Category Archives: The Wandering Microbiologist

“Trying to escape microbiology”

Confessions of a Microbiologist, The Science of Microbiology, The Wandering Microbiologist, , ,

“You can take the microbiologist out of the lab, but you can’t take the lab out of the microbiologist”

I was fortunate enough to attend the Olympics in Paris last month, the first time I have ever been to the Olympics. It was a fantastic experience, and we managed to see several events, including football, tennis, athletics, cycling, Rugby 7s and triathlon. Moreover, Paris is my favourite city, so I take every opportunity to visit!

I was hoping to forget all about all things microbiological for a month, and to a large extent this happened, until I was watching the triathletes swimming in the Seine!

You are probably aware of the story, but it was a big thing, and something of a propaganda stunt, allowing the Olympic athletes to swim in the River Seine, and the French Government invested heavily in cleaning up the Seine in order to facilitate this. 

In the end it was touch and go. Heavy rain before the Olympics put the E.coli counts up in the river, and at least one of the training sessions and the men’s individual event had to be postponed due to levels exceeding the acceptable limits.

A few athletes got sick after swimming in the Seine but of course it was virtually impossible to prove that the river swimming caused the illnesses.

Which got me thinking. “What are the acceptable faecal contamination limits for swimming in rivers, and is the risk any different for elite athletes in the Olympics?

There are safety standards set by World Triathlon, which indicate that colony-forming units (CFU) of E. coli per 100 milliliters of water should not exceed 1,000 and enterococci levels should be below 400 CFU/100ml. As one can see from this report, levels were acceptable on the day of the race, but not on several other days.

Of course, the cut-offs for E. coli and enterococci are completely arbitrary… The higher the counts, the higher the level of faecal contamination, and thus the higher the risk. E. coli and enterococci are of course only indicators, as most E. coli and enterococci do not cause gastrointestinal illness. There are a whole range of infections that one can acquire by swimming in faecally contaminated river water, including bacteria, viruses, & spirochaetes. Gastroenteritis is likely the highest risk but ear infections and skin infections can also occur.

There are several other factors that may affect the overall risk. The risk will depend on the range of gastrointestinal pathogens present in the water. I.e. swimming in a river in India might carry a different risk to swimming in a river in Paris even if the E. coli levels are equivalent. The amount of water ingested will also be a factor. I imagine an elite athlete going hell for leather in the Olympic triathlon will be intaking a lot more water whilst swimming than if President Macron goes for a leisurely dip in the Seine, if he ever does. The exposure time will also be a factor. The athletes competing in the 10km distance swimming event will have a lot more cumulative exposure than the triathletes swimming 1500m. Finally, the “host” needs to be taken into account. The cohort swimming in the Olympics will be overwhelmingly young, fit and immunocompetent thus potentially at less risk than the general population.

So clearly it is not as simple as just saying >1000 E. coli per 100ml of water is unsafe and less than that is safe. It is far more nuanced than that.

For elite athletes, whose livelihoods depend on competing in such events, they really have little choice in the matter. For myself however, who is definitely not an elite athlete, I like looking at the Seine, and it certainly appears cleaner than in years gone by, but I will pass on the swimming just for now.

Michael

 

 

 

“A Smorgasbord of Microbiology”

Future of Microbiology, The Art of Microbiology, The Wandering Microbiologist,

I was fortunate enough to have attended the ECCMID conference in Barcelona a couple of weeks ago, the so-called “Glastonbury” of microbiology conferences. (it is just the drugs that are different…). In general, the conference venue wasn’t great, but the industry exhibition was very impressive, a massive well-lit hall with a true smorgasbord of microbiology tests & platforms available. There were literally hundreds of stands offering a vast array of products. Some of the stands were very flashy affairs, demonstrating fully functioning microbiology platforms. Most importantly, some were even offering free coffee!, although we all know there is no such thing as a “free lunch”. Microbiology is big business now. It can’t have been cheap to hire the floor space at ECCMID, so it must be worth their while.

