The Laboratorian - Volume 1, Issue 2

The Laboratorian - Volume 2, Issue 2
Laboratorian header logo

October 2009 - Volume 1, Issue 2

Article Index

- Fighting the Flu
- NBS Expansion Update
- PKU Summer Camp
- Studying Tuberculosis
- Stress Management


My fascination with nearly all things medical probably started with my mother’s stories of her work as a Labor and Delivery nurse. When I read my first account of the 1918 influenza pandemic, that fascination turned to stories related to the epidemiology of how viruses spread and the public health measures taken to prevent, when possible, or contain when not. I knew that I would see a flu outbreak in my lifetime, but I never expected to have such a close experience with the response efforts.

When I was offered my current position as the Information Specialist for the DSHS Laboratory, I was thrilled to combine my interests with my skills. That is how, in early May 2009, I found myself elbow-deep in disseminating flu-related information through the Laboratory website and coordinating Laboratory documents with the DSHS. At the peak of the DSHS flu response, I briefly served as FAQ Coordinator in the MACC (Multi-Agency Coordination Center). I was the smallest cog in a tremendously complex response effort—much of it done by people whose expertise I could grasp just enough to admire. Seeing the flu response unfold from inside a public health laboratory was everything and nothing like I had imagined.

Read the article on the DSHS Laboratory influenza response, “Fighting the Flu,” for a look at the tremendous work done by some very dedicated laboratorians, and for an overview of how our laboratory is preparing for the anticipated fall flu resurgence.

The amazing thing is that, during the flu response, the Laboratory was still completing its usual testing load. This Issue also highlights some of the testing efforts in other areas. The “Newborn Screening Expansion Update” gives an overview of how Newborn Screening testing has changed and is still growing, and it is accompanied by an article about children whose lives are better for this type of testing. The article on "Studying Mycobacterium Tuberculosis” exhibits a research plan to explore new treatment of a certain strain of tuberculosis. After reading about the Laboratory’s complex and diverse testing, please relax with us by reviewing some “Stress Management” tips and fun historical tidbits in “Did you know?”

I am proud of the work that our laboratorians accomplish, and it is my hope that each issue of The Laboratorian will help readers better appreciate the important public health work of the DSHS Laboratory.

by Jimi Ripley-Black

Did you know?

In 1876, the Governor of Texas was authorized by the legislature to appoint a State Health Officer—a physician who would coordinate quarantines in areas where epidemic disease had broken out. In 1903, the name was changed from Texas Quarantine Department to the Texas Department of Public Health. However, it was three years later in 1879 that the first officer took the job.

The job qualifications for the first State Health officer were: “Must know yellow fever and smallpox.”

Fighting the Flu

Laboratorians sort flu specimens

During the coming autumn months, a resurgance of H1N1 influenza is anticipated as seasonal flu makes its regular appearance. The confluence of both strains will make for a busy flu season this year. The DSHS Laboratory is building on experience to provide optimal testing response.

H1N1 flu is a novel form of the influenza virus that first sickened humans in the United States this past April and has since caused 42 deaths in Texas. In June, the World Health Organization declared that the widespread H1N1 outbreak, while unexpectedly mild to moderate, had developed into a pandemic, the term for a global outbreak. During a regular flu season, the DSHS Laboratory tests approximately 22 specimens per day with two technical staff performing polymerase chain reaction (PCR) testing on 1,000 to 1,500 specimens received during the entire season (October through May).

On April 24, 2009, the Multi-Agency Coordination Center (MACC) was activated. By May, during the peak of the H1N1 flu response, the DSHS Laboratory received 1,410 specimens in a single day and 13,500 specimens total (from late April through early July). Specimen throughput was ramped up over a period of nine days. To support this response, staffing was increased to 25 trained laboratory staff, 15 temporary laboratory employees, and 66 non-technical laboratory staff.
Due to the massive number of specimens submitted for H1N1 testing, extra equipment was also needed. This included the use of four ABI (Applied Biosystems Incorporated) 7500 FAST instruments doing real time PCR testing. One upgraded instrument was housed in Virology, one in Biothreat, and two were on loan from the manufacturer. On the ABI 7500 FAST instruments alone, 20 trained staff processed 252 specimens per 14.5-hour shift.

