Kimberlee A. Musser
A5025055624- Mycobacterium research and diagnosis
- Tuberculosis Research and Epidemiology
- Bacterial Identification and Susceptibility Testing
- Antibiotic Resistance in Bacteria
- Viral gastroenteritis research and epidemiology
- Salmonella and Campylobacter epidemiology
- Legionella and Acanthamoeba research
- Vibrio bacteria research studies
- Infective Endocarditis Diagnosis and Management
- Bacteriophages and microbial interactions
- Bacterial biofilms and quorum sensing
- Escherichia coli research studies
- Genomics and Phylogenetic Studies
- Bacterial Infections and Vaccines
- Antimicrobial Resistance in Staphylococcus
- Listeria monocytogenes in Food Safety
- Pneumonia and Respiratory Infections
- Actinomycetales infections and treatment
- Diagnosis and treatment of tuberculosis
- Streptococcal Infections and Treatments
- Infectious Diseases and Tuberculosis
- Infectious Diseases and Mycology
- Antifungal resistance and susceptibility
- Clostridium difficile and Clostridium perfringens research
- Microscopic Colitis
Wadsworth Center
2016-2025
New York State Department of Health
2016-2025
Mississippi State University
2022
University at Albany, State University of New York
2010-2017
Centers for Disease Control and Prevention
2011-2017
New York City Department of Health and Mental Hygiene
2017
Albany State University
2010-2014
Office of Chief Medical Examiner
2014
Abstract Background The US’ coronavirus disease 2019 (COVID-19) epidemic has grown extensively since February 2020, with substantial associated hospitalizations and mortality; New York State emerged as the national epicenter. We report on extent of testing test results during month March in State, along risk factors, outcomes, household prevalence among initial cases subject to in-depth investigations. Methods Specimen collection for COVID-19 was conducted healthcare settings,...
The Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) presents here a data compendium of 12,289 Mycobacterium tuberculosis global clinical isolates, all which have undergone whole-genome sequencing and had their minimum inhibitory concentrations to 13 antitubercular drugs measured in single assay. It is the largest matched phenotypic genotypic dataset M. date. Here, we provide summary detailing breadth collected, along with description how isolates...
The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis. However, molecular diagnostics to date have focused largely on first-line drugs and predicting susceptibilities in binary manner (classifying strains as either susceptible or resistant). Here, we used multivariable linear mixed model alongside whole genome sequencing quantitative microtiter plate assay relate genomic mutations minimum inhibitory concentration (MIC) 15,211...
Glycopeptides such as vancomycin are the treatment of choice for infections due to methicillin-resistant Staphylococcus aureus. This study describes identification high-level vancomycin-resistant S. aureus (VRSA) isolates in a polymicrobial biofilm within an indwelling nephrostomy tube patient New York. aureus, Enterococcus faecalis, faecium, Micrococcus species, Morganella morganii, and Pseudomonas aeruginosa were isolated from biofilm. For VRSA isolates, MICs ranged 32 >128 microg/ml. also...
For Salmonella enterica serovar Enteritidis, 85% of isolates can be classified into 5 pulsed-field gel electrophoresis (PFGE) types. However, PFGE has limited discriminatory power for outbreak detection. Although whole-genome sequencing been found to improve discrimination clusters, whether this procedure used in real-time a public health laboratory is not known. Therefore, we conducted retrospective and prospective analysis. The study investigated from 1 confirmed outbreak. Additional cases...
Escherichia coli O157:H7 is a Shiga toxin-producing E. (STEC) associated with numerous foodborne outbreaks in the United States and an important cause of bacterial gastrointestinal illness. In May 2009, we investigated multistate outbreak infections. Outbreak-associated cases were identified using serotyping molecular subtyping procedures. Traceback investigation product testing performed. A matched case-control study was conducted to identify exposures illness age-, sex-, state-matched...
ABSTRACT Whole-genome sequencing (WGS) is a newer alternative for tuberculosis (TB) diagnostics and capable of providing rapid drug resistance profiles while performing species identification capturing the data necessary genotyping. Our laboratory developed validated comprehensive sensitive WGS assay to characterize Mycobacterium other M. complex (MTBC) strains, composed novel DNA extraction, optimized library preparation, paired-end WGS, an in-house-developed bioinformatics pipeline. This...
Bedaquiline is a core drug for the treatment of multidrug-resistant tuberculosis; however, understanding resistance mechanisms poor, which hampering rapid molecular diagnostics. Some bedaquiline-resistant mutants are also cross-resistant to clofazimine. To decipher bedaquiline and clofazimine determinants, we combined experimental evolution, protein modelling, genome sequencing, phenotypic data.
Mycobacterium tuberculosis complex (MTBC) infections are treated with combinations of antibiotics; however, these regimens not as efficacious against multidrug and extensively drug resistant MTBC. Phenotypic (growth-based) susceptibility testing on slow growing bacteria like MTBC requires many weeks to months complete, whereas sequencing-based approaches can predict resistance (DR) reduced turnaround time. We sought develop a multiplexed, targeted next generation sequencing (tNGS) assay that...
