When Rapid Blood Culture Identification Results Don’t Correlate, Part 2: Contamination

All laboratories are prone to contamination events. Blood products, analyzers, reagents, media, etc. all have the potential to be contaminated. If you are a molecular microbiologist, then you have to worry about not only bacterial, but also nucleic acid contamination. 

The Issue

The topic of my blog last month focused on discrepant results between blood culture and PCR. Traditional blood culture workflow involves correlating the Gram stain result to what grows in culture. Nowadays, many laboratories are also performing PCR on positive blood cultures. Because we know PCR is more sensitive, it may be easy for some to justify discrepancies. Let’s image that gram positive cocci in clusters were observed in the Gram stain, the PCR detected Staphylococcus and Enterococcus DNA, but only S. aureus grew in the culture. Where did the Enterococcus come from and where did it go? It was not observed in the Gram stain and it didn’t grow in cultures, so was it “real”? Possibly. It could be a contaminant or it could be real, just present in low numbers. It’s difficult to say without having to invest more effort.

When this type of situation occurs in my laboratory, three things happen. First, we review the data. For example, if the Gram stain is discrepant, then we review the Gram stain or perform an acridine orange stain (in the case of positive PCR, but negative culture). If it’s the PCR, then we would make sure that a result entry error did not occur, etc. Second, we add the comment, “clinical correlation needed”. We have found little value in going back to the blood culture bottle and trying to recover the missing organism because in most cases when we look hard enough, using selective agar and other strategies, we do find the organism from the PCR results buried among overgrowth. Therefore, our approach is to let the clinician know that they must use other clinical data to aid in their diagnosis. Third, we document all discrepant blood culture PCR results; which includes an automatic notification to the doctoral director.

Next, let’s imagine that two more blood cultures (from different patients) become positive all within a relatively short period of time from the first discrepant result noted above. gram negative bacilli are observed in one culture and the other displays gram positive bacilli. PCR detects Enterococcus DNA in both cases. What are the odds of that happening? Not good. Something strange is going on!

The Solution

A contamination investigation needs to immediately occur. The two likely sources of contamination are 1) the PCR assay or 2) the blood culture bottles. To determine whether the issue is due to amplicon or target contamination of the PCR assay, we need to identify which instruments reported the Enterococcus. Was it a single instrument or were different instruments involved? Our laboratory performs routine “swipe” tests of the environment as part of our quality control, which allows us to monitor contamination. Swipe tests may also be performed 1) after a known contamination event (i.e., spill due to cracked or leaky product) to ensure that decontamination was properly carried out, 2) to investigate increased positivity rates, or 3) follow up on unusual results, such as the scenario outlined above.

PCR may be performed on a random sampling of uninoculated bottles to determine whether the issue is due to contamination of the blood culture media. If the contamination is high density, this may be useful; however if it is low density, then all bottles you test may still be negative. If the contamination is due to bacterial DNA, then Gram stain or culture will not be useful, hence the need for PCR. It is important to note that the presence non-viable organisms and/or nucleic acids (at levels that can be detected by PCR) is a known limitation noted in the package insert of some blood culture media and PCR manufacturers. If contamination is suspected, then immediately file a report with the manufacturer. Be sure to document lot numbers and expiration dates so that they may alert other customers.
The Conclusion

Human error contributes to the majority of discordant laboratory results. However, errors in interpretation and result entry/clerical errors are only part of the problem. Contamination events only complicate matters. If the test volume is significant, then the number of discordant results should be quickly realized, especially if there truly is a contamination issue. It is important to have a process in place to help reconcile contamination events as quickly as possible as they have the potential to majorly impact operations and patient care.



  1. https://labmedicineblog.com/2018/02/20/when-rapid-blood-culture-identification-results-dont-correlate-part-1-clinical-correlation-needed/


Martinez Headshot-small 2017

-Raquel Martinez, PhD, D(ABMM), was named an ASCP 40 Under Forty TOP FIVE honoree for 2017. She is one of two System Directors of Clinical and Molecular Microbiology at Geisinger Health System in Danville, Pennsylvania. Her research interests focus on infectious disease diagnostics, specifically rapid molecular technologies for the detection of bloodstream and respiratory virus infections, and antimicrobial resistance, with the overall goal to improve patient outcomes.