A supplemental testing platform was brought in to complement real time PCR testing. Based here in Austin, the biotech company, Luminex developed the xTAG RVP respiratory virus panel to provide detection and identification of respiratory virus nucleic acids. This platform uses reverse transcription PCR and target specific primer extension to generate viral DNA templates and works with the Luminex 100/200 IS system to analyzes up to 96 specimens per run. Specimens are analyzed using the Universal-Tag sorting system, which relies on specifically tagged beads to classify the viral templates. Once the beads are mixed with the generated viral DNA template, the Luminex system files the beads one by one past a laser. The laser then analyzes the tagged beads and provides a possible result call for that specimen.

Temp doing Luminex testing

During the height of H1N1 sample submission, technicians were able to analyze up to 360 specimens a day using the Luminex system. Specimens that tested presumptive positive for indicators of the H1N1 virus could then be confirmed using real time PCR. With the addition of the Luminex testing platform, approximately 1,000 specimens could be analyzed each week for the presence of respiratory viruses, increasing the overall efficiency of the surveillance and testing provided by the DSHS Laboratory.

The Laboratory Response Network (LRN) is a national network, of mostly state laboratories, that provides support against biological and chemical threats as well as public health emergencies. Texas has 11 LRN labs located in various areas of the state, including the state laboratory in Austin. The LRN labs proved essential in dealing with the influx of specimens received during the H1N1 outbreak in the spring.

The total number of specimens received by Texas laboratories was over 38,000, through early July 2009. For all specimens tested at the DSHS Laboratory, 21.1 percent tested positive for H1N1 and 74.9 percent tested negative for influenza A. Texas had 4,463 confirmed and probable cases of novel H1N1 flu. The DSHS Laboratory also requested assistance from laboratories outside of the state; Tennessee and Virginia tested a total of 900 specimens, which allowed them to test their surge capacity.

Employees throughout DSHS have been busy for months making preparations for the anticipated fall resurgence of both H1N1 and seasonal flu. This includes the Laboratory, which will build on experience gained during the April 2009 outbreak. Our focus will be on surveillance activities, including monitoring virus distribution and spread, and the detection of new variants.

Requirements for submitting flu specimens to the DSHS Laboratory and LRN laboratories have been updated and distributed to Texas hospitals. New instruments have been acquired to help process specimens faster, and thus help to report results faster. Plans are in place for triaging specimens, so that high priority specimens are tested first; this includes new specimen storage plans for novel and unique strains that can be sent to the CDC for further characterization. Plans for surge capacity include the LRN laboratories, other state laboratories, and possibly the Galveston National Laboratory.

Laboratory staff are being cross-trained for all aspects of H1N1 testing. Other staff have been identified to work in the MACC and to staff a Laboratory-specific MACC-like operations center. A Laboratory work group that includes members from Virology, Specimen Acquisition, Container Preparation, Results Reporting, and management meets weekly to review plans and strategies, complete assignments, and address unmet needs. Twice a week, the heads of Emergency Response and Microbiology meet with the MACC Response Team to ensure that plans and procedures are in place for a coordinated response during the anticipated fall resurgence of flu.

Dr. Lakey has a succinct way of putting it: “We used to say that it wasn’t a matter of if a pandemic would strike, but when,” he says. “Well, the time is now.”


