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Kimberlee A. Musser, Ph.D.

Kimberlee A. Musser, Ph.D.

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

Research Interests

Dr. Musser is the Chief of Bacterial Diseases which includes the Bacteriology Laboratory (reference identification of bacteria, bacterial meningitis testing, Legionella and pertussis testing and tickborne bacterial testing), the Foodborne Bacteriology Laboratory, the Mycobacteriology Laboratory, the Northeast Regional PulseNet Laboratory, and the Northeast Regional Antimicrobial Resistance Laboratory. This laboratory provides diagnostic reference testing for the detection of various pathogenic bacteria in New York State. This testing includes the use of both molecular-based and culture-based methods. The molecular diagnostics include real-time PCR assays, DNA sequencing by pyrosequencing, Sanger and Whole-Genome Sequencing (WGS) as well as molecular typing using Next Generation Sequencing (NGS) for analyzing outbreaks of foodborne, waterborne, and healthcare associated illness and source tracking.

Our laboratory is also involved in developing new molecular detection methods and researching sequence-based methods for bacterial pathogens including those aimed at direct primary specimen detection, characterization and typing. We are interested in molecular diagnostic assays that characterize the bacteria of interest to determine if genes that confer pathogenicity, antimicrobial resistance, or determine the serogroup are present.  This laboratory also has incorporated clinical reporting of whole-genome sequencing for comprehensive testing of Mycobacterium tuberculosis and comprehensive detection of antimicrobial resistance genes as well as utilization of NGS methods for prospective and retrospective investigations of outbreaks. New studies incorporating the use of long read NGS, highly multiplexed real-time PCR, direct specimen NGS and automated bioinformatic analysis are also in progress.

Select Publications

Prussing C, Snavely EA, Singh N, Lapierre P, Lasek-Nesselquist E, Mitchell K, Haas W, Owsiak R, Nazarian E, Musser KA.
Nanopore MinION Sequencing Reveals Possible Transfer of bla KPC-2 Plasmid Across Bacterial Species in Two Healthcare Facilities.
Front Microbiol.
August 19
DOI: 10.3389/fmicb.2020.02007
Ramautar AE, Halse TA, Arakaki L, Antwi M, Del Rosso P, Dorsinville M, Nazarian E, Steiner-Sichel L, Lee L, Dickinson M, Wroblewski D, Dumas N, Musser K, Isaac B, Rakeman J, Weiss D.
Direct molecular testing to assess the incidence of meningococcal and other bacterial causes of meningitis among persons reported with unspecified bacterial meningitis.
Diagn Microbiol Infect Dis.
Bardossy AC, Snavely EA, Nazarian E, Annambhotla P, Basavaraju SV, Pepe D, Maloney M, Musser KA, Haas W, Barros N, Pierce VM, Walters M, Epstein L.
Donor-derived transmission through lung transplantation of carbapenem-resistant Acinetobacter baumannii producing the OXA-23 carbapenemase during an ongoing healthcare facility outbreak..
Transpl Infect Dis.
DOI: 10.1111/tid.13256
Banaei N, Musser KA, Salfinger M, Somoskovi A, Zelazny AM.
Novel Assays/Applications for Patients Suspected of Mycobacterial Diseases.
Clin Lab Med.
DOI: 10.1016/j.cll.2020.08.010
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.
Sept 30
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.
Oct 14
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.
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.
DOI: 10.1128/JCM.00307-19