Synergistic Decision Making

Contrary to common belief, the group is NOT as strong as the weakest link. Instead, a group is as strong as its capacity to compensate for the weakest link. We have all experienced this when, for example, a colleague does not do their share for a presentation or project. This does not mean that the project or presentation fails; it means that other team members will compensate and do additional work that was initially assigned to the unproductive team member. The group thus does not sink to the level of the unproductive member. Instead, it rises to the level of how well others can do that members’ job.

When teams reach synergy, they reach a high level of effectiveness and productivity. In order to find out if your team is synergistic, this course conducts a simulation. The team-building simulation, designed by Human Synergistics International, revolves around some type of emergency situation: people are stranded in the desert, a tsunami is coming, they are surrounded by incoming bush fire, there is a severe snowstorm on the way, or people are stranded on a float plane in the middle of the subarctic. Through a video story, participants of this course are introduced to their situation and then asked to rank available items in order of importance. This is first done individually and then with a group while being observed by one person who is assessing their discussion. Once the correct ranking is revealed, participants will see the difference between their individual and group scores and they receive insights about how effectively they worked together.

Understanding the challenges of a team and how to move ineffective behaviors to productive ones is essential for team synergy. This course follows the Human Synergistics circumplex, explained in more detail in the Organizational Savvy and Reacting to Change course blog. In short, this circumplex indicates which behaviors are constructive, passive/defensive or passive/aggressive. Awareness of the constructive and ineffective behaviors will increase a team’s synergy. The idea behind this model is that when a team adopts constructive behavior, their collaborative results will produce greater results than the sum of their individual efforts. These groups are not as strong as their weakest link, nor are they as strong as their capacity to compensate for the weakest link. Rather, these groups are as strong as their syngeristic capacity.


-Lotte Mulder earned her Master’s of Education from the Harvard Graduate School of Education in 2013, where she focused on Leadership and Group Development. She’s currently working toward a PhD in Organizational Leadership. At ASCP, Lotte designs and facilitates the ASCP Leadership Institute, an online leadership certificate program. She has also built ASCP’s first patient ambassador program, called Patient Champions, which leverages patient stories as they relate to the value of the lab.

“Doctor! We need your help STAT … in Antarctica!”

As a pathologist based in Denver, Colorado, I can easily say this is not a statement I ever expected to hear. Because of my sub-specialty expertise in surgical and cytopathology, and my role as chairman of the pathology department in a tertiary care facility, it was not unusual for colleagues, staff and administrators to stop by my office or to phone me for a matter in need of immediate attention. The conversation would usually start with, “Doctor Sirgi, we need your help as soon as possible with …”. I always welcomed these opportunities to assist with whatever matter needed attention, knowing full well the ultimate beneficiary of these calls would be a patient or an anxious family member. However, I could not hide my surprise when I heard the second part. “You need me where?!” I asked, thinking I had misheard the latter part of the phrase. It turns out my assistance really was immediately needed in Antarctica!

That moment in June 1999 I learned the headquarters of Antarctic Support Associates (ASA) is based in Englewood, Colorado (a suburb of Denver). ASA is contracted by the National Science Foundation to provide science support to the United States Antarctic Program (USAP), based at the Amundsen-Scott South Pole Station (ASSPS). The ASA director told me they had received a desperate call from the scientific team deployed in the South Pole informing them their only medical doctor on site, Dr. Jerri Nielsen, had discovered a breast lump worrisome for cancer during self-palpation. Considering Antarctica was in deep winter, with outside temperatures hovering around negative 85 degrees Fahrenheit evacuating the doctor for medical tests and treatment was completely impossible. This was a full-fledged “Houston we have a problem!” kind of situation.

As soon as I arrived at ASA, a videoconference was established with the afflicted doctor and a few non-medical scientists on site via satellite link-up; the first order of business was to understand the elements of the problem and offer a potential course of action. We only had a few precious minutes of satellite connection before lost of signal. We learned the following:

  • The doctor had self-detected a sizable breast mass of hard consistency.
  • Nobody around her had any experience at performing a biopsy or fine needle aspiration, let alone surgery.
  • There was no laboratory facility or expertise to offer pathology examination, should a sample be obtained.
  • There was no mammography or ultrasound equipment adequate for the evaluation of a breast mass.
  • There was no adequate medication, should a diagnosis of malignancy be established.

