Rapid identification of respiratory pathogens, such as influenza virus A (FluA), influenza virus B (FluB), and respiratory syncytial virus (RSV), reduces unnecessary antimicrobial use and enhances infection control practice. We performed a comparative evaluation of three molecular methods: (i) the Aries Flu A/B & RSV, (ii) the Xpert Xpress Flu/RSV, and (iii) the Cobas Flu A/B & RSV assays. The clinical performances of the three methods were evaluated using 200 remnant nasopharyngeal swab (NPS) specimens against a combined reference standard. The limits of detection (LODs) were determined using FluA, FluB, and RSV control strains with known titers. The 95% LODs were between 1.702 and 0.0003 50% tissue culture infective dose (TCID), with no significant differences revealed among the three assays. Perfect qualitative detection agreement was obtained in the reproducibility study. The Cobas assay failed at the first run on 13 clinical specimens, resulting in an invalid rate of 6.5%. The sensitivities and specificities for all assays were 96.0 to 100.0% and 99.3 to 100% for all three viruses. For on-demand single-specimen and batched 12-specimen workflows, the test turnaround times were 115.5 and 128.8 min for the Aries assay (12 sample capacity), 34.2 and 44.2 min for the Xpress assay (16 sample capacity), and 21.0 and 254.4 min for the Cobas assay (one instrument), respectively. In summary, the Aries, Xpress, and Cobas Liat assays demonstrated excellent sensitivities and specificities for simultaneous detection and identification of FluA, FluB, and RSV from NPS specimens in cancer patients. Test turnaround time was significantly shorter on the Xpress when instrument scalability is unlimited.
CNS infections are potentially life threatening if not diagnosed and treated early. The initial clinical presentations of many CNS infections are nonspecific making a definitive etiologic diagnosis challenging. Nucleic acid in vitro amplification-based molecular methods are increasingly being applied for routine microbial detection. These methods are a vast improvement over conventional techniques with the advantage of rapid turnaround and higher sensitivity and specificity. Additionally, molecular methods performed on cerebrospinal fluid samples are considered the new gold standard for diagnosis of CNS infection caused by pathogens which are otherwise difficult to detect. Commercial diagnostic platforms offer various monoplex and multiplex PCR assays for convenient testing of targets that cause similar clinical illness. Pan-omic molecular platforms possess potential for use in this area. Although molecular methods are predicted to be widely used in diagnosing and monitoring CNS infections, results generated by these methods need to be carefully interpreted in combination with clinical findings. This review summarizes the currently available armamentarium of molecular assays for diagnosis of central nervous system infections, their application, and future approaches.
BackgroundThe majority of patients diagnosed with oropharyngeal squamous cell cancer (OPSCC) are due to HPV infection. At present, there are no reliable tests for screening HPV in patients with OPSCC. The objective of this study was to assess the Cobas® HPV Test on oral rinse specimens as an early, non-invasive tool for HPV-related OPSCC.MethodsOral rinse specimens were collected from 187 patients (45 with OPSCC, 61 with oral cavity SCC (OCSCC) and 81 control patients who had benign or malignant thyroid nodules) treated at MSKCC. The Cobas® HPV Test was used to detect 14 high-risk HPV types in these samples. Performance of the HPV Test was correlated with p16 tumor immunohistochemistry as gold standard.Results91.1% of the oropharynx cancer patients had p16 positive tumors compared to 3.3% of oral cavity cancer. Of the 81 control patients, 79 (97.5%) had no HPV in their oral rinse giving a specificity of the HPV test of 98%. For the combined oral cavity oropharynx cancer cohort, the sensitivity, specificity, positive predictive value and negative predictive value of the HPV Test were 79.1%, 90.5%, 85.0% and 86.4% respectively when p16 immunohistochemistry was used as the reference.ConclusionThe Cobas® HPV Test on oral rinse is a highly specific and potentially sensitive test for oropharyngeal cancer and may be a potentially useful screening test for early oropharyngeal cancer.ImpactWe describe an oral rinse test for the detection of HPV related oropharyngeal cancer.
multilocus sequence type 37 (ST37), which mainly corresponds to ribotype 017, has been a dominant genotype circulating in China. In this study, we report the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to analyze and characterize 204 clinical isolates, including 49 ST37 and 155 non-ST37 isolates collected in China and other countries. The distributions of two major protein peaks ( 3,242 and 3,286) were significantly different between ST37 and non-ST37 prototype strains and clinical isolates. This difference was reproducible when analysis was performed on different colonies in different runs. This finding was repeated and confirmed by both bioMérieux Vitek MS and Bruker Microflex LT systems on isolates recovered from a variety of geographic regions worldwide. The combination of the two peaks was present in 47 of 49 ST37 isolates, resulting in a sensitivity of 95.9%. In contrast, the peak combination was absent in 153 of 155 non-ST37 isolates, resulting in a specificity of 98.7%. Our results suggest that MALDI-TOF MS is a rapid and reliable tool to identify genotype ST37. Work is in progress to characterize the two molecules having peaks at 3,242 and 3,286, which appear to be specific to genotype ST37.
Fecal calprotectin (fCPT) has been used as a surrogate marker for assessment of intestinal inflammation. We explore the utility of fCPT values as a diagnostic aid in cancer patients with suspected Clostridium difficile infection (CDI). A total of 232 stool specimens submitted for GeneXpert C. difficile PCR testing were included in the study. All specimens were tested for fCPT and toxin/GDH antigens. Clinical severity of CDI cases was determined by the IDSA/SHEA criteria. Significant differences of median fCPT values (μg/g) between CDI (n=117, Median 183.6 μg/g) and non-CDI (n=115, 145.6 μg/g, p=0.006) patients were seen. In CDI patents, significantly lower f CPT values were found in patients with mild to moderate (n=95, 182.1 μg/g) than those with severe & severe to complicated (n=22, 218.5 μg/g, p=0.014) scores, and among those that were toxin positive (n=24, 200.2 μg/g) versus toxin negative (n=86, 182.8 μg/g, p=0.044). Despite this overall trend, wide variations in fCPT values were found in all categories examined. A logistic regression analysis revealed that the fCPT values correlated independently with the severity of clinical manifestations (OR=2.021, 95%CI=1.132–3.608); however, it did not correlate with other clinical outcomes. Our study findings show that high fecal calprotectin levels correlate with toxin positive and clinically severe CDI; however wide variations in individual measurements preclude establishment of reliable cut-offs for routine diagnostic use in cancer patients.
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