Prevalence of respiratory viruses by Multiplex PCR: a four-and-a-half year retrospective study in an Italian general hospital.

Viruses are frequent causal agents of acute respiratory infections and the most common are influenza virus, respiratory syncytial virus (RSV), human parainfluenza virus (HPIV), human metapneumovirus (HMPV), rhinovirus (RV), adenovirus (AdV) and the four endemic human coronaviruses (HCoV) -229E, -NL63, -OC43, -HKU1. Multiplex real-time PCR platforms are becoming increasingly common in laboratories mostly in relation to the increased diagnostic sensitivity and reduced turnaround time. The aim of our study was to determine the prevalence of respiratory viruses in a population of patients within the S.S. Antonio e Biagio e Cesare Arrigo General Hospital catchment area of Alessandria, Italy, from January 2016 to June 2020. Therefore, we retrospectively analyzed the results of multiplex real-time PCR performed on nasopharyngeal swabs collected from consecutive patients with symptoms of respiratory infection. A total of 572 patients were included in the study subdivided as follows: pediatric 197/572 (34.4%), adults 200/572 (35%) and elderly 175/572 (30.6%). Among all samples, 235/572 (41.1%) were positive for a respiratory virus, of whom 189/235 (80.4%) were monomicrobial. The prevalence was: 15.5% (89/572) of rhinovirus/enterovirus (RV/EV); 9.4% (54/572) of RSV; 8.9% (51/572) of influenza virus; 5.4% (31/572) of AdV; 3.1% (18/572) of HCoV; 2.8% (16/572) of HPIV; and 2.3% (13/572) of HMPV. RV/EV were the pathogens most frequently involved in coinfections (34.7%, 16/46), followed by AdV (19.6%, 9/46) and influenza virus (19.6%, 9/46). Samples collected from the pediatric group were more frequently positive. The prevalence of positive pediatric samples compared to adults and elderly, respectively was: 28.4% (56/197) for RV/EV vs 10.5% (21/200) vs 6.9% (12/175), p<0.0001; 18.8% (37/197) for RSV vs 2% (4/200) vs 7.4% (13/175), p<0.0001; 13.7% (27/197) for AdV vs 1% (2/200) vs 1.1% (2/175), p<0.0001; and 6.6% (13/197) for HPIV vs 0.5% (1/200) vs 1.1% (2/175), (p<0.0001). With regard to seasonality, a significantly higher prevalence of influenza virus (p<0.0001) and RSV (p=0.029) was found during winter, with peaks in January-February. AdV peaked during winter 2018-2019 (p=0.004), while HCoV were detected with a significantly higher prevalence during winter 2019-2020 (p=0.037). With regard to HPIV, a significant peak from summer to fall 2018 was observed (p=0.016). Most viral respiratory infections have seasonal patterns and the prevalence of respiratory viruses varies according to the method, geographic area and population considered. Knowledge of local epidemiology is therefore crucial for implementation of prevention and treatment strategies.

Clinical Utility of Platelet Count for Screening of Malaria.

Light microscopy, immunochromatographic rapid diagnostic tests and molecular methods are widely used to diagnose malaria. The aim of this study was to find variables among commonly available urgent blood tests to identify patients with low probability of having malaria in small-scale healthcare facilities in which none of the described methods is feasible within a short time. Diagnosis of malaria was made by examining both stained thick and thin blood films by light microscopy. Two hundred and eleven samples were included. Reduced platelet count and increased values of C-reactive protein (CRP) and total bilirubin were the variables most strongly associated with malaria (P<0.0001). The best screening cut-off values obtained by receiver operating characteristic curve analysis for a negative result for malaria were: platelets ≥185,000 cells/µl; CRP ≤2 mg/dl; total bilirubin ≤0.28 mg/dl. The logistic regression model of log-transformed variables showed how platelet count was the only independent variable related to the odds of having a negative blood film result for malaria (odds ratio: 2.621; 95% confidence interval: 1.441-4.768; P=0.002). A platelet count of ≥185,000 cells/µl can be considered a screening value to identify patients with high-probability of a negative blood film result for malaria.

Evaluation of a multiplex gastrointestinal PCR panel for the aetiological diagnosis of infectious diarrhoea.

Background: Infectious diarrhoea is a significant cause of morbidity worldwide. Culture and microscopy are time-consuming and have a low yield. New rapid molecular methods such as multiplex PCR, have been recently introduced for aetiological diagnosis. Aim of this study was to compare the diagnostic yield of the FilmArray gastrointestinal panel with that of standard culture for aetiological diagnosis of infectious diarrhoea.Methods: We performed a retrospective analysis of results of stool samples already processed as part of routine clinical care in the interval from March 2016 to March 2019.Results: One hundred and eighty-three stool samples from as many patients were both cultured and tested by FilmArray and the comparison of diagnostic accuracy between culture and FilmArray with respect to Campylobacter spp., Salmonella spp., Shigella spp., Yersinia enterocolitica and Shiga-like toxin producing E. coli O157 gave the following results: 100% (95% confidence interval (CI): 85-100%) sensitivity; 93.4% (95% CI: 87.9-96.6%) specificity; 74.3% (95% CI: 57.5-86.4%) positive predictive value; 100% (95% CI: 96.7-100%) negative predictive value; 2.9 (95% CI: 1.6-5.1) positive likelihood ratio; zero negative likelihood ratio. By means of FilmArray gastrointestinal (GI) panel, we could identify 34.5% more pathogens (p = .001). Bacteria were mostly detected in patients with 6 or more years of age (χ2=17.1; p = .009) during summer.Conclusions: FilmArray GI panel showed a very good diagnostic performance compared to culture for diagnosis of infectious diarrhoea and gave a more detailed picture of the spectrum of the pathogens involved.