserved rural communities will continue unabated. Our hope is that this pandemic shines a big light on the many challenges of providing quality care to geographically large, sparsely populated rural communities.

-Evelyn Rubinas is a Medical Technologist at Community Health and Emergency Services, Inc. (CHESI) in Cairo, IL. She is a graduate of Southern Illinois University and the University of Arizona and has been a laboratory generalist for over two decades. She lives in Cairo, IL with her wife and a small menagerie of rescue animals.

Testing (Our Patience)

Hi everyone, and welcome back!

I’ll get straight to the point this time: there’s a legitimate crisis happening in our world that is highlighting a multitude of things. Just to name a of few: the complex intersection of state-sponsored healthcare as a human right, the availability of resources to clinical personnel, the logistics and implications of public health measures to the average person, our global connectivity, and lack of damn tests!

And that’s our stop. Please take a minute to locate your exits, as they may be behind you, and get ready to talk about this SUPER CRITICAL aspect of the COVID-19 pandemic. What are clinical tests?

I know, this “viral” topic right now will be shared and spread to a vast array of audiences. So, I’m going to try something new here. The last four years of posts on this blog have been aimed somewhere between laboratory professionals and working clinicians. I open a rare window into our clinical world from time to time, but this pandemic is something affecting everyone. Today, we’ve got a major problem about what’s being said in the media and who understands which parts of it…so, as I discuss some major points below, I will take short pauses to highlight clinically relevant information as well as put things in plain, simple terms for all of us to get up to speed together.

(If you are one of my clinical colleagues, from the bench to the bedside, your notes will be in BLUE. If you are not in the healthcare world, or just want some simple clarification, your notes are going to be GREEN. Let’s run an example so you can see what I mean…)

Image 1. I realize that there are people who ware blue-green colorblind, so if you have a hard time differentiating one from the other in this picture, I’ll keep the clinical/general labels. If you have no issues with these colors, the image above uses green to demonstrate where the coronavirus pandemic currently exists. Colorful humor? Fine, keep reading…

Last month I talked about the background and biology of the SARS-CoV-2 virus as a novel, emerging pathogen and potential pandemic and discussed how we must contextualize these epidemics with proper understanding of data and statistics. Numbers are important and if we’re going to combat a super bug, we’ve got to know what it is, how it acts, where it came from, and what’s happening in the field. A subsequent and fantastic post right after mine by Dr. SoRelle at UTSW, discussed how to validate a COVID-19 test in your laboratory. Basically, he presented a snapshot of the current climate of academic hospital labs now depending on LDTs to respond to the pandemic and discussed where to read more, what limitations testing might have, and how to address things like designing/purchasing primers, cross-reactivity, detection capabilities, and EUAs under the new FDA guidance.

But back to business, this month we’re talking about testing, and if you just google search “COVID-19” in the states, you’re met with a myriad of failure stories…

“As US fumbles COVID-19 testing, WHO warns social distancing not enough” (source)

“Limited access to COVID-19 tests frustrates patients, health professionals” (source)

“What went wrong with coronavirus testing in the US” (source)

“Why coronavirus testing in the US is so delayed” (source)

“America’s shamefully slow coronavirus testing threatens all of us” (source)

Image 2. This novel coronavirus pandemic has caused another pandemic of fake news. Fake cures, misinformation, false panic, mistrust, and a whole mess of non-scientifically accurate claims that have slowed the responses of public health officials in China, Italy, and even here. (Image source: BBC)

I’ll stop torturing you. You’re forced to watch and/or read enough news as it is nowadays (you’re social distancing, right? …right?) I mean, even Norway took a jab and called us “underdeveloped” citing our poorly developed healthcare delivery system—ouch. So, what’s the big problem with testing? What stark revelation exists between all these different news sources and highlights our “laboratory failures” in America? Well, luckily nearly all of these lab-fail stories aren’t aimed at our labs at all, they’re aimed at governmental decisions and red tape traps. But that’s hard to get to in a sea of clickbait. So instead of giving you more rabbit-hole lab talk, let’s talk about two main tenets of this narrative that everyone should be aware of: what laws affect lab tests and what does it mean to create a new lab test? After we clear the air for those two key points, we’ll come back around and tell you what COVID-19 looks like in the medical laboratory.

