Laboratory and Basic Science Research Commons^™

Biographical Feature: Karen C. Carroll, M.D., Erik Munson

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Confidential Machine Learning On Untrusted Platforms: A Survey, Sharma Sagar, Keke Chen

Clinical Lab Sciences Faculty Research and Publications

With the ever-growing data and the need for developing powerful machine learning models, data owners increasingly depend on various untrusted platforms (e.g., public clouds, edges, and machine learning service providers) for scalable processing or collaborative learning. Thus, sensitive data and models are in danger of unauthorized access, misuse, and privacy compromises. A relatively new body of research confidentially trains machine learning models on protected data to address these concerns. In this survey, we summarize notable studies in this emerging area of research. With a unified framework, we highlight the critical challenges and innovations in outsourcing machine learning confidentially. We focus …

Sgx-Mr: Regulating Dataflows For Protecting Access Patterns Of Data-Intensive Sgx Applications, A.K.M. Mubashwir Alam, Sagar Sharma, Keke Chen

Clinical Lab Sciences Faculty Research and Publications

Intel SGX has been a popular trusted execution environment (TEE) for protecting the integrity and confidentiality of applications running on untrusted platforms such as cloud. However, the access patterns of SGX-based programs can still be observed by adversaries, which may leak important information for successful attacks. Researchers have been experimenting with Oblivious RAM (ORAM) to address the privacy of access patterns. ORAM is a powerful low-level primitive that provides application-agnostic protection for any I/O operations, however, at a high cost. We find that some application-specific access patterns, such as sequential block I/O, do not provide additional information to adversaries. Others, …

Biographical Feature: William A. Hinton, M.D., Erik Munson

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Comprehensive Molecular Screening In A Cohort Of Young Men Who Have Sex With Men And Transgender Women: Effect Of Additive Rectal Specimen Source Collection And Analyte Testing, Erik Munson, Alyssa Reynoso, Morena Pass, Kathleen Buehler, Daniel Ryan, Antonia Clifford, Ethan Morgan, Brian Mustanski

Clinical Lab Sciences Faculty Research and Publications

Background

This study's purposes were to characterize detection rates of several sexually transmitted infection (STI) agents and describe the effect additional specimen source and analyte screening has on STI detection within a cohort of young men who have sex with men and transgender women.

Methods

Within a 16-month interval, 1966 encounters involved dual urine and rectal swab submissions assessed by commercial transcription-mediated amplification–based assays for Chlamydia trachomatis and Neisseria gonorrhoeae and by off-label transcription-mediated amplification–based Trichomonas vaginalis and Mycoplasma genitalium testing. Identification of STI carriers used algorithms involving Food and Drug Administration–cleared screening methods, laboratory-modified testing for extraurogenital C. trachomatis …

Biographical Feature: Robin Patel, M.D.(C.M.), D(Abmm), F(Aam), Fidsa, Facp, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Moving Targets Of Bacterial Taxonomy Revision: What Are They And Why Should We Care?, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

Due to the increased widespread use of molecular diagnostics, genome sequencing, and microbiome analysis in microbiology, the field has experienced a massive influx of novel taxa and nomenclature revisions. A subset of these changes is relevant to the clinical microbiology laboratory, particularly in the context of appropriate antimicrobial susceptibility testing and epidemiology of emerging infections. However, assimilation of these changes into daily clinical microbiology laboratory operations can be challenging for a variety of reasons. Recent taxonomic revisions to Enterobacteriaceae, as well as the genera Borrelia, Mycoplasma, and Mycobacterium, are reviewed as examples that illustrate discrepancies between resources …

Assessment Of Dual Schistosome Infection Prevalence From Urine In An Endemic Community Of Ghana By Molecular Diagnostic Approach, William K. Anyan, Brittany R. Pulkkila, Clare E. Dyra, Miriam Price, Jean M. Naples, Joseph Quartey, Abraham K. Anang, Nilanjan Lodh

Clinical Lab Sciences Faculty Research and Publications

Schistosomiasis is an important Neglected Tropical Disease caused by blood parasites called schistosomes. In sub-Saharan Africa, two major human schistosomes, namely Schistosoma mansoni and S. haematobium, often occur sympatrically and is responsible for almost 90% of the affected 290 million people worldwide. We have utilized a highly sensitive and specific assay by amplifying species-specific cell-free repeat DNA fragments by polymerase chain reaction to detect either single or dual schistosome infection from a single urine sample from a broad age group. In this study, we have tested filtered urine samples collected from 163 individuals aged 3–63 years, mostly children (median …

Whither Extensive Genomic-Based Microbial Taxonomic Revision?, Erik Munson, Karen C. Carroll

