The challenge of COVID-19 for a Clinical Microbiology Department

Abstract

Objectives To quantify the workload and cost overload that the COVID-19 pandemic has meant for a Clinical Microbiology laboratory in a real-life scenario. Methods We compared the number of samples received, their distribution, the human resources, and the budget of a Microbiology laboratory in the COVID pandemic (March-December 2020) with the same months of the previous year. Results the total number of samples processed in the Clinical Microbiology laboratory in March-December 2020 increased 96.70% with respect to 2019 (from 246,060 to 483,993 samples), reflecting an increment of 127.50% when expressed as samples/1000 admissions (from 6,057 to 13,780). The increase in workload was mainly at the expense of the virology (+2,058%) and serology (+86%) areas. Despite additional personnel hiring, the samples processed per technician increased 12.5%. The extra cost attributed to Microbiology amounts to 6,616,511 euros (114.8%). Conclusions This is the first study to provide quantitative figures about workload and cost increase caused by the COVID-19 in a Microbiology laboratory.

Epidemiology and outcomes of culture-positive bloodstream pathogens prior to and during the SARS-CoV-2 pandemic: a multicenter evaluation

“…Moreover, because prior studies have shown that central line-associated infection is a common cause of BSIs in patients with COVID-19, a fear of prolonged patient contact, the practice of pronation for ventilated patients [18], and aerosolization of SARS-CoV-2 could be a barrier to catheter hygiene and maintenance [7]. Finally, the pandemic has revealed staffing constraints and supply chain weaknesses that limit the ability of microbiology labs and infectious disease specialists to fully support infection prevention and antimicrobial stewardship policies, which also may affect BSI rates and outcomes [19,20].…”

Establishing a molecular laboratory in COVID-19 pandemic: The experience of a regional laboratory in Spain

“…Considering this situation, regional laboratories implemented molecular areas to expand diagnostic capacity beyond these main centers [7]. The literature describes the adaptation of COVID-19 diagnosis in Microbiology departments with previous experience in PCR-performing [1,4,8] and also in laboratories from low-resource countries [9]. However, to the best of our knowledge, there is no work describing the creation of a molecular area from scratch in the context of the COVID-19 emergency in a regional hospital.…”

“…Since Nucleic Acid Amplification Techniques (NAAT), based on real-time RT-PCR (RT-qPCR), are the main tools for the detection of SARS-CoV-2, the diagnosis was initially centralized at reference hospitals, with well-equipped microbiology departments and qualified staff [2,3]. Within a few weeks, new technology was introduced, additional diagnostic circuits were created and trained staff were incorporated, reinforcing work shifts [1,4].…”

Performing under Pressure: Insights into the Diagnostic Testing Burden at a UK National Health Service Clinical Virology Laboratory during the SARS-CoV-2 Pandemic

“…There have been relatively few studies on the impact of SARS-CoV-2 testing on other diagnostic tests. One Spanish study, from a more general microbiology laboratory, covering the early part of the pandemic (2019–2020), demonstrated a massive rise in the number of virology tests, without breaking these down into those for specific viruses [ 22 ]. Our study covering a longer period before and during the pandemic (2018–2022), focusing on just virology testing, is therefore a useful complementary study to this one.…”