The Law of the Lab

There are SO MANY regulations and accrediting bodies that govern the way labs operate, deliver results, and function in clinical settings. Let’s name some! Various federal, state, and local laws ensure the highest calibers of safety and accountability for clinical and research laboratories; laws from OHSA, the FDA, recommendations from the CDC and local health departments; regulations for mechanical, noise, chemical, exposure, pathogen/infectious safety, pollution, radiation, blah blah blah! Trust me, there are a ton. What feels ever present to us laboratorians are the accrediting and inspection agencies that grant us authority to continue performing our clinically vital roles. Joint Commission, FDA, and other inspections make sure hospitals are up to snuff. Laws that govern what labs can do what tests fall under CLIA. They help us define high complexity to waived (not complex) testing. There’s a massive difference in a clinical office’s medical assistant obtaining a point of care (POCT) glycated hemoglobin (Hgb A1c) than a medical laboratory scientist conducting a hemoglobin electrophoresis study, and that difference highlights specialized training, laboratory ability, safety and quality requirements.

Image 3. I know we’ve had this debate a few years ago, but your average nurse probably couldn’t help too much with a bone marrow aspirate evaluation or running quality control on the chemistry analyzers before morning run. Just the same, I remember being an MLS and I wouldn’t have been the most confident IV or foley catheter placer…now I have the distinct pleasure of living in both worlds. Yay. Bottom line: the laboratory, and de facto the hospital, COULD NOT FUNCTION without the team of medical laboratory scientists that make its wheels turn! (Image source: labtestsonline.com)

Accreditations and recommendations can come from many professional societies like the CAP, ASCP, AABB, AACC, ASM, ASH, and many subspecialized groups. Laboratorian trigger warning: I’m a certified CAP inspector. No; you don’t have to put away your desktop coffee…for now. But I’ve certainly—along with all of you—been wholly immersed in the endless accreditation and regulation protocols we follow. We know exactly why these regulations exist and we should talk more about them, since they define our role as such a critical one.

Feeling Validated Yet?

Some of you lost a breath when I said CAP inspector. The rest of you may now spit out your coffee and run for the hills because I’m talking about VALIDATIONS. Rotating MLS students sometimes do their capstones or theses on validating a test or instrument, but we do them because that’s just a part of our job! So what goes into validating a test? The short answer: a whole lot. The long answer: a whole lot more! Let’s take PCR testing for example, it’s topical because we’re talking about COVID-19 testing and that’s the prime modality so let’s explore that validation.

Image 4. A LOT goes into validation. Lots of biostatistics. I know there’s labels, but let’s walk through this graph. The red line is the best line, good correlation with minimal errors. The purple/pink like is permanently off the red line, therefore its in constant error. The blue line represents errors associated with too much or too little specimen, maybe too little reagent, or some other ratio issue. The salmon line might be another test, or another method of the same test. What do you think? Is it a better test? A little sharper of a test, maybe more sensitive, should we use less specimen? Maybe just a drop or two—BAM you’ve been sued for running a sham lab test company. Trade in that black turtleneck, do not pass go, do not collect $200. A newly validated test, or a validation of a new method comes with BINDERS full of runs and analyses, not for the faint of heart. (Image source: AACC)

So, you want to add a qPCR to your lab’s test menu, eh? You first have to decide quantitative or qualitative. If its quantitative you’re in for a treat—yay statistical variant analysis! You have to prove applicability, practical application, specificity, sensitivity, efficiency, correlatable translation into useful clinical data. Detecting a number or degree of mutations? Make sure its accurate and precise (and repeatable). Buying commercial kits or making your own in-house assay? What about a qualitative test, just a simple yes or no. Easier right? Not really, you need to prove most of the same data and statistical soundness depending on methodology used, instrumentation, nature of variation, etc. AND: it all must be documented, proven, up to regulatory standards, and you better have a database FULL of data that proves your test works. Now, I have good news and bad news.

The good news: this is pretty routine, and pretty easy to follow even for simple new tests your incorporating from commercial vendors with ready-to-validate test kits. The bad news: COVID-19 is not this type of test. Say what you will about the US’s decision to NOT utilize the WHO testing model available weeks ago, the CDC responded in kind here by providing a two-control kit that SLOWLY started to break out. Using this as a model, many labs in academic hospital pulled the trigger on their LDT work. (LDT = laboratory developed tests) I’ve already revealed myself as a CAP inspector (pshh, not even my final form!) and I can tell you that there are hundreds of citations for how to validate already existing tests, compare tests across different instruments, compare them across the same instrument, prove your statistical ability to ensure quality results, and even how to make your own test from scratch! Talk about extra work!




