Description, validation, and review of a decade of experience with a laboratory-developed PCR test for detection of Mycobacterium tuberculosis complex in pulmonary and extrapulmonary specimens.

Rapid detection of Mycobacterium tuberculosis complex directly from clinical specimens is critical for patient care. Mycobacterial culture requires days to weeks for results and therefore many laboratories employ rapid molecular methods for the diagnosis of tuberculosis. There are two FDA-cleared molecular assays for the detection of M. tuberculosis complex in the United States and both are cleared for testing of respiratory specimens only. The detection of M. tuberculosis complex in extrapulmonary specimens is often done using laboratory-developed PCR methods. In this work, the verification and subsequent validation of test performance over a decade is detailed for a laboratory-developed PCR assay (MTBRP) that detects M. tuberculosis complex from respiratory and non-respiratory specimens. The assay also provides information about potential isoniazid resistance. The performance of the MTBRP PCR assay was compared to the Cepheid Xpert MTB/RIF assay in acid-fast smear positive and smear negative specimens and mycobacterial culture for acid-fast smear positive specimens. The MTBRP assay demonstrated 99% correlation with the Xpert MTB/RIF assay using 499 respiratory specimens. The performance of the MTBRP PCR assay compared with mycobacterial culture for 867 AFB smear positive respiratory and non-respiratory specimens demonstrated a sensitivity of 100% and a specificity of 99.1%. This work provides longitudinal evidence using real-world clinical laboratory conditions and specimens to demonstrate that laboratory-developed PCR assays such as the MTBRP can provide a rapid and sensitive method for detection of pulmonary and extra-pulmonary tuberculosis from a wide-variety of smear positive specimen sources.

Effectiveness of Physical Distancing: Staying 6 Feet Over to Put Respiratory Viruses 6 Feet Under.

Community transmission of severe acute respiratory illness Coronavirus-2 (SARS-CoV-2) in Arizona was noted in March 2020. It was our hypothesis that the associated implementation of physical distancing and masking led to a decline in circulation and detection of common respiratory viruses. Nasopharyngeal swabs processed with the Biofire, Film Array respiratory panel at Mayo Clinic Arizona were reviewed from January 1, 2017, to July 31, 2020. A total of 13,324 nasopharyngeal swabs were analyzed. Between April and July 2017- 2019 (Period A) a mean of 262 tests were performed monthly, falling to 128 for the corresponding months of 2020 (Period B). A reduction in the monthly mean number of positive tests (Period A 71.5; Period B 2.8) and mean positivity rate (Period A 25.04%; Period B 2.07%) was observed. Rhinovirus/enterovirus was the most prevalent virus, with a monthly mean of 21.6 cases (30.2% of positives) for Period A and 2 cases (72.7% of positives) for Period B. Positivity for a second virus occurred in a mean of 2.1 positive tests (3.3%) in Period A but was absent in Period B. Implementation of distancing and masking coincides with a marked reduction in respiratory virus detection and likely circulation. Data from the fall/winter of 2020 will help clarify the potential role for distancing and masking as a mitigation strategy, not only for SARS-CoV-2 but also in the seasonal battle against common respiratory viruses.

Evaluation of 4 molecular assays as part of a 2-step algorithm for the detection of Clostridium difficile in stool specimens.

Detection of Clostridium difficile infection is important for clinical laboratories, owing to debilitating disease, severe outcomes, patient awareness, and public reporting of hospital data. This study evaluated the performance of 4 nucleic acid amplification test (NAAT) assays as part of a 2-step algorithm that involves reflexive NAAT following enzyme immunoassay (EIA) testing that is indeterminate for glutamate dehydrogenase (GDH) antigen and toxin A/B (GDH+/toxin- or GDH-/toxin+). A total of 500 stool specimens from consecutive patients were tested by each of the 5 methods and also evaluated as part of a 2-step algorithm. A specimen was considered positive for presence of C. difficile if it tested positive by 3 of 4 molecular methods or toxigenic culture. The sensitivity and specificity of the GDH-EIA method were each 93%. The toxin EIA had only 48% sensitivity, but it had 99% specificity. Sensitivity and specificity of 2-step algorithmic testing ranged from 88% to 93% and 99% to 100%, respectively, offering similar performance to stand-alone NAAT testing.