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

The Photo Quiz: A Look Back And A Look Forward, Erik Munson, Alexander J. Mcadam

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Testing The Infection Prevalence Of Schistosoma Mansoni After Mass Drug Administration By Comparing Sensitivity And Specificity Of Species- Specific Repeat Fragment Amplification By Pcr And Loop-Mediated Isothermal Amplification, Miriam Price, Austin Cyrs, Chummy Sikasunge, James C. L. Mwansa, Nilanjan Lodh

Clinical Lab Sciences Faculty Research and Publications

Schistosomiasis is a blood parasitic disease caused by trematode parasites of the

genus Schistosoma. Schistosoma mansoni is one of the main contributors of the disease and 90% of the global burden of schistosomiasis is in Africa. Mass drug administration (MDA) has been implemented to reduce the disease burden in endemic areas. Because of MDA, the diagnostic sensitivity and specificity for classical diagnostic tests are reduced. In any disease situation, diagnosis is vital in determining asymptomatic, concurrent, current, new, and reinfection cases to evaluate the efficacy of any control program. We have evaluated the positive infection for S. mansoni from …

Strengthening Public Health In Wisconsin Through The Wisconsin Clinical Laboratory Network, Allen C. Bateman, Erin J. Bowles, Erik Munson, Raymond P. Podzorski, Eric T. Beck, Richard Dern, Alana K. Sterkel, David M. Warshauer, Peter A. Shult

Clinical Lab Sciences Faculty Research and Publications

The Wisconsin Clinical Laboratory Network (WCLN) at the University of Wisconsin–Madison is a partnership of 138 clinical and public health laboratories (as of February 2019) coordinated by the Wisconsin State Laboratory of Hygiene. This article describes the WCLN, its current activities, and lessons learned through this partnership. A laboratory technical advisory group, which consists of representatives from clinical laboratories, provides clinical laboratory perspective to the WCLN and fosters communication among laboratories. Activities and resources available through the WCLN include annual regional meetings, annual technical workshops, webinars, an email listserv, laboratory informational messages, in-person visits by a WCLN coordinator to clinical …

Determination Of Mic And Disk Diffusion Quality Control Guidelines For Meropenem–Vaborbactam, A Novel Carbapenem/Boronic Acid Β-Lactamase Inhibitor Combination, Erik Munson, Michael D. Huband, Mariana Castanheira, Kelley A. Fedler, Robert K. Flamm

Clinical Lab Sciences Faculty Research and Publications

Meropenem–vaborbactam is a carbapenem/cyclic boronic acid β-lactamase inhibitor combination primarily active against Gram-negative bacilli, including those harboring class A serine carbapenemases such as Klebsiella pneumoniae carbapenemase (KPC). A Clinical and Laboratory Standards Institute M23-A4 (Tier 2) quality control study established broth microdilution and disk diffusion ranges for reference strains. Two KPC-producing K. pneumoniae ATCC strains are recommended for quality control testing.

Biographical Feature: Richard B. (Tom) Thomson, Jr., Ph.D., D(Abmm), F(Aam), Erik Munson

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Laboratory Focus On Improving The Culture Of Biosafety: Statewide Risk Assessment Of Clinical Laboratories That Process Specimens For Microbiologic Analysis, Erik Munson, Erin J. Bowles, Richard Dern, Eric Beck, Raymond P. Podzorski, Allen C. Batemman, Timothy K. Block, Joshua L. Kropp, Tyler Radke, Karen Siebers, Brian Simmons, Mary A. Smith, Frances Spray-Larson, David M. Warshauer

Clinical Lab Sciences Faculty Research and Publications

The Wisconsin State Laboratory of Hygiene challenged Wisconsin laboratories to examine their biosafety practices and improve their culture of biosafety. One hundred three clinical and public health laboratories completed a questionnaire-based, microbiology-focused biosafety risk assessment. Greater than 96% of the respondents performed activities related to specimen processing, direct microscopic examination, and rapid nonmolecular testing, while approximately 60% performed culture interpretation. Although they are important to the assessment of risk, data specific to patient occupation, symptoms, and travel history were often unavailable to the laboratory and, therefore, less contributory to a microbiology-focused biosafety risk assessment than information on the specimen source …

A Retrospective Analysis Of Treatment And Clinical Outcomes Among Patients With Methicillin-Susceptible Staphlococcus Aureus Bloodstream Isolates Possessing Detecable Meca By A Commercial Pcr Assay Compared To Patients With Methicillin-Resistant Staphylococcus Aureus Bloodstream Isolates, Dylan Jones, Ramy Elshaboury, Erik Munson, Thomas J. Dilworth

Clinical Lab Sciences Faculty Research and Publications

mecA-positive Staphylococcus aureus isolates phenotypically susceptible to cefoxitin (mecA-methicillin-sensitive S. aureus[MSSA]) have been identified. We describe the treatment and outcomes among patients with mecA-MSSA bloodstream infections (BSI) and MRSA BSI matched 1:1 for age, BSI origin, and BSI type (n = 17 per group). Compared to MRSA BSI patients, mecA-MSSA BSI patients more often experienced clinical failure (58.8% and 11.8%, P = 0.010), driven largely by persistent bacteremia (35.3% and 11.8%). mecA-MSSA BSI patients may be at higher risk for poor clinical outcomes.

