This paper develops mechanistic ODE models to predict Valley fever outbreaks by integrating climate and ecological factors, showing improved forecasting over statistical models when including wildlife reservoirs.

bioRxiv · Apr 23, 2026 · PreprintEcology

Unpacking bedaquiline hetero-resistance: the importance of intermediate profiles for phenotypic drug-susceptibility testing

Nabila A. Ismail, Frik A. Sirgel, Shaheed Vally Omar, Shatha Omar, Marianna de Kock, Claudia Spies, Megan Folkerts, Grant Theron, David M. Engelthaler, John Z. Metcalfe, Robin M. Warren

This paper shows that considering intermediate results in phenotypic drug susceptibility testing can detect bedaquiline heteroresistance at low frequencies, improving resistance determination.

Antimicrobial Agents and Chemotherapy · Jul 21, 2025Peer-reviewedMicrobiology

Bacterial Genome wide association studies (bGWAS) and transcriptomics identifies cryptic antimicrobial resistance mechanisms in Acinetobacter baumannii

Chandler C. Roe, Charles H. D. Williamson, Adam J. Vazquez, Kristen Kyger, Michael Valentine, Jolene R. Bowers, Paul D. Phillips, Veronica Harrison, Elizabeth M. Driebe, David M. Engelthaler, Jason W. Sahl

Frontiers in Public Health · Sep 2, 2020Peer-reviewedGenomics

Phylogenetic Analysis of St. Louis Encephalitis Virus within Two Southwestern United State Counties: a case for a bulk introduction event into the southwest United States

Chase L. Ridenour, Jill Hager Cocking, Samuel Poidmore, Daryn E. Erickson, Breezy N. Brock, Michael Valentine, Steven J Young, Jennifer A. Henke, Kim Y Hung, Jeremy Wittie, Heidie Hornstra, Krystal Lee Sheridan, Heather Centner, Darrin Lemmer, Viacheslav Y. Fofanov, , Crystal M. Hepp

The paper uses phylogenetic analysis to determine if St. Louis Encephalitis Virus (SLEV) in Arizona and California originated from local cycling or new imports, finding evidence of annual imports in California and local cycling in Arizona.

bioRxiv · Jun 10, 2020 · PreprintBioinformatics

Genomic variant identification methods alter Mycobacterium tuberculosis transmission inference

Katharine S. Walter, Caroline Colijn, Ted Cohen, Barun Mathema, Qingyun Liu, Jolene R. Bowers, David M. Engelthaler, Apurva Narechania, Júlio Croda, Jason Randolph Andrews

This study shows that different genomic variant calling methods lead to inconsistent transmission inferences and phylogenies in Mycobacterium tuberculosis outbreaks.

bioRxiv · Aug 24, 2019 · PreprintGenomics

Population Genomics Of Cryptococcus neoformans var. grubii Reveals New Biogeographic Relationships And Finely Maps Hybridization

Johanna L. Rhodes, Christopher A. Desjardins, Sean M. Sykes, Mathew A. Beale, Mathieu Vanhove, Sharadha Sakthikumar, Yuan Chen, Sharvari Gujja, Sakina Saif, Anuradha Chowdhary, Daniel John Lawson, Vinícius Ponzio, Arnaldo Lopes Colombo, Wieland Meyer, David M. Engelthaler, , Christina A. Cuomo

This study analyzes the population genomics of Cryptococcus neoformans var. grubii, revealing hybridization, biogeographic relationships, and genetic structure across global isolates.

Genetics · Jul 5, 2017Peer-reviewedGenomics

KlebSeq: A Diagnostic Tool for Healthcare Surveillance and Antimicrobial Resistance Monitoring of Klebsiella pneumoniae

Jolene R. Bowers, Darrin Lemmer, Jason W. Sahl, Talima Pearson, Elizabeth M. Driebe, David M. Engelthaler, Paul Keim

KlebSeq is a diagnostic tool that detects Klebsiella pneumoniae and identifies antimicrobial resistance and virulence traits using amplicon sequencing for healthcare surveillance.

bioRxiv · Mar 14, 2016 · PreprintMolecular Biology