1 | LGM Division Newsletter Summer 2018

Scientists Annual Meeting for Academy of Clinical Laboratory Physicians and Scientists by Suzanne Thibodeaux, MD, PhD

The Division of Laboratory and Genomic Medicine (LGM) had a strong showing at the Academy of Clinical Laboratory Physicians and Scientists (ACLPS) Annual Meeting, hosted by Houston Methodist Hospital and Research Institute in Houston TX. ACLPS is an interdisciplinary society comprised of clinical laboratorians across all subspecialties, which allows for unique networking and collaborative opportunities among trainees, junior faculty, and senior faculty with different professional backgrounds

The Young Investigator Session is a major highlight of the meeting, and LGM trainees presented seven abstracts. Three of these trainees, Jonathan Brestoff-Parker,

Sophonie Jean, and Abraham Qavi, were honored with the Young Investigator Awards. Two of our faculty, Suzanne Thibodeaux and Melanie Yarbrough, presented findings from projects supported by the Young Investigator Grant, which they both received in 2017.

A newsletter distributed by the Division of Laboratory & Genomic Medicine in the Department of Pathology & Immunology at Washington University School of Medicine

Summer 2018 - Volume 5, Issue 1

LGM | NEWSCONTACT US

If you have an idea for a story or have questions about the information in this newsletter, please contact the editors.

Suzie Thibodeaux srthibodeaux@wustl.edu

Tammy Robisontammyrobison@wustl.edu

2 | LGM Division Newsletter Summer 2018

LymphoTrack – A New NGS Assay for Assessment of IGH, TCRG and IGHV Clonality by Lindsay Lay & Julie Neidich, MD

New access to technological advances has allowed the BJH Molecular Diagnostic Laboratory to migrate its immunoglobulin heavy chain (IGH), T cell receptor gamma (TCRG), and IGHV Clonality testing to Next-Generation Sequencing (NGS)-based assays as of April 9, 2018. This assay replaces the PCR-based fragment size capillary electrophoresis assay.

The IGH, TCRG, and IGHV Clonality assays employ massively parallel sequencing technology with InvivoScribe LymphoTrack® reagents and Ion Torrent S5 sequencing instrument. The assays determine the relative proportions of TRG or IGH gene rearrangements formed by the recombination and somatic mutation of the V, D, and J gene segments in lymphocytes. Assessment of clonality of TRG or IGH gene rearrangements is used in the diagnosis and monitoring of T or B lymphoid cancers, including leukemias and lymphomas. The assay is run once per week (typically on Tuesdays), and the estimated turnaround time is approximately 7-10 business days.

Due to the greater analytical sensitivity and higher resolution of the LymphoTrack® NGS assays, there were differences in the clonality results for patient samples tested side-by-side with the older PCR-fragment analysis during the validation of the new NGS assays. Specifically, the NGS LymphoTrack® assay detected clonal rearrangements in 40% (IGH) and 42% (TRG) of samples that were polyclonal by fragment analysis, demonstrating higher analytical sensitivity of the assay. In addition, the NGS LymphoTrack® assay detected only polyclonal rearrangements in 4% (IGH) and 15% (TRG) of samples that were clonal by fragment analysis, demonstrating higher resolution of the assay (i.e., multiple different clonal rearrangements of the same size).

Questions about these changes may be directed to Lindsay Lay, Manager of the Molecular Diagnostics Laboratory, 314-454-7601, Lindsay.Lay@bjc.org, or to Julie Neidich, M.D., Interim Medical Director, 314-273-7120, jneidich@wustl.edu.

To contact an LGM faculty member, please email them or call 314-362-2998.