Image 5. [MLS]: You’re a good analyzer, a smart analyzer. We all appreciate your efforts and you’ve really contributed to a positive work environment. We appreciate you, so we got you these reagents. They’re nice and fresh, what do you think? [Instrument]: *BEEP* *BEEP* *ERROR* *MORE VALIDATION REQUIRED*, [MLS]: okay, okay, have you lost weight?…**RESULTS VERIFIED** (Image source)

Running COVID-19 testing alongside B. burgdorferi: Corona…with Lyme?

Now we’ve come to the heart of the current discussion. Dr. SoRelle talked about validating a COVID-19 assay last month, so I’m letting him take point on that—read his piece, its great! What we’re talking about today is what exactly regulations and validations have to do with COVID-19 testing. Remember the regulations that say how laboratories run tests and operate clinically? Okay, well there are issues with this narrative. You’ll see plenty of news stories about the regulatory red tape that has hindered lab professionals from providing COVID testing. This makes it sound like because of “rules” we just can’t give them out to everyone, or we can’t set up testing for whatever regulatory reason. This is not the case. This is how the relationship between those aforementioned regulatory bodies work. The FDA makes sure labs operate up to federal standards and, and specifically, enforce regulations outlined in CLIA. While the FDA would like to call tests/results products of analyzers/devices to fall in their prevue, the interpretation and translation of that clinical data is not a print out but a MEDICAL SPECIALTY—hi, I’m pathologist #2465827, part of the FDA regional lab result response team—nope. Lab developed tests (LDTs) are not FDA products, but CLIA certified processes that only CLIA certified laboratories can perform. No CLIA no LDT—it’s as simple as that. You now understand that a lot goes into a single test, and that not every lab can perform high-complexity testing, thus, not every lab is CLIA certified to do LDTs… which means no COVID testing for them.

Image 6. It’s not that there aren’t enough tests. Like we ran out or something. This very fast global pandemic happened and pulled the rug out from under us. Because of a number of challenges, we’ve just been behind developing a NEW test for a NEW bug. And we’re catching up quick, but like ASCP addressed their concerns to the White House, we are in need of resources and support. Vendors can’t just jump in and help because THEIR hands are tied by the FDA even if they have readily available test kits. Other countries have done better than us, and we can still do better. (data as of 3/14/2020, source: AEI)

Okay, the other half of the narrative says that because of a lack of supplies from industry vendors, commercial kits were unavailable either from them or the CDC and if they got them, their reagents were not good. Frustrated, scorned immunology/chemistry lab specialists decide, “we’ll show them…we’ll make our own test! *evil laugh*” A bit dramatic, because it is dramatic. That’s not how LDTs work. How, then, do we get to LDTs? That answer is simple: regardless of politics, resources, or any other social concerns, medical laboratorians and clinical pathologists are part of the essential healthcare team that strives to care for the sick and hopes to prevent unnecessary infection or illness. We’re in this together and if one system can’t provide tests for the whole country, hundreds of thousands of hospitals will rise to the occasion and share partial LDTs or create their own. Just like with any other test, labs know full well how to get this done and work together to do it.

But what about the stories that say some tests take 8 hours vs others that take 4 days to turn around results? How come some kits came with 2 swabs, and some with 3? Why did other countries like South Korea do a lot better than us in testing their population? Did we wait too long to set up LDTs? Can’t I just go to my doctor and get tested now? Okay, okay, I hear you. This is where it gets heavy, especially in the media. The takeaway can be a simple comparison: look back to the Zika epidemic. Zika is an Arbovirus/Flavivirus that we knew about for roughly 60 years. As such, we had time to understand it and create tests quickly that measured exposed patients’ antibody response to acute or resolved infections. Even simpler, Zika is part of a family of mosquito-borne illnesses that we generally understand pretty well. SARS-CoV-2 is not like Zika. The word “novel” is used because it’s just that: brand spankin’ new. And, even though it’s a cousin of its predecessor in the old SARS epidemic, we’ve been racing the clock to create accurate and reliable testing. That’s why there’s so much variability happening across commercial industry to academic hospital laboratories.

