The recent reports of human-to-human transmission of the novel coronavirus that’s been identified in China certainly raise the stakes. While this virus still seems to be less transmissible and less virulent than its relative, the SARS coronavirus, it’s pretty early to have a lot of confidence in that. Lessons seem to have been learned from SARS, but at the start of an outbreak it’s hard to predict too much.

What’s the companion animal spin?

Human infections were first linked to an animal (seafood) market. That’s not surprising, since SARS also started at an animal market, and lots of undiscovered coronaviruses are lurking in different animal species (especially bats). The fact that the outbreak was first linked to an animal market doesn’t mean the animals were the source (because there are also lots of people in markets), but it would make sense.

If that’s the case, it’s a bit optimistic for us to think that this virus would be able to infect only its host species and people.

Looking back at SARS, we know that virus can infect a few different mammals, including cats. When SARS was a problem in Canada, people who were exposed underwent voluntary household quarantine, meaning they were supposed to stay at home and away from family members for a period of time. Yet, nothing was said about pets. I could have been quarantined in my basement, away from my family, but still have had regular contact with my cat, who then could have had contact with the rest of the family (and if he was an indoor-outdoor cat, contact with other cats). Think what would have happened if SARS was able to establish itself in the feral cat population of a city like Toronto. It’s probably not transmissible enough between cats to do that, but we didn’t know that at the time. I remember emailing someone who was dealing with the SARS crisis in Ontario at the time about the pet issue, and the response basically was “Good point. Gotta go.” When dealing with a crisis, something ancillary like that isn’t high on the priority list.  We wrote a commentary about the potential risk of pets in household quarantines related to SARS a little while later that got some attention, but I’m not sure there was much action.

That’s why we need to be proactive. For containment measures for SARS, this new coronavirus or any other new disease, we need to assume that multiple species can be affected until proven otherwise, and we need to act accordingly. That doesn’t necessarily need to be complex. It might just be making sure animal contact questions are asked along with human contact questions, that quarantine protocols consider what to do with exposed animals, and that quarantined individuals are kept away from animals. We developed guidelines for management of pets related to Ebola exposure a few years ago, and it took a lot of time to get it right.

Hopefully we don’t have to worry about it, but it’s better to plan ahead than try to catch up.

I saw a TV commercial yesterday talking about a skin product and how it “protects your microbiome.” Microbiome is a big buzzword now, but do what do we really know?

A lot, and almost nothing.

The microbiome is the vast population of microorganisms (mainly bacteria) that live in a site like the intestinal tract, respiratory tract or on the skin. While we often think about bacteria as causes of disease, they’re also critical for our survival. The overall population of microorganisms (the microbiome) provides many benefits to the host (be it a person or animal), but how it interacts with the body is complex and poorly understood.

I’ve been working on microbiota for quite a few years and I think I understand a fair bit about it, but I also think I understand little about it in the grand scheme of things. People often think it’s this cutting edge new technology (it is) that can tell us a lot about ourselves or our patients (it can) and guide medical decisions (not yet). The problem is, there’s a difference between information and knowledge. If you give me a fecal sample (or sample from any other site), I can tell you lots about what’s in it. I can tell you how that fits on a population level with normal or healthy groups. But, I can’t say much with confidence about that individual.


While we’re getting more and more information about the microbiome in healthy and sick animals and people, we don’t really know what we’re looking at. There’s a wide variety of “normal” microbiomes, not just one. If you take 100 healthy dogs and 100 dogs with inflammatory bowel disease, there will be some clear differences between the overall groups. However, some of the sick dogs will have microbiomes that look just like normal dogs, and some perfectly healthy individuals will have microbiomes that I’d consider completely screwed up.

Also, while we get reams of data, and there are lots of ways to analyse them, we still don’t really know what the most important elements are. Is it the overall richness (number of different bacterial species)? Their diversity? The presence of specific bugs? Ratios of specific bugs or groups?

There are still many other issuses as well. For example, does a single sample tells us the whole story? Do data from one geographic region apply to another? Do we need to account for diet, age and various other factors? Should a healthy vegan’s microbiota, for example, be expected to be the same as a healthy meat eater? How good is testing feces when disease occurs higher up in the intestinal tract?

Lots of questions still need answers.  This isn’t meant to dismiss the importance of the field. Like many other groups, we continue to work to try to figure out the microbiome. However, we need to make sure we stay grounded and remember how little we actually “know”.

You can pay to get your dog’s (or your) microbiome tested, get recommendations about whether it’s “normal,” and sometimes be sold treatments as a result of that interpretation. You can buy products to “protect” your microbiome (without much or any evidence behind them). However, remember that marketing often outpaces evidence.

The microbiome’s a wonderful thing. I can’t wait until we understand it better.

