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

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

Also of interest are molecular diagnostic assays that detect the serotype or characterize bacteria to determine if genes that confer pathogenicity, toxin genes, or mobile genetic elements such as plasmids or transposons associated with 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 symptom-based molecular testing panels
  • Development of whole-genome sequence (WGS) based methods for strain typing and diagnostic characterization including Mycobacterium tuberculosis as well as foodborne, waterborne and healthcare associated bacterial pathogens.
  • 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 
  • Characterization and maintenance of a historic bacterial culture collection 
  • Evaluation of commercially available tests and other methodologies
  • Development of real-time PCR assays for newly emerged pathogens
  • Development of novel diagnostic real-time PCR assays  
  • Development and optimization of direct specimen (culture independent) next generation sequencing (NGS) approaches
  • Research into the diversity of bacterial strains within isolates from clinical specimens
  • Research into novel antimicrobial resistant bacteria
  • Evaluation of NGS and WGS approaches for understanding the spread of antimicrobial resistance
  • Creation of a database of circulating transmissible plasmids conferring antimicrobial resistance in New York.
  • Bioinformatic pipeline development for bacterial pathogens including Legionella, foodborne bacteria, antimicrobial resistant bacteria


The Bacteriology Laboratory is also one of ten public health laboratories in the country that participates 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 The Foodborne Diseases Active Surveillance Network (FoodNet), Active Bacterial Core surveillance (ABCs), and Healthcare Associated Infections-Community Interface (HAIC) projects.

The Bacteriology Laboratory participates in several U.S Food & Drug Administration (FDA) funded programs including the The National Antimicrobial Resistance Monitoring System (NARMS) including the Retail Meat Study grant and the GenomeTrakr network. These programs allow our laboratory the ability to contribute to the understanding of foodborne bacteria in retail meats and environmental sampling along with other public health labs and university partners to improve available genomic and geographic data and improve outbreak investigations.

The Bacteriology Laboratory has been a recipient of the Epidemiology and Laboratory Capacity for Prevention and Control of Emerging Infectious Diseases (ELC) Cooperative Agreement since 1996. This funding has been critical to U.S. health departments’ ability to combat infectious diseases and has had a major impact on our laboratory’s ability to detect, respond to, control, and prevent infectious diseases in New York. We continue to have funded projects in the following areas- Laboratory Capacity, PulseNet, PulseNet Area Laboratory, NARMS, Antibiotic Resistance Laboratory Network (AR Lab Network).

The Bacteriology Laboratory has several long-term contracts through the CDC and Association of Public Health Laboratories (APHL) focused on the improvement of new technologies for including whole-genome sequencing (WGS) and culture independent WGS for Legionella and Mycobacterium tuberculosis. These have included the following Request for Proposals (RFPs):


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
Musser E, Smith C, Halse TA, Kohlerschmidt D, Rourke A, Fiero A, Musser KA, Escuyer V, Lapierre P. Characterization of Mycobacterium salfingeri sp. nov.: A novel nontuberculous mycobacteria isolated from a human wound infection. Front Microbiol. 2022; (13): 992610. DOI: 10.3389/fmicb.2022.992610
The CRyPTIC Consortium. Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms. PLoS Biol. 2022; 20 (8): e3001755. DOI: 10.1371/journal.pbio.3001755
The CRyPTIC Consortium. A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics. PLoS Biol. 2022; 20 (8): e3001721. DOI: 10.1371/journal.pbio.3001721
Prussing C, Southwick K, Snavely E, Kidney A, Randall L, Sossei A, Dentinger L, Shushe O, Fernandez R, Haas W, Lapierre P, Singh N, Nazarian EJ, Musser KA, Mitchell K. Comparative analysis of multiplexed PCR and short- and long-read whole genome sequencing to investigate a large Klebsiella pneumoniae outbreak in New York State. Diagn Microbiol Infect Dis. 2022; 104 (2): 115765. DOI: 10.1016/j.diagmicrobio.2022.115765
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; 28 (7): 1431-1436. DOI: 10.3201/eid2807.212353
Fowler PW, Wright C, Spiers H, Zhu T, Baeten EML, Hoosdally SW, Gibertoni Cruz AL, Roohi A, Kouchaki S, Walker TM, Peto TEA, Miller G, Lintott C, Clifton D, Crook DW, Walker AS; Zooniverse Volunteer Community; CRyPTIC Consortium. A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates. Elife. 2022; (11): e75046. DOI: 10.7554/eLife.75046
Walker TM, Miotto P, Köser CU, Fowler PW, Knaggs J, Iqbal Z, Hunt M, Chindelevitch L, Farhat M, Cirillo DM, Comas I, Posey J, Omar SV, Peto TE, Suresh A, Uplekar S, Laurent S, Colman RE, Nathanson CM, Zignol M, Walker AS; CRyPTIC Consortium; Seq&Treat Consortium, Crook DW, Ismail N, Rodwell TC. The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A genotypic analysis. Lancet Microbe. 2022; 3 (4): e265-e273. DOI: 10.1016/S2666-5247(21)00301-3
Simner PJ, Musser KA, Mitchell K, Wise MG, Lewis S, Yee R, Bergman Y, Good CE, Abdelhamed AM, Li H, Laseman EM, Sahm D, Pitzer K, Quan J, Walker GT, Jacobs MR, Rhoads DD. Multicenter Evaluation of the Acuitas AMR Gene Panel for Detection of an Extended Panel of Antimicrobial Resistance Genes among Bacterial Isolates. J Clin Microbiol. 2022; 60 (3): e0209821. DOI: 10.1128/JCM.02098-21
Chan JL, Nazarian E, Musser KA, Snavely EA, Fung M, Doernberg SB, Pouch SM, Leekha S, Anesi JA, Kodiyanplakkal RPL, Turbett SE, Spalding Walters M, Epstein L. Prevalence of carbapenemase-producing organisms among hospitalized solid organ transplant recipients, five US hospitals, 2019-2020. Transpl Infect Dis. 2022; 24 (2): e13785. DOI: 10.1111/tid.13785
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
Haas W, Lapierre P, Musser KA. A Bioinformatic Pipeline for Improved Genome Analysis and Clustering of Isolates during Outbreaks of Legionnaires' Disease. J Clin Microbiol. 2021; 59 (2): e00967-20. DOI: 10.1128/JCM.00967-20
Carey J, Cole J, Venkata SLG, Hoyt H, Mingle L, Nicholas D, Musser KA, Wolfgang WJ. Determination of Genomic Epidemiology of Historical Clostridium perfringens Outbreaks in New York State by Use of Two Web-Based Platforms: National Center for Biotechnology Information Pathogen Detection and FDA GalaxyTrakr. J Clin Microbiol. 2021; 59 (2): e02200-20. DOI: 10.1128/JCM.02200-20
Banaei N, Musser KA, Salfinger M, Somoskovi A, Zelazny AM. Novel Assays/Applications for Patients Suspected of Mycobacterial Diseases. Clin Lab Med. 2020; 40 (4): 535-552. 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. 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
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. 2020; August 19 (11): 2007. DOI: 10.3389/fmicb.2020.02007
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. 2020; April 22 (2): e13256. DOI: 10.1111/tid.13256