Introduction

Rapid and accurate diagnosis was critical to face COVID-19 emergency leading to an unprecedented adaptation of clinical microbiology services to the spread of the pandemic [1].

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].

Despite the great adaptation of these reference laboratories, the development of the outbreak overwhelmed health-care systems worldwide and exceeded their diagnostic capacity [5]. To support the growing testing demand, regional and small laboratories had to incorporate molecular technology by changing their settings and infrastructure, implementing new procedures, and training personnel.

This work describes the implementation of a molecular diagnosis area and the activity load of SARS-CoV-2 RNA detection, in a regional hospital with no previous experience in molecular techniques.

Materials and methods

This is a retrospective study performed at Hospital de Sierrallana y Tres Mares (HSLL) (Cantabria, Spain), a 265-bed regional hospital attending a population of 161,000 inhabitants, from October 2020 to March 2022. The Microbiology department is part of the Clinical Analysis Service and operated from 8 am to 3 pm from Monday to Friday.

To analyse the implementation of a molecular diagnosis area, we describe: structural changes in the microbiology laboratory, the number of human resources recruited, their training and the working shifts established.

Nasopharyngeal swab samples were investigated for SARS-CoV-2 detection when required. The laboratory activity was divided into two different periods: from October 2020 to February 2021, processing mainly samples of hospital origin (inpatients and hospital workers) and from February 2021 to March 2022, assuming the diagnosis and surveillance of primary-care outpatients in our health-area.

For COVID-19 diagnosis workload analysis data were obtained from the laboratory records and reported as number of samples processed per day.

Results

SARS-CoV-2 diagnosis activity

HSLL processed 144,442 nasopharyngeal swab samples during the study period, comprising the second to the sixth waves of SARS-CoV-2. COVID-19 laboratory activity involved: from October 2020 to February 2021, a total of 12,737 samples were analysed (mean 124.87, range 53–222); while from February 2021 to March 2022, the activity increased to 131,705 nasopharyngeal swabs processed (mean 305.58 samples, range 48 to 1,326), assuming samples from our primary care area.

Overall, primary care centres and surveillance samples represented 56.06% (80,968/144,442) of the PCRs performed, 41.34% (59,715/144,442) correspond to hospital origin samples, and 2.6% (3,759/144,442) were from health-care workers.

The largest peaks of work occurred during the fifth and sixth wave, with 25,285 samples processed in July 2021, and 32,245 between December 2021 and January 2022, representing 14.5% and 22.3% of the total activity, respectively. Epidemiological surveillance accounting for the largest volume of work (Fig. 1).

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Distribution by origin of sample of the PCRs for SARS-CoV-2 performed from October 2020 to March 2022. The line separates the two different periods of SARS-CoV-2 detection activity in the laboratory

Citation: Acta Microbiologica et Immunologica Hungarica 70, 1; 10.1556/030.2023.01972

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Discussion

Our results show the major transformation of a regional laboratory during the SARS-CoV-2 pandemic. Our microbiology department was able to process a large volume of samples in short response times. To handle this large volume of samples, the laboratory organisation underwent substantial changes; new staff were recruited and thoroughly trained, and work shifts were implemented.

In the first months of the outbreak, most reference hospitals struggled to provide rapid results [6]. 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.

One of the biggest challenges faced, was transforming the laboratory structure to integrate the new molecular area. Further than point-of-care testing (POCT), our lab had never performed routine molecular diagnosis, referring such tests to the reference hospital in the area. A great effort was made in the infrastructure project, the implementation of new techniques and the installation of new equipment. It is well known that poorly expertise and performance in NAAT methodology can lead to contaminations or misinterpretations involving serious consequences [10]. To avoid this, personnel were thoroughly trained to meet quality criteria and ensure the reliability of the results.

During the study period, we adapted to the different waves and changes in the surveillance policies of our autonomous community. It should be considered that most of the major hospitals in our country had open robotic systems available to increase their diagnostic capacity [11, 12]. However, as a small setting, we did not have such platforms accessible, mainly due to space beyond economic reasons. It is remarkable, despite not having the technological and human resources of a reference centre, we reached peaks of 1,326 samples/day with a response time of less than 12 h.

The main limitation of this study is its retrospective nature. Also, multiple and follow-up samples were not excluded, and antigen-test diagnosis was not included in the analysis. However, this work was not intended to show positivity or prevalence data in our area, already reflected in many official reports throughout the pandemic.

COVID-19 pandemic has represented not only the challenge, but the opportunity to introduce NAAT methodology in inexperienced environments. In a globalised world where pathogens can easily spread or emerge, tools for rapid identification are essential. Positively, from now on, applications of molecular diagnostics in small settings can go beyond COVID-19, improving the detection of many infectious diseases and acquiring better independence from reference centres. This work can be useful for other regional hospitals. Secondary laboratories have shown an extraordinary ability to adapt and cannot be left behind in technological advances in the field of Clinical Microbiology.

Conflict of interest

The authors report no conflicts of interest relevant to this article.