Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants

The rapid and presumptive detection of SARS-CoV-2 variants may be performed using multiplex RT-PCR assays. The aim of this study was to evaluate the diagnostic performance of five qualitative RT-PCR tests as compared with next-generation sequencing (NGS). We retrospectively examined a multi-variant panel (n = 72) of SARS-CoV-2-positive nasopharyngeal swabs categorized as variants of concern (Alpha, Beta, Gamma and Delta), variants under monitoring (Iota and Kappa) and wild-type strains circulating in Liguria (Italy) from January to August 2021. First, NGS libraries of study samples were prepared and mapped to the reference genome. Then, specimens were screened for the detection of L452R, W152C, K417T, K417N, E484Q, E484K and N501Y mutations using the SARS-CoV-2 Variants II Assay Allplex, UltraGene Assay SARS-CoV-2 452R & 484K & 484Q Mutations V1, COVID-19 Ultra Variant Catcher, SARS-CoV-2 Extended ELITe MGB and Simplexa SARS-CoV-2 Variants Direct. The overall accuracy of these assays ranged from 96.9% to 100%. Specificity and sensitivity were 100% and 96-100%, respectively. We highly recommend the use of these assays as second-level tests in the routine workflow of SARS-CoV-2 laboratory diagnostics, as they are accurate, user friendly, low cost, may identify specific mutations in about 2-3 h and, therefore, optimize the surveillance of SARS-CoV-2 variants

Indagine sulla diffusione di stafilococchi resistenti alla meticillina in Liguria

Introduction. Staphylococcus aureus is a major opportunistic pathogen especially in nosocomial settings. An increasing proportion of strains has intrinsic resistance to methicillin (MRSA) and recent reports documented the emergence of MRSA also in the community.The aim of this study was to evaluate methicillin-resistance in Liguria. Methods. 767 isolates of Staphylococcus spp have been collected from 10 laboratories, including 508 S. aureus: 292 (57.5%) hospital-acquired, 188 (37%) community-acquired, and 28 (5.5%) from healthcare settings; 259 coagulase- negative staphylococci (CNS): (193 (74.5%) hospital-acquired, 56 (21.6%) community-acquired, and 10 (3.9%) healthcare settings. Susceptibility tests were carried out by the disk diffusion method (CLSI, 2006) using cefoxitin (CFX) (Oxoid, Milan). MRSA has been also evaluated by PBP2’ latex agglutination test (Oxoid, Milan) on 52 randomly selected S. aureus. Results. The data obtained indicated an incidence of MRSA in nosocomial settings up to 45.2%, while among the community-acquired isolates the percentage was 6.4%. With respect to CNS the figures were 61,8% and 10,6% for the nosocomial-and community-acquired organisms respectively. A 99% agreement between data of the coordinating centre and the various laboratories was found. Methicillin-resistance was confirmed in 52 S. aureus by PBP2’ latex agglutination test. Conclusions. Present findings indicate that MRSA in community in the Ligurian area exists and this phenomenon requires future surveillance