With the possibility (or the wishful thinking) that we could still be dealing with a benign lesion, I recommended that we first focus our efforts on securing a diagnosis. Luckily, the rudimentary equipment available to Dr. Nielsen included needles, glass slides, Giemsa stain, an antiquated microscope (with no camera attachment), and a medium resolution digital camera borrowed from scientists working in another area of the research facility. I explained in detail to Dr. Nielsen and her team of worried volunteers how to use these seemingly unrelated pieces of material and equipment. Keep in mind that all this happened at a time when digital pathology was still in its infancy (if not fetal stage), and a hefty dose of DIY had to be improvised on the spot.

I had brought a needle, an orange, a couple of glass slides, and three jars filled with the fluids needed for a quick staining of the material obtained. Dr. Nielsen had herself and her crew of non-medical scientists. I demonstrated how to perform a fine needle aspiration, smear the material obtained on a glass slide, and how to properly stain it for microscopic examination.

These were but the very first steps of a long journey toward obtaining a diagnosis. Considering Dr. Nielsen had no expertise in the examination of pathology material, she needed to follow steps completely unfamiliar to her in order for me (and other experts mobilized around the country) to establish a diagnosis:

  • Perform a medical procedure she had never performed before … on herself!
  • Prepare smears of the material aspirated from the mass
  • Have those smears stained
  • Use a microscope to identify areas of cellularity on the slides obtained
  • Use a camera to take pictures of these areas
  • Load the pictures in an email
  • Transmit an email “heavy in data” across the planet, on a very slow satellite linked connection

Dr. Nielsen performed the procedure on herself the next day. The pictures I received a day later were impossible to interpret because the slides had been improperly stained; areas photographed had abundant red blood cells but no breast epithelial cells to evaluate. The team was understandably quite discouraged when they received our feedback. I sent them an email commending them on their efforts and further guiding them on:

  • Troubleshooting the staining process
  • Focus on the best areas to take pictures, using a breast cytopathology atlas as a visual aide

Their second attempt was much improved and allowed us to unequivocally establish a diagnosis of malignancy affecting Dr. Nielsen’s breast. Reaching a diagnosis was good; however, the tragic reality still remained that the patient had cancer and it was completely impossible to evacuate her from her current location.

The “home team” (anybody not based on the other end of the world) immediately started mobilizing resources from different areas of expertise to:

  • Get Dr. Nielsen the treatment she needed while stuck in Antarctica
  • Get Dr. Nielsen out of the South Pole as soon as meteorological conditions allowed

The following immediate priorities were then identified and acted upon:

  • Per the oncologists consulted, adequate chemotherapy could not be started in the absence of knowing the tumor’s biomarkers status
  • To establish this status, better tissue was needed for further immunohistochemical testing
  • Each medical specialty involved with the rescue effort made recommendations for the type of equipment and material that needed to be transported to the South Pole (including specialized medical atlases, ultrasound equipment, newer microscopes equipped with high resolution digital cameras, regular and immunohistochemical stains with appropriate easy to use instructions, various chemotherapy drugs for different treatment possibilities).

The equipment, with duplicate units of everything sent, was placed in crates and flown to the US Air Force base in New Zealand. Ace pilots volunteered to drop the equipment over the Amundsen-Scott South Pole Station, despite terrible weather conditions, zero visibility over the drop zone, and no chance of landing or refueling during the mission. Ultimately, a couple of attempts were necessary to successfully drop the needed equipment over the area. The station personnel worked for hours in negative 85 degrees Fahrenheit temperatures and near zero visibility to collect the dropped material, much of it severely damaged, and transport the surviving equipment back to the base.

Treatment began, the tumor was stabilized, and Dr. Nielsen returned to the U.S., where she continued treatment as soon as weather allowed it. Unfortunately, she succumbed to her illness several months later.

