The Laboratorian - Volume 6, Issue 2


The Laboratorian - Volume 6, Issue 2
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October 2014 - Volume 6, Issue 2

Article Index

- Ebola Testing
- Lab Reporting
- CQI Project Update






DSHS Laboratory Meets the Challenges of Ebola Testing

On September 30, 2014, the Centers for Disease Control and Prevention (CDC) confirmed the first case of travel-related Ebola in the United States. Laboratory testing that confirmed the case was performed concurrently at the CDC laboratory in Atlanta Georgia and at the Department of State Health Services (DSHS), Biosafety Level 3 Laboratory in Austin, Texas. The DSHS laboratory received its certification to run the Ebola assay just a month earlier and was one of only 13 laboratories in the United States initially certified to do so. More laboratories have been certified since then, making a total of 21 ready to test for Ebola.

The DSHS Laboratory was approached to perform Ebola screening because of its participation in the CDC Laboratory Response Network (LRN). Emergency response protocols, including results reporting, were already in place. The Biothreat Team already had the appropriate environmental controls in place in the Biosafety Level 3 laboratory (BSL3) and personnel with extensive experience handling select infectious agents. This made them uniquely qualified to deal with the Ebola virus.

On August 5, 2014, the United States Food and Drug Administration (FDA) granted emergency use authorization for the screen assay that the laboratory would use. On August 7, at the request of the United States Department of Defense (DOD), the CDC-LRN asked DSHS to accept the Ebola testing assay. On August 12, DSHS received the assay kit and the next day received proficiency testing specimens containing deactivated Ebola virus. The proficiency test was performed the following week and the Laboratory received notification on August 22 that they had passed and were cleared to perform the assay. The whole process was completed in less than a month due to the urgency of the situation. Little did they know they would receive their first real specimen a little more than a month later.

Through the hard work and dedication of a number of individuals, the task of bringing the testing online was quickly and effectively accomplished.

So how does the DSHS Lab end up with an Ebola specimen? When a patient under investigation is identified, hospital officials first contact their local health department. The local health department then contacts a DSHS epidemiologist who does a preliminary screen based on symptoms and history of contact with infected individuals in the countries where Ebola is currently active. In essence, they do an assessment to determine if a patient has a high risk of being infected by the virus. DSHS then consults with CDC Emergency Operations and they give ultimate approval for testing at the DSHS laboratory. After this approval is granted, the submission process begins.

Ebola specimens can consist of either whole blood or plasma. They are shipped to the Lab following all Department of Transportation, CDC and DSHS protocols and regulations. The infectious material is packaged in a watertight primary container surrounded by absorbent material. This is placed inside a secondary watertight container which is then placed in a rigid outer packaging. Appropriate identifying labels are placed on the outside of the package.

On September 30, at around 9am, the DSHS laboratory received its first Ebola specimen. The Biothreat Team microbiologists donned their personal protective equipment (PPE) and got to work in the BSL3 laboratory.

While working with potentially live virus, the microbiologists on the Biothreat Team take a number of precautions to eliminate any possibility of infection. They wear personal air purifying respirators (PAPR), water resistant Tyvek suits and booties, and double gloves with the inner pair taped to their suit. This PPE covers them from head to toe. They avoid the use of glass and other sharps that may damage the integrity of their suits. They are slow, deliberate and safe at all times. The team of three was able to ensure the procedure was properly followed, that all required documentation was completed, and that everything was performed safely.

All Biothreat Team personnel are thoroughly trained in BSL3 safety procedures and they always work using the buddy system. No one is ever in the BSL3 lab alone. In addition to PPE, the BSL3 lab has restricted access, interlocking doors, and single-pass, directional airflow into the lab. All exhaust air is HEPA filtered. Everything that comes out of the lab is either autoclaved or decontaminated with chemicals to eliminate the possibility that anything infectious might escape.

