Laboratory and Basic Science Research Commons^™

Antimicrobial Activity Of Sulbactam-Durlobactam Against Acinetobacter Baumannii-Calcoaceticus Complex Strains Causing Non-Respiratory And Non-Bloodstream Infections From The United States (2023–2025), Erik Munson

Clinical Lab Sciences Faculty Research and Publications

Acinetobacter baumannii most often causes pneumonia in critically ill patients. However, A. baumannii is also an important cause of a broader range of infections, including skin/wound and urinary tract infections. This study aims to evaluate the in vitro activity of sulbactam-durlobactam and comparator antibiotics, including meropenem and cefiderocol against A. baumannii-calcoaceticus complex isolates from non-respiratory and non-bloodstream sources. Samples included 285 A. baumannii-calcoaceticus complex isolates enriched for carbapenem resistance collected across 17 states in the United States (January 2023–May 2025). Antimicrobial susceptibility tests were conducted by manual broth microdilution and interpreted according to Clinical and Laboratory Standards Institute (CLSI) and …

An Update On Novel Taxa And Revised Taxonomic Status Of Bacteria Isolated From Human Clinical Specimens Described In 2024, Arianna Carella, Karen C. Carroll, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

Knowledge of novel and revised bacterial taxonomy facilitates routine operations in the medical microbiology laboratory and communication with important stakeholders. Notable new gram-positive taxa accepted in 2024 include the clinically significant Staphylococcus brunensis sp. nov., as well as Streptococcus suis subsp. hashimotonensis subsp. nov., which can be delineated from other Streptococcus suis subsp. by possession of the Lancefield group A antigen. Four novel Enterobacterales species are discussed, plus a novel eighth family Gallaecimonadaceae. One of these, Providencia huashanensis sp. nov. is clinically significant and harbors multiple genetic determinants that encode antimicrobial resistance mechanisms. Stenotrophomonas forensis sp. nov., derived from …

Update On Novel, Validly Published, And Included Bacterial Taxa Derived From Nondomestic Animals And Taxonomic Revisions Published In 2024, Claire R. Burbick, Sara D. Lawhon, Trinity Krueger, Elena Ruiz-Reyes, Mallory Lenmark, Ayden Wisney-Leonard, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

Description of new and revised taxa originating from non-domestic animal species continues to be pursued. The majority are bacteria isolated from the alimentary system of a variety of healthy wildlife, adding to our understanding of microbial flora present in the normal state. A few new and revised taxa are associated with disease, including a novel Erysipelothrix species associated with sepsis in albatross and a revised species, Allocoenonia anatina comb. nov., associated with Riemerella anatipestifera-like disease in ducks and geese. Representative bacteria from genera that are additionally under study for the remediation of pollutants and bacteria that are related to …

Valid And Accepted Novel Bacterial Taxa Isolated From Domestic Companion And Agricultural Animals Described In 2024, Sara D. Lawhon, Claire R. Burbick, Trinity Krueger, Elena Ruiz-Reyes, Ayden Wisney-Leonard, Mallory Lenmark, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

Recognizing and updating bacterial names is key to communication between the veterinary clinical microbiology laboratory, veterinarians, and clients. Moraxella oculi sp. nov., distinct from Moraxella bovis and Moraxella bovoculi, was isolated from a cow with infectious bovine keratoconjunctivitis. Several respiratory pathogens were recognized, including Neisseria leonii sp. nov. described from rabbits, Mannheimia indoligenes sp. nov. described from cattle in Europe, and Moraxella haemolytica sp. nov. described from a goat in China. Stenotrophomonas forensis sp. nov. is a novel designation within the Stenotrophomonas maltophilia complex associated with isolates derived from horses. New additions to the Campylobacter genus included Campylobacter californiensis …

Helminth And Malaria Co-Infection Among Pregnant Women In Battor And Adidome Towns Of The Volta Region Of Ghana, Navneet Kaur, William K. Anyan, Abraham K. Anang, Nilanjan Lodh

Clinical Lab Sciences Faculty Research and Publications

Aim: In sub-Saharan Africa, approximately 40 million pregnant women are exposed to parasitic diseases such as malaria caused by Plasmodium falciparum, Schistosome parasites, and soil-transmitted helminths (STHs). When parasitic diseases share the same habitat and overlap in distribution, then high co-infection rates occur. The co-infection can lead to consequences for the child, such as intrauterine growth retardation, low birth weight, pre-term delivery, and neonatal mortality.

