key: cord-0982842-18h92306
authors: Catalán, Pilar; Alonso, Roberto; Alcalá, Luís; Marín, Mercedes; Moure, Zaira; Pescador, Paula; Bouza, Emilio; Munoz, Patricia
title: The challenge of COVID-19 for a Clinical Microbiology Department
date: 2021-05-13
journal: Diagn Microbiol Infect Dis
DOI: 10.1016/j.diagmicrobio.2021.115426
sha: 370e1424e6e29eb15572c0418d84a931372148b7
doc_id: 982842
cord_uid: 18h92306

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.

In a very short period of time, Clinical Microbiology Departments had to adapt their structure to respond to an unprecedented massive diagnostic demand of a new disease (COVID-19) (1) . However, up to the present time, we were not able to find reports quantifying the change for Clinical Microbiology Departments in aspects like variation in type of samples, human resources and cost. This paper compares the workload of the pandemic in our Microbiology Department (March-December 2020) with the same period of time of the previous year. We evaluate changes in samples submission, in personnel and in laboratory budget. We hope that our experience can be useful for other laboratories planning how to deal with possible future epidemics.

Setting. The Hospital General Universitario Gregorio Marañón (HGUGM) is a public tertiary and reference hospital in Madrid, Spain. The hospital attends a population of 350,000 inhabitants and, in normal circumstances, the Microbiology Department processes more than 300,000 samples per year. We report the activity of the Microbiology Department during the coronavirus pandemic in our country (March-December 2020), as compared to the same months in 2019. The data were obtained from the laboratory records. The main diversity of techniques occurred specially in the first months of the pandemic coinciding with the greatest shortage of products on the market. Except for the very earliest start, when RUO tests were used, we have always used CE marked systems.

Multiplex kits or combinations of singleplex kits have been always used, so samples were considered positive when at least 2 different targets were amplified. The runs always included positive and negative controls provided by the corresponding manufacturers, as well as laboratory own controls consisting of previously characterized, diluted and aliquoted samples. From May-June 2020 we preferentially used the TaqPath system by ThermoFisher, using the KingFisher as extraction system and QuantStudio-5 as Thermocycler as a standard technique and GeneXpert system by Cepheid on its platform Infinity as a rapid system. The latter, due to its higher price and its limitation for processing large numbers of samples at once, was used only when a very fast result was required, patients in the emergency room, imminent deliveries or preparation for unscheduled and urgent procedures.

Evaluation of laboratory samples. The workload of the laboratory was reported as samples processed per day, samples/1000 admissions and samples/100.000 inhabitants.

Overall received samples and samples in each area of the laboratory were analyzed. Ethics. The study was approved by the local Ethics Committee (code MICRO.HGUGM.2020-028).

Statistics. Contingency tables were statistically analyzed by means of exact Fisher's test, and Mann-Whitney's U-test was used with numerical variables. Average turnaround times during the study period were 6.7h for PCR (ranging from 1.3h to 8,1h) and 1.4h for antibody testing (range, 57 min to 1,9h). hours/day). Research staff (7 persons) also helped in COVID-19 diagnosis during these months.

Overall, the Microbiology department costs increased 6,616,511 euros (114.8%). Of these, 519,104 euros were allocated to personnel hiring and extended shifts, and the rest to laboratory materials (+242%; from 2,515,756 to 8,613,163 euros). The most expensive items were: PCR reagents (60%), reagents for SARS-CoV-2 IgG detection (12%), SARS-CoV-2 extraction and purification (8%) and nasopharyngeal sampling swabs and transport media (15%).

Our results reflect the enormous adaptation challenge that Microbiology laboratories had to tackle in a very short period of time to provide the diagnosis of a new disease within a worldwide epidemic. In three months, the samples received in the laboratory increased by 96.70%, work shifts were amplified, and need of procurement of diagnostic material in a very competitive market resulted in an excess expense of more than six and a half million euros in ten months.

Several articles have been published analyzing adaptations required in emergency, radiology and intensive care departments (2) (3) (4) . However, we were not able to find virtually nothing about the great challenge that the pandemic has posed to Clinical Microbiology laboratories.

The Microbiology staff had to quickly adapt to the available information and the technologies being used. We had to implement practices never done before under normal circumstances, such as completing the installation of equipment by ourselves, or putting into operation veterinary diagnostic machinery (for nucleic acids extraction).

Training plans for the personnel were fundamental. Most department members (staff, residents and technicians) required specific training on nucleic acid extraction and PCR.

Antibody detection procedures, the use of auto-analyzers for immunoassays and reinforcement in security procedures in the laboratory, were included in the training as well.

