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.

Various times, I’ve asked audiences “What percentage of antimicrobial resistance in humans do you think it attributable to antimicrobial use in animals?

  • Answers pretty much range from 0-100%.

The actual number is probably on the low end of that range, but we really don’t know. It’s such a complex system that a simple number can’t be generated.  In fact, we don’t have the data to even get close to an accurate overall estimate.

However, better estimates can be made for certain resistant bacteria, for which more specific data are available. The estimates are still pretty dodgy given current gaps in surveillance, so the numbers have to be taken with a big grain of salt, and we have to take care extrapolating to other bacteria or different geographic ranges. Regardless, the information can be interesting and useful if we are careful not to overinterpret things.

A recent paper in The Lancet Planetary Health (Mughini-Gras et al. 2019) investigated multidrug-resistant E. coli, specifically E. coli that produced extended spectrum beta-lactamases (ESBLs) or that harboured the AmpC gene. These E. coli are resistant to 3rd generation cephalosporins (an very important drug class for treatment of infections in people) and are often resistant to various other antimicrobials as well. The study evaluated data on ESBLs and AmpC E. coli from different Dutch sources, and developed a transmission model to estimate how people were becoming infected (outside of hospitals).

Here are some highlights from the study:

  • People carrying resistant E. coli likely most often (61%) got it from other people, followed by food, animal and environmental sources (in that order).
  • The graph below shows how common resistant E. coli are in various sources (size of the bar to the left of midline) and how important each source is to humans in terms of potential exposure (size of the bar to the right). As you can see, for some sources (e.g. chickens – the birds, not the meat), resistant E. coli are very common but they are not thought to be important sources of exposure to people, while for others, the likelihood of resistant E. coli is low but the sources pose a disproportionately high risk of exposure to humans (e.g. raw vegetables). The impact on people varies with the overall amount of exposure and how we handle potentially contaminated sources. For example, even though the rate of contamination of raw vegetables is low, we encounter those very frequently and we often don’t cook them. In contrast, the contamination rate in surface water is high, but we don’t have a lot of direct contact with untreated water.
  • Companion animals came up higher than I would have guessed, being estimated to account for 7% of human infections, most often from dogs (3.9%) (although it reinforces why I’m concerned about ESBLs in dogs and cats, and why we’re studying it).

The over-riding conclusion was that humans are the main source of community-acquired resistant E. coli, but that non-human sources still play important roles. They also concluded that, even though non-human sources accounted for a minority of infections, it would be difficult for these resistant E. coli to be maintained in people without transmission to and from non-human source. So, addressing the problem in people alone will help, but won’t eliminate the problem.

We have to remember that these are just estimates and they may just (or at best) apply to the Netherlands. However, it’s an interesting story and should keep us thinking about the multi-disciplinary (One Health) approach that we need to take to combat antimicrobial resistance.

Despite daily updates to spam filters and contact blocking, I wake up every day to a variety of invitations to submit to journals.

  • No good journal does that. They have lots of submissions.

The spam emails highlight the wild west of predatory journals, often with names that try to imitate real journals. Today’s was the “New American Journal of Medicine”, a not-so-subtle variation of the New England Journal of Medicine or the American Journal of Medicine. It looks like that journal has published a total of 8 papers in 2019. I looked at one of them and “crap” is my generous assessment. It’s a paper that recommends a treatment for pregnant women and it’s one page long, does not disclose the funding source, fails to fulfill pretty much every standard reporting requirement for a clinical trial and reports essentially no specific data or analysis. But, it’s “published data” and therefore now on someone’s CV.

The state of the scientific literature is pretty messed up. “Show me the study” has been a common refrain, but it’s not as useful these days because anything can get published.


  • Too many journals.
  • Predatory journals.
  • Profit.

Good journals screen out the weak articles. High impact journals publish a minority (5-25%) of the articles submitted to them (and bear in mind most often people only send their best papers to those journals). Some journals that are still good quality take lower impact papers that are still good science. Some journals take whatever they can get, just trying to screen out the bad science.

Others will take whatever they can get, as long as the authors can pay. Sadly, there are literally thousands of those, and they’re the worst kind.

Some people don’t realize most researchers don’t get paid to write scientific papers, and in some cases it’s quite the opposite. Some journals still publish at no cost, but increasingly, there are publication fees that may range from a few hundred to a few thousand dollars. That, itself, isn’t necessarily the problem. Some journals charge fees so that the papers can be open access (available to anyone, without a need for a subscription). However, some journal charge a couple thousand dollars, make a nice profit and don’t particularly care about the science.

As someone who’s an associate editor, editorial board member and frequent reviewer for many journals, I see the good and bad.

  • I see papers that should be published accepted.
  • I see good quality papers rejected by good journals, knowing they’ll still end up in another good journal.
  • I see bad papers rejected.

However, I also see…

  • Horrible quality papers rejected that I know will (unfortunately) still end up published somewhere else.
  • Published papers that clearly didn’t undergo any/much peer review, or at least peer review of any quality and/or editors that paid any attention.

It’s frustrating to be reviewing a paper that’s complete crap, knowing it will find a home in a journal eventually and still become part of the “published literature.” Yes, it will most likely be in a bottom-feeder journal that many of us in the scientific community know is dodgy, but not everyone will realize the difference. Sometimes that’s just frustrating, because poor quality science shouldn’t be published and just “muddies the water” of what’s out there. However, when it deals with clinical matters (e.g. diagnosis, treatment of disease) it can actually be harmful, because poor quality or invalid data shouldn’t form the basis of decisions. Yet, it happens.

There have been a couple “stings,” where fake (and clearly garbage) papers have been submitted to journals. The highest profile was one that was published in Science (Bohannon, 2013).  The author submitted a paper to several journals.  It was later said of the study that “Any reviewer with more than a high-school knowledge of chemistry and the ability to understand a basic data plot should have spotted the paper’s short-comings immediately. Its experiments are so hopelessly flawed that the results are meaningless.” More than 50% of the open access journals to which it was submitted accepted it.

There are many reasons these dodgy journals are used.

  • “Publish or perish” as they say in academia isn’t quite true, but it’s pretty close. Junior faculty need to show productivity to keep their positions or move into the increasingly elusive tenured positions. Published scientific papers is a key metric, because it’s easy to count.
  • Some people get taken advantage of, not realizing the journal is predatory (or that fees are so high, until after the paper is accepted).
  • Commercial profit. Companies want to say their products are supported by published data. If the data aren’t actually any good, the amount of money that it takes to get something published is inconsequential for most companies (and cheaper than going back to the drawing board).

Open access isn’t inherently bad. There are excellent open access journals that charge a couple of thousand dollars per paper for publication but have high standards. Open access is actually ideal as it means the science is available to everyone. It just has to be acceptable science, and that’s where things start to fall apart.

Anyway… enough ranting. I always like to say “don’t talk about a problem without talking about a solution” but I don’t have an easy solution. More awareness is key, which is why sites that track predatory journals, such as Beall’s List, are important. It’s a good update on a sad state of affairs.