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.

Prevalence and nosocomial spread of methicillin-resistant Staphylococcus aureus in a long-term-care facility in Slovenia.

OBJECTIVES: To determine the prevalence and incidence of methicillin-resistant Staphylococcus aureus (MRSA) colonization among residents and healthcare workers (HCWs) of a long-term-care facility (LTCF), to assess possible routes of nosocomial spread, and to determine genetic relatedness of the isolates. SETTING: A 351-bed community LTCF for the elderly. DESIGN AND PARTICIPANTS: Study investigators made two visits, approximately 3 months apart, to the facility. Samples for cultures were obtained from 107 residents during the first visit, 91 residents during the second visit, and 38 HCWs. RESULTS: The prevalence of MRSA colonization among residents was 9.3% during the first visit and 8.8% during the second visit. During the first visit, two HCWs were colonized. During the second visit, no HCWs were colonized. The colonization of HCWs suggested a potential role in the transmission of MRSA. Molecular typing showed that two of three roommates in one room had the same strain, whereas two in another room differed from one another. All isolates, except one, belonged to two related clonal groups. It seems that the clonal group to which most isolates belonged had the greatest potential for spreading among both residents and HCWs. CONCLUSIONS: Similar prevalence rates of MRSA colonization have been found in other European countries, but such studies have usually involved residents with better functional status than that of the participants in this study. Nosocomial spread of MRSA occurred in the facility examined, but not frequently. More attention should be focused on the hand hygiene of HCWs.

Risk factors for colonization with methicillin-resistant Staphylococcus aureus in a long-term-care facility in Slovenia.

OBJECTIVE: To evaluate risk factors associated with methicillin-resistant Staphylococcus aureus (MRSA) colonization in a long-term-care facility (LTCF) for the elderly in Slovenia. SETTING: A 351-bed community LTCF for the elderly. DESIGN AND PARTICIPANTS: This was a case-control study. MRSA carriage was identified in 102 of 127 residents of the facility's nursing unit. Two swabs were taken: one from the anterior nares and one from the largest skin lesion. If no skin lesions were present, the axillae and the groin area were swabbed. Data were collected regarding gender, age, length of stay in the facility, underlying conditions, functional status, presence of wounds or pressure sores, presence of catheters, antibiotic treatments, and hospital admissions. RESULTS: We detected MRSA in 12 participants. Risk factors independently and significantly associated with MRSA colonization on the multivariate analysis were antibiotic treatments within 1 month before the investigation (odds ratio, 5.087; 95% confidence interval, 1.02 to 25.48; P = .048) and multiple hospital admissions in the 3 months before the investigation (odds ratio, 6.277; 95% confidence interval, 1.31 to 30.05; P = .022). CONCLUSIONS: This is the first assessment of risk factors for colonization with MRSA in an LTCF in Slovenia. MRSA poses a problem in this LTCE Our observations may be valuable in implementing active surveillance cultures in infection control programs in Slovenian LTCFs.