Once a specimen is received at the laboratory, the first step in the process is to deactivate the virus so that it is no longer infectious. This is done by treating the blood specimen with TRIzol and incubating it for five minutes to completely kill the virus. The TRIzol also serves to stabilize the viral RNA by deactivating RNases that might degrade the RNA, therefore reducing the possibility of detection failure. The process is performed in a biosafety cabinet in the BSL3 laboratory.

After inactivating any possible live virus in the specimen, Viral RNA extraction is performed using a QIAamp® Viral RNA extraction kit manufactured by QIAGEN®. The kit uses the selective binding properties of a silica gel based membrane to capture the RNA.

First, a lysis buffer is added to the inactivated Ebola specimen. This aids in binding the RNA to the membrane. The specimen is placed in a mini spin column, which is essentially a tube open on both ends with a membrane stretched across the inside. The specimen is passed through the membrane using the force of centrifugation and the viral RNA and other components of the specimen bind to it. Two separate washes are forced through the membrane to remove the non-RNA components that have been captured. Finally, a special elution buffer is used to remove the purified viral RNA from the membrane, again using the force of centrifugation. The eluted viral RNA is then ready for real-time reverse transcriptase polymerase chain reaction (rRT-PCR).

In rRT-PCR, the specimen is combined with a solution of DNA primers specific for the Ebola virus, reporter probes, nucleotides (the building blocks of DNA) and Taq polymerase. Reverse transcription is the first step in the process. During this step, the specimen is held at a slightly elevated temperature to allow for the conversion of the viral RNA to DNA.

The solution is then run through repeated cycles of hot and cool temperature. When the solution heats up the DNA is denatured (the two strands of the double helix are separated), and when it cools down, the primers and reporter probes attach to their complimentary base sequences on the separated strands. Then the Taq polymerase begins the task of DNA replication starting at the primers. As it moves down the strand adding complimentary nucleotides, if it encounters a reporter probe, it just munches on through releasing the reporter molecule which fluoresces. This fluorescence is detected and graphed. An increasing fluorescent response over the course of the PCR run indicates the presence of Ebola virus genetic material. An hour later, the result was obtained and confirmed by the CDC.

Thomas Eric Duncan had recently traveled to Dallas from Liberia, when he came down with symptoms typical of Ebola Virus Disease. Duncan had already been isolated and public health officials were beginning the process of identifying individuals that may have come into contact with him so that they could be monitored for the possible onset of symptoms. The DSHS and CDC results confirmed that Duncan was the first person diagnosed with Ebola in the United States.

After the assay was completed, all specimens in-house were immediately destroyed. Throughout the procedure, all surfaces that may have come in contact with viral material, live or inactivated, were meticulously cleaned and all waste from the procedure was autoclaved before entering the biohazard waste stream.

It is important to note that the assay the DSHS performs is only a screen. DSHS receives two specimens, one for testing, and one to forward to the CDC. The DSHS Lab can only issue a presumptive positive or negative result that can aid healthcare workers in determining a course of treatment and proper infection control procedures. Only the CDC can provide definitive confirmatory results, because they have more precise and selective tools for identifying the Ebola virus.

On October 8, Duncan succumbed to the disease. “This is a difficult time for the family, and our thoughts are with them,” said DSHS commissioner Dr. David Lakey. “We will continue to treat Mr. Duncan with dignity and respect, and we're taking great care to make sure there is no additional risk that others could be infected.”

Public health officials are continuing to monitor people who came into contact with the patient before he was isolated.

On October 11, the Biothreat Team received a positive result, from a health care worker who cared for Duncan. Late on October 14, they received a sample from a second health care worker; the test was completed around midnight with a positive result. Teamwork, training and practice – a combined 11 years of BSL3 experience – helped everything go smoothly. Responding to emerging new diseases and being on call 24/7/365 is part of the job.

The DSHS is committed to protecting the public’s health. The Laboratory plays an important role in realizing that commitment. Adaptability and teamwork are crucial, and everyone steps up to accomplish the job that they were trained to do.

For updates on Ebola, visit the DSHS website.

by Andrew Vinyard





Lab Tour: Laboratory Reporting

Lab Reporting employees at work. Photo courtesy of Andrew Vinyard.