What started as a “Dr. Sirgi, we need your help STAT … in Antarctica” developed into a medical rescue mission of monumental proportion. Ordinary people from different walks of life and medical expertise worked synergistically to develop on-the-fly life-saving solutions that had never been tried before. In the end:

  • A heroic doctor performed diagnostic procedures on herself and braved all kinds of challenges in an attempt to survive.
  • A staff of scientists with limited to no medical experience rose to the occasion to act as capable and devoted medical assistants.
  • Physicians and medical technologists from around the country, who were previously strangers, synergistically worked together to coordinate efforts to save a colleague who was trapped in some of the harshest conditions in the world.
  • Administrators of the Antarctic Support Associates (ASA) organization worked day and night to secure any and all expertise and needed equipment for the rescue mission.
  • Air Force pilots voluntarily risked their lives to rescue a fellow human being.

No one involved woke up on that first day thinking they would be called for such a noble endeavor. All parties involved were ordinary citizens, and every single one tapped into his or her infinite leadership potential to collaborate with colleagues in order to resolve an almost impossible situation. Although There were many links of uncertain strength in this effort due to lack of experience or expertise, the common resolve and demonstrated leadership of all players involved created an indestructible chain of potential and led ultimately to the mission’s resounding success.


Sirgi pic-small

-Karim E. Sirgi, MD, MBA is board certified in anatomic and clinical Pathology, with additional board certification in cytopathology. He is active as an independent healthcare consultant, and is the current president of the CAP Foundation. Additional biographical information can be accessed at www.karimsirgimd.com

Hematology Case Study: The Race to Save a 48 Year Old Man from a Rare Disease

A 48-year-old Caucasian male presented to a Baltimore Emergency Room complaining of fever, chills, and aches. He stated he had not been feeling well for the past week. His symptoms had progressed rapidly over the last 3 days to include night sweats, nausea and excessive somnolence. History taken in the ER revealed the patient had returned 10 days prior from a Safari in Botswana and Zambia. The patient was admitted to the ICU, in shock, with a BP of 75/50. Even though the patient had taken anti-malarial medication, the doctors suspected malaria. Blood was sent to the lab for a blood parasite exam and treatment for malaria was started while the doctors waited for the confirmation.

In the Hematology laboratory, technologists perform microscopy of thick and thin blood smears to look for malarial parasites. The thin smear is a typical Wright Giemsa stained wedge smear, and the thick smears are prepared and stained so that the red blood cells are lysed, and the sample is concentrated, making examination easier. Thorough, careful examination of the thick smear is aimed to identify whether a particular parasite is present, but they require a long drying period and take several hours to prepare and read. Thin smears can detect the parasites but also permit identification of particular species of malaria. While the thick smears were drying the technologist examined the thin smear.

The technologist who examined this patient’s thin smears saw parasites (image 1) under her microscope. She consulted with a supervisor and pathologist to confirm, and the patient’s doctor was notified that the patient did not have malaria, but instead, had Trypanosoma! This was an exciting find in the laboratory, as there have been only 40 cases seen in the US in the past 50 years.

Image 1. This slide shows the parasite, in dark blue. The parasite causes
African trypanosomiasis, also known as sleeping sickness
(Courtesy of Greater Baltimore Medical Center).

The race for diagnosis and treatment did not stop there, as there are 2 types of African trypanosomiasis, or African sleeping sickness, and effective and appropriate treatment must be started in a timely fashion. Both types look identical on a blood smear and both are considered universally fatal, if not treated. West African trypanosomiasis and East African trypanosomiasis are caused by the tsetse fly, which only lives in rural Africa. The patient stated he did remember being bitten by tsetse flies, and because there had been such a short span of time between being bitten and the onset of symptoms, doctors concluded that the patient had the rarer and fast-acting East African trypanosomiasis, which can kill within months.

Epidemiologists at CDC were contacted, who then consulted other infectious disease specialists at CDC. There are 2 treatments depending the stage of the disease. Surinam is the first line of defense, but melarsoprol, which is arsenic-like and very toxic, must be used if the parasites have reached the central nervous system. Because of the urgent need to start treatment, emergency shipments of both drugs were flown to Baltimore. The patient was started on Surinam to reduce the number of parasites in his blood to a level low enough to allow a spinal tap to be performed. After confirming that the CSF showed no signs of the parasite, treatment with surinam was continued and the patient was discharged a week later and has made a full recovery.

