#FEMSmicroBlog: Life during the COVID-19 outbreak as a clinical microbiologist

02-07-2020

Clinical microbiologists are doing frontline work along with other essential professionals during the current SARS-CoV-2 outbreak. The author of this new blog entry for the #FEMSmicroBlog, Killian O’Hara, tells us about his contribution in setting up a rapid test system for COVID-19 and the current situation in the Republic of Ireland. #QuarantineDiary

“The days all seem to fall into one but behind all the personal protective equipment we know that the job that we are doing will have incalculable benefits for the patient.

I am a Medical Scientist based in Midland Regional Hospital Portlaoise, a tertiary hospital in the Midlands in the Republic of Ireland. My specialist area is Clinical Microbiology and I have been working on the frontline trying to battle COVID-19 since it began to ravage our island.

Setting up a validated test system for COVID-19

My work has changed radically since the onset of SARS-CoV-2. Microbiologists are playing a crucial and everlasting role in this fight. My colleagues and I played an instrumental role in the testing of the suspect SARS-CoV-2 samples, and in setting up a whole new laboratory testing algorithm and information management system. This has not been easy as we had to go about setting this up in a rapid and efficient manner to expedite the testing and subsequent reporting of COVID-19 results.

We called the National Virus Reference Laboratory (NVRL) in Dublin to source commercial controls to run in our laboratory. We needed these controls to make sure that our GeneXpert testing assay, which is based on real-time PCR, could deliver accurate and timely results from time of sampling to time of reporting. When it comes to any type of viral testing, we liaise with the NVRL on a regular basis.

We set about validating the new controls by running daily tests on the positive, negative, and commercial quality control aliquotes. After about two weeks of constant testing our instrument was validated for COVID-19 testing. The next step was to interface the instrument with the computer system so that we could report the results rapidly to the clinicians. We worked diligently with our IT colleagues to set up new test requests for COVID-19 on our computer system and they assisted us in installing an interface programme on the instrument so that it could automatically transfer the results to the computer when testing was completed.

This expedited the reporting of positive and negative results and it meant that we as a laboratory could guarantee a turnaround time of two hours from sampling to reporting.

GeneXpert Instrument and Xpress SARS-CoV-2 cartridge (top right box, approximate size  3.3 x 3.5 cm)
On the current situation in Ireland

The situation in Ireland has now calmed down quite significantly and we are starting to see a small chink of light at the end of the tunnel. The statistics show that there has been 25,437 cases and 1,734 deaths recorded that are attributable to COVID-19 (as of 28 June 2020). For a small island nation with a population of just over five million people these figures are quite significant. Also, a worrying statistic that emerged last week shows that in Ireland we have the highest amount of cases of COVID-19 linked to healthcare workers in the world.

One day soon hopefully this will all be over. The people that we have lost along the way will forever be in my thoughts but conversely, I know that I have left my mark on this fight day in and day out and it’s my proudest moment to date. For now, let us all dream of a future without SARS-CoV-2 and rest assured my colleagues and I at Midland Regional Hospital Portlaoise will do our best to accelerate its elimination.”

About the author of this blog

Killian O’Hara is a Medical Scientist in Microbiology working in the Clinical Microbiology laboratory of the Midland Regional Hospital in Portlaoise (Republic of Ireland). He is interested in antimicrobial resistance, emerging and re-emerging infections and epidemiology and global health. Killian has been a volunteer with FEMS since 2017 (#OnThisDay project and Antimicrobial Resistance Taskforce). Killian’s key objective moving forward is to collaborate with like-minded microbiologists to help spread awareness and knowledge pertaining to Microbiology to all corners of the continent.

About this blog section

In #QuarantineDiary for the #FEMSmicroBlog, microbiologists tell us about the challenges and opportunities from a personal and professional (development) perspective during the current SARS-CoV-2 pandemic. These can range from a list of useful resources to keep learning, to how researchers can offer their help, to a personal view of current events.

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