In a short timeframe the number of samples increased rapidly (37% in March, 63% in April) mostly due to high complexity samples such as SARS-CoV-2 PCR, which increased by 2,058% in the whole period. In ten months almost 240,000 SARS-CoV-2

PCRs and more than 55.000 serological tests were performed and results were provided every single day.

During the pandemic, there has been excellent communication and collaboration between the Microbiology and Infectious Diseases department and the Hospital management. The management has accepted the scientific and technical expertise of our department and we always have ensured the optimization of resources. In choosing the diagnostic platforms we have considered the reputation of the suppliers, the quality of the products and their adaptation to our circumstances and needs. Economic issues have also been taken into account, although they have not been a limiting factor for decisionmaking.

We have implemented some cost saving measures whenever possible. For instance, sample pooling was performed occasionally when the expected positivity rate was low.

It was carried out in two low prevalence population studies, one carried out in employees of our Hospital (5) and the other in asymptomatic volunteers. At some point, sterile saline solution was also used instead of transport medium due to the lack of supply.

The number of Microbiology laboratory technicians increased during the first 10 months of the pandemic, although not enough so as to stabilize the personnel workload, that increased by 12.5%. The daily number of samples processed by a microbiology technician to maintain a proper quality standard is not established (6) . In fact, there very few reports have analyzed the workload of different infections in Microbiology laboratories. This field has traditionally been of interest to our group (7) (8) (9) .

Despite the extensive use of antimicrobials in patients with COVID-19 samples reflecting suspected concomitant nosocomial infection did not raise and even was reduced (blood cultures, respiratory samples, intravenous catheters and samples searching for colonization by multi-resistant pathogens). In fact, it has been shown that critical COVID-19 patients frequently suffer from nosocomial infection (10) and in some centers the blood culture utilization has increased by up to 35%, with a high percentage of false positives (11) .

The areas of the laboratory that experienced exponential growth in their workload were those related to the diagnosis of COVID-19, specially the Virology and Serology units.

The rest of the areas saw their demand clearly reduced, probably due to the reduction in surgical and outpatient clinics activity at the Hospital. This fact, together with the reinforcement of material and human resources, has allowed us to maintain the quality of care and our response times. We have not submitted samples at any time to external laboratories, however we have received samples from other canters and laboratories that do not usually depend on us.

There are virtually no data in the literature on the 'normal budget' of a Clinical Microbiology laboratory. Undoubtedly this budget is very much influenced locally by salaries and healthcare model. This epidemic has shown that hospitals must be prepared to spend large amounts of money to properly attend the diagnosis of the epidemic. In our center, Microbiology laboratory costs rose by 114% in ten months, mainly due to the purchase of diagnostic tests (increase of 242%). This meant a cost increase of 6,616,511 euros over the normal Microbiology budget. The increase in the cost of diagnostic material was much more relevant than that of personnel (519,104 euros), which reflects the significant work overload assumed by the technicians and staff of the Microbiology laboratory.

The main limitation of our study is its unicentric nature, which reflects the experience of a Clinical Microbiology laboratory in a tertiary hospital located in Europe, in a country with public health care and which has suffered a large number of cases of COVID-19.

However, we believe that it may be useful to other hospitals due to the absence of data in the literature, both on the overload that the emergence of the epidemic has meant and its cost. This is the first study to provide quantitative figures about workload and cost increase caused by the first wave of the COVID-19 in a Microbiology laboratory. 

The Laboratory Diagnosis of COVID-19--Frequently-Asked Questions

Strategies for radiology departments in handling the COVID-19 pandemic

Containing COVID-19 in the Emergency Department: The Role of Improved Case Detection and Segregation of Suspect Cases

Logistic and organizational aspects of a dedicated intensive care unit for COVID-19 patients

Sample pooling is efficient in PCR testing of SARS-CoV-2: a study in 7400 healthcare professionals

Practical Guidance for Clinical Microbiology Laboratories: Implementing a Quality Management System in the Medical Microbiology Laboratory

Workload due to Aspergillus fumigatus and significance of the organism in the microbiology laboratory of a general hospital

A European perspective on intravascular catheter-related infections: report on the microbiology workload, aetiology and antimicrobial susceptibility (ESGNI-005 Study)

A European perspective on nosocomial urinary tract infections I. Report on the microbiology workload, etiology and antimicrobial susceptibility (ESGNI-003 study). European Study Group on Nosocomial Infections

Nosocomial infection among patients with coronavirus disease-2019: a retrospective data analysis of 918 cases from a single center in Wuhan city

Bacteremia and Blood Culture Utilization During COVID-19 Surge

Nothing to declare a. All differences in the distribution of samples were statistically significant with p<0.0001 b. 5,973 extra hours were also hired for staff and residents, besides the new staff c. 385,343€ euros were dedicated to personnel hiring and extended shifts in March-December 2020 for the COVID-19 pandemic