Because of the excellent work done by the medical technologists who made the first discovery, the speed with which the critical calls were made, the actions of the doctors involved, and the cooperation of the CDC, this patient received his first dose of Surinam a little over 24 hours after his blood was sent to the lab. This case shows the importance of a thorough medical and travel history in differential diagnosis. It also illustrates the importance of the competency evaluations and surveys in which all laboratory professionals are required to participate. None of the technologists, doctors or scientists involved had ever actually seen a case of African Trypanosomiasis, they had only read about it in books and seen it on competency assessments.

This case is based on an actual case from 2016. My coworker, Gail Wilson, was the technologist who first saw the Trypanosoma on the slides. Many thanks to Gail for her keen eye and attention to detail!

Image 2: L&R: Trypanosoma brucei in thin blood smears stained with Giemsa. Center: A close up of a tsetse fly. Credit: DPDx



  1. Jon E. Rosenblatt Barth Reller Melvin P. Weinstein.pages 1103-1108, Laboratory Diagnosis of Infections Due to Blood and Tissue Parasites Clinical Infectious Diseases, Volume 49, Issue 7, 1 October 2009; retrieved March 2018 from https://academic.oup.com/cid/article/49/7/1103/316703
  1. Ivo Elliott, Trupti PatelJagrit Shah, and Pradhib Venkatesan. West-African trypanosomiasis in a returned traveller from Ghana: an unusual cause of progressive neurological decline BMJ Case Rep. 2014; 2014: bcr2014204451. Published online 2014 Aug 14.doi: 1136/bcr-2014-204451; retrieved March 2018 from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139564/
  1. Lena H. Sun. Medical Detectives raced to save a man from a rare, ‘universally lethal’ disease; retrieved March 2018 from https://www.washingtonpost.com/news/to-your-health/wp/2016/12/22/medical-detectives-raced-to-save-a-man-from-a-rare-universally-lethal-disease/?utm_term=.16d7b136bc47
  1. Parasites – African Trypanosomiasis (also known as Sleeping Sickness). Retrieved March 2018 from https://www.cdc.gov/parasites/sleepingsickness/
  1. DPDx- Laboratory Identification of parasites of Public Health Concern; retrieved March 2018 from https://www.cdc.gov/dpdx/



-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.


Microbiology Case Study: A 52 Year Old Man with End Stage Renal Disease

Case History

A 52-year-old man with multiple medical issues including a history of end stage renal disease on hemodialysis, chronic pancreatitis status post distal pancreatectomy, intravenous drug use through dialysis catheter, and multiple types of bacteremia presented with chills and abdominal pain. Labs on admission included a white blood cell count of 28.64 k/cmm, hemoglobin 8.8 g/dL, and platelets 581 K. He was diagnosed with a pancreatitis flare and admitted for pain management, with further labs drawn. After one day, he felt much better and was discharged with a pending blood culture to follow up on. At 61 hours, one bottle flagged positive with yeast seen on gram stain.

Laboratory findings

Image 1: potato flake agar with creamy tan-white colonies.
Image 2: calcofluor white fluorescent stain showing round yeast forms.

The organism was identified as Cryptococcus laurentii via MALDI-ToF MS. A follow-up fungal culture was negative, however, repeat blood culture grew Stenotrophomonas maltophilia. His tunneled catheter was removed, and two days later the patient required urgent interventional radiology access for dialysis. He completed a two-week course of ceftazidime and was discharged. 


Cryptococcus laurentii is a very rare fungal pathogen. It is a psychrophilic organism, growing ideally at 15 °C, and is the most common yeast found in tundra.1 Major reservoirs include soil, food, and pigeon excrement.2 C. laurentii usually causes infection in immunocompromised hosts, although rare incidents of infection in immunocompetent patients have been reported. Reported manifestations have included fungemia, meningitis, peritonitis, pneumonia, pyelonephritis, keratitis, and skin infection.3

