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We're only two weeks into the school year, and already Burlington, Ont., public school teacher Joanne Stewart is looking at empty desks.

Of the 22 students in her Grade 3/4 class, two girls have been out sick – one of them for several days – and nearly half a dozen are noticeably sniffling or otherwise "fighting a bug."

Welcome to the cesspool known as your child's classroom.

Kids succumb to an average of eight respiratory infections each year; whether and when they'll miss school over it is less well documented. According to a 2010 British study, 50 per cent of parents send their children to school even though they're aware the kids are sick. It's just so complicated for working parents: The negotiation over which parent stays home (which ultimately becomes an argument over whose job is more "important"), followed by the booking off of your own sick days because you caught the bug your kid brought home.

These classroom-borne illnesses aren't limited to the common cold either; some infectious bad boys are about to get so medieval on your butt, you might wish for a good ol' case of pink eye.

Dr. Michael Dickinson, a pediatrician in Miramichi, N.B., spent the summer looking into children's blister-covered mouths. With kids back in close quarters and balmy temperatures keeping things contagious, he predicts he'll see even more before the frost descends.

"We're hoping that we've seen the worst of hand, foot and mouth disease for 2012," he says, using the common name for an ailment that looks like it couldn't possibly exist in the 21st century. But it does.

Three to six days after exposure to Coxsackie or echovirus, sores appear in the most uncomfortable places: hands, feet, buttocks, throat. Hand, foot, and mouth disease is sure to strike playdate-cancelling fear into the hearts of other parents.

Once cooler fall weather descends, it will drive out the icky virus. But Dickinson is already bracing for an onslaught of pertussis – whooping cough – which is on the rise, despite publicly funded vaccination here in Canada.

It has infected an estimated 2,000 people in four provinces this year and in the United States the story is grimmer: more than 18,000 cases make this year's outbreak the worst in more than half a century.

What the two illnesses have in common is how they're primarily transmitted: through coughs and sneezes. When you get a bunch of kids coughing and sneezing in an enclosed space – and not necessarily using the best "cough etiquette" or hand-washing habits – there's an outbreak waiting to happen, says Dr. Vinita Dubey, associate medical officer of health in Toronto Public Health's Division of Communicable Diseases.

Get this: Even if your kid doesn't get sick, Dubey says there's a good chance the bacterium that causes pertussis will find a happy home at the back of your child's nose, growing and multiplying so that the one time your child forgets to sneeze into her sleeve, the droplets that shoot out of her nostrils will be especially potent. She may not get sick herself, but could pass whooping cough along to a younger brother or sister.

It doesn't help that the pertussis vaccine your child got as a baby doesn't offer lifelong protection. Plus, the bacterium's ability to hang around in our nasal passages makes vaccination less effective. So Dubey advises adults and teens to get a booster shot. And if you have a cough that just won't go away, even without the signature "whoop" sound, get tested for pertussis to ensure you don't spread it.

Next up on the fun agenda? Flu season, right around the corner. Dickinson is already nagging his patients about the vaccine, even though it won't be available until next month. The newer intranasal version, he says, provides better protection than the injected vaccine, which is contrary to the norm. It's also far less drama-inducing if your kid (or you) has a needle phobia.

Meanwhile, Joanne Stewart has a sore throat, and something funny is going on with her ears – no doubt symptoms of the bug responsible for her students' absences.

Most years, she'll succumb to three or four infections, which seems a modest number; Ms. Stewart credits her rigorous hand-washing regime.

When the kids go to lunch, she says, "I make sure they wash their hands. And I check that they've used soap."

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