Kimberlee A. Musser

Kimberlee A. Musser, Ph.D.

Clinical Director, Wadsworth Center David Axelrod Institute
Laboratory Chief of Bacterial Disease
Ph.D., Albany Medical College (1998)
Postdoctoral training: CDC/APHL Emerging Infectious Diseases Research Fellow, Wadsworth Center, New York State Department of Health

Research Interests

Dr. Musser is the Clinical Director of the Wadsworth Center’s David Axelrod Institute which includes the Infectious Disease Laboratories: Bacteriology, Biodefense, Bloodborne Virus, Diagnostic Immunology, Mycobacteriology, Mycology, Parasitology and Virology, as well as the Newborn Screening Program. She is also the center’s Chief of Bacterial Diseases overseeing reference identification of bacteria, bacterial meningitis testing, Legionella, tickborne bacterial testing, foodborne bacteriology, mycobacteriology, and antimicrobial resistance testing. 

Under her leadership, her team at Wadsworth Center has developed and validated dozens of bacterial and mycobacterial laboratory-developed tests including real-time PCR assays, MALDI-TOF Mass Spectrometry, pyrosequencing and most recently next generation sequencing (NGS) methods including whole-genome sequencing (WGS) and targeted NGS for both clinical and surveillance testing. Notably, Wadsworth was the first public health laboratory in the nation to utilize WGS clinically for TB and to utilize WGS to investigate a large outbreak of Legionnaires’ disease. The lab continues to expand WGS use for foodborne bacteria, Legionella, healthcare-associated, vaccine preventable and antibiotic-resistant bacteria, as well as for prospective and retrospective investigations of outbreaks. New studies incorporating the use of long read next generation sequencing (NGS), direct specimen NGS and automated bioinformatic analysis are also in progress.

Dr. Musser frequently shares her experience shepherding new tests from research, development, and validation through regulatory approval. She has given over 50 invited seminars at local, national, and international meetings and has published more than 90 peer-reviewed articles.. She was an ASM Distinguished Lecturer from 2020-2022. Dr. Musser has also served on numerous national committees including as Chair of the APHL Antimicrobial Resistance Laboratory Workgroup, as a member of the APHL Workforce Development Committee, and as a member of the APHL Annual Conference Planning Committee. She is currently as the Chair of the APHL TB Subcommittee and a member of the APHL Infectious Diseases Committee.

Awards and Honors

  • 2018 Commissioner’s Recognition Award, NYSDOH (Public Health Impact-Legionella)  

  • 2017 APHL Gold Standard Award

  • 2012 National TB Controller Association, Ed Desmond Laboratorian Award

  • 2011 Pangborn Award, Wadsworth Center

  • 2011 Commissioner’s Recognition Award, NYSDOH (Pertussis Outbreak Team)

  • 2002 Commissioner’s Recognition Award, NYSDOH (Bioterrorism Response Team)

  • 1999 Commissioner’s Recognition Award, NYSDOH (E.coli Outbreak Team)