Image 7. We’ve got a lot of work to do. At a rough estimate there are roughly 6000 cases of confirmed COVID-19 in the US, and we’re only testing that much…we can’t even collect this data fast enough. This is was scares most healthcare people, myself included. (Source: Medscape)

Pandemic Proportions

I love to make puns but let me be clear: this is a serious global pandemic, as defined by the CDC and WHO and we must understand this fully and appropriately. We’re still in the dark about a lot of data, mostly because of missing numbers. What we do know continues to inform our daily-changing climate of public health awareness in the US. The following images speak for themselves and I’ve collected them as a resource and snapshot for you to look through, just to get your SARS-CoV-2 bearings.

Image 8. If you haven’t yet locked this into your computer desktop, this dashboard from Johns Hopkins pulls data from various trusted sources (WHO, CDC, ECDC, NHC, and DXY) and local info to create a live, updating dashboard to follow along with the pandemic. (Source)
Image 9. I posted these for my pieces on Zika in Sint Maarten, so let’s not be strangers to the epidemiological week graph. Take note, after the first week of March 2020, things get messy. Read: the great lab test debacle. (Source: CDC)
Image 10. This is an uncomfortable graphic. Outside of China, the worse of the (then labeled) epidemic was Italy. Fast forward, we’re in full global pandemic mode and we’re starting to overtake the Italians a bit with cases detected/reported over time. Living, breathing, coughing data. (Source: @elipariser on Twitter)
Image 11. Could I write a piece about literal lab testing and ignore this gem of a post from @TrustMeImAMedTech ? No, I could not. Very cool, clinical snapshot of an average COVID-19 patient’s labs based on data from a Clinical Chemistry Lab Medicine article from this month.
Image 12. The UCSF ID working group established a diagnostic profile of a suspected COVID-19 infected patient. Anecdotally, I’ve read about cases that present with lymphocytopenia or lymphocytosis, the latter of which may correlate to prognostic factors. (Source: J Babik, UCSF)
Image 13. What? I’m still on Reddit. There’s always good stuff on there. This post by u/RadOncDoc shares intensivist Dr. Nick Mark’s take on acutely infected, critical COVID-19 patients. I’m reading and absorbing… (Source: reddit, r/medicine)
Image 14. You’ve heard of #FlatteningTheCurve, what does this mean? If we do nothing, the daily number of cases increases dramatically. If we take measures to preserve the capacity of the health care delivery system (social distancing) we won’t over tax the ERs and critical care units that might be needed during this pandemic, thus, flattening the curve of daily cases. (Source: Vox)

What can I say? It’s hard to write a conclusion about something that’s changing every day. I’ve been doing my best editing to keep this as up to date as it could possibly be for publication, but there are a million more resources sitting in the queue that I wish I could walk you all through. But I think, at the end of the day, what we need to remember is one simple thing: we’ve been here before and we’ll be here again. Public health epidemics and our responsiveness is one of the more serious aspects of laboratory medicine and pathology, not to mention healthcare at large. I said it last month that we’re lucky that this isn’t an influenza-type virus, because that would look a lot different. There are still some highly serious infectious etiologies out there more lethal than COVID-19, but this pandemic is bringing to light a lot of public health awareness and an opportunity to examine our population’s medical/health literacy, our policy priorities, our strength and resolve, as well as our ability to adapt.

Image 15. If you have a few minutes, please watch this CNN clip from one of my friends, colleagues, and mentors discussing how to be safe and smart during this period of social distancing and compassion-informed protective changes! (Source: CNN, video here)
Image 16. “I’ve never seen anything like this before,” said the pundit, reporter, bystander, and/or concerned citizen. The sad part is, they say it every time we have a public health crisis. The time is now to break the cycle and learn from the past. (@CEKanakisMD, #PathDoodles 2020)

In the coming days, weeks, months you’re going to most likely hear about municipal infrastructures cutting back on things in order to prevent the spread of the virus. Listen to these warnings and heed the advice of the medical community. If you think you’re being a hero by braving the storm, you’re no better than a mosquito that carries malaria with no symptoms itself. Wash your hands, practice appropriate social distancing, continue your daily life with your necessary trips out being mindful of what those of us in healthcare live with on a daily basis. Practice compassion as well, just because we’re social distancing to “flatten the curve” doesn’t mean its time for martial law and cleaning supply hoarding. I know these are serious times, but humor and compassion can be infectious too.

Thank you for reading.

Please remember to follow the most updated, verified, and trusted sources on this starting with the CDC and your local public health organizations.

Wash your hands. Change your clothes. Minimize exposures. Take time to reflect and keep as close to your normal routine as possible while remembering things will get better.

