ABSTRACT
Background. Hospital-onset bloodstream infection (HOBSI) incidence has been proposed as a complementary quality metric to central line-associated bloodstream infection (CLABSI) surveillance. Several recent studies have detailed increases in median HOBSI and CLABSI rates during the COVID-19 pandemic. We sought to understand trends in HOBSI and CLABSI rates at a single health system in the context of COVID-19. Methods. We conducted a retrospective analysis of HOBSIs and CLABSIs at a three-hospital health system from 2017 to 2021 (Figure 1). We compared counts, denominators, and demographic data for HOBSIs and CLABSIs between the prepandemic (1/1/2017-3/30/2020) and pandemic period (4/1/2020-12/31/2021) (Table 1). We applied Poisson or negative binomial regression models to estimate the monthly change in incidence of HO-BSI and CLABSI rates over the study period. Figure 1: Definitions applied for hospital-onset bloodstream infections (HO-BSIs) and central line-associated bloodstream infections (CLABSIs). Potentially contaminated blood cultures were identified by microbiology laboratory technicians as any set of blood culture in which a single bottle was positive for organisms typically considered as skin contaminants. Uncertain cases undergo secondary review by senior lab technicians. Table 1: Count, denominator, and device utilization ratio data for hospital-onset bloodstream infections (HO-BSIs) and central line-associated bloodstream infections (CLABSIs) Note that central line utilization increased upon regression analysis (p<0.001). Results. The median monthly HOBSI rate per 1,000 patient days increased from 1.0 in the pre-pandemic to 1.3 (p< 0.01) in the pandemic period, whereas the median monthly CLABSI rate per central line days was stable (1.01 to 0.88;p=0.1;Table 2). Our regression analysis found that monthly rates of HO-BSIs increased throughout the study, but the increase was not associated with the onset of the COVID-19 pandemic based on comparisons of model fit (Figure 2;Table 3). Despite an increase in central line utilization, regression modelling found no changes in monthly CLABSIs rates with respect to time and the COVID-19 pandemic. Incidence of HOBSIs and CLABSIs by common nosocomial organisms generally increased over this time period, though time to infection onset remained unchanged in our studied population (Table 2). Conclusion. HOBSIs rates did not correlate with CLABSI incidence across a three-hospital health system from 2017 and 2021, as rates of HOBSI increased but CLABSI rates remained flat. Our observed increase in HOBSI rates did not correlate with the onset of the COVID-19 pandemic, and caution should be used in modeling the effects of COVID-19 without time-trended analysis. Further evaluation is needed to understand the etiology, epidemiology, and preventability of HO-BSI.
ABSTRACT
Background: Detection and surveillance of SARS-CoV-2 is of eminent importance, particularly due to the rapid emergence of variants of concern (VOCs). Since September 2020, the TaqPath COVID-19 assay (Thermo Fisher Scientific, Waltham, MA, USA) has been used to identify viral strains of the new lineage B.1.1.7, since it previously failed to detect the S-gene 69/70 deletion. Rapid detection of these variants of concern can help to contain them and prevent widely spreading throughout the population. This study evaluated S-gene mutations screening with a commercially available qualitative real-time PCR (RT-PCR) assay to detect likely variant of SARS-CoV-2 by the S gene amplification curve non-sigmoidal fluorescence profile. Method(s): The viral RNA of the samples was extracted using the Seegene STARlet automated system combined with StarMag 96x4 Viral DNA/RNA 200C. All samples were subjected to Real Time RT-PCR with the AllplexTM SARS-CoV-2 Assay kit (Seegene Inc, Seul, South Korea) for the qualitative detection of four target genes: E, N, RdRp, and S genes. PCR has been performed by a CFX-96 real-time thermocycler (Bio-Rad Laboratories Inc, Hercules, CA, USA) and Ct values were acquired from the fluorescence channels by the fluorophores FAM (E gene), Quasar 670 (N gene), Cal Red 610 (RdRp and S genes), and HEX (internal control). Gene target amplification curve analysis was performed using Seegene Viewer ver 3.24 (Seegene). The samples tested positive for SARS-CoV-2 viral genome, which presented abnormalities in the fluorescence profile of the amplification curve of the RdRP/S genes, were further subjected to the amplification protocol by the GSD NovaTYpe SARS-CoV-2 amplification kit (Nova Tec Immunodiagnostica, Dietzenbach, Hessen, Germany), and to definitively confirm the presence of the English variant (lineage B.1.1.7), subsequently subjected to Next Generation Sequencing (NGS). Result(s): Thirty respiratory samples subjected to amplification using the AllplexTM SARS-CoV-2 Assay in early January 2021, showed a reduction in amplification efficiency on the fluorescence profile of RdRP/S genes with slope and inflection point variations. The profile of the SARS-CoV-2 English variant (lineage B.1.1.7) for the 30 samples, was performed first by qualitative test in RT-PCR, GSD Nova TYpe SARS-CoV-2, and subsequently confirmed by NGS technology (analysis performed in an external laboratory). Both analytical methodologies identified all 30 samples with the B.1.1.7. lineage of SARS-CoV-2. This last diagnostic proof pushed our working group to evaluate the presence and degree of spread of the English variant in the area of the Napoli 3 Sud ASL, testing the viral genome of 900 samples to RT-PCR using the Allplex TM SARS-Cov-2 kit, alterations in the fluorescence profile of the amplification curves related to the S gene were observed and confirmed using the GSD NovaTYpe SARS-CoV-2 kit. Conclusion(s): Since late 2020, several variants of SARS-CoV-2 have emerged around the world. The gold standard molecular method to detect a specific variant consists in the total or partial sequencing of the virus genome, but today the latter remains expensive and time-consuming, limiting its implementation in all diagnostic samples. PCR-based screening approaches are relatively cheaper, and results can be verified in a few hours. The indirect approach in RT-PCR, on SARS-Cov-2 diagnostic tests of positive samples, of the non-sigmoidal fluorescence profile of the S gene using AllplexTM SARS-CoV-2 PCR assay allows a quick and cheaper prediction of the lineage B.1.1.7. Therefore, using Allplex SARS-COV 2 can be used as an early and first-line screening, before eventually using the sequencing of the viral genome. Copyright © 2022 EDIZIONI MINERVA MEDICA.