SARS-CoV-2 diagnostics in the virology laboratory of a University Hospital in Rome during the lockdown period

Italy was one of the most affected nations by coronavirus disease 2019 outside China. The infections, initially limited to Northern Italy, spread to all other Italian regions. This study aims to provide a snapshot of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) epidemiology based on a single-center laboratory experience in Rome. The study retrospectively included 6565 subjects tested for SARS-CoV-2 at the Laboratory of Virology of Sapienza University Hospital in Rome from 6 March to 4 May. A total of 9995 clinical specimens were analyzed, including nasopharyngeal swabs, bronchoalveolar lavage fluids, gargle lavages, stools, pleural fluids, and cerebrospinal fluids. Positivity to SARS-CoV-2 was detected in 8% (527/6565) of individuals, increased with age, and was higher in male patients (P <.001). The number of new confirmed cases reached a peak on 18 March and then decreased. The virus was detected in respiratory samples, in stool and in pleural fluids, while none of gargle lavage or cerebrospinal fluid samples gave a positive result. This analysis allowed to gather comprehensive information on SARS-CoV-2 epidemiology in our area, highlighting positivity variations over time and in different sex and age group and the need for a continuous surveillance of the infection, mostly because the pandemic evolution remains unknown

La fecondità degli stranieri in Italia: tra indizi e valutazioni presuntive

Fonti e strumenti n. 5, Dipartimento di Scienze Demografiche, Università di Roma "La Sapienza

Nati da almeno un genitore straniero

collana Fonti e Strumenti del Dipartimento di Scienze Demografich

Colistin resistance beyond carbapenems: molecular epidemiology of multi-drug resistant Klebsiella pneumoniae from an Italian hospital

Purpose: Multidrug resistant (MDR) Klebsiella pneumoniae (Kp) is a worldwide concern worsened by colistin resistance emergence. In this study, molecular epidemiology of clinical MDR Kp strains is described, assessing clonal relationships and resistance genes profiles. Prevalence of Extended-Spectrum Beta-Lactamase (ESBL) blaCTX-M, blaTEM and blaSHV genes was evaluated, as well as that associated to carbapenems (blaKPC, blaGES, blaVIM, blaIMP, blaNDM, blaOXA-48) and colistin resistance (mcr-1,2,3,4 and mgrB). Methods & Materials: Twenty-six Kp cultures were collected from âŁœA.Cardarelli⣞ hospital in Molise Region (Central Italy), 57.7% from Intensive Care Unit (ICU). The Minimum Inhibitory Concentration (MIC) was assessed by BD Phoenixâ„¢. Genotyping was achieved through Pulsed-Field Gel Electrophoresis (PFGE) withXbaI and MultiLocus Sequence Typing (MLST). PCRs for resistance genes detection and mgrB sequencing were performed. Results: Most (n = 20, 77%) strains were carbapenems resistant (imipenem, meropenem, ertapenem), and 53% (n = 14) to colistin. A higher prevalence of blaKPC (100%) and blaSHV (96.2%) was found compared with blaTEM (88.5%), blaVIM (69.0%) and blaCTX-M (7.7%). While none colistin-resistant (col-R) strain carried mcr-1,2,3,4 variants, 42.8% (n = 6) had an Insertion Sequence (IS) in mgrB, identified as IS5-like (5/14, 36%) and ISKpn14 (1/14, 7%). The prevalent Sequence Type was ST512 (50%), followed by ST101 (38.5%) and ST307 (11.5%). PFGE detected 12 clusters and 18 pulsotypes (95% similarity), and was more discriminating than MLST (Simpson’s Index 95%vs 61%). An ICU outbreak, during November 2014-January 2015, included five ST512 strains, blaTEM/blaSHV/blaVIM/blaKPC positive, and col-R due to mgrB IS5-like. Conclusion: Molecular epidemiology study identified an outbreak caused by poor compliance with hygienic standards because of reduced personnel during Christmas holidays. Although ST258 is the most prevalent in Italy, half strains were typed as ST512 that represents its monoallelic variant. Our results confirm the endemic blaKPC distribution and blaTEM/blaSHV as the prevalent ESBLs in Kp hospital outbreaks. According to epidemiological data, plasmid mcr variants were not found in col-R strains. Conversely, IS elements prevalence in mgrB explain resistance in about half col-R strains, and was in line with Italian data. Further investigations are needed to identify mgrB mutations in IS negative col-R strains

Comparison of FTD SARS-CoV-2 Assay and RealStar RT-PCR kit 1.0 for the detection of SARS-CoV-2

The aim of the study was to evaluate the clinical performance of FTD SARS-CoV-2 compared to the RealStar RT-PCR kit 1.0. The analysis of 100 nasopharyngeal swabs showed an overall agreement of 88 %. The positive percentage agreement was 85.6 % and the negative percentage agreement was 91 %. In conclusion we observed a substantial agreement among the two methods, with discrepancies mainly observed in specimens with relatively low amount of viral RNA

KI and WU polyomavirus in respiratory samples of sars‐cov‐2 infected patients

Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) has been declared a global pandemic. Our goal was to determine whether co‐infections with respiratory polyomaviruses, such as Karolinska Institutet polyomavirus (KIPyV) and Washington University polyomavirus (WUPyV) occur in SARS‐CoV‐2 infected patients. Oropharyngeal swabs from 150 individuals, 112 symptomatic COVID‐19 patients and 38 healthcare workers not infected by SARS‐ CoV‐2, were collected from March 2020 through May 2020 and tested for KIPyV and WUPyV DNA presence. Of the 112 SARS‐CoV‐2 positive patients, 27 (24.1%) were co‐infected with KIPyV, 5 (4.5%) were positive for WUPyV, and 3 (2.7%) were infected simultaneously by KIPyV and WUPyV. Neither KIPyV nor WUPyV DNA was detected in samples of healthcare workers. Significant correlations were found in patients co‐infected with SARS‐CoV‐2 and KIPyV (p < 0.05) and between SARS‐CoV‐2 cycle threshold values and KIPyV, WUPyV and KIPyV and WUPyV concurrently detected (p < 0.05). These results suggest that KIPyV and WUPyV may behave as opportunistic respiratory pathogens. Additional investigations are needed to understand the epidemiology and the prevalence of respiratory polyomavirus in COVID‐19 patients and whether KIPyV and WUPyV could potentially drive viral interference or influence disease outcomes by upregulating SARS‐CoV‐ 2 replicative potential