This is a smaller outbreak than the puppy outbreak from the previous post, probably in large part because fewer people have contact with geckos, but… Contact with reptiles such as geckos has been a known risk factor for human salmonellosis for years. That’s a big part of the reason for recommending that high risk people (i.e. those less than 5 years of age, over 65 years of age, pregnant, or immunocompromised) have no contact (direct or indirect) with reptiles.

In this outbreak (Koski et al, Zoonoses and Public Health 2019), Salmonella Fluntern was the cause of infection in 12 people in 4 US states (Oregon, California, Iowa and New York). The median age of those affected was 5 years, with a range from less than 1 to 58 years of age (so much for the “keep young kids away from reptiles” recommendation). No one died, but 3 people (25%) were hospitalized. Most people reported contact with leopard geckos, and the same bacterium was isolated from a gecko owned by one affected person.

No common source of geckos was identified and their bacteria were different enough genetically that a point source isn’t likely. Other gecko- or reptile-associated Salmonella Fluntern isolates were identified in bacterial databases from Europe. So, this suggests that Salmonella Fluntern is a reptile (or even gecko) associated strain, posing a broad risk to reptile/gecko owners.

This report doesn’t change any recommendations, but just shows (again) the issues that are involved. Reptiles shouldn’t be in high risk households. People with reptiles need to use some basic hygiene precautions to reduce their risk of infection. It’s not rocket science, but it’s often neglected.

More information about reducing the risk of infection associated with reptiles can be found in on the Worms & Germs Resources – Pets page.

A couple of recent outbreak reports are interesting, though unsurprising, and they help raise awareness about some important issues.  Here’s the first one.

The CDC recently released an update on the ongoing investigation into antibiotic-resistant Campylobacter infections from puppies. Contact with puppies (and kittens) has been shown to be a risk  factor for people developing campylobacteriosis, a bacterial intestinal infection.  Campylobacter is most often associated with poultry but can be shed in the feces of numerous species, including dogs and cats. When you combine the general increased risk of pathogen shedding in young animals, the higher rates of shedding in commercially produced animals (e.g. from puppy mills), rampant antibiotic use in commercial breeding operations, and the close contact that people have with new puppies (and their feces, particularly during the house training period), it’s a great recipe for infection with Campylobacter, particularly antibiotic resistant strains.

The ongoing US outbreak of Campylobacter jejuni infections in people has now reached 30 confirmed cases, presumably with many other undiagnosed cases (see graph below).

  • Affected people have come from 13 US states (see map below).
  • Four people have been hospitalized as a result of the infection.
  • Campylobacter isolates have been resistant to a variety of antibiotics, including those that are commonly used to treat severe infections.

Petland pet stores have been implicated as a /the source.  Twenty-four affected people were interviewed, and 21 had had contact with a puppy in the week before they got sick, and 16 of those had contact with a puppy from a pet store. Of those, 80% were people who had a puppy from a Petland store or that worked at Petland.

Laboratory evidence indicates that bacteria from ill people in this outbreak are closely related genetically to bacteria from ill people in the 2016–2018 outbreak of multidrug-resistant Campylobacter infections linked to pet store puppies, which was also linked to Petland.

A single source of puppies hasn’t yet been identified. Presumably they are focusing on commercial puppy suppliers but stores likely get puppies from a variety of sources, making the investigation a challenge.

A few take-home messages:

  • Don’t be afraid of puppies. They’re biohazardous but also a lot of fun. There’s always risk in life and the disease risk associated with puppies can be reduced with some common sense precautions.
  • Campylobacter is one of many “don’t eat poop” diseases. The bacterium has to go from the puppy’s intestinal tract to a person’s mouth for someone to get infected. There are lots of ways to reduce this risk, such as hand washing, picking up feces promptly and good house training.
  • While you shouldn’t be afraid, you should be aware. So should your physician. If you get sick after having obtained a new puppy, make sure your healthcare provider knows that you have a puppy.

More information about reducing the risks associated with puppies, and about Campylobacter, can be found on the Worms & Germs Resources – Pets page.

“One Health” is getting a lot of talk (but still not enough action) these days. It deals with the intersection of human health, animal health and the environment. Unfortunately, all of these components don’t get treated equally, and the environment often gets ignored. There are a variety of reasons for that, which I won’t get into (at least in this post).

The environment plays an often-forgotten role in antibiotic resistance, through things like contamination of soil and water sources by agricultural runoff, human sewage, and waste produced during pharmaceutical manufacturing, not to mention the ongoing biological warfare that bacteria in the environment wage on each other (most of our natural antibiotics were originally derived from environmental bacteria or fungi). While we focus on use of antimicrobials in animals and humans, they’re also used in plants. Recently, there has been attention focused on the potential role of antifungals use in plants (e.g. vegetables, fruits) on resistance in a very nasty emerging pathogenic fungus called Candida auris. This fungus is (currently) a rare cause of disease in people, but kills ~35% of people who get infected with the resistant form, and infection rates have been increasing internationally.