Co-Chief Laboratory & Genomic MedicineCharles Eby, MD*

BJH Clinical ChemistryMitch Scott, PhD*Ann Gronowski, PhD*

BJH Drug Monitoring ∙ ToxicologyJohn Turk, MD, PhD*

BJH Serology ∙ ImmunologyAnn Gronowski, PhD*Neil Anderson, MD*

BJH MicrobiologyCarey-Ann Burnham, PhD*Neil Anderson, MD*Melanie Yarbrough, PhD*

BJH Blood Bank ∙ Transfusion MedicineBrenda Grossman, MD*Ron Jackups, MD, PhDChang Liu, MD, PhD*Charles Eby, MD George Despotis, MDSuzie Thibodeaux, MD, PhD*

BJH Hematology ∙ HemostasisJohn Frater, MD*Ron Jackups, MD, PhD*Charles Eby, MD*

BJH Flow CytometryFriederike Kreisel, MD*

BJH Cytogenomics Julie Neidich, M.D.*Ina Amarillo, Ph.D.Yang Cao, Ph.D.

BJH Molecular DiagnosticsJackie Payton, MD, PhD*Julie Neidich, MDWojciech Swat, PhD

BJH HistocompatibilityChang Liu, MD, PhD*

BJH Clinical & Translational GenomicsJon Heusel, MD, PhD*Latisha Love-Gregory, PhDSamantha McNulty, PhDMolly Schroder, PhD

SLCH Core LaboratoryDennis Dietzen, PhD*Stephen Roper, PhD*Ron Jackups, MD, PhD*

CLINICAL FACULTY CONTACT INFO* denotes laboratory director

3 | LGM Division Newsletter Summer 2018

Microbiology Update: Eswabs for Cultureby Lindsay Lay & Julie Neidich, MD

Beginning August 1, 2018, if swabs are used for specimen collection, each microbiology culture type/orderable test (example: bacterial, fungal, mycobacteria) will require

a separate ESwab. Sending tissue or fluid in a sterile container is preferred, with swabs being reserved for cases when tissue or fluid cannot be obtained.

HistoTrac – New Information System for the HLA Laboratoryby Lindsay Lay & Chang Liu, MD, PhD

On June 2, 2018, the BJH Histocompatibility (HLA) Laboratory launched HistoTrac, a laboratory information system for all HLA testing and reporting, which replaces the Cerner HLA module that was previously in use. Developed by HLA specialists, HistoTrac is a versatile system poised to streamline BJH HLA Laboratory services by meeting the needs of the complex and challenging HLA Laboratory.

With this system, we anticipate the following improvements:

• Custom-built HLA EPIC order sets that integrate with both Cerner and HistoTrac to allow a smooth interface of information between all systems

• Custom-built reports for HLA typing, antibody screen, crossmatch, and donor-specific antibody (DSA) interpretation with improved clarity

• Reduction of paper-heavy processes, which will streamline the laboratory workflow

• Reduction of manual data entry for testing results by interfacing with instruments and databases

• Interface capabilities with national transplant databases such as UNOS and NMDP, with plans to make active in the future, with the goal of reducing the time for data transfer and entry between all parties and systems

• Improved lab management tools such as turn-around-time monitors

The BJH HLA Laboratory faced a monumental undertaking by pairing the launch of HistoTrac alongside that of EPIC, with a timeline for launch ultimately being under a year. The build and launch of HistoTrac required an immense effort and time commitment that speak to the dedication of the HLA team members and their collaborators in IS, LIS, SystemLink (the vendor of HistoTrac), and beyond. We express our gratitude to the BJH HLA Laboratory team for the efforts that went into this project. Every person in the lab played a critical role in the ability to launch HistoTrac, all while operating and maintaining a busy clinical HLA laboratory. The BJH HLA Laboratory will continue to work through the post-go-live improvements that will only serve to realize all of the intended system goals and optimize our internal workflows.

DID YOU KNOW?By Kim Zohner

In 2018 BJH labs called an average of 4242 critical results per month, 99.6% of which are completed within 30 minutes of the result being available.