The work in Laboratory Reporting isn’t flashy. It lacks the wow factor of the fancy scientific testing machines in many other areas of the Laboratory, and yet, the work that the Laboratory Reporting group does is a crucial component of Microbiology, Texas Health Steps (THSteps), and Newborn Screening (NBS). “In order for test results to be released, the NBS, THSteps and Microbiology form data must be entered, verified and released by our group first,” said Tiffunee Odoms, Laboratory Reporting Group Micro/THSteps Team Lead. “We are often asked to pull, enter and release a specific form in order to hasten the process for the Lab to report results to the submitter.”

A Lab Reporting employee sits at her desk, smiling at the camera. Photo courtesy of Andrew Vinyard.

Laboratory Reporting processes 1.5 million samples annually with only 32 employees. Broken down monthly, Microbiology averages 15,000 samples, THSteps averages 27,000 samples and NBS averages 65,000 samples. Despite the high volume, all result requests are handled individually.

“To us, all requests are memorable, as we provide a service that affects the people of Texas,” said Odoms. “One parent call does stand out. A mother was trying to get her son’s Sickle test but, due to HIPAA (Health Insurance Portability and Accountability Act of 1996) regulations, we were unable to help her. The mother stated that she was driving to our lab from Dallas because she needed the results today. A Customer Service Representative was able to walk her through the steps to prevent her four-hour drive to Austin and get her son’s results to the school in 10 minutes. The mother called back and gave the department kudos for a quick response and saving her a long drive.”

Laboratory Reporting responds primarily to healthcare providers who need results from tests on their patients. Requests also come from Universities and parents who need Sickle Cell results, because NCAA rules require them to prove that they have been tested. This is extremely important. If they do have Sickle Cell, they have to take extra safety measures during team practice.

Lab Reporting employees entering information into the LIMS. Photo courtesy of Andrew Vinyard.

The Laboratory Reporting staff consists of 25 full-time and two part-time Data Entry Operators with five Lab Reporting staff who answer phones. The daily work load is impressive. Data Entry receives an average of 4,500 submission forms daily with same-day turn-around time; the same number of results is reported out daily. Lab reporting staff receive an average of 210 calls a day. In addition, daily fax requests arrive from healthcare providers looking for test results for their patients. An average of 6,200 duplicate reports monthly. That translates to 295 daily. Lab reporting staff also verbally report Rabies results twice daily. If a result is positive, decomposed or unsatisfactory, a staff member will also contact officials in the appropriate public health region. The total number of samples varies and can be higher during the summer time, especially for bats.

Sometimes bats don’t arrive in the traditional manner. One time a bat made its way into the Laboratory building and somehow ended up in the Reporting room. Fortunately, the Safety Officer came to their rescue and captured the bat in a box.

The busiest times of year are August through April. August is the beginning of the school year, so THSteps specimens and requests increase due to Head Start programs ensuring that Medicaid kids are properly tested. This is also the busiest time for Sickle Cell requests. NBS peaks nine months after the beginning of winter. “Yes, NBS increases depending on how cold a winter we have had,” said Odoms.

Why is data entry still handled manually in this electronic age? Because the department has yet to find software and equipment to accommodate all three Laboratory Information Management Systems (LIMS) and their varied form sizes. All Data Entry Operators are cross-trained in all three LIMS. The phone staff are also cross-trained to perform searches on all three LIMS, and they can also do data entry.

Laboratory Reporting is a loyal and dedicated group. “Many of the Lab Reporting staff have been with us for many years – 10 employees have a total work experience of 177 years,” said Odoms.

A long-term Lab Reporting employee at her desk. Photo courtesy of Andrew Vinyard.

Lab Reporting staff work with people who are also passionate about results and how they impact patients. For example, a foster parent had no information on a foster child's birth mother and she needed a newborn screen. The lab reporting staff, the nurse, and the foster parent worked together diligently to search every parameter possible to locate the baby’s NBS screen, which had abnormal results.