Cryptococcus laurentii is a urease-positive organism. Gram stain shows large budding yeasts without hyphae. The yeast grows on routine agar as whitish-yellow creamy colonies and on birdseed agar as whitish or greenish colonies. Staining with calcofluor highlights encapsulated yeast forms. Molecular diagnosis can be accomplished by ribosomal RNA sequencing of the internal transcribed spacer and D1/D2 regions. Treatment in most cases has been with fluconazole, although in one case of peritoneal dialysis catheter-related peritonitis, voriconazole was used due to low fluconazole susceptibility.4


  1. Molina-Leyva A, Ruiz-Carrascosa JC, Leyva-Garcia A, Husein-Elahmed H. Cutaneous Cryptococcus laurentii infection in an immunocompetent child. International Journal of Infectious Diseases. 2013;17(12). doi:10.1016/j.ijid.2013.04.017.
  2. Johnson, L. B., Bradley, S. F. and Kauffman, C. A. Fungaemia due to Cryptococcus laurentii and a review of non-neoformans cryptococcaemia. Mycoses. 1998;41: 277–280. doi:10.1111/j.1439-0507.1998.tb00338.x
  3. Furman-Kuklińska K, Naumnik B, Myśliwiec M. Fungaemia due to Cryptococcus laurentii as a complication of immunosuppressive therapy – a case report. Advances in Medical Sciences. 2009;54(1). doi:10.2478/v10039-009-0014-7.
  4. Asano M, Mizutani M, Nagahara Y, et al. Successful Treatment of Cryptococcus laurentii Peritonitis in a Patient on Peritoneal Dialysis. Internal Medicine. 2015;54(8):941-944. doi:10.2169/internalmedicine.54.3586.


-Prajesh Adhikari, 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.

Is It Possible to Have Coexistence of Hepatitis B Surface Antigen and Antibody?

Hepatitis B surface antigen (HBsAg) is the serologic hallmark of acute Hepatitis B virus (HBV) infection. It can be detected in serum using immunoassays a few weeks after HBV infection, and normally disappears after 4-6 months in recovered patients (1). Antibodies against HBsAg (anti-HBs) appears as a response from the host immune system, and these antibodies neutralize HBV infectivity and clear circulating HBsAg (2). Anti-HBs generally persist in life, indicating recovery and immunity from HBV infection.

Some of us may simply assume that the presence of anti-HBs should always associated with the loss of HBsAg. However, it is possible to see concurrent anti-HBs and HBsAg in patients. In fact, coexistence of HBsAg and anti-HBs is not rare, and has been reported in 10 to 25 percent of HBV chronic carriers in previous studies (3-4).  The underlying mechanism is not fully understood but several reports explained it as HBsAg mutants escaping the immune system (2-4). HBsAg mutants are believed to arise under the selective pressure from the host immune system, or from vaccinations (4-6).

“a” determinant in HBsAg is one of the main target of anti-HBs. It has been reported that mutations in the “a” determinant of the surface gene (S-gene) result in amino acid substitutions in HBsAg, and reduce the binding of anti-HBs to HBsAg, leading to immune escape (4). The first HBV mutant was reported by Zanetti et al in 1988 as G145R mutation. In their report, infants born to HBsAg carrier mothers developed breakthrough infections despite receiving HBIG and HBV vaccine at birth (5). Since this report, several other HBsAg mutations have been reported (4, 6).

Currently, there is no easily available assay to diagnose individuals who are suspected of harboring HBsAg escape mutants. Moreover, mutated HBsAg may leads to false negativity in some serologic assays, leading to a missed diagnosis of chronic HBV infection (6). Another concern is the potential risk of transmission to others, as vaccination does not provide protection from these mutated viruses (8); this is especially important in liver transplant recipient and newborns from HBsAg positive mothers.