4 | LGM Division Newsletter Summer 2018

FEATURED COLLEAGUE

Molly Schroeder, PhD

Molly Schroeder, PhD joined Washington University as Assistant Professor of Pathology and Immunology in April 2018. Dr. Schroeder is a Clinical Laboratory Geneticist certified by the ABMGG in Clinical Molecular Genetics and Cytogenetics. She obtained her BS at Saint Louis University and her PhD from Baylor College of Medicine, where she investigated the roles of developmental growth control signals and cell competition in epithelial tumor suppression. She then completed a Clinical Laboratory Fellowship in the Center for Human Genetics Laboratory at Case Western Reserve University/University Hospitals, where she led several validation projects, including the lab’s first next generation sequencing (NGS) assay. After fellowship, she joined the HudsonAlpha Institute for Biotechnology as a senior scientist and laboratory director.

Dr. Schroeder is a member of the LGM division, Clinical and Translational Genomics, and is an Associate Medical Director of the Cytogenomics and Molecular Pathology Laboratory. Her clinical and research interests include genome-scale sequencing, assay development, and the application of evidence-based medicine approaches to laboratory genomics.

We welcome Dr. Schroeder!

Enhanced Recovery of Fastidious Microorganisms from Urine Specimans in the Setting of Total Laboratory Automation for Urine Culture by William Lainhart, PhD & Carey-Ann Burnham, PhD

The BJH Microbiology Laboratory has recently adopted automated instrumentation (the Kiestra Total Laboratory Automation System) for processing of some culture-based testing. The laboratory has been using this system for culture of urine specimens since 2016. To understand the impact of automation on the recovery of microorganisms from urine specimens in the BJH Microbiology laboratory, we compared urine culture data from the pre-automation (July 2015-June 2016) and post-automation (October 2016-September 2017) time periods. In the post-automation time period, we observed a significant increase in the number of organisms reported (199 per 1,000 cultures pre-automation compared to 224 per 1,000 cultures post-automation, p <0.0001), and increases

in recovery (proportion of positive urine cultures) of some common (Escherichia coli) and less common uropathogens, such as Aerococcus urine and Staphylococcus saprophyticus (Table).

An interesting finding of this study is the increase in detection of Neisseria gonorrhoeae on blood agar plates in the post-automation time period. We hypothesize that this increased recovery can be attributed to the plates remaining in optimal incubation conditions continuously and review of culture plates on high-resolution monitors. While molecular methods remain the gold standard for the diagnosis of N. gonorrhoeae infections, improved recovery of N. gonorrhoeae using TLA has the potential to support public health and surveillance programs.

Organism Pre-TLA (n per 1000 cultures)

Post-TLA (n per 1000 cultures)

Percent Change p-value

Escherichia coli 79.4 101.2 +27% <0.0001Klebsiella spp. 22.9 24.0 +5% 0.24Streptococcus agalactiae 22.2 36.7 +66% <0.0001Aerococcus urinae 2.2 4.4 +103% <0.0001Staphylococcus saprophyticus

1.0 2.3 +126% <0.0001

Neisseria gonorrhoeae 0.2 1.0 +371% <0.0001Actinotignum schaalii 0.1 0.13 +33% 0.77Streptococcus pneumoniae 0.02 0.1 +312% 0.27Alloscardovia omnicolens 0.0 0.06 n/a 0.30

TLA – total laboratory automation; n/a – not applicable

5 | LGM Division Newsletter Summer 2018

HistoTrac - New Information System for the HLA Laboratory by William Lainhart, PhD & Carey-Ann Burnham, PhD