“All patients are important. Each form represents a face, not just a name or number,” Odoms said. Supplying accurate, legible information about patients ensures that results are reported correctly with shorter turnaround times so that every patient in Texas can remain healthy.

by Jimi Ripley-Black




CQI Project Update: Completed Green Belt Project Saves $23,565 per year

In Lean Six Sigma, a method for making continuous quality improvements (CQI), waste is not defined with the common meaning. In Lean terminology, waste can be anything beyond the minimum amount of people, effort or material necessary to add value to a process. There are typically eight different types of waste in Lean. A few examples include: inventory, having too much or too little; over production, producing more than will be used then having excess sitting in inventory; defects, errors that need to be reworked; and waiting, for signatures, coworkers, approvals, product, etc.

There are currently eight individuals working on Green Belt projects in the Lab. Three are in the Media Preparation Group and five are in Newborn Screening. The first completed project in Media Prep focused on identifying and reducing internal waste. Green Belt Nora Berrios, and her team, defined internal waste as:  (1) errors made during media production and (2) media that failed quality control (QC). Errors were examined over a 24-month period during which 8,446 recipes were made with only 325 errors. While this is a very low error rate of only 3.85 percent, the cost of these errors was more than $62,000. The objective of this project was to reduce the error rate of the media that fail the most often by 10 percent, from 3.85 percent to 3.46 percent.

In order to accomplish this reduction, four Lean tools were used: (1) the 5 Whys, (2) mistake proofing, (3) the 5Ss, and (4) the spaghetti diagram. The 5 Whys literally asks the question “why” five times in order to get to the root cause of a problem. In this case, why are human errors occurring in media production? Once the root cause was determined, the team was able to implement simple, yet effective solutions, such as more on-the-job training for new technicians.

Mistake proofing is just what it sounds like – setting up visual cues to help prevent errors from occurring. Visual cues are around us every day, for example, the light on your stove top that tells you a burner is on to help prevent you from burning yourself. Or when the gas light in your car comes on to remind you to fill up so you don’t get stranded on the side of the road. In this project, a mistake proofing solution was as simple as highlighting the glassware required for a media recipe. This step ensures the technician will look closely at the procedure and prevent mistakes from happening by selecting the correct glassware.

5S is a familiar process in the DSHS Laboratory, because almost everyone has participated in a 5S project. 5S enhances organization, reduces clutter and facilitates a productive work environment. It was implemented in a common area for weighing out reagents – an important step in media production.

The spaghetti diagram maps a process and all the different routes taken to accomplish a task. Often, the maps are so convoluted it looks like spaghetti, hence the name. One media was selected for mapping that involved travel to and from another area on another floor and back and forth in the same room.

Spaghetti diagram - before

A little rearranging and preparation eliminated the travel during the process and the steps in the map were much cleaner and less spaghetti-like.

Spaghetti diagram - after

These changes may sound simple, and they are, however, these simple changes made a surprisingly significant impact. After implementing the improvements listed above, the error rate decreased from 3.85 percent to 0.63 percent – a huge improvement and an estimated cost savings of nearly $23,565 per year!

This project highlights the importance of organizations applying Continuous Quality Improvement, a management philosophy which contends that most things can be improved. Recommendations were provided to the Media Preparation Team Lead who will continue implementation and sustainability. The reduction in error rate was not due to an automated solution, but rather to implementation of recommendations identified by team members. It was a group effort. Periodic monitoring of issues will be critical for continued quality improvement. The dedicated team members who worked with Nora to make this project successful were Charles Harris, Miriam Udoye, Hong Trinh, Megan Snyder, Chris Goben, and Gayathri Kamalammal. Great teamwork!

by Vanessa Telles




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October 2014, Volume Six, Issue Two   (Publication #E14-13156)
Published by DSHS Laboratory Services Section
PO Box 149347, MC 1947
Austin, TX 78714

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email The Laboratorian


Grace Kubin, PhD
512 776 7318
email Grace

Jimi Ripley-Black
512 776 6505
email Jimi

Last updated May 19, 2015