It could be said that in combating COVID-19 we microbiologists have not covered ourselves in glory. A big failing is that we haven’t jumped up and down vigorously enough in response to policy errors.
A sensitive and specific test – in other words a very good test – for the virus in the nose and throat (RT-PCR) was developed during the second week of January. It used technology that was already being employed in many NHS microbiology labs as well as many biomedical research labs throughout Scotland.
But we didn’t agitate enough about its rapid implementation for COVID-19 in these labs, or publicly reinforce strongly enough the WHO Director-General’s March 16 message of test, test, test. Or shout loudly enough when the then Chief Medical Officer announced on 2 April the abandonment of contact tracing, a system that we have successfully used to investigate and control outbreaks of infection ever since microbiology developed as a scientific discipline 150 years ago. Or refute with enough vigour her incorrect statement on that day that testing was only going to be positive when there were symptoms. Neither did we agitate enough to get the prevent, prevent, prevent, message across for care homes by insisting that all residents and staff going into them were virus-free; as microbiologists our experience over decades of influenza and E.coli O157 (commoner in Scotland than anywhere else in the world) in them has been that once the pathogens enter, outbreaks and mortality commonly follow.
It seems certain that there will be a public inquiry into the COVID catastrophe. Counsel to the inquiry will probe policy errors with forensic exactitude. But we microbiologists will have at least two excuses for our failings as a discipline. It is the diminution in our influence, and in our numbers, in recent decades. It is as though the much-quoted words allegedly said in the 1960s by a former US Surgeon General, William Stewart – “It is time to close the books on infectious diseases and declare the war on pestilence won” – were actually said, believed, and acted on. But he never uttered them. He said the opposite. Fake news, indeed. Nevertheless, there are many fewer of us now than in the past, and our habitats, laboratories, are diminished in number too.
Lab rat(s)
Certain occupations are high risk for contracting COVID-19 infections. As we discovered again this week at Millers of Speyside abattoir in Grantown. They have indeed occurred very commonly in meat plant workers who spread the virus to each other either in the cold working environment or in cramped living conditions, or both; many are migrant workers. The recent outbreak at the 2 Sisters Coupar Angus poultry plant means that Scotland has joined Wales, Ireland, Germany, the US and other countries in this regard.
Other microbes have also been associated with food processing. John Smith ran the City Laboratory in Aberdeen. His work on fish gutters and filleters in the 1930s is a microbiological classic. They caught leptospirosis, a bacterial infection mild in most but with measurable mortality in older workers, just like COVID-19, and, like that virus, having a gender bias, being significantly more lethal to men. The fish house workers (fortunately for them mostly local quines in their late teens and early twenties) contracted it from bacteria in slimy working surfaces contaminated with rat urine. Rats carry the organism in their kidneys. Smith told the fish house owners how to remedy the problem. They acted. The infections stopped.
But the excellence of work done at the laboratory did not prevent its closure in 1991, after a process called by managers “laboratory rationalisation”. We called it “lab rat”, and a very mild colleague called the negotiations “mangling meetings”.
In the mid-1990s I chaired a group that tried to prevent the closure of another laboratory in Aberdeen, the Torry Research Station, that worked on fish microbiology and preservation. For years its microbiology lab was run by James Shewan, held in such high regard internationally that a bacterial genus is named after him, Shewanella. But we failed.
Lest it be thought that only microbiologists in Scotland might have to defend themselves when the time comes, the dismemberment of Public Health England indicates that scapegoating south of the border is under way, and President Trump has already mounted massive attacks on the budget of the Centers for Disease Control and Prevention in Atlanta.
Image of pork processing plant via Wikimedia Commons
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Shona MacIver says
A balanced, thoughtful, short essay by Sir Professor Hugh Pennington. Thank you!