  1. Lok A, Esteban R, Mitty J. Hepatitis B virus: Screening and diagnosis. UpToDate. Retrieved Feb 2018 from https://www.uptodate.com/contents/hepatitis-b-virus-screening-and-diagnosis#H3
  2. Liu W, Hu T, Wang X, Chen Y, Huang M, Yuan C, Guan M. Coexistence of hepatitis B surface antigen and anti-HBs in Chinese chronic hepatitis B virus patients relating to genotype C and mutations in the S and P gene reverse transcriptase region. Arch Virol 2012;157:627–34.
  3. Colson P, Borentain P, Motte A, Henry M, Moal V, Botta-Fridlund D, Tamalet C, Gérolami R. Clinical and virological significance of the co-existence of HBsAg and anti-HBs antibodies in hepatitis B chronic carriers. Virology 2007;367:30–40.
  4. Lada O, Benhamou Y, Poynard T, Thibault V. Coexistence of hepatitis B surface antigen (HBs Ag) and anti-HBs antibodies in chronic hepatitis B virus carriers: influence of “a” determinant variants. J Virol. 2006 Mar;80(6):2968-75.
  5. Zanetti AR, Tanzi E, Manzillo G, Maio G, Sbreglia C, Caporaso N, Thomas H, Zuckerman AJ. Hepatitis B variant in Europe. 1988 Nov 12; 2(8620):1132-3.
  6. Leong J, Lin D, Nguyen M. Hepatitis B surface antigen escape mutations: Indications for initiation of antiviral therapy revisited. World J Clin Cases 2016;4:71.
  7. Colson P, Borentain P, Motte A, Henry M, Moal V, Botta-Fridlund D, Tamalet C, Gérolami R. Clinical and virological significance of the co-existence of HBsAg and anti-HBs antibodies in hepatitis B chronic carriers. 2007;367:30–40.
  8. Thakur V, Kazim S, Guptan R, Hasnain S, Bartholomeusz A, Malhotra V, Sarin S. Transmission of G145R mutant of HBV to an unrelated contact. J Med Virol 2005;76:40–6.



-Xin Yi, PhD, DABCC, FACB, is a board-certified clinical chemist, currently serving as the Co-director of Clinical Chemistry at Houston Methodist Hospital in Houston, TX and an Assistant Professor of Clinical Pathology and Laboratory Medicine at Weill Cornell Medical College.

Critical Care, Critical Labs

Sepsis is a medical emergency and a global public health concern. The Surviving Sepsis Campaign started in 2012 and has since issued International Guidelines for Management of Sepsis and Septic Shock. These Guidelines have been updated several times, and the 4th edition of the 2016 guideline have been issued. The Guidelines are written from the perspective of developed (“resource-rich”) countries, where critical care settings are equipped with tools for managing these patients. Yet, the developing world carries the greatest burden of sepsis-related mortality. Unfortunately, the developing world lacks access to many of the necessary tools for managing the critically ill patient – including basic laboratory testing.

Laboratory values are a significant part of the management of the septic patient. Take a look at the sepsis screening tool. Analytes and lab tests included in screening patients for sepsis include: lactate, creatinine, bilirubin, INR, and blood gases. The Surviving Sepsis bundles require a lactate concentration within 3 hours of presentation, and a subsequent lactate within 6 hours. The care bundle also requires a blood culture within 3 hours of presentation and prior to administration of antibiotics. Early-goal directed therapy for sepsis requires administration of crystalloid based on lactate concentrations. Basics of laboratories in the US, lactate and blood cultures are both difficult to obtain and far from routine in the resource-poor care settings.

Blood gases and lactate are particularly difficult to find and to maintain in the developing world. While there are a number of point-of-care or small benchtop devices – like the iStat (Abbott), the Piccolo (Abaxis), and the Stat Profile pHOx (Nova), it is often cost-prohibitive to maintain these devices.  The iStat and the Piccolo are examples of cartridge-based devices. All of the chemistry takes place in single-use cartridges and the device itself is basically a timer. In my experience, cartridge based devices hold up in environmental extremes better than open reagent systems. However, they are not cheap and this can be prohibitive. Cost of a single cartridge can range from $3-10 USD. In countries where patients and their families are expected to pay upfront or as they go for even inpatient medical care, and the income for a family is $2USD/day, routine monitoring of blood gases and lactate by cartridge is just not feasible. Reagent based devices like the Stat Profile use cartons of reagent for many uses. This is much cheaper – if all the reagent is used before it expires! Some healthcare settings can accommodate only 1-3 critical patients, and might not be able to use a whole carton before the expiry, even when adhering to Surviving Sepsis guidelines.