Select Publications
Murphy SG, Smith C, Lapierre P, Shea J, Patel K, Halse TA,
Dickinson M, Escuyer V, Rowlinson MC, Musser KA. Direct detection of drug-resistant Mycobacterium tuberculosis using targeted next generation sequencing. Sec. Infectious Diseases: Epidemiology and Prevention. 2023; 11 DOI:
Haas W, Singh N, Lainhart W, Mingle L, Nazarian E, Mitchell K, Baker D, Nattanmai G, Kohlerschmidt D, Dickinson MC, Kacica M, Dumas N, Musser KA. Genomic Analysis of Vancomycin-Resistant Staphylococcus aureus Isolates from the 3rd Case Identified in the United States Reveals Chromosomal Integration of the vanA Locus. Microbiol Spectr. 2023; 11 (2): DOI: 10.1128/spectrum.04317-22
Long JR, Mitchell K, Edwards J, Wroblewski D, Luke E, Dickinson M, Kidney A, Dumas N, DelRosso P, Dorsinville M, Antwi M, Weiss D, Nazarian E, Limberger RJ, Musser KA, Halse TA. Laboratory Diagnosis of Bacterial Meningitis by Direct Detection, Serotyping and Next Generation Sequencing: How 10 years of Testing in New York State has evolved to improve laboratory diagnosis and public health. Mol Cell Probes. 2022; (61): 101786. DOI: 10.1016/j.mcp.2021.101786
Prussing C, Southwick K, Snavely E, Kidney A, Sossei A, Dentinger L, Shushe O, Fernandez R, Haas W, Lapierre P, Singh N, Nazarian EJ, Musser KA, Mitchell K. Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission. J Antimicrob Chemother. 2022; 104 (2): 3025-3034. DOI: 10.1093/jac/dkx264
Shea J, Smith C, Halse TA, Kohlerschmidt D, Rourke AK, Musser KA, Escuyer V, Lapierre P. Novel Mycobacterium tuberculosis Complex Genotype Related to M. caprae. Emerg Infect Dis. 2022; 104 (2): DOI: 10.3201/eid2807.212353
Rowlinson MC, Musser KA. Current Methods and Role of Next-Generation Sequencing in the Diagnosis of Antimicrobial Resistance in Tuberculosis. Clinical Microbiology Newsletter. 2022; 40 (1): 1-12. DOI: 10.1016/j.clinmicnews.2021.12.001
Prussing C, Canulla T, Singh N, McAuley P, Gosciminski M, King E, Bandy U, Machado MJ, Karlsson M, Musser KA, Huard RC, Nazarian EJ. Characterization of the First Carbapenem-Resistant Pseudomonas aeruginosa Clinical Isolate Harboring blaSIM-1 from the United States. Antimicrob Agents Chemother. 2021; 65 (10): e0106621. DOI: 10.1128/AAC.01066-21
Schoonmaker-Bopp D, Nazarian E, Dziewulski D, Clement E, Baker DJ, Dickinson MC, Saylors A, Codru N, Thompson L, Lapierre P, Dumas N, Limberger R, Musser KA. Improvements to the Success of Outbreak Investigations of Legionnaires' Disease: 40 Years of Testing and Investigation in New York State. Appl Environ Microbiol. 2021; 87 (16): e0058021. DOI: 10.1128/AEM.00580-21
Shea J, Halse TA, Kohlerschmidt D, Lapierre P, Modestil HA, Kearns CH, Dworkin FF, Rakeman JL, Escuyer V, Musser KA. Low-level rifampin resistance and rpoB mutations in Mycobacterium tuberculosis: An analysis of whole-genome sequencing and drug susceptibility test data in New York. J Clin Microbiol. 2020; Sept 30 (JCM): 01885-20. DOI: 10.1128/JCM.01885-20
Smith C, Halse TA, Shea J, Modestil H, Fowler RC, Musser KA, Escuyer V, Lapierre P. Assessing Nanopore sequencing for clinical diagnostics: A comparison of NGS methods for Mycobacterium tuberculosis. J Clin Microbiol. 2020; Oct 14 (JCM): 00583-20. DOI: 10.1128/JCM.00583-20
Bhattacharyya RP, Bandyopadhyay N, Ma P, Son SS, Liu J, He LL, Wu L, Khafizov R, Boykin R, Cerqueira GC, Pironti A, Rudy RF, Patel MM, Yang R, Skerry J, Nazarian E, Musser KA, Taylor J, Pierce VM, Earl AM, Cosimi LA, Shoresh N, Beechem J, Livny J, Hung DT. Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination. Nat Med. 2019; 25 (12): 1858-1864. DOI: 10.1038/s41591-019-0650-9
Singh N, Lapierre P, Quinlan TM, Halse TA, Wirth S, Dickinson MC, Lasek-Nesselquist E, Musser KA. Whole-Genome Single-Nucleotide Polymorphism (SNP) Analysis Applied Directly to Stool for Genotyping Shiga Toxin-Producing Escherichia coli: an Advanced Molecular Detection Method for Foodborne Disease Surveillance and Outbreak Tracking.. J Clin Microbiol. 2019; 57 (7): e00307-19. DOI: 10.1128/JCM.00307-19
Lapierre P, Nazarian E, Zhu Y, Wroblewski D, Saylors A, Passaretti T, Hughes S, Tran A, Lin Y, Kornblum J, Morrison SS, Mercante JW, Fitzhenry R, Weiss D, Raphael BH, Varma JK, Zucker HA, Rakeman JL, Musser KA. Legionnaires' Disease Outbreak Caused by Endemic Strain of Legionella pneumophila, New York, New York, USA, 2015. Emerg Infect Dis. 2017; 23 (11): 1784-1791. DOI: 10.3201/eid2311.170308
Shea J, Halse TA, Lapierre P, Shudt M, Kohlerschmidt D, Van Roey P, Limberger R, Taylor J, Escuyer V, Musser KA. Comprehensive Whole-Genome Sequencing and Reporting of Drug Resistance Profiles on Clinical Cases of Mycobacterium tuberculosis in New York State. J Clin Microbiol. 2017; 55 (6): 1871-1182. DOI: 10.1128/JCM.00298-17
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