Biomedical subjects

Kimberlee A Musser

Publications and source records attributed to Kimberlee A Musser.

9 recordsLinked to original sources

PubMed2026

Presence of globally prominent multidrug-resistant genotypes of Salmonella enterica serovar Typhi in New York State, 2016-2023.

The human-restricted enteric pathogen Salmonella enterica serovar Typhi (S. Typhi) is the causative agent of the life-threatening typhoid fever. Although S. Typhi incidence is relatively low in the USA, routine surveillance of S. Typhi is critical to track the emergence and spread of high-risk lineages in non-endemic areas. In this study, we analysed 151 genomes of S. Typhi isolates from patients who were clinically confirmed with typhoid fever across New York State between 2016 and 2023. We used the GenoTyphi classification scheme and identified established multidrug-resistant and extensively drug-resistant lineages. We detected the presence of the globally widespread genotype 4.3.1 (haplotype 58) and its derivative 4.3.1.1.P1, which recently emerged in Pakistan, as well as the Bangladesh-restricted lineages 3.3.2.Bd1 and 3.3.2.Bd2 in our dataset. Ten mutations and 14 acquired genes associated with antimicrobial resistance (AMR) were present across the entire population, with 86.8% of the genomes possessing at least one of these AMR determinants. The gyrA S83F mutation conferring quinolone and triclosan resistance was the most frequently detected (94 genomes). Combinations of dfrA7+catA1 (resistance to trimethoprim and chloramphenicol, respectively) and sul2+aph(3″)-Ib+aph(6)-Id (resistance to sulphonamide and aminoglycosides, respectively) co-occurred frequently and were associated with IncQ and IncY plasmid replicons. Phylogenetic contextualization against a global dataset of 1,643 genomes from 20 countries across five continents, including other parts of the USA, from the same time period showed geographic intermingling, suggesting the spread of high-risk genotypes of international origins to New York State. Altogether, these findings reveal the presence of globally dominant resistant genotypes that are likely facilitated by human travel in New York State, where typhoid fever is not endemic. Long-term genomic surveillance is critical to AMR profiling, identifying genotypic shifts in regional S. Typhi populations, monitoring transmission routes and guiding effective public health interventions.

Salmonella typhi↗

PubMed2026

Clustering and Source Association of Clinical and Nonclinical Listeria monocytogenes Isolates, New York, USA, 2000-20211.

We analyzed whole-genome sequencing data for 1,046 human clinical and 1,332 nonclinical Listeria monocytogenes isolates collected across New York, USA, during 2000-2021. Several hypervirulent clonal complexes (CCs) were significantly associated with clinical isolates, and several hypovirulent CCs were associated with nonclinical isolates. Specific CCs also showed association with specific food categories (e.g., processed meat); specific genetic markers (e.g., inlA premature stop codons) were also significantly associated with processed meat isolates. Analysis of clusters that contained food isolates, as well as subsequently identified clinical isolates, showed that time of isolation between food isolates and clinical isolates was significantly shorter for produce isolates than for isolates from meat, dairy, or fish. This finding suggests unique transmission pathways for produce, which might reflect short shelf life or limited L. monocytogenes persistence (e.g., in agricultural environments). This study highlights new opportunities for use of whole-genome sequencing to improve outbreak investigations and source attribution.

Listeria monocytogenes↗

PubMed2006

High-level vancomycin-resistant Staphylococcus aureus isolates associated with a polymicrobial biofilm.