A Preliminary Investigation Of Acculturative Stress And Diurnal Cortisol Among Latina Women, Lucas Torres, Felicia Mata-Greve, April L. Harkins

Clinical Lab Sciences Faculty Research and Publications

The interplay between biological and cultural factors has remained understudied among ethnic minority groups, including Latinos. To the best of our knowledge, minimal to no research has examined the relationship between acculturative stressors and diurnal cortisol among Latina women. This initial exploratory study sought to examine the relationship between cortisol and acculturative stress. Among a small sample of adult Latina women, salivary cortisol was collected at 3 time points (waking, 30 min postwaking, and bedtime) to assess the cortisol awakening response (CAR) and diurnal cortisol response. Information regarding acculturative stress and acculturation was also collected. The major results showed that …

Detection Of Duo-Schistosome Infection From Filtered Urine Samples From School Children In Zambia After Mda, Megan J. Hessler, Austin Cyrs, Steven C. Krenzke, El Shaimaa Mahmoud, Chummy Sikasunge, James C. L. Mwansa, Nilanjan Lodh

Clinical Lab Sciences Faculty Research and Publications

Schistosomiasis is one of the major Neglected Tropical Diseases (NTDs) in sub-Saharan Africa. In sub-Saharan Africa, two major human schistosome species namely Schistosoma mansoniand S. haematobium often occur sympatrically largely affecting children. Recognizing the public health impact of Schistosomiasis, the World Health Organization (WHO) is urging member states to regularly treat at least 75% and up to 100%, of all school-aged children at risk of morbidity. For control strategies based on targeted mass drug administration (MDA) to succeed it is essential to have a simple and sensitive test for monitoring the success of these interventions. Current available diagnostic …

Surveillance Of Wisconsin Organisms For Trends In Antimicrobial Resistance And Epidemiology (Swotare): Epidemiologic Correlates For 2016 Surveillance Isolates, Erik Munson, Heather Zeman, Erin Hueppchen

Clinical Lab Sciences Faculty Research and Publications

Background: The Centers for Disease Control and Prevention advocate data collection and monitoring as one facet of a comprehensive approach to combat antimicrobial resistance in the United States. However, a paucity of such data exists at the local/state level for common disease-causing organisms.

Methods: To begin to characterize epidemiologic correlates of antibacterial resistance in Wisconsin, data analyses were performed with respect to isolates in the Surveillance of Wisconsin Organisms for Trends in Antimicrobial Resistance and Epidemiology (SWOTARE) 2016 collection. In addition to submitting isolates of Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa, and Streptococcus pneumoniae, participating laboratories were also requested to …

Answer To November Photo Quiz: Campylobacter Jejuni Pleuritis, Robin Olson, Kimber L. Munson, Maureen Napierala, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Photo Quiz: A 69-Year-Old Immunosuppressed Male With Chest Pain And Shortness Of Breath, Robin Olson, Kimber L. Munson, Maureen Napierala, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Molecular Diagnostics Update For The Emerging (If Not Already Widespread) Sexually Transmitted Infection Agent Mycoplasma Genitalium: Just About Ready For Prime Time, Munson Erik

Clinical Lab Sciences Faculty Research and Publications

Mycoplasma genitalium is an important and emerging agent of sexually transmitted infection in females and males, carrying the potential for postinfection genital tract sequelae. Past efforts to identify this organism on a routine basis, which were problematic due to the fastidious nature of the bacterium and its antigenic intricacies, have recently become supplemented by molecular diagnostics. A number of these assays are available commercially. This minireview describes the format and performance indices of a number of M. genitalium DNA- and RNA-based amplification assays; many of these assays have contributed to an improved clinical and epidemiologic understanding of this organism.