Gram Negative BacilliAchromobacter spp. (respiratory) 35 20 69 17 74 86Achromobacter spp. (non-respiratory) 45 7 98 24 7 95Acinetobacter spp. 57 95 88 91 96 93 93 84Acinetobacter calcoaceticus-baumannii complex 78 74 41 44 36 76 45 36 40Citrobacter freundii complex 204 • • • 98 • • 94 94 95 99 • 86 •Citrobacter koseri 176 93 100 97 98 95 100 98Enterobacter aerogenes 226 • • • 98 • • 98 100 51 98 • 96 •Enterobacter cloacae 509 • • • 92 • • 95 98 60 99 • 87 •Escherichia coli 7091 47 50 87 95 93 95 75 93 100 98 72 Escherichia coli - URINE ONLY 6290 47 31 91 95 94 96 76 93 98 100 98 73Klebsiella oxytoca 293 • 72 54 96 93 96 96 96 96 100 94 90Klebsiella pneumoniae 1522 • 63 91 94 94 94 93 97 66 99 95 80Klebsiella variicola 144 • 93 98 99 99 99 99 99 86 99 99 90Morganella morganii 123 • • • 98 94 91 80 84 ‡ 100 • 67 •Proteus mirabilis 969 82 96 73 99 98 99 70 93 ‡ 100 100 75Proteus vulgaris/hauseri 41 • • • 100 95 98 88 95 ‡ 100 • 85 •Providencia stuartii 61 • • • 100 98 97 48 82 ‡ 97 • 59 •Providencia rettgeri 55 • • • 100 100 100 82 98 ‡ 100 • 69 •Pseudomonas aeruginosa 1430 93 97 92 83 91 87 90 77Pseudomonas aeruginosa (mucoid phenotype) 215 85 94 91 77 83 88 89 80Serratia marcescens 207 • • • 99 • • 97 99 99 • 93 •Stenotrophomonas maltophilia 205 85 99 94

‡ Intrinsically resistant to nitrofurantoin.Shaded boxes indicate organism/antimicrobial combinations not tested routinely.Data based on first isolate per patient.

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Percent of Strains Susceptible to Antimicrobial IndicatedRegional Antibiogram - 2017 Patients ≥18 years of age Alton Memorial Hospital, Barnes-Jewish Hospital, Christian Hospital, Parkland Health Center, St. Louis Children's Hospital

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Gram PositiveStaphylococcus aureus 4023 99 55 74 98 40 100 55 98 99 MRSA* 1791 99 0 65 97 11 100 0 96 99 MSSA** 2231 100 100 81 98 63 100 100 99 99 VISA*** 36 100 56 64 94 36 100 56 100 0Staphylococcus capitis 34 85 79 100 79 100 85 97 100Staphylococcus epidermidis 506 35 60 88 34 100 35 44 100Staphylococcus hominis 63 41 67 74 23 100 41 39 100Staphylococcus intermedius group 46 98 67 80 69 100 98 63 100Staphylococcus lugdunensis 369 93 79 96 74 100 93 98 100Enterococcus faecalis 1111 99 31 75 100 100 94Enterococcus faecium 329 8 47 91 98 34 29Streptococcus agalactiae 93 100 49 42 100 100Streptococcus anginosus 156 99 80 69 98 100Streptococcus constellatus 95 100 80 78 96 100Streptococcus intermedius 98 100 76 62 99 100Streptococcus mitis group 95 97 88 42 65 100Streptococcus pneumoniae 182 99 90 91 84 53‡ 98 66 100Corynebacterium striatum 105 2 28 100 0 100

** Methicillin-Susceptible Staphylococcus aureus.

Shaded boxes indicate organism/antimicrobial combinations not tested routinely.Data based on first isolate per patient.

† Only indicated for uncomplicated cystitis.

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Percent of Strains Susceptible to Antimicrobial IndicatedRegional Antibiogram - 2017 Patients ≥18 years of age Alton Memorial Hospital, Barnes-Jewish Hospital, Christian Hospital, Parkland Health Center, St. Louis Children's Hospital

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The BJH Microbiology Laboratory now provides microbiology services for five hospitals in the BJC healthcare system. As a result of this consolidation of services, we have the opportunity to examine antimicrobial resistance patterns on a more regional level.

This year, for the first time, we have had the ability to produce regional antibiograms for adult and pediatric patients. The 2017 adult regional antibiograms for Gram-positive and Gram-negative bacteria are shown below. Regional and hospital-specific antibiograms are available in Dorsata.