Issue #127
August 2022
COVID-19: Diaries of a microbiologist

Microbiologists have been integral to everything that has happened in the laboratory throughout COVID-19. Without microbiology pathologists, it would not have been possible to manage the pandemic. But at what cost? Dr Lyn Waring, Chair of the RCPA’s microbiology advisory committee, explains the pressures of working in the laboratory over the past 2.5 years.

“Back in March 2020 when we had our first few cases in Australia, microbiology pathologists were involved in liaising with the state reference laboratories and the state health departments to set up COVID-19 testing so that we could offer some kind of wide diagnostic support for the government. We needed to work out which tests would be used whilst also making sure that we had enough internal redundancy in case something went wrong. As we were using tests which had never been used before, we were working with the reference laboratories with samples they had sent as gold standards to validate the performance of our tests.

“In the very early days, we were running tests that we weren’t fully confident with, so we were having to double check everything before it went out. We had to phone the positive patients and the Department of Health (DOH) ourselves because at that stage there were no mechanisms in place to manage that. There was a lot of confusion in the public about what positive results meant to them and their families. There were lots of questions and every single case was different. In Melbourne, many of the early patients were from non-English speaking backgrounds and many had poor or very limited knowledge of English, making it difficult to communicate with them. Some people were really terrified that they were going to die.

“Initially, many patients had attended drive through collection centres, or had been screened at aged care facilities or in quarantine hotels where there were no referring doctors. It therefore fell on the Medical Microbiologist to talk to patients. It quickly became clear that this was going to go crazy, and we needed to find new, better ways of efficiently and confidentially communicating results with both the patients and the DOH.

“The increase in pathology testing was huge, and this was all in addition to our normal case load. We were all very tired, but we kept going because we had to. My microbiology team were working from 8 o’clock in the morning until midnight every night, every day. It was hard on all of us, because it impacted whole families, but everyone willingly stepped up. It was never a question – everyone just mucked in and did whatever they could to help. In my laboratory at Melbourne Pathology, anyone that could pipette was in the molecular lab pipetting thousands and thousands of samples. If you had a lab coat on, then you were doing something.

“In the midst of the dramatically increasing numbers of samples requiring COVID PCR testing, the number of meetings and phone calls from doctors and patients requesting assistance also increased. These meetings were to communicate with our Public and Private Pathology colleagues to assist each other to deliver the service needed in our state. Also there were a lot of meetings with our referring hospitals and infection control coordinators about management of testing and patient movement and infection control. The microbiologists were instrumental in prioritising sample testing in keeping with the urgency of each case as well as assisting with interpretation of reports.

“One of the other roles as a microbiologist is what we do when things go wrong. You can’t just let it slide, you’ve got to follow it up and explain to the patient, the doctors involved, or the DOH, what happened, how it happened and how you’re going to prevent it happening again. We had to keep changing and find a solution, a better way of doing things.

“It was all terribly stressful because everyone wanted something from you, and I think it is such a huge testament to my colleagues that we were all able to support our community the way we did. It was a huge amount of effort and work, and it was very different to how we normally work. Microbiologists these days do not generally have a high profile, but here we were on the front line. Everything had to move like lightening and the pathologists throughout this had to maintain good humour, calm and a sense of balance whilst maintaining a quality service.

“The good thing was that we were all in the same ship and rowing in the same direction. People were very much engaged and wanting to do the right thing, even though people were (and still are) getting tired. Yes, we all got very tired but if we hadn’t worked together then none of it would have been possible. That includes the whole pathology cohort – the collectors out there in the rain, cold, sleet and heat – if they weren’t doing that then we wouldn’t have the samples to start with.

“All the while, each of us had our personal challenges with our own families, not just how the COVID pandemic impacted them, but also how the lockdowns impaired our abilities to attend to our families’ needs. My husband was working remotely overseas during the initial lockdown and had to go through several quarantine periods to be able to come home to see me. In addition, I had to admit my mother into an aged care facility, a move she was strongly against, in the town she lives in north Queensland in late 2020. This was due to increasing inability to care for herself and the absence of any family close-by who could help. I was not able to get to see her until the borders opened very briefly in March 2021, but then I too almost got locked out of my home state by the rapidly evolving quarantine border closures.

“I’m hoping that the silver lining is that everyone now has a better understanding of what pathology entails and more specifically what the role of the Medical Microbiologist involves. We have also got a lot more equipment and trained scientists so some of the services that we provide have been improved because of COVID-19, which we wouldn’t have been able to do otherwise. We have upskilled and hopefully improved awareness in the general community and in the medical community too. But, the pandemic is still not over and we are ever ready to take on the next challenges!”



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