Point Of Care Diagnosis Of Multiple Schistosome Parasites: Species-Specific Dna Detection In Urine By Loop-Mediated Isothermal Amplification (Lamp), Nilanjan Lodh, Kei Mikita, Kwabena M. Bosompem, William K. Anyan, Joseph K. Quartey, Joseph Otchere, Clive J. Shiff

Clinical Lab Sciences Faculty Research and Publications

Schistosomes are easily transmitted and high chance of repeat infection, so if control strategies based on targeted mass drug administration (MDA) are to succeed it is essential to have a test that is sensitive, accurate and simple to use. It is known and regularly demonstrated that praziquantel does not always eliminate an infection so in spite of the successes of control programs a residual of the reservoir survives to re-infect snails. The issue of diagnostic sensitivity becomes more critical in the assessment of program effectiveness. While serology, such as antigen capture tests might improve sensitivity, it has been shown that …

Results Of A Local Combination Therapy Antibiogram For Pseudomonas Aeruginosa Isolates: Is Double Worth The Trouble?, Matthew Song, Thomas J. Dilworth, Erik Munson, Jim Davis, Ramy Elshaboury

Clinical Lab Sciences Faculty Research and Publications

Purpose:

To determine the frequency at which fluoroquinolones and aminoglycosides demonstrate in vitro activity against non-urinary, non-skin/skin structure Pseudomonas aeruginosa isolates exhibiting decreased susceptibilities to one or more β-lactam agents.

Methods:

β-lactam-non-susceptible P. aeruginosa isolates recovered from blood, bone, lower respiratory tract, pleural fluid, cerebrospinal fluid, or peritoneal fluid cultures between October 2010 and October 2014 were reviewed from four community hospitals within a single health-system. Only the first isolate per patient was included for analysis. The likelihood that each isolate was susceptible to a non-β-lactam antimicrobial was then determined and summarized within a combination antibiogram.

Results:

In total, 179 …

Biographical Feature: Thomas F. Smith, Ph.D., Erik Munson

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Correction For Munson And Carroll, “What’S In A Name? New Bacterial Species And Changes To Taxonomic Status From 2012 Through 2015”, Erik Munson, Karen C. Carroll

Clinical Lab Sciences Faculty Research and Publications

Author Correction.

Diagnosis Of Strongyloides Stercoralis: Detection Of Parasite-Derived Dna In Urine, Nilanjan Lodh, Reynaldo Caro, Shterna Sofer, Alan Scott, Alejandro Krolewiecki, Clive J. Shiff

Clinical Lab Sciences Faculty Research and Publications

Detecting infections of Strongyloides stercoralis is arduous and has low sensitivity. Clinically this is a major problem because chronic infections may disseminate in the host and lead to a life threatening condition. Epidemiologically, S. stercoralis is often missed in surveys as it is difficult to identify by standard stool examination procedures. We present, for the first time, evidence that the infection can be detected in filtered urine samples collected and processed in the field and subsequently assayed for the presence of parasite DNA. Urine specimens (∼40 mL) were collected from 125 test and control individuals living in rural and peri-urban …

Update On Laboratory Diagnosis And Epidemiology Of Trichomonas Vaginalis: You Can Teach An “Old” Dog “New” Trichs, Erik Munson, Maureen Napierala, Kimber L. Munson

Clinical Lab Sciences Faculty Research and Publications

Past viewpoints on Trichomonas vaginalis infection have characterized the associated clinical disease as a “nuisance” condition, with affected demographics largely being older African American females residing in urban centers. The advent of commercial molecular assays specific for T. vaginalis has offered a new outlook on trichomoniasis. Within high-prevalence sexually transmitted infection populations, parasite distribution is not localized to specific population centers, and T. vaginalis prevalence is elevated among both younger and older age groups. Adaptation of these molecular assays can additionally facilitate male screening and subsequent epidemiologic characterization. These findings, combined with associations between T. vaginalis infection and human immunodeficiency …

Arthritis Is Developed In Borrelia-Primed And -Infected Mice Deficient Of Interleukin-17, Joseph Kuo, Thomas F. Warner, Erik Munson, Dean T. Nardelli, Ronald F. Schell

Clinical Lab Sciences Faculty Research and Publications

Interleukin-17 (IL-17) has been shown to participate in the development of Lyme arthritis in experimental mice. For example, neutralization of IL-17 with antibodies inhibits induction of arthritis in Borrelia-primed and -infected C57BL/6 wild-type mice. We hypothesized that mice lacking IL-17 would fail to develop Borrelia-induced arthritis. IL-17-deficient and wild-type C57BL/6 mice were primed with heat-inactivated Borrelia and then infected with viable spirochetes 3 weeks later. No swelling or major histopathological changes of the hind paws were detected in IL-17-deficient or wild-type mice that were primed with Borrelia or infected with viable spirochetes. By contrast, IL-17-deficient and wild-type mice …

Acute Respiratory Distress Syndrome Caused By Plasmodium Falciparum Infection, Erik Munson, Patricia G. Luedke, William D. Timm

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.