Glycopeptides such as vancomycin are the treatment of choice for infections due to methicillin-resistant Staphylococcus aureus. This study describes the identification of high-level vancomycin-resistant S. aureus (VRSA) isolates in a polymicrobial biofilm within an indwelling nephrostomy tube in a patient in New York. S. aureus, Enterococcus faecalis, Enterococcus faecium, Micrococcus species, Morganella morganii, and Pseudomonas aeruginosa were isolated from the biofilm. For VRSA isolates, vancomycin MICs ranged from 32 to >128 microg/ml. VRSA isolates were also resistant to aminoglycosides, fluoroquinolones, macrolides, penicillin, and tetracycline but remained susceptible to chloramphenicol, linezolid, rifampin, and trimethoprim-sulfamethoxazole. The vanA gene was localized to a plasmid of approximately 100 kb in VRSA and E. faecium isolates from the biofilm. Plasmid analysis revealed that the VRSA isolate acquired the 100-kb E. faecium plasmid, which was then maintained without integration into the MRSA plasmid. The tetracycline resistance genes tet(U) and tet(S), not previously detected in S. aureus isolates, were identified in the VRSA isolates. Additional resistance elements in the VRSA isolate included a multiresistance gene cluster, ermB-aadE-sat4-aphA-3, msrA (macrolide efflux), and the bifunctional aminoglycoside resistance gene aac(6')-aph(2")-Ia. Multiple combinations of resistance genes among the various isolates of staphylococci and enterococci, including vanA, tet(S), and tet(U), illustrate the dynamic nature of gene acquisition and loss within and between bacterial species throughout the course of infection. The potential for interspecies transfer of antimicrobial resistance genes, including resistance to vancomycin, may be enhanced by the microenvironment of a biofilm.

Acetamides↗

PubMed2006

Development and evaluation of a 4-target multiplex real-time polymerase chain reaction assay for the detection and characterization of Yersinia pestis.

A multiplexed, 4-target real-time polymerase chain reaction (PCR) assay for the detection and characterization of Yersinia pestis was designed and optimized for respiratory and environmental samples. The target sequences include the entF3 gene of the chromosome, pla (plasminogen activator) on the pPCP1 virulence plasmid, caf1 (F1 capsule antigen) on the pMT1 virulence plasmid, and a region located on the pCD1 plasmid. The sensitivity of this assay was determined to be less than 85 CFU per reaction for each specimen type analyzed. This assay was also determined to be 100% specific with strains of Y. pestis, 9 additional Yersinia species, and related enteric and respiratory organisms. The results show that this multiplex real-time PCR assay using TaqMan(R) (Roche Molecular Systems, Inc., Alameda, CA) chemistry is sensitive and specific, requires minimal sample input, and can yield results in approximately 4 h. This assay is the first 4-target multiplex real-time PCR assay for Y. pestis in which detection and virulence assessment of Y. pestis can occur in one reaction, from clinical and environmental samples.

Antigens, Bacterial↗

PubMed2006

A multiplexed real-time PCR assay for rapid detection of Chlamydia trachomatis and identification of serovar L-2, the major cause of Lymphogranuloma venereum in New York.

Lymphogranuloma venereum (LGV) is caused by a rare form of Chlamydia trachomatis that is difficult to diagnose, since culture is not readily available, and since other methods are not reliable or lack sensitivity. We report here a rapid, sensitive, and specific real-time multiplex polymerase chain reaction (PCR) assay capable of detecting C. trachomatis and identifying serovar L-2 in the same reaction, directly from rectal swabs. The analytical sensitivity of the assay was 25 genome copies for C. trachomatis, and 50 genome copies for L-2. The analytical specificity was 100%, as demonstrated with a diverse range of C. trachomatis serovars and other site-specific bacterial pathogens. With the use of a rapid DNA extraction method, a blinded validation of spiked rectal swabs correctly identified 30 samples containing C. trachomatis cells, L-2 DNA, or negative samples. The multiplexed PCR assay also identified serovar L-2 in 13 of 70 rectal swab samples taken from symptomatic patients. Twelve additional samples were positive for C. trachomatis only, and omp1 sequencing determined these samples as either serovar D, E, G, J, or K. This assay represents the first real-time PCR method capable of detecting C. trachomatis DNA, and of simultaneously identifying C. trachomatis infection as serovar L-2.