ABSTRACT The largest reported outbreak of waterborne Escherichia coli O157:H7 in the United States occurred upstate New York following a county fair August 1999. Culture methods were used to isolate E. from specimens 128 775 patients with suspected infections. Campylobacter jejuni was also isolated stools 44 persons who developed diarrheal illness after attending this fair. There one case confirmed coinfection and C. . Molecular detection stx 1 2 Shiga toxin genes, immunomagnetic separation...
In this study, we report a whole-genome single nucleotide polymorphism (SNP)-based evolutionary approach to study the epidemiology of multistate outbreak Salmonella enterica subsp. serovar Montevideo. This included 272 cases that occurred in 44 states between July 2009 and April 2010. A case-control linked consumption salami made with contaminated black red pepper outbreak. We sequenced, on SOLiD System, 47 isolates XbaI PFGE pattern JIXX01.0011, common pulsed-field gel electrophoresis...
Next-generation sequencing technologies are being rapidly adopted as a tool of choice for diagnostic and outbreak investigation in public health laboratories. However, costs operation the need specialized staff remain major hurdles laboratories with limited resources implementing these technologies. This project aimed to assess feasibility using Oxford Nanopore MinION whole-genome data Mycobacterium tuberculosis isolates species identification, silico spoligotyping, detection mutations...
Objectives: Infections caused by Legionella are the leading cause of waterborne disease outbreaks in United States. We investigated a large outbreak Legionnaires’ New York City summer 2015 to characterize patients, risk factors for mortality, and environmental exposures. Methods: defined cases as patients with pneumonia laboratory evidence infection from July 2 through August 3, 2015, history residing or visiting 1 several South Bronx neighborhoods City. describe epidemiologic,...
Rapid and reliable detection of rifampin (RIF) resistance is critical for the diagnosis treatment drug-resistant multidrug-resistant (MDR) tuberculosis. Discordant RIF phenotype/genotype susceptibility results remain a challenge due to presence rpoB mutations that do not confer high levels resistance, as have been exhibited in strains with such Ser450Leu.
Members of the Mycobacterium tuberculosis complex (MTBC) differ in virulence attributes, drug resistance patterns, and host preferences. The rapid differentiation these species to determine zoonotic or human sources disease direct treatment can benefit both public health patient management. Commercially available assays cannot differentiate species, published have not been evaluated directly on clinical specimens. A real-time PCR assay for M. tuberculosis, bovis, bovis BCG, africanum,...
ABSTRACT Campylobacter enteritis is a food-borne or waterborne illness caused almost exclusively by jejuni and, to lesser extent, coli . These organisms produce indistinguishable clinical diseases and together represent the second most common cause of bacterial diarrhea in United States leading enteric infection throughout world. The conventional approach laboratory diagnosis based on recovery organism from stool specimen, which requires use specialized medium incubated at 42°C for several...
The aim of this study was to compare the clinical and laboratory characteristics Clostridium difficile infection (CDI) in patients with discordant test results for cytotoxin assay (CYT) PCR assays. A retrospective from May August 2008 March 2010 performed. CDI diagnosed 128 patients. increased yield C. cases by 2-fold compared that CYT assay. Fifty-six (44%) were detected only (CYT negative). Forty-nine percent non-NAP1 strains only, 28% those infected NAP1 (P < 0.05). No significant...
Plumbing systems are an infrequent but known reservoir for opportunistic microbial pathogens that can infect hospitalized patients. In 2016, a cluster of clinical sphingomonas infections prompted investigation.We performed whole-genome DNA sequencing on isolates multidrug-resistant Sphingomonas koreensis identified from 2006 through 2016 at the National Institutes Health (NIH) Clinical Center. We cultured S. sinks in patient rooms and both shotgun metagenomic to identify within...
Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains are a serious health problem in India, also contributing to one-fourth of the global MDR (TB) burden. About 36% MTBC reported fluoroquinolone (FQ) resistant leading high pre-extensively drug-resistant (pre-XDR) and XDR-TB (further resistance against bedaquiline and/or linezolid) rates. Still, factors driving MDR/pre-XDR epidemic India not well defined. In retrospective study, we analyzed 1852 consecutive obtained...
Our laboratory has developed a rapid, sensitive, and specific molecular approach for detection in clinical specimens, within 48 h of receipt, both Mycobacterium tuberculosis complex (MTBC) DNA mutations the 81-bp core region rpoB gene that are associated with rifampin (RIF) resistance. This approach, which combines an initial real-time PCR internal inhibition assessment pyrosequencing assay, was validated direct use specimens. To assess suitability respiratory, nonrespiratory, acid-fast...
ABSTRACT A total of 30 Legionella pneumophila serogroup 1 isolates representing 10 separate legionellosis laboratory investigations (“outbreaks”) that occurred in New York State between 2004 and 2012 were selected for evaluation whole-genome sequencing (WGS) approaches molecular subtyping this organism. Clinical environmental available each outbreak initially examined by pulsed-field gel electrophoresis (PFGE). Sequence-based typing alleles extracted from WGS data yielding complete sequence...