A recent paper in Emerging Infectious Diseases (Chen et al. 2019) highlights another related issue. The authors looked a different fungus, Aspergillus fumigatus, found in agricultural fields in China. About 10% of the A. fumigatus that they found were resistant to azoles, a common class of antifungal drugs. Eighteen of 21 (86%) of the resistant isolates were from strawberry fields. They also found residual antifungal levels in the soil at many sites, including the drug defenoconazole in 8/10 strawberry fields, and prochloraz in 7/10 strawberry fields.

It’s hard to say what this means for human or animal health, but it’s a concern.  The authors concluded “The management of fungicide use in agricultural fields, especially those serving as potential resistance hotspots, such as strawberry fields, is needed to curb the emergence of antifungal drug resistance in clinics.”

People sometimes get frustrated when I won’t say “absolutely, positively that cannot happen.” It’s not that I don’t understand or am afraid to make a decision, it’s biology. I can say something is “exceedingly unlikely to happen,”not something I’d be concerned about” or
there’s no evidence that’s a concern.” However, Mother Nature likes to keep us on our toes and strange things can happen.

A paper in this month’s Emerging Infectious Diseases (Jung et al, Rare case of enteric Ancylostoma caninum hookworm infection, South Korea) is an example of that.

Ancylostoma caninum is a hookworm that typically infects dogs. It lives in the dog’s intestinal tract, and dogs poop out the parasite eggs. Those eggs hatch into larvae in the environment, and people can be infected by the larvae by touching a contaminated surface. The parasite larvae actually burrow into the skin and cause an incredibly itchy condition as the larvae migrate through the skin for a short period of time. Since people aren’t the natural host, the larvae typically die at that stage in people.  In contrast, in dogs the larvae continue to migrate through the body, eventually making it to the intestine, where they mature into adult worms, produce more eggs and continue the life cycle.

This case report describes an intestinal infection with A. caninum in a person. This isn’t the first time it’s been reported, but it’s rare. The affected person was a 60-year-old man who underwent a colonoscopy. During the procedure, a worm was found attached to the intestine (images A and B below). It was removed and identified as the dog hookworm (image C shows a close up of the worm’s mouth where you can see the “hooks”). He was treated with a dewormer in case that hookworm left any friends behind, and the man recovered. He had some abdominal pain, but whether the parasite was the cause is hard to say. However, he did have an increase in blood eosinophils, a type of white blood cell that’s associated with allergic and parasitic infections.

What does this change?

Nothing.  It’s just interesting oddball infection for physicians to keep in mind, especially in people who live in or have visited areas where canine hookworms are common (e.g. a lot of tropical regions – fecal contamination on beachs is a common source of exposure to hookworm larvae).

Preventing hookworm infections, human or canine, involves proper fecal handling (e.g. stoop and scoop), good hygiene (e.g. wash your hands) and deworming of dogs. Those precautions are nothing special, but these basic measures are often overlooked.

This is one of these “I’m not sure it’s really news” stories, but I guess is should be because it’s still a problem. We know there is a clear link between reptiles and Salmonella in people.  Reptiles are common carriers of this bacterium, and human infections from handling reptiles or having contact with their environment are far from rare.

Similarly, outbreaks of salmonellosis in people linked to feeder rodents (rodents bred to be fed to reptiles) also aren’t uncommon.  Such outbreaks can be even more wide reaching because of large scale rodent production and subsequent widespread distribution of a lot of infected rodents.

The Public Health Agency of Canada recently released a public health notice about an ongoing outbreak of Salmonella infections linked to snakes and feeder rodents that has affected people in multiple provinces over the last two years.

Details are pretty limited, but as of December 10, 2019, there had been 92 confirmed cases of infection with the outbreak strain of Salmonella Typhimurium in 6 provinces, spanning the country from east to west (Newfoundland and Labrador, Nova Scotia, New Brunswick, Quebec, Ontario and British Columbia). The largest number of cases was in Quebec (52) followed by Ontario (16). As with other outbreaks, this probably represents a minority of the true number of infections.  Cases occurred between April 2017 and October 2019 (see graph of the “epidemiological curve” from the public health notice below).

Six people were hospitalized but no one has died.

In general, it is recommended that high risk people (children less than 5 years of age, people  over 65 years of age, pregnant women and people with compromised immune systems) not have contact with reptiles. That includes living with them, since many cases have occurred in individuals who lived in the same house as a reptile but didn’t handle the animal directly, presumably because the household environment was contaminated. People in those high-risk groups should also avoid contact with feeder rodents. Feeder rodents pose more risk than pet rodents, because a rodent that’s been living in a household is less likely to be infectious than one that was just brought in (alive or frozen) as food for a reptile. Regardless, some common sense hygiene, particularly handwashing, goes a long way.