Bacteriological Techniques↗

PubMed2005

Use of a multiplex molecular beacon platform for rapid detection of methicillin and vancomycin resistance in Staphylococcus aureus.

Drug resistance, particularly vancomycin and methicillin resistance, in Staphylococcus aureus continues to emerge as a significant public health threat in both the hospital and community settings. In addition to the limited treatment options, S. aureus strains acquire and express numerous virulence factors that continue to increase its ability to cause a wide spectrum of human disease. As a result, empirical treatment decisions are confounded and there is a heightened need for a diagnostic test (or assay) to rapidly identify antibiotic resistance and specific virulence determinants and indicate the appropriate treatment. To that end we developed a platform using multiplex molecular beacon probes with real-time PCR for the rapid detection of drug resistance-determining genes and virulence factors in S. aureus. In this study, we demonstrate the specificity and sensitivity of our platform for detection of the genes conferring methicillin (mecA) and vancomycin (vanA) resistance as well as a gene encoding the virulence factor Panton-Valentine leucocidin (lukF) in S. aureus isolates.

Anti-Bacterial Agents↗

PubMed2004

A real-time multiplexed PCR assay for rapid detection and differentiation of Campylobacter jejuni and Campylobacter coli.

Campylobacter species are the leading agents of bacterial gastroenteritis worldwide. C. jejuni and C. coli together are responsible for more than 95% of all cases of Campylobacter-induced diarrheal disease in the United States. Detection of campylobacteria in clinical samples by conventional culture is problematic and slow due to their complex taxonomy, fastidious growth requirements, and biochemical inertness. The current study describes a rapid, sensitive, and specific real-time polymerase chain reaction (PCR) assay capable of detecting and differentiating C. jejuni (hippuricase gene, hipO) and C. coli (serine hydroxymethyltransferase gene, glyA) in a single reaction, directly from clinical isolates and human feces. The analytical specificity of the assay was demonstrated with a diverse range of Campylobacter species, related organisms, and other diarrhea-inducing bacterial pathogens. The analytical sensitivity of the multiplexed, PCR assay was 10 genome copies for both C. jejuni and C. coli. Following a rapid DNA extraction method (QIAGEN QIAamp DNA stool Mini Kit), the multiplexed PCR identified C. jejuni or C. coli in 100% of fecal samples containing 10(3) colony-forming units (CFU) per gram of feces. This assay represents the first real-time PCR method capable of detecting and differentiating C. jejuni and C. coli in a single reaction.

Base Sequence↗

PubMed2004

Laboratory confirmation of generalized vaccinia following smallpox vaccination.

The reinitiation of smallpox vaccination has renewed interest in implementing modern diagnostic methods to assess orthopoxvirus infection and adverse events following vaccination. We report here the laboratory confirmation of vaccinia virus in pustular lesions of a healthy adult vaccinee by use of a two-tier algorithm incorporating TaqMan PCR and electron microscopy.

Adult↗

PubMed2004

Multiplex diagnostic platforms for detection of biothreat agents.

The availability of rapid, sensitive and cost-effective diagnostic methods is paramount to the success of a comprehensive national health security system in the USA. The national networks that were established to safeguard US infrastructures (e.g., public health, livestock, agriculture and water supply) have developed sufficient capability and capacity for monitoring. However, additional advanced methods will be required to maintain operational readiness. Currently available methods, although sensitive and specific, are generally costly and not amenable to high-throughput analyses. Critical to the success of biothreat surveillance is the ability to screen for and detect multiple agents rapidly in a single reaction and with minimal sample processing. This review will examine currently available diagnostic platforms (i.e., PCR-, immuno- and array-based) and biosensors that can detect multiple biothreat analytes in a single reaction (i.e., multiplex assays). The maturity, benefits and limitations of each platform will be described and a prospective view, from current to future state of the art, will be proposed.

Bioterrorism↗