Methods: The objective of the study was to determine the nature and extent of coinfection from 100 samples collected from the Battor (50) and Adidome (50) towns of Ghana in collaboration with the Noguchi …

Advanced Specificity And Sensitivity Studies Relative To A Research Use Only Transcription-Mediated Amplification-Based Assay For Treponema Pallidum Rna Detection, Trinity Krueger, Grace Kadonsky, Elizabeth Thelen, Amanda Zapp, Josephine Moore, Ahmet Muslu, Allan Pillay, Irene A. Stafford, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

Preliminary experimentation has suggested that a research-use-only real-time transcription-mediated amplification assay for Treponema pallidum (RUO T. pallidum TMA) yields instances of T. pallidum nucleic acid detection that coincide with non-treponemal serology in men who have sex with men (MSM) at increased risk for sexually transmitted infection. To further characterize the specificity of RUO T. pallidum TMA testing, 3,586 rectal swab specimens reported as “not detected” by the assay generated a mean endpoint FAM fluorescence of 637.5 units. Introduction of Treponema denticola, Treponema phagedenis, and Treponema refringens nucleic acid into matrices generated mean endpoint FAM fluorescence ranging from 620.7 …

Editorial: The Role Of Diagnostics In Eliminating Schistosomiasis As A Public Health Problem: Trend And Need, James Mwansa, Moses J. Chimbari, Nilanjan Lodh

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Automated Mycoplasma Genitalium Molecular Macrolide Resistance Detection And Nucleic Acid Target Semi-Quantitation: Patient Demographic Considerations, Josephine Moore, Trinity Krueger, Amanda Zapp, Stephen C. Lavey, Kimber L. Munson, Irene A. Stafford, Michael E. Newcomb, Brian Mustanski, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

Recent work has optimized parameters of a real-time reverse transcriptase PCR-based laboratory-developed test on the Panther Fusion system which detects Mycoplasma genitalium-specific macrolide resistance-associated mutations LDT (MRM-LDT) from primary swab and urine specimens. In this study, MRM-LDT was applied to a large multi-demographic study set to further characterize M. genitalium resistance in the United States. A total of 2,145 primary clinical specimens testing positive for M. genitalium 16S rRNA by transcription-mediated amplification (TMA) were initially titered by the same assay using serial 10-fold dilutions to determine relative target nucleic acid burden. Specimens were then processed for MRM-LDT. Findings were stratified …

Activity Of Novel Ceftibuten-Avibactam, Ceftazidime-Avibactam, And Comparators Against A Challenge Set Of Enterobacterales From Outpatient Centers And Nursing Homes Across The United States (2022–2024), Aliaa Fouad, April M. Bobenchik, Robin Chamberland, Andrew E. Clark, Holly K. Huse, Isabella W. Martin, A. Brian Mochon, Erik Munson, Maroun M. Sfeir, Monica Srodon, Kimberly Taylor, Yungchou Wang, Lars F. Westblade, David P. Nicolau, Tomefa E. Asempa

Clinical Lab Sciences Faculty Research and Publications

Ceftibuten is being developed in combination with the oral prodrug of avibactam. Outpatient isolates (n = 500) from 11 US states underwent susceptibility testing with manual broth microdilution. Ceftibuten had susceptibility rates of 64% (CLSI) and 23% (EUCAST). Ceftibuten-avibactam achieved 96.4% inhibition at MIC ≤ 1 µg/mL. Susceptibility rates were as follows: cefpodoxime (2.6%), ceftriaxone (1%), ceftazidime-avibactam (99.6%), tebipenem (89%), ertapenem (94.4%), levofloxacin (26.6%), trimethoprim-sulfamethoxazole (40.2%), and fosfomycin (96.8%). Ceftibuten-avibactam demonstrates potent in vitro activity against cephalosporin non-susceptible isolates.

Comparative Dna Extraction Methods To Use For Lamp Assay As Molecular Diagnosis Of Human Schistosomes From Urine Samples, Brittany R. Pulkkila, Chummy Sikasunge, James Mwansa, Nilanjan Lodh

Clinical Lab Sciences Faculty Research and Publications

Background

Schistosomiasis in Africa is an ongoing public health problem that is caused by two major human species, Schistosoma mansoni and S. haematobium, which often cause concurrent infections. Due to the global goal of controlling or eliminating schistosomiasis as a public health problem, the issue of diagnostic sensitivity has become more critical in the assessment of program success. In that regard, the World Health Organization (WHO) has drawn attention to the need for field-applicable tests with high specificity and sensitivity.