Blood cultures and subsequent treatment with appropriate antibiotics is a large part of the surviving sepsis campaign. Microbiology in the developing world is often limited to a few reference laboratories in country. Also, the number of potential infectious agents is larger in the developing world where diseases like malaria and dengue fever are common. Multiplexed nucleic acid tests might fill the gap here. Again, the cost is a major factor. Just reagents alone for a single multiplexed NAT can be over $250 USD.

In short, if the surviving sepsis guidelines really do help decrease sepsis mortality, the developing world doesn’t have a chance unless it has a greater laboratory capacity. Basic labs that we don’t think twice about can be very hard to come by in resource-poor environments. The tests already exist in forms that can be used in resource-poor settings – they just need to be cheaper, at least for those in limited resource settings. Are you listening, Abbott?


Sarah Brown Headshot_small

Sarah Riley, PhD, DABCC, is an Assistant Professor of Pediatrics and Pathology and Immunology at Washington University in St. Louis School of Medicine. She is passionate about bringing the lab out of the basement and into the forefront of global health.  

Microbiology Case Study: A 21 Year Old Female with a Sore Throat

A 21 year-old female presented to the emergency department with a sore throat. Her symptoms started two weeks prior to presentation. She was seen at student health last week and given Tamiflu, but her sore throat has grown progressively worse. She now has pain with swallowing and cannot swallow liquids. Upon examination the patient has no rash, no fever, and is not in respiratory distress. She does have left tonsillar fullness causing her uvula to be slightly deviated to the right along with an enlarged left cervical lymph node. Her complete blood count (CBC) was elevated at 19.7 x103/ul (reference range 4-10 x103/ul) with 12% lymphocytes, 2% monocytes, and 83% neutrophils. A rapid antigen test for S. pyogenes or Group A Streptococcus was negative. A CT exam of the neck was performed and a peritonsillar abscess of 1 x 1.3 x 1.6 cm was identified. The abscess was drained resulting in 1 ml of yellow purulent fluid which was sent to the microbiology lab for culture. The following was Gram stain was prepared from the abscess material.

Fusobacterium necrophorum Gram stain


The Gram stain of this abscess showed 4+ PMNs and 4+ small, pleomorphic gram negative bacilli. Anaerobic culture grew Fusobacterium necrophorum, identified by MALDI-TOF MS with a confidence score of 2.2. F. necrophorum is a non-motile, non-pigment forming, pleomorphic gram negative bacilli. It is a strict anaerobe that tests catalase negative, indole positive, and lipase positive on egg yolk agar. Anaerobic antibiotic disk testing for this organism shows susceptibility to kanamycin and colistin with resistance to vancomycin.

The two most clinically relevant species of Fusobacterium are F. nucleatum and F. necrophorum. Because they are strict anaerobes which are often not recovered in culture, Fusobacterium spp. are an under-recognized cause of disease. F. necrophorum colonizes the oral cavity, and like other colonizing anaerobes, it tends to cause infections near the mucosal surface where it resides. F. necrophorum most commonly causes pharyngitis, recurrent tonsillitis, and other odontogenic infections. In adolescents, 10% of tonsillitis that is not caused by S. pyogenes can be attributed to F. necrophorum. These infections can progress to septic thrombophlebitis of the internal jugular vein (Lemierre’s syndrome), bacteremia, and rarely F. necrophorum can cause abscesses throughout the body. Because it is an anaerobic bacterium, susceptibility testing is rarely performed on isolates of F. necrophorum. They are highly susceptible to β-lactam–β-lactamase inhibitor combinations, carbapenems, and metronidazole.

Lemierre’s syndrome was of great concern in our patient since it is most commonly observed in adolescents and young adults that were previously healthy, like our patient. Fortunately, CT scan of the neck showed no indication of thrombophlebitis in our patient. After drainage of the abscess, she felt much better and was able to tolerate liquids. The patient was discharged from the ED with a course of amoxicillin/clavulanate (augmentin). Upon follow up in ENT clinic she gave a more through history of 4-5 episodes of sore throat over the past year.


  1. Manual of Clinical Microbiology, 11th edition
  2. Principles and Practices of Infectious Disease, 7th edition


-Erin McElvania, PhD, D(ABMM), is the Director of Clinical Microbiology NorthShore University Health System in Evanston, Illinois.