Candida auris is an emerging multidrug-resistant fungal pathogen that has been associated with nosocomial bloodstream and deep wound infections causing a high mortality rate mainly in intensive care unit (ICU) patients. Laboratories currently rely on phenotypic testing using commercial automated systems for identification of yeasts; however, this technique has often led to misidentification of C. auris to other closely related species. We developed and validated a TaqMan-based real-time PCR assay on the BD Max platform targeting ribosomal DNA (rDNA) region nucleotide sequences to quickly and accurately test for C. auris infection from culture and clinical specimens. The assay is highly specific, reproducible, and sensitive, allowing detection of as low as 1 C. auris CFU per reaction within 3 h.
As the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) begins to overlap with the traditional respiratory season in the Northern Hemisphere, simultaneous testing for SARS-CoV-2 and the other common causes of respiratory infections is imperative. This has led to the development of multiplex respiratory assays that include SARS-CoV-2 as a target. One such assay is the BioFire respiratory panel 2.1 (RP2.1), which is an expansion of the original BioFire FilmArray respiratory panel 2 (RP2) to include SARS-CoV-2.
Bacterial whole-genome sequencing (WGS) provides clinical and public health laboratories an unprecedented level of information on species identification, antimicrobial resistance, and epidemiologic typing. However, multiple barriers to widespread adoption still exist. This research describes bacterial WGS using the Illumina iSeq 100 instrument to overcome some of these barriers. Using an in-house, high-quality single-nucleotide polymorphism analysis pipeline and a commercial whole-genome multilocus sequence typing program, the sequencing of Acinetobacter baumannii, Burkholderia cepacia, Clostridioides difficile, Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa, Serratia marcescens, and Staphylococcus aureus isolates was validated. The genome coverage range was 17Â to 149Â, with a mean of 59Â. The limit of detection for single-nucleotide polymorphisms was 30Â. Overall platform base calling accuracy was >99.999%. Reproducibility and repeatability of base calling inferred from whole-genome multilocus sequence typing was species dependent and ranged from >97% similarity for P. aeruginosa to >99.9% similarity for S. aureus. Resistance gene and multilocus sequence typing allele identification was 100% concordant with expected results. A simple, modified library preparation reduces the per-sample cost by half to give overall theoretical sample costs ranging from approximately $50 to $100 for library preparation and sequencing. The iSeq 100 provides a cost-effective and easy-to-use platform for clinical and public health laboratories to sequence bacterial isolates for a wide range of potential applications.
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