Newborn Screening Expansion Update

In 1965, Texas began screening newborns for heritable disorders. Phenylketonuria (PKU) was the first disorder mandated for widespread population screening. Children with PKU cannot metabolize the amino acid phenylalanine (phe), and it’s accumulation in the blood can lead to severe mental retardation. Initially, newborn dried blood spot specimens were screened for PKU by a bacterial inhibition assay called the “Guthrie assay.” The analysis required the daily preparation of a phe-free media and the addition of a bacterial growth inhibitor and B. subtilis spores. When dried blood spot dots were applied to the agar plate and allowed to Photo of Newborn Screening heelstick
incubate for 16-18 hours, the phe present in the blood spots diffused into the media, blocked the inhibitor, and allowed the growth of B. subtilis. The B. subtilis growth zone was proportional to the concentration of phenylalanine in the blood spot. In 2001, a fluorometric assay was implemented that reduced the PKU assay incubation steps from 16 hours to 2.5 hours.

On December 6, 2006, the DSHS Laboratory began screening infants for metabolic disorders using tandem mass spectrometry (MS/MS). The MS/MS method dramatically changed screening for metabolic disorders in Texas. The MS/MS method transformed screening for PKU to a procedure that measures 30 amino acids and acylcarnitines in two minutes, after a two hour sample preparation step. The analysis requires thirty microliters of each sample, which are injected into an MS/MS instrument. Each sample is ionized and the ions are then sorted and separated by their mass-to-charge ratio. The measurement of the ions produces a mass spectrum used to determine the relative amount of each the 30 amino acids and acylcarnitines.

By analyzing the levels of the different amino acids and acylcarnatines, the Newborn MS/MS Screening Laboratory is now able to screen infants for 20 different metabolic disorders, including PKU. The metabolic disorders screened by MS/MS include six amino acid disorders, five fatty acid oxidation disorders, and nine organic acid disorders.

Metabolic disorders often result from inborn errors that effect the production of essential enzymes, which the body uses to breakdown nutrients into their basic components. Early intervention can prevent many of the life-altering symptoms associated with metabolic disorders. The most frequent metabolic disorder identified in Texas by MS/MS screening is Medium Chain Acyl CoA Dehydrogenase Deficiency (MCAD), a fatty acid oxidation disorder. Each year, approximately 20 children are diagnosed with MCAD as a result of newborn screening. Children with fatty acid oxidation disorders have to eat regularly, especially when they are sick, because fasting puts them at increased risk of death due to hypoglycemia. To learn more about the disorders screened by MS/MS analysis at DSHS, visit the newborn screening website:

More than 1,583,000 dried blood spot specimens submitted for approximately 812,000 Texas infants were analyzed by MS/MS in Texas by the end of 2008. A total of 4,619 specimens were flagged and required follow-up by Newborn Screening Case Management nurses and public health technicians. Of those flagged with abnormal results, confirmatory testing was recommended for about 900 infants. From December 2006 to December 2008, a total of 137 infants, affected by one of the 20 disorders screened, have been diagnosed following an abnormal newborn screen result by the DSHS Newborn Screening Laboratory. As outlined in the second part of the table below, an additional 62 infants with varying forms of metabolic conditions have been identified and several metabolic conditions have also been detected in the mother as a result of screening the baby.

Disorders reported to the DSHS since Newborn Screening began (Dec. 2006)



Phenylketonuria (PKU)


Maple syrup urine disease (MSUD)




Argininosuccinic acidemia (ASA)


Citrullinemia (CIT)


Tyrosinemia type I (TYR)


Medium-chain acyl-CoA dehydrogenase deficiency (MCAD)


Long-chain hydroxyacyl-CoA dehydrogenase deficiency (LCHAD)


Trifunctional protein deficiency (TFP)


Very-long-chain acyl-CoA dehydrogenase deficiency (VLCAD)


Glutaric acidemia type I (GA I)


Beta-ketothiolase deficiency (BKT)


Hydroxymethylglutaric aciduria (HMG)


Isovaleric acidemia (IVA)


3-methylcrotonyl-CoA carboxylase deficiency (3MCC)


Methylmalonic acidemia, Cbl A and Cbl B forms


Methylmalonic acidemia, mutase deficiency form


Multiple carboxylase deficiency (MCD)


Propionic acidemia (PA)


Carnitine uptake defect (CUD)


Other Disorders Detected


Benign Persistent Hyperphe


Hyperphe Variants


Methylmalonic acidemia, Cbl C


Tyrosinemia type II (TYRII)


2-Methylbutrylglycinuria (2MBG)


Carnitine Acylcarnitine translocase deficiency (CACT)


Carnitine Palmitoyl Transferase I deficiency (CPT 1)


*Disorders are reported to the NBS program by metabolic specialists.

