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Research & Development

Research and Development

Since 1995, the Bacteriology Laboratory has been developing diagnostic molecular assays to supplement the classical testing available.

The assays are for public health purposes and are rarely commercially available. The tests used include real-time PCR and DNA sequencing analysis.

Also of interest are molecular diagnostic assays that molecularly serotype or characterize bacteria to determine if genes that confer pathogenicity, express toxins, or produce antibiotic resistance are present.

Research Projects

The Bacteriology Laboratory has developed many molecular based assays to rapidly detect and/or identify/characterize bacterial pathogens.

  • Development of rapid sequence-based assays for the characterization and typing of bacterial pathogens
  • Development of novel diagnostic real-time PCR assays  
  • Development of symptom-based molecular testing panels
  • Evaluation of broad-range PCR assays for bacterial identification
  • Development of whole genome sequence (WGS) based methods for strain typing and diagnostic characterization
  • Implementation of a national surveillance system for foodborne diseases based on WGS in collaboration with the CDC and FDA.
  • Discovery and characterization of new species of bacteria recovered from New York State patients.
  • Evaluation of MALDI-TOF MS technology for strain typing and susceptibility testing
  • Characterization and maintenance of a historic bacterial culture collection 
  • Evaluation of commercially available tests and other methodologies
  • Development of Pulsed-field Gel Electrophoresis (PFGE) protocols
  • Development of real-time PCR assays for newly emerged pathogens.


The Bacteriology Laboratory is also one of ten public health laboratories in the country that participate in the Emerging Infections Program (EIP), a national program funded by the Centers for Disease Control and Prevention (CDC) to establish and strengthen surveillance for new and emerging infections, and to develop prevention and control measures. The laboratory components of the EIP include FoodNet, PulseNet, Active Bacterial Core (ABC) surveillance and the National Antimicrobial Resistance Monitoring System (NARMS).


  • den Bakker HC, Allard MW, Bopp D, Brown EW, Fontana J, Iqbal Z, Kinney A, Limberger R, Musser KA, Shudt M, Strain E, Wiedmann M, Wolfgang WJ . Rapid whole-genome sequencing for surveillance of Salmonella entericaserovar enteritidis. Emerging Infectious Disease. 2014;20(8):1306-1314.
  • Pubmed Web Address

  • Halse TA, Edwards J, Cunningham PL, Wolfgang WJ, Dumas NB, Escuyer VE, Musser KA. Combined real-time PCR and rpoB gene pyrosequencing for rapid identification of Mycobacterium tuberculosis and determination of rifampin resistance directly in clinical specimens. J Clin Microbiol. 2010;48(4):1182-1188.
  • Pubmed Web Address

  • Mitchell K, Halse T, Kohlerschmidt D, Bennett T, Vanner C, King E, Musser K, Escuyer V. A Model of Shared Mycobacteriology Testing Services: Lessons Learned.
  • Pubmed Web Address

  • 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.
  • Pubmed Web Address

  • Bopp DJ, Baker DJ, Thompson L, Saylors A, Root TP, Armstrong L, Mitchell K, Dumas NB, Musser KA. Implementation of Salmonella serotype determination using pulsed-field gel electrophoresis in a state public health laboratory.
  • Pubmed Web Address

  • Raphael BH, Baker DJ, Nazarian E, Lapierre P, Bopp D, Kozak-Muiznieks NA, Morrison SS, Lucas CE, Mercante JW, Musser KA, Winchell JM. Genomic Resolution of Outbreak-Associated Legionella pneumophila Serogroup 1 Isolates from New York State.
  • Pubmed Web Address