If you have specific questions, comments, or concerns leave them in the comments below. Feel free to contact me anytime, and follow my social media (@CEKanakisMD on Twitter) for more/updated material.

Take care, see you next time!


-Constantine E. Kanakis MD, MSc, MLS (ASCP)CM is a new first year resident physician in the Pathology and Laboratory Medicine Department at Loyola University Medical Center in Chicago with interests in hematopathology, transfusion medicine, bioethics, public health, and graphic medicine. His posts focus on the broader issues important to the practice of clinical laboratory medicine and their applications to global/public health, outreach/education, and advancing medical science. He is actively involved in public health and education, advocating for visibility and advancement of pathology and lab medicine. Watch his TEDx talk entitled “Unrecognizable Medicine” and follow him on Twitter @CEKanakisMD.

Playlist for the Apocalypse and Other Rays of Hope…

While washing my hands in an airport restroom, “Until the End of the World” by U2 (Achtung Baby, 1991, Island Records) was playing over the toilet speakers. As I watched several people incorrectly wash their hands during this current pandemic, the songs lyrics (which I have known by heart since 1991) rang through my brain and struck a new chord with me. There are plenty of doomsday songs that actually make us happy (Prince’s 1999, from 1999, 1982, Warner Bros.; R.E.M.’s “It’s the End of the World as We Know It,” from Document, 1987, I.R.S. Records) despite the dark images in the lyrics. And then here are a whole host of doomsday songs that are dark and brooding (“Man Comes Around” by Johnny Cash, “Waiting for the End of the World” by Elvis Costello, “It’s Not the End of the World but I Can See it from Here” by Lostprophets, and “Preaching the End of the World” by Chris Cornell, etc.). It turns out you can write a doomsday song after a breakup with your partner (“The End of the World” by Skeeter Davis) or in response to nuclear war fears (“Everyday is Like Sunday”by Morrissey).

What struck me in my new feeling of U2’s track was the dichotomy of viewpoint by the two principal voices in the song. The speaking voice is in it for the short game, in it for “me.” The listener in the song is in it for the long game, in it for “we.” Considering both the inspiration for the song personally for Bono as well as the historical character about which the song is based, this might be kind of obvious to most of us. However, in 2020, as we face what can only be described as a venomous divergence of voices, the lyrics force me to think about individuals’ motivations, agendas, messages, points of view, and goals when they speak, text, post, or otherwise communicate their opinions and that such opinions come in two flavors. There are those that are in this for themselves. There is no other valid observation than selfishness, conceit, arrogance, and disrespect for others. There are those that are in this for everyone. There is no other valid observation than collaboration, caring, selflessness, humility, and respect.

Considering that, regardless of your moral compass or who your parents were, most children are theoretically raised to be like the latter but the innate, instinctive traits of our evolution are really the former. Thus, as many great philosophers and thinkers have concluded, the intellectual evolution of the human mind and personality is such that seeing and caring for “the other”, even more than for ourselves, is a mark of high achievement while base, crude attacks on “the other” are marks of devolved, unintelligent individuals. Notice that there is no good and evil in this argument. There is only awareness of self and awareness of others and choosing one over the other. Naturally, the best life is to balance our care for ourselves and our care for others, which, some would argue, is one of the most valuable aspects of organized religion. As I am a non-religious person—despite the fact that the U2 track is one of my favorites—I strive to achieve that balance through a universal moral compass perspective which includes a great deal of importance on the safety, security, health, well-being, and happiness of others.

COVID-19 and its viral cause, SARS-CoV-2, have sent incredible ripples, waves, and tsunamis across every aspect of human life in the last 6 months. Pandemic preparedness and responsiveness is a “we” activity. China very much had a “we” approach to health (among many other sectors) which was evident by their incredible response to SARS originally in 2002. Some would argue that had SARS emerged in any other country, it would have gone pandemic at a much faster rate with horrible consequences; yet, emergence in China meant the virus was facing a huge pre-programmed response. But importantly in the 2002 outbreak, CDC officials from the US were relocated to China and work closely with the Chinese government to plan, implement, and execute daily changes to the management of the outbreak. Relationships being what they are, China did not interact as closely with the US for COVID-19 and, thus, the response was not as successful. In healthcare, as in many areas of human life, we are stronger together, and we will be more successful with transparency and communication than with secrecy and seclusion. The health of humanity should not be a geopolitical issue.