Newborn Screening in Texas continues to change and improve the lives of infants and their families as the entire program continues to expand and identify ideas to improve laboratory and newborn screening practices.

by Patricia Ramos Hunt

Camp PHEver: Summer Camp with a Mission

Camp PHEver participants 2009Camp PHEver fun

Since newborn screening began in Texas, over 600 children have been diagnosed with Phenylketonuria (PKU), a disorder that can lead to severe mental retardation if it is not detected and treated. Children with PKU cannot metabolize phenylalanine (phe)—an essential amino acid that is present in many of the foods we eat. PKU has traditionally been treated by restricting the dietary intake of protein and phe; although recently, a new drug has been approved that has loosened some of the dietary restrictions.

Metabolic centers and metabolic specialists have played a central role in ensuring that affected infants receive proper care and treatment. In addition to providing medical services and nutrition counseling, metabolic staff from across the state often provide emotional support and help build a safe environment for affected children and their families. For the past 13 years, two special people, Barbara Dominguez, RN and Kerri Lamance, RN, BSN, have directed an annual summer camp that they co-founded for children affected with PKU. The camp—called Camp PHEver—is sponsored by Texas Children's Hospital. Camp PHEver’s mission is to provide a typical summer camp experience for children and adolescents with PKU; they can meet new friends, reunite with old camp buddies, feel comfortable about PKU, and just have fun.

The camp is held every July in Brenham, Texas. This year, 68 kids from across the nation attended the camp. In addition to the fun activities, the staff prepares special low protein meals to demonstrate that meals can be tasty and still meet the requirements of the special diets that the kids are required to maintain. A PKU dietary monitoring specimen is collected from each child at the beginning of camp and at the end of camp in order to demonstrate, to the kids, that eating low protein meals can improve the phenylalanine level in their blood.

After the specimens are collected, they are sent to the DSHS Laboratory for analysis. Each year, the Chemistry Check-In Group, Data Entry and Laboratory Reporting Group, and Newborn Tandem Mass Spectrometry Screening Laboratory await the specimens with anticipation. This annual event increases the typical PKU dietary monitoring program workload (5-10 daily specimens) by more than ten-fold, with an average of 120 specimens received. Laboratory staff work together to ensure that specimen results are ready and available in a timely manner—helping to do their part to make certain that another Camp PHEver comes to a successful conclusion.

When the laboratory analysis is complete, test results are sent to the Camp PHEver directors who share the test results with the kids and their families at their next appointment. The helps demonstrate, to the kids and their families, that eating low protein meals can improve the phenylalanine level in their blood, which promotes continued positive patient outcomes.

by Patricia Ramos Hunt

Studying Mycobacterium Tuberculosis

The DSHS Laboratory is involved in an ongoing grant-funded project to investigate whether mycobacterium tuberculosis (MTB) is susceptible to moxifloxacin. Moxifloxacin is one of a class of antibiotics called fluoroquinolones that are used as second-line anti-TB drugs. Patient samples, in this case isolated from patients in the Houston, Texas area, are analyzed for reduced susceptibility to moxifloxacin and other fluoroquinolone antibiotics, as well as first-line antibiotics. This study will further identify mutations in genes associated with reduced susceptibility to the fluoroquinolone antibiotics—work that should help in the design of better treatment regimens and provide a basis for further monitoring and research on TB drug resistance. moxifloxacin