Healthcare in general is becoming ever more expensive to fund. There are good reasons for this. There is so much more that we can do now than even a generation ago. Stem cell transplants, CAR-T therapy, new anti-cancer drugs, minimally invasive cardiac procedures (e.g. TAVI) to name but a few. In addition, we have a lot more elderly people. Good healthcare and its associated cost will keep a patient alive, who will then inevitably present later in life with further health issues to manage. Spending on healthcare undoubtedly improves life expectancy, but there is a ceiling on life expectancy and there is a law of diminishing returns which eventually kicks in…

With regards to microbiology, there is no difference really. There are so many more things we can offer in a microbiology lab which we could not offer even 20 years ago. Multi-plex & rapid turnaround PCRs, 16s RNA sequencing, metagenomics are a few examples. There are more antibiotics to perform susceptibilities on, and we can now perform both phenotypic and genotypic susceptibility testing. There are a lot more infectious conditions we can now effectively diagnose, usually with PCR based methods. We are also required to spend a lot more money on good quality assurance frameworks, and rightly so, it’s critically important! The landscape has changed out of all recognition in the microbiology lab. A generation ago, it was mainly culture-based bacteriology. Times have changed…

All of this means that diagnostic stewardship plays an increasingly important role in the microbiology laboratory, if we are to have any hope of limiting costs whilst providing good value to the clinicians and patients. What tests and platforms should we have in the laboratory, and which patients should we perform these tests on? Personally, I think diagnostic stewardship should be a key component and focus of the jobs of both clinical microbiologists and laboratory managers alike.

“Diagnostic Stewardship is a never-ending process…”

When wandering around the industry exhibition hall, it is easy to get caught up in the euphoria and hype; “I’ll have one of those, and I’ll take that as well”, but there is now an almost infinite array of things that a microbiology lab can have… The key is to listen to what the industry reps have to offer, and then work out what is going to give most value to your particular patient cohort. Will that 24-plex respiratory PCR improve patient management over and above the incumbent 16-plex? Will this assay which gives me susceptibility results from positive blood cultures in 2 hours instead of 6 hours decrease patient mortality? 

Diagnostic stewardship is a fascinating area. Industry presents us with all these options. It takes an effective team working together in the lab to make the right decisions.

Michael

“Flu in Kathmandu”

Confessions of a Microbiologist, The Wandering Microbiologist, ,

When I was offered the chance to go to a WHO influenza meeting in Kathmandu, I grabbed it with both hands. Such opportunities certainly don’t come by every day…

However the trip to Nepal did not get off to the best of starts.

On the flight to Kathmandu, I started to get toothache. By the time we landed I was in agony. The pain was compounded by the fact that my suitcase didn’t make the connection at Singapore. Ouch!

Things could only get better…

However my initial impressions of Kathmandu did little to lift my spirits. There were three power cuts in the first 24 hours, apparently a hangover from the 2015 earthquake. I had to pass on coffee in my hotel room as the tapwater had a distinct greeny brown tinge to it. I then attempted to do some initial exploration of the city on foot, but crossing roads in this city is not for the faint-hearted! Eventually fatigue and my nerves got the better of me and I retreated to the safer confines of my hotel room, wondering just what I had got myself into…

But things did eventually improve (as they almost always do!). The conference started the next day and it was good to focus for a change on just one microbiological subject (influenza) for two and a half days, as this allowed the acquisition of some in-depth knowledge. It was also good to speak to representatives from countries that I have very little knowledge of and have certainly never met anybody from before , i.e.  Timor Leste, Mongolia, Bhutan. The Nepalese people themselves were very friendly and as most of them knew a little bit of English, it was easy to strike up a conversation.

And my suitcase eventually turned up, albeit the day before I was due to leave (carry-on bag next time!). As for my toothache, the hotel concierge kept me going with a steady supply of paracetamol, which took the edge off the pain and allowed me to function. I fear a visit to the dentist will be required though on return to NZ.

The highlight of the whole trip was the final day visit of local hospitals, public health laboratories, and the Nepal National Influenza Centre. This was a fantastic opportunity to meet local laboratory professionals, and to discuss what particular challenges they faced in a sometimes challenging environment. I was extremely impressed at the systems they had in place.


“Lab and hospital tour in Kathmandu”

So despite the challenges the trip turned out to be hugely educational, both in an academic and cultural sense. I learnt a good deal about Influenza, and even more about Nepal. It is very different to New Zealand! I look forward to going back there one day,  hopefully to do some trekking in the Himalayas.

And I have made a new resolution:- to attend at least one microbiology conference a year in a place I have never been to before, even if I have to pay for it myself.

Michael