The diagnostic medical team (DMT), composed of pathologists and laboratory professionals, is the backbone of modern healthcare. However, these are also people who have underlying conditions, have elderly parents, have to ride the train to work, etc. Everyday, even when there isn’t a pandemic, members of the DMT place their own personal health and safety on the line to provide patients with rapid, accurate diagnoses and continuous care. Fortunately, laboratorians are well versed in protecting themselves within the laboratory from potential risks; however, in a pandemic situation, they must also protect themselves from external risks, else the laboratory staffing falls below the levels that insure high quality patient care is available.

COVID19 testing by RT-PCR of SARS-Cov-2, for example, is a high complexity laboratory test that is often performed by a select number of laboratorians and not by all laboratory staff. When we hear discussions of laboratory testing for COVID and money for such testing or availability of kits, it must also be noted that the laboratory is the only segment in the system who can take money and tests and turn it into data that saves lives—but only if they have sufficient people to make this happen. Healthcare facility leadership and national leadership must support those teams by providing all necessary resources to meet the needs of patients including the laboratory direct and indirect needs. Expanding the ability of personnel in the laboratory to meet this emergent need through cross-training and potential emergency staffing coverages is essential to successfully navigating this pandemic.

The DMT is always practicing the “we.” But now that the pandemic requires transparency and communication for success, the entire health system must amplify the practice of “we” and advocate with external leaders for every member of the healthcare team, but especially the laboratories. It is no time for “me” in this situation. Hand washing, social distancing, and self-quarantine may seem like things that protect “me” but it is clear that the goal is rooted in protecting “we.” Flattening the curve may prevent the healthcare systems from becoming overburden; however, laboratories are going to be massively overburdened regardless. Asymptomatic, symptomatic with other diseases, and true cases of COVID19 all have to be tested and there isn’t a precedent for the pace the disease is moving. Laboratories are coming online this week (March 16th) with testing that needed to be available in January. Laboratory staff must be enabled and mobilized to meet this current needs. We are all behind the curve on this one, but I have full confidence in our DMTs to get this done if they can be supported. There will be struggle but the tenacity and perseverance of our nation’s laboratory professionals and pathologists will see this through to its end. Because we, the DMT, don’t have a choice but to always consider the “we” in our daily practice, our patients WILL BE tested and diagnosed. We will beat this together and in being together, we will be stronger.

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-Dan Milner, MD, MSc, spent 10 years at Harvard where he taught pathology, microbiology, and infectious disease. He began working in Africa in 1997 as a medical student and has built an international reputation as an expert in cerebral malaria. In his current role as Chief Medical officer of ASCP, he leads all PEPFAR activities as well as the Partners for Cancer Diagnosis and Treatment in Africa Initiative.

A Day in the Life

Who are medical laboratory scientists? We call ourselves clinical laboratory scientists, medical technologists, med techs, medical laboratory technicians, MLTs, or simply “techs.” Around the clock each day we provide vital information to physicians. We perform a variety of laboratory procedures from identifying microorganisms to providing blood for emergency transfusions. We’re trained in clinical chemistry, hematology, microbiology, and transfusion medicine. We are dedicated to delivering accurate and precise, high quality results to physicians. These providers rely on us for the diagnosis and monitoring of patients. I’ve heard it said that “without the lab, you’re just guessing.” We are a somewhat unknown but very important part of the medical field.

Many of us joined this profession because we are organized, have a strong attention to detail, are intrigued by science, and want to help others. We want to work in the medical field, but may not really want patient contact. In my case, I knew I loved biology, chemistry and math, had an analytical mind, and pay a great deal of attention to detail, but I didn’t really want to deal with “people,” so I thought I had found the perfect profession. Working in a lab, in the basement, I wouldn’t have any patient contact. Little did I know that for many years I’d be looked up to as an “expert phlebotomist;” the tech the phlebotomists would come to when they missed a “tough stick.” I was often called to the floors and the outpatient lab to draw patients. I worked 3rd shift where we were our own phlebotomists. And little did I know that I’d discover a love of teaching, and actually enjoy standing in front of a group of students, teaching them. I never thought I’d enjoy public speaking, but now I speak at conferences and symposiums and love sharing my love and knowledge of Hematology and Transfusions Medicine with my audiences.