Methods

To address this, we have evaluated the amplification of S. mansoni and S. haematobium cell-free repeat DNA by …

An Update On Novel Taxa And Revised Taxonomic Status Of Bacteria Isolated From Domestic Companion And Agricultural Animals Described In 2023, Sara D. Lawhon, Claire R. Burbick, Trinity Kreuger, Elena Ruiz-Reyes, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

With the proliferation of abundant bacterial genomic data comes the recognition of new organisms as well as a better understanding of the relatedness of known bacteria. Recognizing the associated taxonomic changes enhances communication and understanding about the significance of novel organisms and deeper understanding of known pathogens. This review addresses the addition of multiple gastrointestinal bacteria that form the normal microbiota in a variety of animals including honeybees as well as novel bacteria from domestic animals including an alpha-hemolytic Streptococcus species from guinea pigs, two Moraxella spp. from cows and goats, a new Capnocytophaga species from cats, a thermophilic Campylobacter …

An Update On Novel Taxa And Revised Taxonomic Status Of Bacteria Isolated From Aquatic Host Species Described In 2022–2023, Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

The description of new taxa and nomenclature updates to currently known taxa from aquatic animal species continues. After a review of the literature from 2022 and 2023, multiple lists of bacteria, including members of Phylum Planctomycetota, were compiled. As with the previous review, most bacteria are oxidase-positive Gram-negative bacilli with familiar families including new taxa in Aeromonadaceae, Flavobacteriaceae, and Vibrionaceae. A number of Gram-positive bacilli are described including new taxa in the Nocardioides, Paenibacillus, and Streptomyces genera. Two anaerobic species are listed, and one new member of Family Planctomycetaceae is noted. Revised taxa are …

Valid And Accepted Novel Bacterial Taxa Isolated From Non-Domestic Animals And Taxonomic Revisions Published In 2023, Erik Munson, Claire R. Burbick, Sara D. Lawhon, Trinity Krueger, Elena Ruiz-Reyes

Clinical Lab Sciences Faculty Research and Publications

Continued investigation into the bacteria associated with non-domestic animals provides important information for recognizing normal flora, assessing the health status of these unique species of animals, and identifying new or emerging pathogens of concern. In this summary of novel taxa and taxonomic revisions, considerable additions have been made toward understanding fecal and mucosal flora in multiple wild animal species. In addition, novel pathogenic bacteria are discussed, including multiple Chlamydia spp. causing disease in a hawk and crocodile, two Corynebacterium spp. causing oral lesions in penguins and a lesser-known genus, Mergibacter within Family Pasteurellaceae, causing disease in multiple wild bird …

Mycoplasmoides Genitalium Nucleic Acid Semi-Quantitation And Molecular Macrolide Resistance Detection Via Automated Assays: Gender And Specimen Source Considerations, Erik Munson, Josephine Moore, Trinity Kreuger, Amanda Zapp, Stephen C. Lavey, Kimber L. Munson, Irene A. Stafford, Brian Mustanksi

Clinical Lab Sciences Faculty Research and Publications

A laboratory-developed test (LDT) using analyte-specific reagents has been optimized on a commercial platform to detect macrolide resistance-associated mutations (MRM) in 23S rRNA from Mycoplasmoides genitalium from primary clinical specimens. In this study, MRM-LDT was applied to a multi-specimen source study set. One thousand four hundred ninety-five primary specimens testing positive for M. genitalium by commercial transcription-mediated amplification (TMA) were initially titered by the TMA assay using serial 10-fold dilutions to semi-quantitate target nucleic acid burden. Primary specimens were then processed for MRM detection using the MRM-LDT. Findings were stratified by gender and specimen source. The mean log₁₀ target …

Mycoplasmoides Genitalium Macrolide Resistance Detection Is Needed In University Settings, Stephen C. Lavey, Brittany Cassel, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

Background: Mycoplasmoides genitalium remains a difficult sexually-transmitted infection (STI) to manage due to its potential for antimicrobial resistance and post-infection sequelae. University students are especially vulnerable, as this demographic has the highest rate of STI in the United States. As a result, investigating prevalence rates and therapeutic outcomes in this population is essential to minimize future impact of M. genitalium. The purpose of this study was to investigate a university student population for M. genitalium distribution and treatment outcome.

Design: Retrospective chart-review of university health clinic attendees, augmented by laboratory detection of M. genitalium following therapeutic intervention.

Methods: A total …

Female Genital Schistosomiasis (Fgs) Prevalence And Burden Across Endemic Countries, Timelines, And Age Groups: A Retrospective Study, Navneet Kaur, Lilianna Buss, Lauren Zorn, James Mwansa, Mable M. Mutengo, Nilanjan Lodh

Clinical Lab Sciences Faculty Research and Publications

Female Genital Schistosomiasis (FGS) is caused by Schistosoma haematobium, which causes chronic gynecological conditions that lead to substantial morbidity and infertility. This study’s objective is to determine the prevalence and burden of FGS based on the presence of S. haematobium-specific DNA in females across age groups using our previously field-acquired filtered human urine samples from Zambia, Tanzania, and Ghana, collected over multiple years. For Ghana (2013), 39 out of 90 samples were from females, of which 31 (79.5%) were positive and 8 (20.5%) were negative. In Zambia (2016), 80 out of 133 samples were from females, of which …

