Accuracy of Allplex SARS-CoV-2 assay amplification curve analysis for the detection of SARS-CoV-2 variant Alpha.

Aim: To evaluate the accuracy of two PCR-based techniques for detecting SARS-CoV-2 variant Alpha (B.1.1.7). Materials & methods: A multicenter prospective cohort with 1137 positive specimens from Slovenia was studied. A mutation-based assay (rTEST-COVID-19 qPCR B.1.1.7 assay) and amplification curve pattern analysis of the Allplex SARS-CoV-2 assay were compared with whole-genome sequencing. Results: SARS-CoV-2 variant Alpha was detected in 155 samples (13.6%). Sensitivity and specificity were 98.1 and 98.0%, respectively, for the rTEST-COVID-19 qPCR B.1.1.7 assay and 97.4 and 97.5%, respectively, for amplification curve pattern analysis. Conclusion: The good analytical performance of both methods was confirmed for the preliminary identification of SARS-CoV-2 variant Alpha. This cost-effective principle for screening SARS-CoV-2 populations is also applicable to other emerging variants and may help to conserve some whole-genome sequencing resources.

Analysis of Slovenian MRSA strains with susceptibility patterns suggestive of CA-MRSA.

BACKGROUND: Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) differs from healthcare-associated MRSA (HA-MRSA) in its molecular and microbiological characteristics. MATERIALS AND METHODS: Six Slovenian regional public health institutes and the National Institute of Public Health took part in monitoring CA-MRSA infections. S. aureus isolates resistant to oxacillin and susceptible to > or = two of the four antibiotics ciprofloxacin, erythromycin, clindamycin or gentamicin were defined as CA-MRSA and further analyzed. The presence of the gene for Panton-Valentine leukocidin (PVL) was confirmed using PCR, the type of staphylococcal cassette chromosome (SCCmec) using multiplex PCR, and macrorestriction analysis of chromosomal DNA using pulsed-field gel electrophoresis (PFGE). RESULTS: A total of 31 strains from 31 patients were analyzed during a period of 21 months: 23 specimens were sent from hospitals, six from primary care, two from a long-term care facility. All 31 isolates contained the gene mecA. Sixteen (51.6%) isolates were identified as SCCmec type IV, three isolates were PVL positive. Using PFGE, the CA-MRSA strains were classified into 15 similarity groups. Results of antibiotic susceptibility showed there were five resistance types among the 31 strains. Simultaneous resistance against ciprofloxacin and gentamicin was often associated with the presence of SCCmec type I, strongly resembling HA-MRSA. CONCLUSIONS: PVL-positive strains of CA-MRSA have been isolated in Slovenia only rarely. We will continue to monitor strains of MRSA in order to obtain the complete microbiological and epidemiological features.