I’ve been teaching for years, but continue working in the laboratory as well, because I feel the best teachers are the ones with first hand, current experiences to share. When I work with my students, I like to coach them to think problems through and to solve puzzles instead of simply memorizing facts. Med techs often choose the profession because they have a strong ability in science, but also keen investigative instincts, and enjoy the challenge of solving puzzles. We graduate with a plethora of knowledge, but it doesn’t stop there. We need to take this with us to our jobs, build on it, and use it every day to learn to think through and solve these puzzles and problems quickly and accurately. It’s a profession where you never stop learning.

So, where is this going? Graduation is coming, and a new set of med techs will be set forth into the labs of the world, armed with knowledge and ready to learn yet even more. So, what is it really like working in a hospital lab? Here’s a little glimpse of a typical day in the Hematology lab.

It starts a lot like the Beatles tune: “Woke up, fell out of bed, dragged a comb across my head. Found my way downstairs and drank a cup, and looking up I noticed I was late…” Which reminds me, I remember reading somewhere that medical technologists are the profession that drinks the most coffee. But, so much for being side tracked. Waking up at the crack of dawn, rushing in the door, clocking in before 7 am, on a typical morning we all check the schedule to see where we are scheduled for the day and to see who called out sick. On this day, there was only one sick call, which necessitated a little juggling of the schedule because we were already short staffed. (We can’t wait for you new grads to start!) That was our first problem of the day solved. And then we got a call that the 2nd heme tech was stuck in traffic. Techs are very adaptable, and can think on their feet. Looking around, I suddenly noticed I was alone in Hematology, and our CellaVision was down. On top of sick and late calls, the overnight tech had left early. I jumped right in. I took inventory of the situation, and saw messages about 2 pathology review fluid slides that were left from the previous shift. I took out QC to warm up, started finishing up the morning run and worked on the CellaVision. Soon my partner for the day arrived, just in time to hear the XN analyzer start beeping. Did I mention that techs are really good at multi-tasking?

I got the CellaVision up and running again: second problem of the day fixed. After shutting off the alarm on the XN, we began investigating, reran the specimen, called the floor, and discovered it was a contaminated sample: third problem of the day solved. We had a morning of calling critical labs to the providers, trekking across to the other building to bring the pathology reviews to the pathologists, and handling sample barcode issues. I took a quick look at the clock and realized it was 9:30 am, and we had just finished the morning QC and maintenance. Time for that coffee! (I actually am apparently one of the few med techs who doesn’t drink coffee, but I managed a quick break and a cup of tea.) Our hematology techs assist with bone marrow collections, making the slides, processing them and bringing the slides to the pathologists, then to surgical pathology and cytology. The whole process can take 1 ½ – 2 or more hours, and this day was our lucky day. We had two scheduled bone marrows, and another one that was a surprise. Three bone marrow and only two techs in the department!

While we were up in oncology and interventional radiology and processing bone marrows, the CellaVision acted up again, and I had to call service. I left a message for evening shift that service would be coming in that afternoon. A reagent ran out and I had to fill out the reagent replacement log. One other things that med techs do very well, is documenting what we did. There is a saying in the lab that “if it’s not documented, it didn’t happen.” We had a couple racks of unreceived specimens delivered to the department, and had to resolve the unregistered samples. Stats kept coming in, we had a T4T8 to run, and lunch time came and went, with neither of us getting a real lunch. Body fluids started coming in, three in a row. And guess what? One of them needed a pathology review! Med techs also get plenty of exercise when the pathologists are in a different building than the lab. The next phone call I got was from a second-shift tech who was running late. It seemed like the start of the day all over again! Before we knew it, it was 3:30 and time to go home.

We had a full day, a great day. It makes me feel good to know that we are doing such vital work. I feel proud that our team works well together. Not every day is quite this busy, but the busy ones are when we learn the most.

To all the students I have worked with this year, and all students everywhere, welcome to the lab! We need curious minds, and new techs who are ready to unravel the puzzles and solve the problems we see every day. We need new “diagnostic detectives.” I am very proud every year to see or new graduates accept the challenge and become medical laboratory professionals. 2020 Graduates, welcome to our world!

-Becky Socha, MS, MLS(ASCP)CM BB CM graduated from Merrimack College in N. Andover, Massachusetts with a BS in Medical Technology and completed her MS in Clinical Laboratory Sciences at the University of Massachusetts, Lowell. She has worked as a Medical Technologist for over 30 years. She’s worked in all areas of the clinical laboratory, but has a special interest in Hematology and Blood Banking. When she’s not busy being a mad scientist, she can be found outside riding her bicycle.