Quick Facts

  • Global TB:  One infection occurs every second; 32 percent of the earth’s population is infected with TB; and 9-10 million people develop active TB annually.
  • Moxifloxacin is a topoisomerase inhibitor (it inhibits DNA replication) fourth generation fluoroquinolone. The Laboratory tests Ofloxacin (a second generation drug) in our secondary anti-TB drug panel. Ofloxacin is currently considered to be a class representative of all other fluoroquinolones.
  • Moxifloxacin is as bactericidal as Isoniazid and has higher activity than Ofloxacin.
  • During 2007-2008, there were 634 culture positive TB cases in Houston, Texas.
  • Six of the 314 Laboratory samples have Moxifloxacin Resistance.
  • Serum concentration of Moxifloxacin can be at a higher level than other fluoroquinolones in treatment of Tuberculosis.

The grant is funded by the National Institutes of Health (NIH) for the principal investigator (PI) Hana M. El Sahly, MD, at Baylor College of Medicine. Dr. El Sahly is coordinating with members of the DSHS Laboratory—Denise Dunbar, Mycobacteriology/Mycology supervisor and Ken Jost, Tuberculosis Applications Scientist—and various TB Experts in the Houston area to conduct this project. The PI’s group now works at the Methodist Hospital Research Institute, Department of Pathology, and Molecular Tuberculosis Laboratory, Houston, Texas. The grant provides for the contract cost of each specimen’s drug susceptibility testing (DST). Genotyping is provided by the Centers for Disease Control and Prevention (CDC) Universal Genotyping Program.

This study will help establish background levels of moxifloxacin resistance occurring in a general population. At the DSHS Laboratory, DST includes Isoniazid, Rifampin, and Ethambutol in a primary panel. Further DST includes Streptomycin, Ethionamide, Kanamycin, Rifabutine, Ofloxacin, Pyrazinamide and Capreomycin. Multidrug-resistant TB (MDR-TB) is defined as resistant to Isoniazid and Rifampin while extensively drug-resistant TB (XDR-TB) is defined as MDR-TB that is also resistant to any fluoroquinolone and an injectable drug (Capreomycin, Kanamycin or Amikacin). Moxifloxacin, a fourth generation fluoroquinolone, is sometimes used by physicians to treat TB throughout the country. Moxifloxacin is as bactericidal as Isoniazid and has a higher bactericidal activity than Ofloxacin.

Treatment of TB requires patients to take at least six months of multiple anti-tuberculosis drugs. If the patient does not take the medications regularly for the full treatment period, or if medications are not prescribed properly, the disease may not be cured—resulting in recurrence or emergence of drug resistant TB. First-line drugs are very effective in the treatment of drug susceptible TB, although in the United States, the rate of TB drug resistance to at least one of the four first-line drugs stands at 7.4 percent, as of 2007. It has been 36 years since the last FDA-approved drug to treat TB, Rifampin, was introduced into the drug market. A difference between Isoniazid and Moxifloxacin is that Isoniazid is used only to treat TB; however, fluoroquinolones are used to treat a broad range of bacterial infections. It is helpful to have very effective drugs held back as second line anti-TB drugs; in the event there is resistance or intolerance to first-line drugs, there remain effective drugs for treatment.

Patient samples are analyzed, over a two-year sample period, for reduced susceptibility to moxifloxacin and other fluoroquinolone antibiotics, as well as first-line antibiotics. No study has yet identified fluoroquinolone resistance of all clinical culture-positive TB isolates in a defined population. This study will identify mutations in the genes associated with reduced susceptibility to the fluoroquinolone antibiotics, which should help to design better treatment regimens and provide a base line for further monitoring and research on TB drug resistance.

Currently, 634 TB culture-positive patients from Houston isolates have been enrolled in the study. The DSHS Laboratory has received MTB isolates from 559 patients. Thus far, 314 isolates have been tested and 6 (1.9 percent) were found to be resistant to Ofloxacin and Moxifloxacin. Future studies involving the Laboratory are anticipated to concern CDC task orders, for example, to define significant clusters for classic epidemiology variables aiding genotyping studies.

