Category Archives: The Science of Microbiology

“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

 

 

 

“When the bugs take their time…”

The Science of Microbiology, ,

You are probably familiar with the scenario… A blood culture takes a couple of days to become positive. A Gram stain shows Gram negative rods. The plates are subbed but after another couple of days there is still no growth on the plates. The clinicians are getting impatient and are phoning the lab looking for an identification…

It is certainly a frustrating situation but one that occurs not infrequently.

Is there anything that can be done to help the clinician, and more importantly the patient, whilst we are waiting for the organism to grow?

There are several organisms to consider in this sort of scenario. We should be thinking about HACEK organisms, anaerobes, Pasteurella spp., oxidative non-fermentors like Burkholderia spp., Capnocytophaga spp. Consider micro-aerophilic bacteria such as Campylobacter spp. and Helicobacter spp.  And don’t forget about exotic organisms such as Brucella spp.  Even then, this list is by no means exhaustive, and I am sure there are others that you have come across that I have forgotten about!

What can the lab/clinical microbiologist do to narrow the differential down and manage accordingly pending plate growth?

A few things come to mind:

Aerobic or anaerobic bottle positive?: If the aerobic bottle only is positive it can point to non-fermentors like Burkholderia spp. If the anaerobic bottle only is positive, then one must think about anaerobes (e.g. Bacteroides spp. Fusobacterium spp. )

Gram stain appearance: A cocco-bacillary appearance should make one think of Haemophilus and Brucella. Longish, pleomorphic spindle-shaped organism on Gram point towards Capnocytophaga. “Seagulls” or “squiggles” should send you in the direction of Campylobacter/Helicobacter

Patient History: A history of dog bites/exposure should make one think of Capnocytophaga. A prosthetic valve or other valve disease, or clinical stigmata of endocarditis can indicate a HACEK organism. A history of injecting drug use makes one suspicious of Burkholderia cepacia. A travel history to an endemic area could make one think of Brucella spp. or Burkholderia pseudomallei. In a patient with neck pain and swelling, you don’t want to miss a Fusobacterium necrophorum. If the patient is frankly septic, you want to make sure they are getting covered for Capnocytophaga and Pasteurella.

Of course, all this is speculation, and our educated guesses may be completely wrong in the end. It is however important speculation… We want to make sure that the patient is being covered for the most likely and the most serious possibilities.

Taking another, but no less important angle, from a lab point of view it is essential that any slow growing Gram-negative organisms are worked up in a biohazard cabinet. Laboratory exposure incidents for organisms such as Brucella spp.  and Burkholderia pseudomallei are resource-intensive, stressful for the staff, and for the most part avoidable.

And sometimes the bugs just like to mock us, even make fools of us. Just recently, I was convinced a wavy Gram negative rod in (multiple) positive blood cultures from a patient was going to turn out to be a Campylobacter, only for it to finally be identified as a Helicobacter cinaedi… Wrong again!

Michael

“The return of the fried egg”

The Science of Microbiology, , ,

After a prolonged COVID-induced hibernation, Mycoplasma pneumoniae is back in NZ. Over the past couple of months there have been a sprinkling of cases throughout NZ picked up on respiratory panel testing by PCR in diagnostic laboratories, including my own.

I can hardly remember the last time I saw a Mycoplasma pneumoniae infection. It was definitely pre-COVID. The low Ro of Mycoplasma pneumoniae infection meant that transmission was brought to an almost instantaneous halt by the introduction of Non-Pharmaceutical Interventions (NPIs or “lockdowns”) following the emergence of the COVID pandemic.

Over the past year or so, it has started making a comeback worldwide. It has taken longer than other pathogens to return post-COVID, and as described in this interesting article in the Lancet, this is likely due to various factors such as the slow generation time (6 h), long incubation period (1–3 weeks), and relatively low transmission rate of Mycoplasma pneumoniae. It has returned later than most in New Zealand, likely due its geographical isolation and relatively sparse population.

In a (slightly perverted) way I am glad it is back. It is a very interesting bug! It is one of the smallest known bacteria, at only 300nm. It lacks a cell wall, which is why you cannot see it on a Gram stain. It is also why Mycoplasma infections do not respond to beta-lactam antibiotics. It most commonly causes respiratory infections but also has the ability to affect a wide range of organ systems, either by direct invasion or autoimmune reaction. This is eloquently summarised on this table.

It is sometimes referred to as a cause of “walking pneumonia” which can be a little misleading as it is certainly well capable of causing hospitalisation in both adults and children.

As for the “fried egg”, this refers to its phenotypic appearance on culture media (e.g. Hayflick media). Of course, fried eggs have not really returned as virtually nobody these days (and certainly no diagnostic labs in NZ) culture for Mycoplasma pneumoniae, with the mainstay of diagnosis now being PCR and to a much lesser extent, serological testing. Having said this, there is some evidence that Mycoplasma serology is more sensitive than PCR, likely due to delayed presentation to Health Services.

With the worldwide resurgence of Mycoplasma pneumoniae, the other thing to consider is whether the re-emerging strains are macrolide resistant.  This is difficult, due to the lack of laboratories culturing for Mycoplasma pneumoniae. However, assays are now being developed to look for the key rRNA mutations coding for macrolide resistance directly from clinical samples. It is certainly something we will need to think about both from a treatment and surveillance point of view.

Which is the optimal sample type for (molecular) diagnosis of Mycoplasma pneumoniae? There does not seem to be a lot of literature on this topic and it probably depends on the clinical presentation of the disease. If presenting as an upper respiratory tract infection, which it can do, then throat or nasopharyngeal swab is likely to be best.  For pneumonia then sputum or BAL are probably optimal.

So, Mycoplasma pneumoniae is back, and because of this, we need to start thinking about it again as a differential diagnosis in our patients. Its return has however, made my job a little more interesting…

Michael