The good, the bad and us in clinical microbiology

Published 28.07.2020
Author Henna Lusa
Photos Suvi Elo
I often get excited about solving new microbiological challenges in my job. In five years, I will still be happily working with clinical laboratory diagnostics and research but the work will be completely different to what we can even imagine at the moment.
I often get excited about solving new microbiological challenges in my job. In five years, I will still be happily working with clinical laboratory diagnostics and research but the work will be completely different to what we can even imagine at the moment.
Antti Hakanen believes that researchers should not become too locked to their organisations. Tyks has a lot of collaboration with different schools, sector research institutes and others.
Antti Hakanen believes that researchers should not become too locked to their organisations. Tyks has a lot of collaboration with different schools, sector research institutes and others.

Antti Hakanen, Director of the Laboratory Division at Turku University Hospital (Tyks), did not think he was working in a job that would arouse media interest until the coronavirus pandemic came to Finland. He foresees great upheavals in future health care and diagnostics.

Hints of Chief Physician Antti Hakanen‘s future career could already be spotted back in his childhood. His parents, both linguists, were amused by their primary school son’s keen interest in the Middle Ages and the plague epidemic.

Back then, Hakanen was in a Boy Scout troop called “Knights of Koroinen” in Turku. In adulthood, the Scouts faded into the background of his life and were replaced with orienteering.

Orienteering is a fitting metaphor for leadership and the researcher mindset. You need to make fast decisions and trust them, but also be brave enough to question them later when you receive more information. The best orienteers keep it together when they run into problems and quickly find a new route, he explains.

It was not immediately clear to Hakanen what to specialise in, because medicine has a myriad of different branches. He was leaning slightly towards specialising in infectious diseases, but for family reasons he chose a field where he would not have to be on call at night.

It was an easy decision to make, since my spouse specialised in internal medicine and endocrinology, which is an on-call speciality, and our children were small.

Science needs seemingly simple questions

As Director of Tyks’ Laboratory Division, Hakanen feels that he is part of a good, multi-disciplinary working community, where doctors, microbiologists, bio-analysts and representatives of other disciplines stick together to form a dynamic team. Medicine and patients are always present in his work. Samples, technological progress, biology, mutation of viruses and bacteria – new information continues to pour in and be refined.

I think laboratory work is central to medicine. As a result of coronavirus, the previously often side-lined diagnostics have suddenly become popular and attractive to the media, he laughs.

It is in Hakanen’s nature to keep asking questions in his work. He carefully reads children’s science questions in the Helsingin Sanomat newspaper. The seemingly simple questions are often the most significant in his opinion.

They have the absolute best questions, such as does the Saimaa ringed seal sweat under the ice? Science cannot go after every question, but we should dare to ask many more questions.

Let us not stray into humbug

Hakanen compares the current situation of diagnostics in clinical microbiology to Renaissance era explorers standing at the edge of an ocean.

Many say that there is nothing beyond the ocean, but the most curious minds wonder how to get over there.

Hakanen believes that the importance of this field will change significantly in the next five to ten years. .

We already know that humans and animals have more microbes in their bodies than cells of their own. The newest figure is that we are 53 percent microbe cells. Microbes have a dramatic effect on our health.

Crohn’s disease and other inflammatory bowel diseases are on the increase, not to mention irritable bowel syndrome or obesity. Hakanen expects to see new kinds of diagnostics that could shed light on what causes these diseases, among others.

Any course of medication and our nutrition have a significant effect on the bacteria, fungi and viruses in our bodies. The effects are primarily seen in the intestine, but also in body cavities and on the skin.

Hakanen thinks diagnostic methods and processes need to be sped up and made more cost-effective. The amount of data is growing exponentially.

I want to be one of the people who create solutions for this. We may not, however, stray onto the wrong tracks such as offering humbug microbiome mappings that tell people how their microbes affect partnering.

New diagnostic implemented in just a few days

Microbiology has come a long way since the great insights of the 19th century. Hakanen wants to use the slightly clichéd phrase that in clinical microbiology, there are the good, the bad and us. That refers to good microbes, bad microbes and our own immune defence system. So far, the discipline has focused on identifying the bad microbes and wiping them out.

A hundred years ago, during the Spanish flu pandemic, pathogenic viruses could not be diagnosed. Bacteria, yes, but there were no antibiotics yet. Case histories from that time make for tragic reading.

He points out that there will be new diseases and mutations every now and again. Healthcare must always have capacity for quick diagnostics, isolation and treatment, whether it is coronavirus or something else.

Very few fields can implement new diagnostics in a few days, as happened with coronavirus gene tests. In this field, you just have to.

A growing mountain of disposable protective equipment waste

In the spring of 2018, Tyks put Finland’s first robotic bacteria cultivation line into operation. According to Hakanen, medicine will become more automated and progressively shift online and to in-room diagnostics. On the other hand, larger laboratories need open diagnostics platforms that can be quickly turned towards meeting new needs.

In the past, to arrange a trip to another country you had to walk into a travel agency and make the booking there. Nowadays that sounds prehistoric. I believe that people in the future will have their own measuring instruments connected to an information system and that you can contact a doctor through a chat. Hospitals would only be visited for compelling reasons, such as big surgeries, he muses.

The transfer of information between systems must be swift and seamless. Culling unnecessary information and interpreting figures are significant challenges for information systems and experts.

Here, we and Mylab have common challenges to solve that will occupy us for a long while.

Hakanen longs for better data about healthcare. In the coronavirus crisis, the world’s leading expert organisations, citizens and decisionmakers are all at the mercy of the same news cycle. Environmental aspects in the crisis are important as well.

We are growing the waste mountain of disposable protective equipment. The smell of burning diesel increases when laboratories are centralised. How can we decrease the amount of by-product plastic waste from diagnostics? Surely there will be solutions to these problems, he hopes.

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