More information about Salmonella and reptiles is available on the Worms & Germs Resources – Pets page.

Calling all backyard poultry owners:

You are invited to participate in a survey regarding backyard chickens that is being conducted by Dr. Scott Weese, a Professor in the Department of Pathobiology, Ontario Veterinary College, University of Guelph, and Public Health Ontario’s Infection Prevention and Control Team (Central-West).  We are interested in hearing from people who have backyard chickens, or who may be interested in getting backyard chickens, to find out what educational resources may be helpful for those involved in raising and handling chickens.

Click here for more information and to participate in this survey.

ProMed Mail just reported on the return of canine flu to Ontario.

The problem is, it’s not true. (I guess that’s not a problem. It’s good that it’s not here.)

Today’s ProMed post on the subject references a news article (which appears to have been removed since) that just seems to be a direct copy of a mainstream media report from January 2018. To my knowledge, we have not had any canine flu activity in Canada since October 2018 (and since canine flu is reportable in Ontario – to both public health and the agriculture ministry – it’s unlikely we wouldn’t know about any diagnosed infections).

Influenza in dogs bound to come back to Ontario, particularly given the massive number of dogs that are imported every year from high-risk areas like Asia, but as far as we know it’s not present here at the moment.

For the full story of our previous outbreak and successful control efforts, check out the recently published report on canine influenza in Ontario (Weese et al. EID 2019).

The headline’s true, but a bit sensational. However, it’s from a recent paper that has attracted a lot of attention: Being licked by a dog can be fatal: Capnocytophaga canimorsus sepsis with purpura fulminans in an immunocompetent man (Mader et al. 2019).

This recent fatal Capnocytophaga canimorsus infection in a German man has gotten a lot of attention. It’s a bit of an obscure bacterium, despite being present in the mouth of pretty much every dog, and one that I disproportionately talk about a lot because it’s not well known but has the potential to cause very serious disease in people. Most veterinary professionals don’t have much background on C. canimorsus, since it doesn’t typically cause disease in animals.  However, it’s important to know about it when talking to dog owners about risks from bites. When I talk to physicians, there’s usually a similar lack of recognition.

While this bug is common in dogs, human infections are rare. They usually occur in people without a functional spleen or in people who have compromised immune systems. In those individuals, a bite or other type of contact with dog saliva in wounds/broken skin or on mucous membranes (e.g. mouth, nose, eyes) creates the potential for infection, and is an indication for prophylactic antibiotics.

In the general population, infections are exceptionally rare, which is why this particular case report is so unique.  It describes a fatal infection in a 63-year-old man who was otherwise healthy and had no known immunocompromise.

  • That’s really rare.

He had a dog and had not been bitten, but had been licked.

  • That’s rare too as far as risk for infection with this bacterium, but it happens.

He developed severely progressive disease and ultimately died after 16 days of aggressive care.

  • Unfortunately, that’s not rare. A large percentage of infected people die, and those who survive often have devastating complications, including loss of digits or limbs.

The authors drew a couple of conclusions:

Pet owners with flu-like symptoms should urgently seek medical advice when their symptoms exceed those of a simple viral infection, which in this case were severe dyspnoea and petechiae. Physicians confronted with such patients should ask about contact with dogs and cats.

  • I’d expand that to contact with any animal, since this bacterium is not the only issue. Furthermore, everyone plays a role here. Patients and their families should report animal contact if  their healthcare provider doesn’t ask.

They [healthcare providers] should consider C. canimorsus infections also in the presence of purpura fulminans and the absence of animal bites or scratches, and any immunodeficiency. In such cases, the clinician should immediately start empiric treatment with a penicillin in combination with a beta-lactam inhibitor until a definite diagnosis is established.

  • It’s hard to say that Capno should be considered in every person. I guess it’s fine to say “think about it,” but common things occur commonly, and this infection in a healthy person isn’t one of them. Early recognition is important and fortunately, someone coming with this severe of an infection would be expected to be immediately started on an antibiotic  anyway that would also kill Capno (since it’s susceptible to a range of antibiotics).

For me, the key is preventing things from getting to this stage in the first place through common sense measures to decrease risk in high-risk individuals, and early recognition of a combination of risk factors. That doesn’t apply to an odd case like this, but it does to the majority of cases where there’s known (but not necessarily recognized) immunosupression of the patient, lack of recognition of the potential problems from a dog bite, and frequent lack of communication about animal exposure and bites. Failure to realize the risk in high-risk persons contributes to many deaths.

More information about Capnocytophaga canimorsus can be found in the fact sheet on the Worms & Germs Resources – Pets page.