2024 American Society For Microbiology Awards And Prize Program: Clinical Microbiology Honorees, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Asymptomatic Rectal Bacterial Pathogens Show Large Prospective Relationships With Hiv Incidence In A Cohort Of Young Sexual And Gender Minorities: Implications For Sti Screening And Hiv Prevention, Ross A. Baiers, Daniel T. Ryan, Antonia Clifford, Erik Munson, Richard D'Aquila, Michael E. Newcomb, Brian Mustanski

Clinical Lab Sciences Faculty Research and Publications

Background

We estimated the predictive value of rectal (bacterial sexually transmitted infection [bSTI]) pathogen detection for future HIV seroconversion among young adult sexual and gender minorities (YSGMs) assigned male at birth (AMAB).

Methods

Data were collected between March 2018 and August 2022 from RADAR, a longitudinal cohort study of YSGMs AMAB living in the Chicago metropolitan area (n = 1022). Rates of rectal bSTIs and the proportion of self-reported rectal bSTI symptoms are reported. We examined whether the presence of rectal bSTIs predicted HIV seroconversion using generalized estimating equations (GEEs).

Results

Participants tested reactive for rectal Mycoplasma genitalium (MGen), Neisseria …

Serologic Correlation Of A Research-Use-Only Treponema Pallidum Transcription-Mediated Amplification Assay Performed On Rectal Swabs From A Longitudinal Cohort Of Young Men Who Have Sex With Men, Amanda Zapp, Hannah Hudson, Erik Munson, Elizabeth Thelen, Daniel Ryan, Richard D'Aquila, Brian Mustanski

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Update On Novel Validly Published And Included Bacterial Taxa Derived From Human Clinical Specimens And Taxonomic Revisions Published In 2023, Arianna Carella, Karen C. Carroll, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

Taxonomy is a systematic practice in which microorganisms are granted names to facilitate and standardize multi-disciplinary communication. We summarize novel bacterial taxa derived from human clinical material that were published in peer-reviewed literature and/or included by the International Journal of Systematic and Evolutionary Microbiology during calendar year 2023, as well as taxonomic revisions that have been published/included by the same entity. While the majority of newly discovered facultative and anaerobic organisms were derived from microbiome surveillance, noteworthy novel taxa in the realm of pathogenicity potential include those related to Aerococcus spp., several Corynebacterium spp., Exercitatus varius gen. nov., sp. nov., …

Biographical Feature: Charles Y. Chiu, M.D., Ph.D., Erik Munson

Clinical Lab Sciences Faculty Research and Publications

No abstract provided.

Changes In Streptococcus Pneumoniae Susceptibility In Wisconsin: Implications For Clinical Treatment Decisions For Respiratory Infections, Erik Munson, Stephen C. Lavey, Megan R. Lasure, Barry C. Fox

Clinical Lab Sciences Faculty Research and Publications

Objective: In 2019, the American Thoracic Society and Infectious Diseases Society of America updated clinical practice guidelines for community-acquired pneumonia (CAP). In contrast to guidelines published in 2007, macrolide monotherapy for outpatients was made a conditional recommendation based on resistance levels. Local knowledge of current antimicrobial susceptibility is needed to guide management of CAP and other bacterial respiratory pathogens. The purpose of this study was to investigate antimicrobial susceptibility profiles and trending for Wisconsin Streptococcus pneumoniae isolates.

Design: Multi-center laboratory surveillance, with testing at a central location utilizing standardized susceptibility testing protocols.

Methods: Data published by the Wisconsin Department of …

Surveillance Of Wisconsin Organisms For Trends In Antimicrobial Resistance And Epidemiology (Swotare): 2018-2019 Report On Enterobacter Cloacae And Klebsiella Pneumoniae Clinical Isolates, Alyssa Reynoso, Erik Munson

Clinical Lab Sciences Faculty Research and Publications

Objectives: Both Enterobacter cloacae and Klebsiella pneumoniae have been regarded as important opportunistic pathogens for humans. Recent data have described the spread of multi-resistant strains of these organisms. Development of novel resistance phenotypes may result in a reduction in anti-infective efficacy, therefore making patient treatment decisions challenging. The Surveillance of Wisconsin Organisms for Trends in Antimicrobial Resistance and Epidemiology (SWOTARE) program aims to combat this issue and improve antibiotic stewardship by monitoring antimicrobial resistance at a local level.

Design: Multi-center laboratory surveillance, with testing at a single location utilizing standardized media and susceptibility testing protocols

Methods: In the years 2018 …

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 …