Me Bungo Pony says
I have to disagree Shona. There is not even an issue here never mind a “balanced” take on it. It is an article that seeks to create an issue, not address it. The only person I have heard trying to “scapegoat” microbiologists for the pandemic is Hugh Pennington …. in this article.
As someone who has worked through the pandemic in a Microbiology lab, I can assure you there was no shortfall in staff numbers available to tackle the virus. In fact, for most of the Summer, the majority of us had little to do as the non-covid workload fell by as much as 80% with hospitals emptying and GPs all but closing.
The capacity for Covid testing was not huge back in January but then, why should it have been? It had not been a “thing” until then. If Health Boards were to staff labs based on the possibility of innumerable as yet unknown sources of pandemics, much of the space would have to be given over to table tennis tables and the like as the bulk of the staff would be struggling to fill their day. However, even now, the Virology section of our lab is more than doubling in size and moving to more generous accommodation with new technology being put in place.
The reasoning, such as it is, in the article is also found wanting. What have the events of the early 20th century got to do with the reality of 21st century circumstances? Someone doing something impressive in a particular place nearly a century ago does not give that place a right to continue its existence for evermore. And just what does the closure of a fish Microbiology lab have to do with any of this?
I would normally be fully behind any article that highlights the work of medical labs. But this article just annoys me. New technology has allowed ambitious managers to climb the greasy pole on the back of small, satellite lab closures and centralisation. I have opposed all in our region as I believe they were short sighted and have led to a diminution in the “routine” service provided to local communities. There are other issues in NHS/Laboratory management I have serious problems with. Had the article been about these issues I would have been in full support of it. But it isn’t.
Scotty13 says
My take on Prof Pennington’s article is written on a day when Scotland’s care homes reported more Covid-19 deaths and a delayed report from Public Health Scotland was publicised.
This is not a good day for our First Minister, Nicola Sturgeon nor for the SNHS.
It’s feared discharges of dozens of confirmed cases – as well as the shifting of untested patients who may have been carrying the virus – contributed to the total of nearly 2,000 deaths in Scotland’s care homes. Dozens of hospital patients had tested positive for Covid-19 but were still discharged into care homes in Scotland at the behest of the Scottish government and its senior advisors.
I can recall the Chief Medical Officer’s announcement on 2 April on the abandonment of contact tracing, and more so that testing was only going to be positive when there were symptoms. This astonishing error of judgement seems not to have been challenged within the First Minister’s advisory groups for reasons best known to themselves. This misunderstanding is perhaps a central issue in the public’s confusion over the role of testing and its place in controlling if not eradicating Covid.
Asymptomatic citizens are capable of being carriers and transmitters of corona and other viral species as they have immune systems that have adapted to the virus in ways we ‘re still learning about. It may well relate to the so-called T-cell memory functions that act to efficiently neutralise pathogens without the typical febrile accompaniments of a viral insult.
Had this practice of discharging infected patients been rejected by clinicians, our death toll would have been less devastating. But it wasn’t and we need to consider why.
We cannot blame ignorance of a new viral genus on our lack of preparedness for this pandemic. We were warned of a possible contagion and its effects on our society when we experienced SARS and MERS in 2003. That showed us the risk of what new coronaviruses could do to swathes of our population. We seemed to have hopelessly failed to set up sufficient defences against covid-19 and other infections, and our elderly folk have paid the ultimate penalty.
Prof. Pennington rightly points out that independent labs have reduced in number and perhaps this centralisation of public science facilities tends to dilute the number of individual scientists who look at ‘science’ from differing angles. Science has always been subject to vigorous peer review and that must be encouraged without political interference.
The lack of viable test and trace systems together with the weekly announcements from politicians who regularly add new rules and regulations based on a numbers system shows no sign of curbing the transmission rate that is leading us into the Winter months, when human immunity always lags.
I would be delighted if the author was permitted to sit on the SG advisory committee and add his experience and wisdom. I would like to think the non-scientists that would sit alongside him would allow him to perhaps educate them a little.