Andrew Clark, PhD

Director, Bacteriology

Andrew Clark, Ph.D., D(ABMM) is an Assistant Professor in the Department of Pathology at the Johns Hopkins University School of Medicine.  Dr. Clark completed his MS and PhD in Microbiology at the University of Arizona, Tucson.  He then completed a CPEP-accredited postdoctoral fellowship in Clinical and Public Health Microbiology at the National Institutes of Health Clinical Center in Bethesda, MD.  Prior to joining Johns Hopkins University, Dr. Clark served on faculty at the University of Texas Southwestern Medical Center where he was the medical director of the microbiology laboratory at Parkland Health and Hospital System.

Dr. Clark serves as the Director of the Bacteriology Laboratory at the Johns Hopkins Hospital and oversees clinical antimicrobial susceptibility testing. His research program focuses on the clinical evaluation and implementation of new and emergent technologies for microbial detection and characterization and antimicrobial resistance.

1. Laboratory diagnosis of bacterial infections and antimicrobial susceptibility testing
2. Evaluation of novel and emergent technologies for the detection and characterization of microbial infections
3. Genetic mechanisms of antibiotic resistance

Antibiotic resistance continues to be a threat to modern medicine, broadly impacting patient management.  Our current research focus examines the efficacy of novel antibiotic compounds and combinations for the management of infections caused by multidrug-resistant organisms, as well as the diagnostic modalities used to assess resistance phenotypes.  Through both traditional phenotypic, molecular, and genomic approaches we have come to appreciate this phenomenon is significantly more nuanced than simple gene acquisition, loss, or mutational change. 

In collaboration with the clinical microbiology laboratory of the Johns Hopkins Hospital, our group works to examine mechanisms underpinning emerging antibiotic resistance.  We evaluate the utility of novel antibiotics and antibiotic combinations, as well as investigate the contribution cryptic resistance phenotypes (including heteroresistance, inoculum effects, and inducible resistance) toward disease progression and outcomes.  Finally we are interested in antimicrobial susceptibility testing modalities themselves, including the development of novel methods to improve the detection of resistance phenotypes.

Bellrose, M.M.*, Clark, A.E.*, Youn,J-H., Weingarten, R.A., Crooks, C.M., Dekker, J.P., and Frank, K.M. Manual Reading of Sensititre Broth Microdilution System Panels Improves Accuracy of Susceptibility Reporting for Polymyxin Antibiotics.  J. Clin. Microbiol. 2021 Aug 18;59(9):e0033221.  PMID: 34165324; *Co-first authored manuscript

Clark, A.E., Wang, Z., Ostman, E., Zheng, H., Yao, H., Cantarel, B., Kanchwala, M., Xing, C., Chen, L., Irwin, P., Xu, Y., Oliver, D., Lee, F., Gagan, J., Filkins, L., Muthukumar, A., Park, J., Sarode, R., and SoRelle, J.  Multiplex Fragment Analysis for Flexible Detection of all SARS-CoV-2 Variants of Concern.  Clin. Chem. 2022 Jul 27;68(8):1042-1052.  PMID: 35616102

Maxwell, D.N., Kim, J., Pybus, C.A., White, L., Medford, R.J., Filkins, L.M., Monogue, M.L., Rae, M.M., Desai, D., Clark, A.E., Zhan, X., and Greenberg, D.E.  Clinically Undetected Polyclonal Heteroresistance among Pseudomonas aeruginosa Isolated from Cystic Fibrosis Respiratory Specimens.  J. Antimicrob. Chemother. 2022 Nov 28;77(12):3321-3330.  PMID: 36227655.

Tisza, M., Smith, D., Clark, A.E., Youn, J-H., NISC Comparative Sequencing Program, Khil, P., and Dekker, J.P. Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in the Bacteroides fragilis group. Nature Commun. 2023 Jul 10;14(1):4082. PMID: 37429841.

Ray, S., Flemming, L.K., Scudder, C.J., Ly, M.A., Porterfield, H.S., Smith, R.D., Clark, A.E., Johnson, J.K., and Das, S. Comparative phenotypic and genotypic antimicrobial susceptibility surveillance in Achromobacter spp. through whole genome sequencing. Microbiol. Spectr. 2025 April;13(4):e0252724. PMID: 40013782

American Society for Microbiology

Southwestern Association for Clinical Microbiology

Clinical Laboratory Standards Institute