Comparison of saliva with oral and nasopharyngeal swabs for SARS-CoV-2 detection on various commercial and laboratory-developed assays.

The accurate laboratory detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial element in the fight against coronavirus disease 2019 (COVID-19). Reverse transcription-polymerase chain reaction testing on combined oral and nasopharyngeal swab (ONPS) suffers from several limitations, including the need for qualified personnel, the discomfort caused by invasive nasopharyngeal sample collection, and the possibility of swab and transport media shortage. Testing on saliva would represent an advancement. The aim of this study was to compare the concordance between saliva samples and ONPS for the detection of SARS-CoV-2 on various commercial and laboratory-developed tests (LDT). Individuals were recruited from eight institutions in Quebec, Canada, if they had SARS-CoV-2 RNA detected on a recently collected ONPS, and accepted to provide another ONPS, paired with saliva. Assays available in the different laboratories (Abbott RealTime SARS-CoV-2, Cobas® SARS-CoV-2, Simplexa™ COVID-19 Direct, Allplex™ 2019-nCoV, RIDA®GENE SARS-CoV-2, and an LDT preceded by three different extraction methods) were used to determine the concordance between saliva and ONPS results. Overall, 320 tests were run from a total of 125 saliva and ONPS sample pairs. All assays yielded similar sensitivity when saliva was compared to ONPS, with the exception of one LDT (67% vs. 93%). The mean difference in cycle threshold (∆C t ) was generally (but not significantly) in favor of the ONPS for all nucleic acid amplification tests. The maximum mean ∆​​​​​C t was 2.0, while individual ∆C t varied importantly from -17.5 to 12.4. Saliva seems to be associated with sensitivity similar to ONPS for the detection of SARS-CoV-2 by various assays.

Comparison of PCR and culture for screening of vancomycin-resistant Enterococci: highly disparate results for vanA and vanB.

We compared PCR to conventional culture for the detection of vancomycin-resistant enterococci (VRE) in 30,835 rectal samples over a 3-year period. The positive and negative predictive values of vanB PCR were 1.42% and 99.9%, respectively. A positive vanB result by PCR is poorly predictive and necessitates culture for differentiation of VRE-positive and -negative individuals.

Mycobacterium haemophilum epididymal abscess in a renal transplant patient.

Mycobacterium haemophilum is an established cause of cutaneous lesions in immunocompromised hosts. We report the first known case of epididymal abscess, which highlights the need to work up all specimens that are acid-fast bacillus-positive for M. haemophilum from immunocompromised hosts, regardless of body site.

Influence of multidrug resistance on tuberculosis treatment outcomes with standardized regimens.

RATIONALE: Multidrug-resistant tuberculosis (TB) poses a major challenge to global TB control. We analyzed the association between estimated prevalence of initial or acquired MDR-TB, and treatment outcomes reported nationally. OBJECTIVES: We analyzed the estimated prevalence of initial or acquired MDR-TB and treatment outcomes reported nationally. METHODS: Countries were analyzed if multidrug resistance prevalence estimates were available, and if they reported outcomes for more than 250 cases treated using standardized regimens in 2003 and/or 2004. Data sources were the World Health Organization for treatment regimens, prevalence of initial multidrug resistance, and reported cases and treatment outcomes in 2003 and 2004; the Joint United Nations Programme on HIV/AIDS for HIV seroprevalence; and the World Bank for income per capita. The adjusted impact of initial multidrug resistance on initial and retreatment outcomes was estimated with weighted multivariate linear regression. MEASUREMENTS AND MAIN RESULTS: Among countries using one of two standardized initial regimens, failure rates averaged 5.0%, and relapse rates averaged 12.8% in the 20 countries where prevalence of initial multidrug resistance exceeded 3%, compared with an average of 1.6% (P < 0.0001) and 8.1% (P = 0.0002), respectively, in 83 countries where initial multidrug resistance prevalence was less than 3%. In 92 countries using one standardized retreatment regimen, failure rates were 2.7%, 3.8%, 6.2%, and 8.1% in quartiles of increasing prevalence of acquired multidrug resistance (P < 0.0001). When stratified by initial multidrug resistance prevalence, initial and retreatment outcomes in the 79 countries using the 6-month rifampin initial regimen were not significantly different from the 24 countries using the 2-month rifampin initial regimen. CONCLUSIONS: Currently recommended standardized TB initial and retreatment regimens should be reevaluated in countries where prevalence of initial multidrug resistance exceeds 3%, in view of poor treatment outcomes.