ABSTRACT
Human coronaviruses (HCoVs) are associated with a range of respiratory symptoms. The discovery of severe acute respiratory syndrome (SARS)-CoV, Middle East respiratory syndrome, and SARS-CoV-2 pose a significant threat to human health. In this study, we developed a method (HCoV-MS) that combines multiplex PCR with matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), to detect and differentiate seven HCoVs simultaneously. The HCoV-MS method had high specificity and sensitivity, with a 1–5 copies/reaction detection limit. To validate the HCoV-MS method, we tested 163 clinical samples, and the results showed good concordance with real-time PCR. Additionally, the detection sensitivity of HCoV-MS and real-time PCR was comparable. The HCoV-MS method is a sensitive assay, requiring only 1 μL of a sample. Moreover, it is a high-throughput method, allowing 384 samples to be processed simultaneously in 30 min. We propose that this method be used to complement real-time PCR for large-scale screening studies.
ABSTRACT
Background As the numbers of people with COVID-19 continue to increase globally, concerns have been raised regarding the widespread use of antibiotics for the treatment of COVID-19 patients and its consequences for antimicrobial resistance during the pandemic and beyond. The scale and determinants of antibiotic use in the early phase of the pandemic, and whether antibiotic prescribing is beneficial to treatment effectiveness in COVID-19 patients, are still unknown. Unwarranted treatment of this viral infection with antibiotics may exacerbate the problem of antibiotic resistance, while antibiotic resistance may render presumptive treatment of secondary infections in COVID-19 patients ineffective. Methods This rapid review was undertaken to identify studies reporting antimicrobial use in the treatment of hospitalised COVID-19 patients. The review was conducted to comply with PRISMA guidelines for Scoping Reviews ( http://www.prisma-statement.org/Extensions/ScopingReviews ) and the protocol was registered with the Open Science Framework (OSF): http://osf.io/vp6t5 . The following databases: Web of Science, EMBASE, PubMed, CNKI & VIP were searched to identify the relevant studies from 1 Dec 2019 up to 15 June 2020; no limits were set on the language or the country where studies were conducted. The search terms used were: ((“Covid-19” or “SARS-CoV-2” or “Coronavirus disease 2019” or “severe acute respiratory syndrome coronavirus-2”) and ((“antibiotic prescribing” or “antibiotic use” or “antibiotic*”) or “antimicrobial *” or “antimicrobial therapy” or “antimicrobial resistance” or “antimicrobial stewardship”)). A total of 1216 records were identified through database searching and 118 clinical studies met the inclusion criteria and were taken into data extraction. A bespoke data extraction form was developed and validated through two independent, duplicate extraction of data from five Records. As all the included studies were descriptive in nature, we conducted descriptive synthesis of data and reported pooled estimates such as mean, percentage and frequency. We created a series of scenarios to capture the range of rationales for antibiotic prescribing presented in the included studies. Results Our results show that during the early phase of the pandemic, 8501 out of 10 329 COVID-19 patients (82·3%) were prescribed antibiotics; antibiotics were prescribed for COVID-19 patients regardless of reported severity, with a similar mean antibiotic prescribing rate between patients with severe or critical illness (75·4%) and patients with mild or moderate illness (75·1%). The top five frequently prescribed antibiotics for hospitalised COVID-19 patients were azithromycin (28·0 % of studies), ceftriaxone (17·8%), moxifloxacin (14·4%), meropenem (14·4%) and piperacillin/tazobactam (12·7%). The proportion of patients prescribed antibiotics without clinical justification was 51·5% vs 41·9 % for patients with mild or moderate illness and those with severe or critical illness respectively. Comparison of patients who were provided antibiotics with a clinical justification with those who were given antibiotics without clinical justification showed lower mortality rates (9·5% vs 13·1%), higher discharge rates (80·9% vs 69·3%) and shorter length of hospital of stay (9·3 days vs 12·2 days). Only 9·7% of patients in our included studies were reported to have secondary infections. Conclusions Antibiotics were prescribed indiscriminately for hospitalised COVID-19 patients regardless of severity of illness during the early phase of the pandemic. COVID-19 related concerns and lack of knowledge drove a large proportion of antibiotic use without specific clinical justification. Although we are still in the midst of the pandemic, the goals of antimicrobial stewardship should remain unchanged for the treatment of COVID-19 patients.