If you would like to learn more about TB, this CDC web page has more details:

by Monty Gomez and Ken Jost


Stress Management

Regulatory requirements, the novel H1N1 influenza A response, and other factors have lead to an increase in work demands at the Laboratory, which has left many laboratorians feeling stressed. This article gives guidance on managing these emotions, as presented by Patrick Clynch, the Laboratory training coordinator and a Licensed Professional Counselor.

What are the signs of stress? First, answer the following questions:

  • Do I take care of myself?
  • Do I eat the right types of foods?
  • Do I get as much sleep as I need?
  • Am I happy?
  • Do I have a positive self esteem?
  • Am I in positive physical shape and physically fit?
  • Do I like my appearance?
  • Do I feel relaxed a lot of the time?
  • Do I manage my emotions in a healthy manner?

Many answer “no” to some of these questions, when looking back over the past couple of years—or sometimes just a couple of months, weeks, or even days. The real problem begins when the long-term answer to these questions is “no.” These are signs of stress. With continual stress, bad habits develop so that the person effected does exactly the opposite of what should be done to take care of physical and emotional health. Examples are: (1) developing bad habits, such as poor nutrition and lack of exercise; (2) neglecting rest and relaxation; and (3) thinking negative thoughts. Staying up late worrying, stress eating, drinking, and smoking do not work well for long-term management of chronic stressors—not to mention the health detriment. These types of behaviors and habits also begin to degrade any sense of positive self esteem. Over time, these patterns become increasingly difficult to break.

Now that stressors have been identified, how can they be managed?

There is simple a way to look at stress management. First, look at lifestyle and realize and accept that the current plan is not working. Think of body, mind, and soul. Look back over the past six years and ask, “How I am doing?” The following areas are referred to as the Six Stress Managers:

  1. Fun and play
  2. Exercise
  3. Nutrition and food
  4. Meditation/prayer (faith and spirituality)
  5. Relaxation and sleep (rest)
  6. Journaling (thoughtful reflection)

Think about the Six Stress Managers. Now, what is the next step?

When there are signs of excessive moodiness, anger, unhappiness, and/or stress, it is good practice to stop and take an inventory in these areas. The idea is that what is going on right now is not working or not working well. Choose to make changes. Changes do not have to be big or done all at once, but there should be enough change to do something different or new. Remember, decide what works on a personal level; not what might work for someone else.

Realize that the way to reduce stress is to change what is not working. Recognize what is not working well, under the current plan, and make a conscious decision and effort to do something different. That may entail journaling thoughts, trying a new hobby, watching a different television show, reading a new magazine, trying new places of worship, going to bed earlier, joining a gym, or eating healthier. The choice is personal. Even the smallest changes can influence future well-being. There is nothing to lose by trying.

No one likes to change, so why is it important?

Thinking about change when stressed or angry is not easy. However, feelings of stress, anger, and unhappiness are indicators of taking on too much. Ask these questions:

  • Am I doing the things that help me lead a happier and more balanced life?
  • Am I in harmony with myself?

Practicing the positive habit of evaluating the Six Stress Managers and focusing on being active—rather than reactive—by doing some things differently, leads to developing the tools for stress management. Use these tools until this statement becomes true: “I have never felt better in my entire life.”

by Cindy Crouch


Note: External links to other sites are intended to be informational and do not have the endorsement of the Texas Department of State Health Services. These sites may not be accessible to people with disabilities.

To receive new issue notifications via email, please click on "Sign Up for E-mail Updates" logo on the main newsletter web page:

October 2009, Volume One, Issue Two
(Publication #E14-13156)
Published by DSHS Laboratory Services Section
PO Box 149347, MC 1947
Austin, TX 78714

512 458 7318
888 963 7111, ext 7318 Toll Free
email The Laboratorian


Susan U. Neill, PhD
512 458 7318
email Susan

Jimi Ripley-Black
512 458 7318, ext 6505
email Jimi

Last updated April 6, 2011